Discrete Biomathematics
Peter F. Stadler
External Scientific Member
Email MPI MIS
Homepage University Leipzig
Phone:
+49 (0) 341 - 9959 - 558
Fax:
+49 (0) 341 - 9959 - 658
Address:
Inselstr. 22
04103 Leipzig
Arguello, A. S.
; Montellano-Ballesteros, J. J.
and P. F. Stadler:
Hamiltonicity in power graphs of a class of abelian groups.
Journal of algebraic combinatorics,
57 (2023) 1, p. 313-328 [DOI]
Bran, A. M. ; Stadler, P. F. ; Jost, J. and G. Restrepo:
The six stages of the convergence of the periodic system to its final structure.
Communications chemistry,
6 (2023), 87 [DOI] [FREELINK]
Kolberg, T. ; Löhneysen, S. v.
; Ozerova, I. ; Weller, K. ; Hartmann, R. K. ; Stadler, P. F. and M. Mörl:
Led-Seq : ligation-enhanced double-end sequence-based structure analysis of RNA.
Nucleic acids research,
Vol. not yet known, pp. not yet known [DOI]
Korchmaros, A. ; Schaller, D. ; Hellmuth, M. and P. F. Stadler:
Quasi-best match graphs.
Discrete applied mathematics,
331 (2023), p. 104-1025 [DOI] [ARXIV]
Nono, C. M.
:
From RNA folding to inverse folding : a computational study.
Dissertation, Universität Leipzig, 2023[FREELINK]
Schaller, D. ; Hartmann, T. ; Lafond, M. ; Wieseke, N. ; Hellmuth, M. and P. F. Stadler:
Relative timing information and orthology in evolutionary scenarios.
[ARXIV]
Seemann, C. R. ; Moulton, V. ; Stadler, P. F. and M. Hellmuth:
Planar median graphs and cubesquare-graphs.
Discrete applied mathematics,
331 (2023), p. 38-58 [DOI] [ARXIV]
Valdivia, D. I. ; Geiß, M. ; Hernández Rosales, M. ; Stadler, P. F. and M. Hellmuth:
Hierarchical and modularly-minimal vertex colorings.
The art of discrete and applied mathematics,
6 (2023) 2, P2.01 [DOI] [ARXIV]
Yao, H.-T. ; Lorenz, R. ; Hofacker, I. L. and P. F. Stadler:
Salt corrections for RNA secondary structures in the ViennaRNA package.
[ARXIV]
Akgül, B. ; Stadler, P. F. ; Hawkins, L. J. ; Hadj-Moussa, H. ; Storey, K. B. ; Ergin, K. ; Çetinkaya, R. ; Paschoal, A. R. ; Nachtigall, P. G. ; Tutar, Y. ; Yousef, M. and J. Allmer:
44 current challenges in miRNomics.
miRNomics : MicroRNA biology and computational analysis / J.
Allmer... (eds.). Humana Press, Springer, 2022. - P. 423-438
(Methods in molecular biology ; 2257)
[DOI]
Arguello, A. S.
and P. F. Stadler:
Whitney's connectivity inequalities for directed hypergraphs.
The art of discrete and applied mathematics,
5 (2022) 1, P1.01 [DOI]
Bonidia, R. P. ; Avila Santos, A. P. ; Almeida, B. L. S. de ; Stadler, P. F. ; da Rocha, U. N.
; Sanches, D. S. and A. C. P. L. F. Carvalho:
BioAutoML : automated feature engineering and metalearning to predict noncoding RNAs
in bacteria.
Briefings in bioinformatics,
23 (2022) 4, bbac218 [DOI]
Bonidia, R. P. ; Avila Santos, A. P. ; Almeida, B. L. S. de ; Stadler, P. F. ; da Rocha, U. N.
; Sanches, D. S. and A. C. P. L. F. Carvalho:
Information theory for biological sequence classification : a novel feature extraction
technique based on tsallis entropy.
Entropy,
24 (2022) 10, 1398 [DOI]
Bruckmann, C. ; Stadler, P. F. and M. Hellmuth:
From modular decomposition trees to rooted median graphs.
Discrete applied mathematics,
310 (2022), p. 1-9 [DOI] [ARXIV]
Changat, M. ; Vaheeda Shanavas, A. and P. F. Stadler:
Transit functions and pyramid-like binary clustering systems.
[ARXIV]
Eggers, D. ; Siederdissen, C. H.
and P. F. Stadler:
Accuracy of RNA structure prediction depends on the pseudoknot grammar.
Advances in bioinformatics and computational biology : 15th Brazilian Symposium on
Bioinformatics, BSB 2022, Buzios, Brazil, September 21-23,2022, Proceedings / N.
M. Scherer... (eds.). Springer, 2022. - P. 20-31
(Lecture notes in computer science ; 13523)
[DOI]
Ender, A. ; Graf, N. ; Kolberg, T. ; Findeiß, S. ; Stadler, P. F. and M. Mörl:
Synthetic riboswitches for the analysis of tRNA processing by eukaryotic RNase P enzymes.
RNA,
28 (2022) 4, p. 551-567 [DOI]
Ender, A. ; Stadler, P. F. ; Mörl, M. and S. Findeiß:
RNA design principles for riboswitches that regulate RNase P-mediated tRNA processing.
Riboregulator design and analysis / J.
Chappell... (eds.). Humana, 2022. - P. 179-202
(Methods in molecular biology ; 2518)
[DOI]
Engelhardt, J. ; Scheer, O. ; Stadler, P. F. and S. J. Prohaska:
Evolution of DNA methylation across Ecdysozoa.
Journal of molecular evolution,
90 (2022) 1, p. 56-72 [DOI] [ARXIV]
Gornik, S. G. ; Flores, V. ; Reinhardt, F. ; Erber, L. ; Salas-Leiva, D. E. ; Douvropoulou, O. ; Lassadi, I. ; Einarsson, E. ; Mörl, M. ; Git, A. ; Stadler, P. F. ; Pain, A. and R. F. Waller:
Mitochondrial genomes in Perkinsus decode conserved frameshifts in all genes.
Molecular biology and evolution,
39 (2022) 10, msac191 [DOI] [ARXIV]
Guzman, G. E. C. ; Stadler, P. F. and A. Fujita:
Efficient eigenvalue counts for tree-like networks.
Journal of complex networks,
10 (2022) 5, cnac040 [DOI]
Hartmann, T. ; Bannach, M. ; Middendorf, M. ; Stadler, P. F. ; Wieseke, N. and M. Hellmuth:
Complete edge-colored permutation graphs.
Advances in applied mathematics,
139 (2022), 102377 [DOI] [ARXIV]
Hellmuth, M. ; Schaller, D. and P. F. Stadler:
Compatibility of partitions with trees, hierarchies, and split systems.
Discrete applied mathematics,
314 (2022), p. 265-283 [DOI] [ARXIV]
Klapproth, C. ; Zöztsche, S. ; Kühnl, F. ; Fallmann, J. ; Stadler, P. F. and S. Findeiß:
Tailored machine learning models for functional RNA detection in genome-wide screens.
[ARXIV]
Krieg, L. ; Didt, K. ; Karkossa, I. ; Bernhart, S. H. ; Kehr, S. ; Subramanian, N. ; Lindhorst, A. ; Schaudinn, A. ; Tabei, S. ; Keller, M. ; Stumvoll, M. ; Dietrich, A. ; von Bergen, M. ; Stadler, P. F. ; Laurencikiene, J. ; Krüger, M. ; Blüher, M. ; Gericke, M. ; Schubert, K. ; Kovacs, P. ; Chakaroun, R. and L. Massier:
Multiomics reveal unique signatures of human epiploic adipose tissue related to systemic
insulin resistance.
Gut : an international journal of gastroenterology and hepatology,
71 (2022) 11, p. 2179-2193 [DOI]
Leal, W.:
Exploration of chemical space.
Dissertation, Universität Leipzig, 2022[FREELINK]
Leal, W. ; Llanos, E. J. ; Bernal, A. ; Stadler, P. F. ; Jost, J. and G. Restrepo:
The expansion of chemical space in 1826 and in the 1840s prompted the convergence
to the periodic system.
Proceedings of the National Academy of Sciences of the United States of America,
119 (2022) 30, e2119083119 [DOI]
Llanos, E. J. ; Leal, W. ; Bernal, A. ; Jost, J. and P. F. Stadler:
Are the chemical families still there? exploration of similarity among elements.
[FREELINK]
Müller, S. ; Flamm, C. and P. F. Stadler:
What makes a reaction network ''chemical''?.
Journal of cheminformatics,
14 (2022), 63 [DOI] [ARXIV]
Nebe, M. ; Kehr, S. ; Schmitz, S. ; Breitfeld, J. ; Lorenz, J. ; Le Duc, D. ; Stadler, P. F. ; Meiler, J. ; Kiess, W. ; Garten, A. and A. S. Kirstein:
Small integral membrane protein 10 like 1 downregulation enhances differentiation
of adipose progenitor cells.
Biochemical and biophysical research communications,
604 (2022), p. 57-62 [DOI]
Nunn, A. ; Otto, C. ; Fasold, M. ; Stadler, P. F. and D. Langenberger:
Manipulating base quality scores enables variant calling from bisulfite sequencing
alignments using conventional bayesian approaches.
BMC genomics,
23 (2022) 1, 477 [DOI] [ARXIV]
Nunn, A. ; Rodríguez-Arévalo, I. ; Tandukar, Z. ; Frels, K. ; Contreras-Garrido, A. ; Carbonell-Bejerano, P. ; Zhang, P. ; Ramos-Cruz, D. ; Jandrasits, K. ; Lanz, C. ; Brusa, A. ; Mirouze, M. ; Dorn, K. ; Galbraith, D. ; Jarvis, B. A. ; Sedbrook, J. C. ; Wyse, D. L. ; Otto, C. ; Langenberger, D. ; Stadler, P. F. ; Weigel, D. ; Marks, M. D.
; Anderson, J. A. ; Becker, C. and R. Chopra:
Chromosome-level Thlaspi arvense genome provides new tools for translational research
and for a newly domesticated cash cover crop of the cooler climates.
Plant biotechnology journal,
20 (2022) 5, p. 944-963 [DOI] [ARXIV]
Reinhardt, F. and P. F. Stadler:
ExceS-A : an exon-centric split aligner.
Journal of integrative bioinformatics,
19 (2022) 1, 20210040 [DOI]
Schaller, D. ; Hellmuth, M. and P. F. Stadler:
AsymmeTree : a flexible Python package for the simulation of complex gene family histories.
Software,
1 (2022) 3, p. 276-298 [DOI]
Stadler, P. F. and S. Will:
Bi-alignments with affine gaps costs.
Algorithms for molecular biology,
17 (2022) 1, 10 [DOI] [FREELINK]
Teich, M. ; Leal, W. and J. Jost:
Corpus-based metaphor analysis through graph theoretical methods.
[ARXIV]
Velandia-Huerto, C. A. ; Yazbeck, A. M. ; Schor, J. and P. F. Stadler:
Evolution and phylogeny of MicroRNAs : protocols, pitfalls, and problems.
miRNomics : MicroRNA biology and computational analysis / J.
Allmer... (eds.). Humana Press, Springer, 2022. - P. 211-233
(Methods in molecular biology ; 2257)
[DOI] [FREELINK]
Wörtz, J. ; Smith, V. ; Fallmann, J. ; König, S. ; Thuraisingam, T. ; Walther, P. ; Urlaub, H. ; Stadler, P. F. ; Allers, T. ; Hille, F. and A. Marchfelder:
Cas1 and Fen1 display equivalent functions during archaeal DNA repair.
Frontiers in microbiology,
13 (2022), 822304 [DOI]
Anders, J. ; Petruschke, H. ; Jehmlich, N. ; Haange, S.-B. ; von Bergen, M. and P. F. Stadler:
A workflow to identify novel proteins based on the direct mapping of peptide-spectrum-matches
to genomic locations.
BMC bioinformatics,
22 (2021) 1, 277 [DOI]
Anders, J. ; Petruschke, H. ; Jehmlich, N. ; Haange, S.-B. ; von Bergen, M. and P. F. Stadler:
Direct mapping of Peptide-to-Spectra-Matches to genome information facilitates qualifying
proteomics information.
BMC bioinformatics,
Vol. not yet known, pp. not yet known [DOI] [FREELINK]
Bedulina, D. ; Drozdova, P. ; Gurkov, A. ; von Bergen, M. ; Stadler, P. F. ; Luckenbach, T. ; Timofeyev, M. and S. Kalkhof:
Proteomics reveals sex-specific heat shock response of Baikal amphipod Eulimnogammarus
cyaneus.
The science of the total environment : an international journal for scientific research
into the environment and its relationship with man,
763 (2021), 143008 [DOI]
Berkemer, S. ; Siederdissen, C. H.
and P. F. Stadler:
Compositional properties of alignments.
Mathematics in computer science,
15 (2021) 4, p. 609-630 [DOI]
Changat, M. ; Narasimha-Shenoi, P. G. ; Nezhad, F. H.
; Kovše, M. ; Mohandas, S. ; Ramachandran, A. and P. F. Stadler:
Transit sets of two-point crossover.
The art of discrete and applied mathematics,
4 (2021) 1, P1.09 [DOI]
Changat, M. ; Nezhad, F. H.
and P. F. Stadler:
Cut vertex transit functions of hypergraphs.
Algorithms and discrete applied mathematics : 7th international conference, CALDAM
2021, Rupnagar, India, February 11-13, 2021 ; proceedings / A.
Mudgal... (eds.). Springer, 2021. - P. 222-233
(Lecture notes in computer science ; 12601)
[DOI]
Costa, M. B.
; Oliveira, J. V.
; da Silvia, W. M. C. ; Sen, R. ; Fallmann, J. ; Stadler, P. F. and M. Emilia M. T. Walter:
Machine learning studies of non-coding RNAs based on artificially constructed training
data.
Proceedings of the 14th international joint conference on biomedical engineering systems
and technologies : volume 3 / R.
Lorenz... (eds.). SciTePress, 2021. - P. 176-183 [DOI]
Di Lavore, E. ; Leal, W. and V. de Paiva:
Dialectica Petri nets.
[ARXIV]
Doncheva, N. T. ; Palasca, O. ; Yarani, R. ; Litman, T. ; Anthon, C. ; Groenen, M. A. M. ; Stadler, P. F. ; Pociot, F. ; Jensen, L. J. and J. Gorodkin:
Human pathways in animal models : possibilities and limitations.
Nucleic acids research,
49 (2021) 4, p. 1859-1871 [DOI]
Ender, A. ; Etzel, M. ; Hammer, S. ; Findeiß, S. ; Stadler, P. F. and M. Mörl:
Ligand-dependent tRNA processing by a rationally designed RNase P riboswitch.
Nucleic acids research,
49 (2021) 3, p. 1784-1800 [DOI]
Fingerhut, J. ; Gomez-Lavin, J. ; Winklmayr, C. and J. J. Prinz:
The aesthetic self : the importance of aesthetic taste in music and art for our perceived
identity.
Frontiers in psychology,
11 (2021), 577703 [DOI]
Gatter, T. and P. F. Stadler:
Ryūtō : Improved multi-sample transcript assembly for differential transcript
expression analysis and more.
Bioinformatics,
37 (2021) 23, p. 4307-4313 [DOI] [CODELINK]
Gatter, T. ; von Löhneysen, S. ; Fallmann, J. ; Drozdova, P. ; Hartmann, T. and P. F. Stadler:
LazyB : fast and cheap genome assembly.
Algorithms for molecular biology,
16 (2021), 8 [DOI]
Geiß, M. ; Chávez, E. ; González Laffitte, M. ; López Sánchez, A. ; Stadler, B. M. R. ; Valdivia, D. I. ; Hellmuth, M. ; Hernández Rosales, M. and P. F. Stadler:
Corrigendum: 'Best match graphs' [In: Journal of mathematical biology, 78 (2019)7,2015-2057].
Journal of mathematical biology,
82 (2021) 6, 47 [DOI] [ARXIV]
Geiß, M. ; Hellmuth, M. and P. F. Stadler:
A linear-time algorithm for the common refinement of rooted phylogenetic trees on
a common leaf set.
[ARXIV]
Guzman, G. E. C. ; Stadler, P. F. and A. Fujita:
Efficient Laplacian spectral density computations for networks with arbitrary degree
distributions.
Network science,
9 (2021) 3, p. 312-327 [DOI]
Gärtner, F. ; Kühnl, F. ; Seemann, C. R. ; Siederdissen, C. H.
and P. F. Stadler:
Superbubbles as an empirical characteristic of directed networks.
Network science,
9 (2021) 1, p. 49-58 [DOI] [ARXIV]
Günzel, C. ; Kühnl, F. ; Arnold, K. ; Findeiß, S. ; Weinberg, C. E. ; Stadler, P. F. and M. Mörl:
Beyond plug and pray : context sensitivity and in silico design of artificial neomycin
riboswitches.
RNA biology,
18 (2021) 4, p. 457-467 [DOI] [ARXIV] [CODELINK]
Hellmuth, M. ; Seemann, C. R. and P. F. Stadler:
Generalized Fitch graphs III : symmetrized Fitch maps and sets of symmetric binary
relations that are explained by unrooted edge-labeled trees.
Discrete mathematics and theoretical computer science,
23 (2021) 1, 13[ARXIV] [FREELINK]
Hoffmann, A. ; Erber, L. ; Betat, H. ; Stadler, P. F. ; Mörl, M. and J. Fallmann:
Changes of the tRNA modification pattern during the development of Dictyostelium discoideum.
Non-coding RNA,
7 (2021) 2, 32 [DOI]
Jakob, L. ; Vereshchagina, K. ; Tillmann, A. ; Rivarola-Duarte, L. ; Axenov-Gribanov, D. ; Bedulina, D. ; Gurkov, A. ; Drozdova, P. ; Timofeyev, M. ; Stadler, P. F. ; Luckenbach, T. ; Pörtner, H.-O. ; Sartoris, F. and M. Lucassen:
Thermal reaction norms of key metabolic enzymes reflect divergent physiological and
behavioral adaptations of closely related amphipod species.
Scientific reports,
11 (2021), 4562 [DOI]
Jorge, N. A.
; Ueberham, U. ; Knobloch, M. ; Stadler, P. F. ; Fallmann, J. and T. Arendt:
Disturbance of phylogenetic layer-specific adaptation of human brain gene expression
in Alzheimer's disease.
Scientific reports,
11 (2021) 1, 20200 [DOI]
Kirstein, A. S. ; Kehr, S. ; Nebe, M. ; Hanschkow, M. ; Barth, L. A. G. ; Lorenz, J. ; Penke, M. ; Breitfeld, J. ; Le Duc, D. ; Landgraf, K. ; Körner, A. ; Kovacs, P. ; Stadler, P. F. ; Kiess, W. and A. Garten:
PTEN regulates adipose progenitor cell growth, differentiation, and replicative aging.
The journal of biological chemistry,
297 (2021) 2, 100968 [DOI] [ARXIV]
Klapproth, C. ; Sen, R. ; Stadler, P. F. ; Findeiß, S. and J. Fallmann:
Common features in lncRNA annotation and classification : a survey.
Non-coding RNA,
7 (2021) 4, 77 [DOI]
Kolora, S. R.
; Gysi, D. M. ; Schaffer, S. ; Grimm-Seyfarth, A. ; Szabolcs, M. ; Faria, R. ; Henle, K. ; Stadler, P. F. ; Schlegel, M. and K. Nowick:
Accelerated evolution of tissue-specific genes mediates divergence amidst gene flow
in European green lizards.
Genome biology and evolution,
13 (2021) 8, evab109 [DOI]
Leal, W. ; Llanos, E. J. ; Bernal, A. ; Stadler, P. F. ; Jost, J. and G. Restrepo:
Computational data analysis shows that key developments towards the periodic system
occurred in the 1840s.
[FREELINK]
Leal, W. ; Restrepo, G. ; Stadler, P. F. and J. Jost:
Forman-Ricci curvature for hypergraphs.
Advances in complex systems,
24 (2021) 1, 2150003 [DOI] [ARXIV]
Lipaeva, P. ; Vereshchagina, K. ; Drozdova, P. ; Jakob, L. ; Kondrateva, E. ; Lucassen, M. ; Bedulina, D. ; Timofeyev, M. ; Stadler, P. F. and T. Luckenbach:
Different ways to play it cool : transcriptomic analysis sheds light on different
activity patterns of three amphipod species under long-term cold exposure.
Molecular ecology,
30 (2021) 22, p. 5735-5751 [DOI]
Lorenz, R. ; Flamm, C. ; Hofacker, I. L. and P. F. Stadler:
Efficient algorithms for co-folding of multiple RNAs.
Biomedical engineering systems and technologies : 13th international joint conference,
BIOSTEC 2020, Valletta, Malta, February 24-26, 2020, revised selected papers / X.
Ye (ed.). Springer, 2021. - P. 193-214
(Communications in computer and information science ; 1400)
[DOI]
Lorenz, R. and P. F. Stadler:
RNA secondary structures with limited base pair span : exact backtracking and an application.
Genes,
12 (2021) 1, 14 [DOI]
Machné, R. ; Murray, D. B. ; Bernhart, S. H. ; Axmann, I. M. and P. F. Stadler:
Pulse-width modulation of gene expression in budding yeast.
[ARXIV]
Meir, A. Y.
; Keller, M. ; Bernhart, S. H. ; Rinott, E. ; Tsaban, G. ; Zelicha, H. ; Kaplan, A. ; Schwarzfuchs, D. ; Shelef, I. ; Gepner, Y. ; Li, J. ; Lin, Y. ; Blüher, M. ; Ceglarek, U. ; Stumvoll, M. ; Stadler, P. F. ; Stampfer, M. J. ; Kovacs, P. ; Liang, L. and I. Shai:
Lifestyle weight-loss intervention may attenuate methylation aging : the CENTRAL MRI
randomized controlled trial.
Clinical epigenetics,
13 (2021) 1, 48 [DOI]
Meir, A. Y.
; Keller, M. ; Müller, L. ; Bernhart, S. H. ; Tsaban, G. ; Zelicha, H. ; Rinott, E. ; Kaplan, A. ; Gepner, Y. ; Shelef, I. ; Schwarzfuchs, D. ; Ceglarek, U. ; Stadler, P. F. ; Blüher, M. ; Stumvoll, M. ; Kovacs, P. and I. Shai:
Effects of lifestyle interventions on epigenetic signatures of liver fat : CENTRAL
randomized controlled trial.
Liver international,
41 (2021) 9, p. 2101-2111 [DOI]
Nitsche, A. ; Arnold, C. ; Ueberham, U. ; Reiche, K. ; Fallmann, J. ; Hackermüller, J. ; Horn, F. ; Stadler, P. F. and T. Arendt:
Alzheimer-related genes show accelerated evolution.
Molecular psychiatry,
26 (2021) 10, p. 5790-5796 [DOI] [ARXIV]
Nunn, A. ; Can, N. ; Otto, C. ; Fasold, M. ; Díez Rodríguez, B. ; Fernández Pozo, N. ; Rensing, S. A. ; Stadler, P. F. and D. Langenberger:
EpiDiverse Toolkit : a pipeline suite for the analysis of bisulfite sequencing data
in ecological plant epigenetics.
NAR : genomics and bioinformatics,
3 (2021) 4, lqab106[FREELINK]
Olzog, V. J.
; Gärtner, C. ; Stadler, P. F. ; Fallmann, J. and C. E. Weinberg:
cyPhyRNA-seq : a genome-scale RNA-seq method to detect active self-cleaving ribozymes
by capturing RNAs with 2 ',3 ' cyclic phosphates and 5 ' hydroxyl ends.
RNA biology,
18 (2021) Sup 2, p. 818-831 [DOI]
Parra-Rincón, E. ; Velandia-Huerto, C. A. ; Fallmann, J. ; Gittenberger, A. A. ; Brown, F. D. ; Stadler, P. F. and C. I. Bermúdez-Santana:
The genome of the ''sea vomit'' Didemnum vexillum.
BMC genomics,
11 (2021) 12, 1377 [DOI]
Rodriguez Fernandez, A. E.
:
On the study of fitness landscapes and the Max-Cut problem.
Dissertation, Universität Leipzig, 2021[FREELINK]
Saraiva, J. P.
; Bartholomaeus, A. ; Kallies, R. ; Gomes, M. ; Bicalho, M. ; Kasmanas, J. C.
; Vogt, C. ; Chatzinotas, A. ; Stadler, P. F. ; Dias, O. and U. N.
da Rocha:
OrtSuite : from genomes to prediction of microbial interactions within targeted ecosystem
processes.
Life science alliance,
4 (2021) 12, e202101167 [DOI] [ARXIV] [CODELINK]
Schaller, D.:
Gene family histories : theory and algorithms.
Dissertation, Universität Leipzig, 2021[FREELINK]
Schaller, D. ; Geiß, M. ; Hellmuth, M. and P. F. Stadler:
Best match graphs with binary trees.
Algorithms for computational biology : 8th International Conference, AlCoB 2021, Missoula,
MT, USA, June 7-11, 2021 ; proceedings / C.
Martín-Vide... (eds.). Springer, 2021. - P. 82-93
(Lecture notes in computer science ; 12715)
[DOI] [ARXIV]
Schaller, D. ; Geiß, M. ; Hellmuth, M. and P. F. Stadler:
Least resolved trees for two-colored best match graphs.
Journal of graph algorithms and applications,
25 (2021) 1, p. 397-416 [DOI] [ARXIV]
Schaller, D. ; Geiß, M. ; Hellmuth, M. and P. F. Stadler:
Heuristic algorithms for best match graph editing.
Algorithms for molecular biology,
16 (2021), 19 [DOI] [ARXIV]
Schaller, D. ; Geiß, M. ; Hellmuth, M. and P. F. Stadler:
Arc-completion of 2-colored best match graphs to binary-explainable best match graphs.
Algorithms,
14 (2021) 4, 110 [DOI] [ARXIV]
Schaller, D. ; Geiß, M. ; Stadler, P. F. and M. Hellmuth:
Complete characterization of incorrect orthology assignments in best match graphs.
Journal of mathematical biology,
82 (2021) 3, 20 [DOI] [ARXIV]
Schaller, D. ; Hellmuth, M. and P. F. Stadler:
A simpler linear-time algorithm for the common refinement of rooted phylogenetic trees
on a common leaf set.
Algorithms for molecular biology,
16 (2021), 23 [DOI] [ARXIV]
Schaller, D. ; Lafond, M. ; Stadler, P. F. ; Wieseke, N. and M. Hellmuth:
Indirect identification of horizontal gene transfer.
Journal of mathematical biology,
83 (2021) 1, 10 [DOI] [ARXIV]
Schaller, D. ; Stadler, P. F. and M. Hellmuth:
Complexity of modification problems for best match graphs.
Theoretical computer science,
865 (2021), p. 63-84 [DOI] [ARXIV]
Stadler, P. F.:
Alignments of biomolecular contact maps.
Interface focus,
11 (2021) 4, 20200066 [DOI]
Stadler, P. F. ; Velandia-Huerto, C. A. and J. Fallmann:
miRNAture : computational detection of microRNA candidates.
Genes,
12 (2021) 3, 348 [DOI]
Vieira, L. M.
; Jorge, N. A.
; de Sousa, J. B.
; Setubal, J. C. ; Stadler, P. F. and M. Emilia M. T. Walter:
Competing endogenous RNA in colorectal cancer : an analysis for colon, rectum, and
rectosigmoid junction.
Frontiers in oncology,
11 (2021), 681579 [DOI]
Wolpert, D. ; Price, M. H. ; Crabtree, S. A. ; Kohler, T. A. ; Jost, J. ; Evans, J. ; Stadler, P. F. ; Shimao, H. and M. D. Laubichler:
The past as a stochastic process.
[ARXIV]
Balogh, G. ; Bernhart, S. H. ; Stadler, P. F. and J. Schor:
A probabilistic version of Sankoff's maximum parsimony algorithm.
Journal of bioinformatics and computational biology,
18 (2020) 1, 2050004 [DOI]
Berkemer, S.:
Towards dynamic programming on generalized data structures and applications of dynamic
programming in bioinformatics.
Dissertation, Universität Leipzig, 2020[FREELINK]
Berkemer, S. ; Maier, L.-K. ; Amman, F. ; Bernhart, S. H. ; Wörtz, J. ; Märkle, P. ; Pfeiffer, F. ; Stadler, P. F. and A. Marchfelder:
Identification of RNA 3' ends and termination sites in Haloferax volcanii.
RNA biology,
17 (2020) 5, p. 663-676 [DOI] [ARXIV]
Berkemer, S. and S. E. McGlynn:
A new analysis of archaea-bacteria domain separation : variable phylogenetic distance
and the tempo of early evolution.
Molecular biology and evolution,
37 (2020) 8, p. 2332-2340 [DOI]
Berkemer, S. and P. F. Stadler:
Street name data as a reflection of migration and settlement history.
Urban science : open access journal,
4 (2020) 4, 74 [DOI]
Binder, S. ; Zipfel, I. ; Friedrich, M. ; Riedel, D. ; Ende, S. ; Kämpf, C. ; Wiedemann, K. ; Buschmann, T. ; Puppel, S.-H. ; Reiche, K. ; Stadler, P. F. and F. Horn:
Master and servant : LINC00152 - a STAT3-induced long noncoding RNA regulates STAT3
in a positive feedback in human multiple myeloma.
BMC medical genomics,
13 (2020), 22 [DOI]
Breitfeld, J. ; Kehr, S. ; Müller, L. ; Stadler, P. F. ; Böttcher, Y. ; Blüher, M. ; Stumvoll, M. and P. Kovacs:
Developmentally driven changes in adipogenesis in different fat depots are related
to obesity.
Frontiers in endocrinology,
11 (2020), 138 [DOI]
Changat, M. ; Narasimha-Shenoi, P. G. ; Nezhad, F. H.
; Kovše, M. ; Mohandas, S. ; Ramachandran, A. and P. F. Stadler:
Transit sets of \(k\)-point crossover operators.
AKCE international journal of graphs and combinatorics,
17 (2020) 1, p. 519-533 [DOI] [ARXIV]
Corona-Gomez, J. A.
; Garica-Lopez, I. J.
; Stadler, P. F. and S. L. Fernandez-Valverde:
Splicing conservation signals in plant long non-coding RNAs.
RNA,
26 (2020) 7, p. 784-793 [DOI] [ARXIV]
Eidi, M. ; Farzam, A. ; Leal, W. ; Samal, A. and J. Jost:
Edge-based analysis of networks : curvatures of graphs and hypergraphs.
Theory in biosciences,
139 (2020) 4, p. 337-348 MIS-Preprint: 103/2020 [DOI] [ARXIV]
Erber, L. ; Hoffmann, A. ; Fallmann, J. ; Betat, H. ; Stadler, P. F. and M. Mörl:
LOTTE-seq (Long hairpin oligonucleotide based tRNA high-throughput sequencing) : specific
selection of tRNAs with 3'-CCA end for high-throughput sequencing.
RNA biology,
17 (2020) 1, p. 23-32 [DOI]
Erber, L. ; Hoffmann, A. ; Fallmann, J. ; Hagedorn, M. ; Hammann, C. ; Stadler, P. F. ; Betat, H. ; Prohaska, S. J. and M. Mörl:
Unusual occurrence of two bona-fide CCA-adding enzymes in Dictyostelium discoideum.
International journal of molecular sciences,
21 (2020) 15, 5210 [DOI]
Fritz, A. ; Hellmuth, M. ; Stadler, P. F. and N. Wieseke:
Cograph editing : merging modules is equivalent to editing P4's.
The art of discrete and applied mathematics,
3 (2020) 2, P2.01 [DOI] [ARXIV]
Gatter, T. ; von Löhneysen, S. ; Drozdova, P. ; Hartmann, T. and P. F. Stadler:
Economic genome assembly from low coverage illumina and nanopore data.
[ARXIV]
Geiß, M. ; González Laffitte, M. ; López Sánchez, A. ; Valdivia, D. I. ; Hellmuth, M. ; Hernández Rosales, M. and P. F. Stadler:
Best match graphs and reconciliation of gene trees with species trees.
Journal of mathematical biology,
80 (2020) 5, p. 1459-1495 [DOI] [ARXIV]
Geiß, M. ; Stadler, P. F. and M. Hellmuth:
Reciprocal best match graphs.
Journal of mathematical biology,
80 (2020) 3, p. 865-953 [DOI] [ARXIV]
Hellmuth, M. ; Geiß, M. and P. F. Stadler:
Complexity of modification problems for reciprocal best match graphs.
Theoretical computer science,
809 (2020), p. 384-393 [DOI] [ARXIV]
Hellmuth, M. ; Seemann, C. R. and P. F. Stadler:
Generalized Fitch graphs II : sets of binary relations that are explained by edge-labeled
trees.
Discrete applied mathematics,
283 (2020), p. 495-511 [DOI] [ARXIV]
Hordijk, W. ; Kaufman, S. A. and P. F. Stadler:
Average fitness differences on NK landscapes.
Theory in biosciences,
139 (2020) 1, p. 1-7 [DOI]
Hoser, S. M. ; Hoffmann, A. ; Meindl, A. ; Fallmann, J. ; Bernhart, S. H. ; Müller, L. ; Ploner, M. ; Misslinger, M. ; Kremser, L. ; Lindner, H. ; Geley, S. ; Schaal, H. ; Stadler, P. F. and A. Hüttenhofer:
Intronic tRNAs of mitochondrial origin regulate constitutive and alternative splicing.
Genome biology,
21 (2020) 1, 299 [DOI]
Keller, M. ; Meir, A. Y.
; Bernhart, S. H. ; Gepner, Y. ; Shelef, I. ; Schwarzfuchs, D. ; Tsaban, G. ; Zelicha, H. ; Hopp, L. ; Müller, L. ; Rohde, K. ; Böttcher, Y. ; Stadler, P. F. ; Stumvoll, M. ; Blüher, M. ; Kovacs, P. and I. Shai:
DNA methylation signature in blood mirrors successful weight-loss during lifestyle
interventions : the CENTRAL trial.
Genome medicine,
12 (2020), 97 [DOI]
Kühnl, F. ; Stadler, P. F. and S. Findeiß:
Assessing the quality of cotranscriptional folding simulations.
[ARXIV]
Leal, W. ; Eidi, M. and J. Jost:
Ricci curvature of random and empirical directed hypernetworks.
Applied network science,
5 (2020), 65 [DOI]
Leal, W. ; Llanos, E. J. ; Bernal, A. ; Restrepo, G. ; Luu, H. D.
; Jost, J. and P. F. Stadler:
Exploring the hypergraph structure underlying the chemical space.
NetSci-X 2020 Tokyo : international school and conference on network Science
Long, Y. and P. F. Stadler:
Exact-2-relation graphs.
Discrete applied mathematics,
285 (2020), p. 212-226 [DOI] [ARXIV]
Lorenz, R. ; Flamm, C. ; Hofacker, I. L. and P. F. Stadler:
Efficient computation of base-pairing probabilities in multi-strand RNA folding.
Proceedings of the 13th international joint conference on biomedical engineering systems
and technologies - Volume 3 : Bioinformatics / E.
De Maria... (eds.). SciTePress, 2020. - P. 23-31 [DOI]
Majumdar, A. and A. Mehta:
Heterogeneous contact networks in COVID-19 spreading : the role of social deprivation.
[ARXIV]
Retzlaff, N.:
Studying evolutionary change transdisciplinary advances in understanding and measuring
evolution.
Dissertation, Universität Leipzig, 2020[FREELINK]
Rodriguez Fernandez, A. E.
; Gonzalez-Torres, B. ; Menchaca-Mendez, R. and P. F. Stadler:
Clustering improves the Goemans-Williamson approximation for the max-cut problem.
Computation : open access journal,
8 (2020) 3, 75 [DOI]
Schwarz, T. S. ; Berkemer, S. ; Bernhart, S. H. ; Weiss, M. ; Ferreira-Cerca, S. ; Stadler, P. F. and A. Marchfelder:
Splicing endonuclease is an important player in rRNA and tRNA maturation in archaea.
Frontiers in microbiology,
11 (2020), 594838 [DOI]
Seal, R. ; Chen, L.-L. ; Griffiths-Jones, S. ; Lowe, T. M. ; Mathews, M. B. ; O'Reilly, D. ; Pierce, A. J. ; Stadler, P. F. ; Ulitsky, I. ; Wolin, S. L. and E. A. Bruford:
A guide to naming human non-coding RNA genes.
The EMBO journal,
39 (2020) 6, e103777 [DOI]
Sen, R. ; Fallmann, J. ; Walter, M. Emilia M. T. and P. F. Stadler:
Are spliced ncRNA host genes distinct classes of lncRNAs?.
Theory in biosciences,
139 (2020) 4, p. 349-359 [DOI]
Sen, R. ; Fallmann, J. ; Walter, M. Emilia M. T. and P. F. Stadler:
Supervised and unsupervised classification of lncRNA subtypes.
[ARXIV]
Shatilina, Z. ; Drozdova, P. ; Bedulina, D. ; Rivarola-Duarte, L. ; Schreiber, S. ; Otto, C. ; Jühling, F. ; Aulhorn, S. ; Busch, W. ; Lubyaga, Y. ; Kondrateva, E. ; Pobezhimova, T. ; Jakob, L. ; Lucassen, M. ; Sartoris, F. ; Hackermüller, J. ; Pörtner, H.-O. ; Stadler, P. F. ; Luckenbach, T. and M. Timofeyev:
Transcriptome-level effects of the model organic pollutant phenanthrene and its solvent
acetone in three amphipod species.
Comparative biochemistry and physiology / D,
33 (2020), 100630 [DOI]
Stadler, P. F. ; Geiß, M. ; Schaller, D. ; López Sánchez, A. ; González Laffitte, M. ; Valdivia, D. I. ; Hellmuth, M. and M. Hernández Rosales:
From pairs of most similar sequences to phylogenetic best matches.
Algorithms for molecular biology,
15 (2020) 1, 5 [DOI] [ARXIV]
Waldl, M. ; Will, S. ; Wolfinger, M. T. ; Hofacker, I. L. and P. F. Stadler:
Bi-alignments as models of incongruent evolution of RNA sequence and secondary structure.
Computational intelligence methods for bioinformatics and biostatistics : 16th international
meeting, CIBB 2019, Bergamo, Italy, September 4-6, 2019, revised selected papers / P.
Cazzaniga (ed.). Springer, 2020. - P. 159-170
(Lecture notes in computer science ; 12313)
[DOI] [ARXIV]
Winklmayr, C. ; Kao, A. B. ; Bak-Coleman, J. B. and P. Romanczuk:
The wisdom of stalemates : consensus and clustering as filtering mechanisms for improving
collective accuracy.
Proceedings of the Royal Society of London / B,
287 (2020) 1938, 20201802 [DOI] [ARXIV] [CODELINK]
Andersen, J. L. ; Flamm, C. ; Merkle, D. and P. F. Stadler:
Information processing in chemical systems.
The energetics of computing in life and machines / D.
Wolpert... (eds.). SFI Press, 2019. - P. 83-102[FREELINK]
Andersen, J. L. ; Flamm, C. ; Merkle, D. and P. F. Stadler:
Chemical transformation motifs : modelling pathways as integer hyperflows.
IEEE ACM transactions on computational biology and bioinformatics,
16 (2019) 2, p. 510-523 [DOI] [ARXIV]
Bašić, N. ; Berkemer, S. ; Fallmann, J. ; Fowler, P. W. ; Gatter, T. ; Pisanski, T. ; Retzlaff, N. ; Stadler, P. F. and S. S. Zemljič:
Convexity deficit of benzenoids.
Croatica chemica acta,
92 (2019) 4, p. 457-466 [DOI] [ARXIV]
Changat, M. ; Narasimha-Shenoi, P. G. and P. F. Stadler:
Axiomatic characterization of transit functions of weak hierarchies.
The art of discrete and applied mathematics,
2 (2019) 1, 1 [DOI] [FREELINK]
Costa, M. B.
; Siederdissen, C. H.
; Dunjic, M. ; Stadler, P. F. and K. Nowick:
SSS-test : a novel test for detecting positive selection on RNA secondary structure.
BMC bioinformatics,
20 (2019) 1, 151 [DOI] [FREELINK]
da Silvia, W. M. C. ; Andersen, J. L. ; Holanda, M. T. ; Walter, M. Emilia M. T. ; Brigido, M. M. ; Stadler, P. F. and C. Flamm:
Exploring plant sesquiterpene diversity by generating chemical networks.
Processes,
7 (2019) 4, 240 [DOI] [FREELINK]
Donath, A. ; Jühling, F. ; Al-Arab, M. ; Bernhart, S. H. ; Reinhardt, F. ; Stadler, P. F. ; Middendorf, M. and M. Bernt:
Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes.
Nucleic acids research,
47 (2019) 20, p. 10543-10552 [DOI]
Drozdova, P. ; Rivarola-Duarte, L. ; Bedulina, D. ; Axenov-Gribanov, D. ; Schreiber, S. ; Gurkov, A. ; Shatilina, Z. ; Vereshchagina, K. ; Lubyaga, Y. ; Madyarova, E. ; Otto, C. ; Jühling, F. ; Busch, W. ; Jakob, L. ; Lucassen, M. ; Sartoris, F. ; Hackermüller, J. ; Hoffmann, S. ; Pörtner, H.-O. ; Luckenbach, T. ; Timofeyev, M. and P. F. Stadler:
Comparison between transcriptomic responses to short-term stress exposures of a common
Holarctic and endemic Lake Baikal amphipods.
BMC genomics,
20 (2019), 712 [DOI] [FREELINK]
Fallmann, J. ; Videm, P. ; Bagnacani, A. ; Batut, B. ; Doyle, M. A. ; Klingstrom, T. ; Eggenhofer, F. ; Stadler, P. F. ; Backofen, R. and B. A. Grüning:
The RNA workbench 2.0 : next generation RNA data analysis.
Nucleic acids research,
47 (2019) W1, p. W511-W515 [DOI]
Gatter, T. and P. F. Stadler:
Ryūtō: network-flow based transcriptome reconstruction.
BMC bioinformatics,
20 (2019), 190 [DOI]
Geiß, M. ; Chávez, E. ; González Laffitte, M. ; López Sánchez, A. ; Stadler, B. M. R. ; Valdivia, D. I. ; Hellmuth, M. ; Hernández Rosales, M. and P. F. Stadler:
Best match graphs.
Journal of mathematical biology,
78 (2019) 7, p. 2015-2057 [DOI] [ARXIV]
Gärtner, F. and P. F. Stadler:
Direct superbubble detection.
Algorithms,
12 (2019) 4, 81 [DOI]
Hellmuth, M. and C. R. Seemann:
Alternative characterizations of Fitch's xenology relation.
Journal of mathematical biology,
79 (2019) 3, p. 969-986 [DOI] [ARXIV]
Kamm, K. ; Osigus, H.-J. ; Stadler, P. F. ; DeSalle, R. and B. Schierwater:
Genome analyses of a placozoan rickettsial endosymbiont show a combination of mutualistic
and parasitic traits.
Scientific reports,
9 (2019) 1, 17561 [DOI]
Kirchner, F. ; Retzlaff, N. and P. F. Stadler:
A general framework for exact partially local alignments.
Proceedings of the 12th international joint conference on biomedical engineering systems
and technologies - Volume 3 : February 22-24, 2019, in Prague, Czech Republic / E.
De Maria... (eds.). SciTePress, 2019. - P. 194-200 [DOI]
Kirsch, R. ; Olzog, V. J.
; Bonin, S. ; Weinberg, C. E. ; Betat, H. ; Stadler, P. F. and M. Mörl:
A streamlined protocol for the detection of mRNA-sRNA interactions using AMT-crosslinking
in vitro.
BioTechniques,
67 (2019) 4, p. 178-183 [DOI]
Kolora, S. R.
; Weigert, A. ; Saffari, A. ; Kehr, S. ; Costa, M. B.
; Spröer, C. ; Indrischek, H. ; Chintalapati, M. ; Lohse, K. ; Doose, G. ; Overmann, J. ; Bunk, B. ; Bleidorn, C. ; Grimm-Seyfarth, A. ; Henle, K. ; Nowick, K. ; Faria, R. ; Stadler, P. F. and M. Schlegel:
Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and
L. bilineata, and implications for speciation.
GigaScience,
8 (2019) 2, giy160 [DOI]
Leal, W. ; Eidi, M. and J. Jost:
Curvature-based analysis of directed hypernetworks.
Complex networks 2019 : the 8th international conference on complex networks and their
applications ; December 10 - 12, 2019 Lisbon, Portugal ; book of abstract / H.
Cherifi (ed.). International conference on complex networks and their applications, 2019. - P. 32-34[FREELINK]
Leal, W. ; Llanos, E. J. ; Stadler, P. F. ; Jost, J. and G. Restrepo:
The chemical space from which the periodic system arose.
Nature chemistry,
Vol. not yet known, pp. not yet known MIS-Preprint: 68/2019 [FREELINK]
Leal, W. and G. Restrepo:
Formal structure of periodic system of elements.
Proceedings of the Royal Society of London / A,
475 (2019) 2224, 20180581 MIS-Preprint: 25/2019 [DOI] [ARXIV]
Llanos, E. J. ; Leal, W. ; Bernal, A. ; Restrepo, G. ; Jost, J. and P. F. Stadler:
A network model of the chemical space provides similarity structure to the system
of chemical elements.
Complex networks 2019 : the 8th international conference on complex networks and their
applications ; December 10 - 12, 2019 Lisbon, Portugal ; book of abstract / H.
Cherifi (ed.). International conference on complex networks and their applications, 2019. - P. 308-310[FREELINK]
Llanos, E. J. ; Leal, W. ; Luu, H. D.
; Jost, J. ; Stadler, P. F. and G. Restrepo:
Correction: 'Exploration of the chemical space and its three historical regimes' [116
(2019) 26, 12660-12665].
Proceedings of the National Academy of Sciences of the United States of America,
116 (2019) 29, p. 14779-14779 [DOI]
Llanos, E. J. ; Leal, W. ; Luu, H. D.
; Jost, J. ; Stadler, P. F. and G. Restrepo:
Exploration of the chemical space and its three historical regimes.
Proceedings of the National Academy of Sciences of the United States of America,
116 (2019) 26, p. 12660-12665 [DOI]
Nowick, K. ; Costa, M. B.
; Siederdissen, C. H.
and P. F. Stadler:
Selection pressures on RNA sequences and structures.
Evolutionary bioinformatics,
15 (2019), 1176934319871919 [DOI]
Prohaska, S. J. ; Stadler, P. F. and M. D. Laubichler:
How and what does a biological system computer?.
The energetics of computing in life and machines / D.
Wolpert... (eds.). SFI Press, 2019. - P. 169-187[FREELINK]
Sousa, I. G.
; Simi, K. C.
; do Almo, M. M.
; Bezerra, M. A.
; Doose, G. ; Raiol, T. ; Stadler, P. F. ; Hoffmann, S. ; Maranhão, A. Q.
and M. M. Brigido:
Gene expression profile of human T cells following a single stimulation of peripheral
blood mononuclear cells with anti-CD3 antibodies.
BMC genomics,
20 (2019), 593 [DOI]
Sweeney, B. A. ; Petrov, A. I. ; Burkov, B. ; Finn, R. D. ; Bateman, A. ; Szymanski, M. ; Karlowski, W. M. ; Gorodkin, J. ; Seemann, S. E. ; Cannone, J. J. ; Gutell, R. R. ; Fey, P. ; Basu, S. ; Kay, S. J. E. ; Cochrane, G. ; Billis, K. ; Emmert, D. ; Marygold, S. J. ; Huntley, R. P. ; Lovering, R. C. ; Frankish, A. ; Chan, P. P. ; Lowe, T. M. ; Bruford, E. A. ; Seal, R. ; Vandesompele, J. ; Volders, P.-J. ; Parakevopoulou, M. ; Ma, L. ; Zhang, Z. ; Griffiths-Jones, S. ; Bujnicki, J. M. ; Boccaletto, P. ; Blake, J. A. ; Bult, C. J. ; Chen, R. ; Zhao, Y. ; Wood, V. ; Rutherford, K. ; Rivas, E. ; Cole, J. R. ; Laulederkind, S. J. F. ; Shimoyama, M. ; Gillespie, M. E. ; Orlic-Milacic, M. ; Kalvari, I. ; Nowrocki, E. ; Engel, S. R. ; Cherry, J. M.
; Beradini, T. ; Hatzigeorgiou, A. G. ; Karagkouni, D. ; Howe, K. L. ; Davis, P. ; Dinger, M. E. ; He, S. ; Yoshihama, M. ; Kenmochi, N. ; Stadler, P. F. and K. P. Williams:
RNAcentral : a hub of information for non-coding RNA sequences.
Nucleic acids research,
47 (2019) D1, p. D221-D229 [DOI]
Sweeney, B. A. ; Petrov, A. I. ; Burkov, B. ; Finn, R. D. ; Bateman, A. ; Szymanski, M. ; Karlowski, W. M. ; Gorodkin, J. ; Seemann, S. E. ; Cannone, J. J. ; Gutell, R. R. ; Fey, P. ; Basu, S. ; Kay, S. J. E. ; Cochrane, G. ; Billis, K. ; Emmert, D. ; Marygold, S. J. ; Huntley, R. P. ; Lovering, R. C. ; Frankish, A. ; Chan, P. P. ; Lowe, T. M. ; Bruford, E. A. ; Seal, R. ; Vandesompele, J. ; Volders, P.-J. ; Parakevopoulou, M. ; Ma, L. ; Zhang, Z. ; Griffiths-Jones, S. ; Bujnicki, J. M. ; Boccaletto, P. ; Blake, J. A. ; Bult, C. J. ; Chen, R. ; Zhao, Y. ; Wood, V. ; Rutherford, K. ; Rivas, E. ; Cole, J. R. ; Laulederkind, S. J. F. ; Shimoyama, M. ; Gillespie, M. E. ; Orlic-Milacic, M. ; Kalvari, I. ; Nowrocki, E. ; Engel, S. R. ; Cherry, J. M.
; Beradini, T. ; Hatzigeorgiou, A. G. ; Karagkouni, D. ; Howe, K. L. ; Davis, P. ; Dinger, M. E. ; He, S. ; Yoshihama, M. ; Kenmochi, N. ; Stadler, P. F. and K. P. Williams:
Corrigendum: ''RNAcentral : a hub of information for non-coding RNA sequences'' [Nucleic
acids research, 47 (2019) D1, p. D221-D229].
Nucleic acids research,
47 (2019) D1, p. D1250-D1251 [DOI]
Uxa, S. ; Bernhart, S. H. ; Mages, C. F. S. ; Fischer, M. ; Kohler, R. ; Hoffmann, S. ; Stadler, P. F. ; Engeland, K. and G. A. Müller:
DREAM and RB cooperate to induce gene repression and cell-cycle arrest in response
to p53 activation.
Nucleic acids research,
47 (2019) 17, p. 9087-9103 [DOI]
Valdivia, D. I. ; Geiß, M. ; Hellmuth, M. ; Hernández Rosales, M. and P. F. Stadler:
Hierarchical colorings of cographs.
[ARXIV]
Wiegreffe, D. ; Alexander, D. ; Stadler, P. F. and D. Zeckzer:
RNApuzzler : efficient outerplanar drawing of RNA-secondary structures.
Bioinformatics,
35 (2019) 8, p. 1342-1349 [DOI] [FREELINK]
Wolpert, D. ; Kempes, C. ; Stadler, P. F. and J. A. Grochow:
Preface.
The energetics of computing in life and machines / D.
Wolpert... (eds.). SFI Press, 2019[FREELINK]
Wolpert, D. ; Kempes, C. ; Stadler, P. F. and J. A. Grochow (eds.):
The energetics of computing in life and machines.
SFI Press, 2019. - XXVIII, 463 p. ISBN 978-1-947864-07-8 [FREELINK]
Yazbeck, A. M. ; Stadler, P. F. ; Tout, K. R. and J. Fallmann:
Automatic curation of large comparative animal microRNA datasets.
Bioinformatics,
35 (2019) 22, p. 4553-4559 [DOI] [FREELINK]
Andersen, J. L. ; Fagerberg, R. ; Flamm, C. ; Kianian, R. ; Merkle, D. and P. F. Stadler:
Towards mechanistic prediction of mass spectra using graph transformation.
Match,
80 (2018) 3, p. 705-731[FREELINK]
Andersen, J. L. ; Flamm, C. ; Merkle, D. and P. F. Stadler:
Rule composition in graph transformation models of chemical reactions.
Match,
80 (2018) 3, p. 661-704[FREELINK]
Backofen, R. ; Gorodkin, J. ; Hofacker, I. L. and P. F. Stadler:
Comparative RNA genomics.
Comparative genomics : methods and protocols / J.
C. Setubal... (eds.). Humana Press, Springer, 2018. - P. 363-400
(Methods in molecular biology ; 1704)
[DOI]
Berkemer, S. ; Siederdissen, C. H.
and P. F. Stadler:
Alignments as compositional structures.
Compositionality : the open-access journal for the mathematics of composition,
Vol. not yet known, pp. not yet known[ARXIV] [FREELINK]
Bhattacharya, T. ; Retzlaff, N. ; Blasi, D. E. ; Croft, W. ; Cysouw, M. ; Hruschka, D. ; Maddieson, I. ; Müller, L. ; Smith, E. ; Stadler, P. F. and G. Starostin:
Studying language evolution in the age of big data.
Journal of language evolution,
3 (2018) 2, p. 94-129 [DOI]
Blasi, D. E.:
Linguistic diversity through data.
Dissertation, Universität Leipzig, 2018[FREELINK]
Canzler, S. ; Stadler, P. F. and J. Schor:
The fungal snoRNAome.
RNA,
24 (2018) 3, p. 342-360 [DOI] [FREELINK]
Changat, M. ; Nezhad, F. H.
and P. F. Stadler:
Axiomatic characterization of transit functions of hierarchies.
Ars mathematica contemporanea,
14 (2018) 1, p. 117-128 [DOI]
Costa, M. B.
; Siederdissen, C. H.
; Tulpan, D. ; Stadler, P. F. and K. Nowick:
Temporal ordering of substitutions in RNA evolution : uncovering the structural evolution
of the Human Accelerated Region 1.
Journal of theoretical biology,
438 (2018), p. 143-150 [DOI] [FREELINK]
Dhiman, I. ; Kimber, S. A. J. ; Mehta, A. and T. Chatterji:
A neutron tomography study : probing the spontaneous crystallization of randomly packed
granular assemblies.
Scientific reports,
8 (2018) 1, 17637 [DOI] [ARXIV]
Donath, A. and P. F. Stadler:
Split-inducing indels in phylogenomic analysis.
Algorithms for molecular biology,
13 (2018), 12 [DOI] [FREELINK]
Ebadi, H. ; Perry, M. ; Short, K. ; Klemm, K. ; Desplan, C. ; Stadler, P. F. and A. Mehta:
Patterning the insect eye : from stochastic to deterministic mechanisms.
PLoS computational biology,
14 (2018) 11, e1006363 [DOI] [ARXIV]
Fagerberg, R. ; Flamm, C. ; Kianian, R. ; Merkle, D. and P. F. Stadler:
Finding the K best synthesis plans.
Journal of cheminformatics,
10 (2018) 1, 19 [DOI]
Geiß, M. ; Anders, J. ; Stadler, P. F. ; Wieseke, N. and M. Hellmuth:
Reconstructing gene trees from Fitch's xenology relation.
Journal of mathematical biology,
77 (2018) 5, p. 1459-1491 [DOI] [ARXIV]
Geiß, M. ; Hellmuth, M. ; Long, Y. and P. F. Stadler:
A short note on undirected fitch graphs.
The art of discrete and applied mathematics,
1 (2018) 1, 8 [DOI] [ARXIV] [FREELINK]
Gröbner, S. N. ; Worst, B. C. ; Weischenfeldt, J. ; Buchhalter, I. ; Kleinheinz, K. ; Rudneva, V. A. ; Johann, P. D. ; Balasubramanian, G. P.
; Segura-Wang, M. ; Brabetz, S. ; Bender, S. ; Hutter, B. ; Sturm, D. ; Pfaff, E. ; Hübschmann, D. ; Zipprich, G. ; Heinold, M. ; Eils, J. ; Lawerenz, C. ; Erkek, S. ; Lambo, S. ; Waszak, S. ; Blattmann, C. ; Borkhardt, A. ; Kuhlen, M. ; Eggert, A. ; Fulda, S. ; Gessler, M. ; Wegert, J. ; Kappler, R. ; Baumhoer, D. ; Burdach, S. ; Kirschner-Schwabe, R. ; Kontny, U. ; Kulozik, A. E. ; Lohmann, D. ; Hettmer, S. ; Eckert, C. ; Bielack, S. ; Nathrath, M. ; Niemeyer, C. ; Richter, G. H. ; Schulte, J. ; Siebert, R. ; Westermann, F. ; Molenaar, J. J. ; Vassal, G. ; Witt, H. ; Lichter, P. ; Weber, U. D. ; Eils, R. ; Korshunov, A. ; Witt, O. ; Pfister, S. M. ; Reifenberger, G. ; Felsberg, J. ; von Kalle, M. ; Schmidt, M. ; Bartholomä, C. ; Taylor, M. ; Jones, D. T. W. ; Jäger, N. ; Korbel, J. O. ; Stütz, A. ; Rausch, T. ; Radlwimmer, B. ; Yaspo, M.-L. ; Lehrach, H. ; Warnatz, H.-J. ; Landgraf, P. ; Brors, B. ; Zapatka, M. ; Wagner, S. ; Haake, A. ; Richter, J. ; Richter, G. ; Kerssemakers, J. ; Jaeger-Schmidt, C. ; Scholz, I. ; Bergmann, A. K. ; Borst, C. ; Burkhardt, B. ; Claviez, A. ; Dreyling, M. ; Eberth, S. ; Einsele, H. ; Frickhofen, N. ; Haas, S. ; Hansmann, M.-L. ; Karsch, D. ; Kneba, M. ; Lisfeld, J. ; Mantovani-Loeffler, L. ; Rohde, M. ; Ott, G. ; Stadler, C. ; Staib, P. ; Stilgenbauer, S. ; Trümper, L. ; Zenz, T. ; Kube, D. ; Küppers, R. ; Weniger, M. A. ; Hummel, M. ; Klapper, W. ; Kostezka, U. ; Lenze, D. ; Moeller, P. ; Rosenwald, A. ; Szczepanowski, M. ; Ammerpohl, O. ; Aukema, S. M. ; Binder, V. ; Hoell, J. I. ; Leich, E. ; López, C. ; Nagel, I. ; Pischimariov, J. ; Rosenstiel, P. ; Schilhabel, M. ; Schreiber, S. ; Vater, I. ; Wagener, R. ; Bernhart, S. H. ; Binder, H. ; Brors, B. ; Doose, G. ; Hoffmann, S. ; Hopp, L. ; Kretzmer, H. ; Kreuz, M. ; Langenberger, D. ; Loeffler, M. ; Rosolowski, M. ; Schlesner, M. ; Stadler, P. F. ; Sungalee, S. ; Kratz, C. P. ; van Tilburg, C. M. ; Kramm, C. M. ; Fleischhack, G. ; Dirksen, U. ; Rutkowski, S. ; Frühwald, M. ; von Hoff, K. ; Wolf, S. ; Klingebiel, T. ; Koscielniak, E. ; Koster, J. ; Resnick, A. C. ; Zhang, J. ; Liu, Y. ; Zhou, X. ; Waanders, A. J. ; Zwijnenburg, D. A. ; Raman, P. ; Northcott, P. A. ; Pajtler, K. W. ; Kool, M. ; Piro, R. M. and L. Chavez:
The landscape of genomic alterations across childhood cancers.
Nature,
555 (2018) 7696, p. 321-327 [DOI]
Gärtner, F. ; Müller, L. and P. F. Stadler:
Superbubbles revisited.
Algorithms for molecular biology,
13 (2018) 1, 16 [DOI]
Gärtner, F. ; Siederdissen, C. H.
; Müller, L. and P. F. Stadler:
Coordinate systems for supergenomes.
Algorithms for molecular biology,
13 (2018), 15 [DOI] [FREELINK]
Hellmuth, M. ; Hernández Rosales, M. ; Long, Y. and P. F. Stadler:
Inferring phylogenetic trees from the knowledge of rare evolutionary events.
Journal of mathematical biology,
76 (2018) 7, p. 1623-1653 [DOI] [ARXIV]
Hoffmann, A. ; Fallmann, J. ; Vilardo, E. ; Mörl, M. ; Stadler, P. F. and F. Amman:
Corrigendum: 'Accurate mapping of tRNA reads' [In: Bioinformatics, 34 (2018) 7, p.
1116-1124].
Bioinformatics,
34 (2018) 13, p. 2339-2339 [DOI]
Hoffmann, A. ; Fallmann, J. ; Vilardo, E. ; Mörl, M. ; Stadler, P. F. and F. Amman:
Accurate mapping of tRNA reads.
Bioinformatics,
34 (2018) 7, p. 1116-1124 [DOI] [FREELINK]
Kianian, R.:
Algorithmic methods for synthesis planning and mass spectrometry.
Dissertation, Universität Leipzig, 2018[FREELINK]
Kirsch, R. ; Seemann, S. E. ; Ruzzo, W. L. ; Cohen, S. M. ; Stadler, P. F. and J. Gorodkin:
Identification and characterization of novel conserved RNA structures in Drosophila.
BMC genomics,
19 (2018) 1, 899 [DOI]
Klemm, K. ; Mehta, A. and P. F. Stadler:
Cover-encodings of fitness landscapes.
Bulletin of mathematical biology,
80 (2018) 8, p. 2154-2176 [DOI] [ARXIV]
Kutsche, L. K. ; Gysi, D. M. ; Fallmann, J. ; Lenk, K. ; Petri, R. ; Swiersy, A. ; Klapper, S. D. ; Pircs, K. ; Khattak, S. ; Stadler, P. F. ; Jakobsson, J. ; Nowick, K. and V. Busskamp:
Combined experimental and system-level analyses reveal the complex regulatory network
of miR-124 during human neurogenesis.
Cell systems,
7 (2018) 4, p. 438-452 [DOI]
Laubichler, M. D. ; Prohaska, S. J. and P. F. Stadler:
Toward a mechanistic explanation of phenotypic evolution : the need for a theory of
theory integration.
Journal of experimental zoology / B,
330 (2018) 1, p. 5-14 [DOI]
Lokits, A. D. ; Indrischek, H. ; Meiler, J. ; Hamm, H. E. and P. F. Stadler:
Tracing the evolution of the heterotrimeric G protein alpha subunit in Metazoa.
BMC evolutionary biology,
18 (2018) 1, 51 [DOI]
Lozada-Chávez, I. ; Stadler, P. F. and S. J. Prohaska:
Genome-wide features of introns are evolutionary decoupled among themselves and from
genome size throughout Eukarya.
[ARXIV]
Mehta, A.:
Storing and retrieving long-term memories : cooperation and competition in synaptic
dynamics.
Advances in physics : X,
3 (2018) 1, p. 755-789 [DOI] [ARXIV]
Nøjgaard, N. ; Geiß, M. ; Merkle, D. ; Stadler, P. F. ; Wieseke, N. and M. Hellmuth:
Time-consistent reconciliation maps and forbidden time travel.
Algorithms for molecular biology,
13 (2018), 2 [DOI] [ARXIV]
Paschoal, A. R.
; Lozada-Chávez, I. ; Domingues, D. S.
and P. F. Stadler:
ceRNAs in plants : computational approaches and associated challenges for target mimic
research.
Briefings in bioinformatics,
19 (2018) 6, p. 1273-1289 [DOI] [FREELINK]
Prohaska, S. J. ; Berkemer, S. ; Gärtner, F. ; Gatter, T. ; Retzlaff, N. ; Siederdissen, C. H.
and P. F. Stadler:
Expansion of gene clusters, circular orders, and the shortest Hamiltonian path problem.
Journal of mathematical biology,
77 (2018) 2, p. 313-341 [DOI]
Restrepo, G. ; Stadler, P. F. and J. Jost:
Proceedings of the ''Mathematics in Chemistry Meeting'', Leipzig, Germany, October
26-28 2016 ; foreword.
Match,
80 (2018) 3, p. 541-545[FREELINK]
Retzlaff, N. and P. F. Stadler:
Phylogenetics beyond biology.
Theory in biosciences,
137 (2018) 2, p. 133-143 [DOI]
Retzlaff, N. and P. F. Stadler:
Partially local multi-way alignments.
Mathematics in computer science,
12 (2018) 2, p. 207-234 [DOI] [FREELINK]
Samal, A. ; Sreejith, R. P. ; Gu, J. ; Liu, S. ; Saucan, E. and J. Jost:
Comparative analysis of two discretizations of Ricci curvature for complex networks.
Scientific reports,
8 (2018), 8650 MIS-Preprint: 83/2017 [DOI] [ARXIV]
Setubal, J. C. and P. F. Stadler:
Gene phylogenies and orthologous groups.
Comparative genomics : methods and protocols / J.
C. Setubal... (eds.). Humana Press, Springer, 2018. - P. 1-28
(Methods in molecular biology ; 1704)
[DOI]
Skrzypczyk, A. ; Kehr, S. ; Krystel, I. ; Bernhart, S. H. ; Giri, S. ; Bader, A. and P. F. Stadler:
Noncoding RNA transcripts during differentiation of induced pluripotent stem cells
into hepatocytes.
Stem cells international,
2018 (2018), 5692840 [DOI]
Stadler, B. M. R. and P. F. Stadler:
Reachability, connectivity, and proximity in chemical spaces.
Match,
80 (2018) 3, p. 639-659[FREELINK]
Stadler, B. M. R. and P. F. Stadler:
Reachability, connectivity, and proximity in chemical spaces.
Match,
80 (2018) 3, p. 639-659[FREELINK]
Waldl, M. ; Thiel, B. C. ; Ochsenreiter, R. ; Holzenleiter, A. ; Oliveira, J. V.
; Walter, M. Emilia M. T. ; Wolfinger, M. T. and P. F. Stadler:
TERribly difficult : searching for Telomerase RNAs in Saccharomycetes.
Genes,
9 (2018) 8, 372 [DOI] [ARXIV]
Wiegreffe, D. ; Müller, L. ; Steuck, J. ; Zeckzer, D. and P. F. Stadler:
The Sierra Platinum Service for generating peak-calls for replicated ChIP-seq experiments.
BMC research notes,
11 (2018), 512 [DOI]
Yazbeck, A. M. ; Tout, K. R. and P. F. Stadler:
Detailed secondary structure models of invertebrate 7SK RNAs.
RNA biology,
15 (2018) 2, p. 158-164 [DOI] [FREELINK]
Al-Arab, M. ; Bernt, M. ; Siederdissen, C. H.
; Tout, K. R. and P. F. Stadler:
Partially local three-way alignments and the sequence signatures of mitochondrial
genome rearrangements.
Algorithms for molecular biology,
12 (2017), 22 [DOI]
Al-Arab, M. ; Siederdissen, C. H.
; Tout, K. R. ; Sahyoun, A. H. ; Stadler, P. F. and M. Bernt:
Accurate annotation of protein-coding genes in mitochondrial genomes.
Molecular phylogenetics and evolution,
106 (2017), p. 209-216 [DOI] [FREELINK]
Alkan, F. ; Wenzel, A. ; Palasca, O. ; Kerpedjiev, P. ; Rudebeck, A. F.
; Stadler, P. F. ; Hofacker, I. L. and J. Gorodkin:
RIsearch2 : suffix array-based large-scale prediction of RNA-RNA interactions and
siRNA off-targets.
Nucleic acids research,
45 (2017) 8, e60 [DOI]
Andersen, J. L. ; Flamm, C. ; Merkle, D. and P. F. Stadler:
Chemical graph transformation with stereo-information.
Graph transformation : 10th international conference, ICGT 2017, held as part of STAF
2017, Marburg, Germany, July 18-19, 2017, proceedings / J.
de Lara... (eds.). Springer, 2017. - P. 54-69
(Lecture notes in computer science ; 10373)
[DOI]
Andersen, J. L. ; Flamm, C. ; Merkle, D. and P. F. Stadler:
An intermediate level of abstraction for computational systems chemistry.
Philosophical transactions of the Royal Society / A,
375 (2017) 2109, 20160337 [DOI] [ARXIV]
Berkemer, S. ; Hoffmann, A. ; Murray, C. R. A. and P. F. Stadler:
SMORE : synteny modulator of repetitive elements.
Life : open access journal,
7 (2017) 4, 42 [DOI]
Berkemer, S. ; Siederdissen, C. H.
and P. F. Stadler:
Algebraic dynamic programming on trees.
Algorithms,
10 (2017) 4, 135 [DOI]
Binder, S. ; Hösler, N. ; Riedel, D. ; Zipfel, I. ; Buschmann, T. ; Kämpf, C. ; Reiche, K. ; Burger, R. ; Gramatzki, M. ; Hackermüller, J. ; Stadler, P. F. and F. Horn:
STAT3-induced long noncoding RNAs in multiple myeloma cells display different properties
in cancer.
Scientific reports,
7 (2017), 7976 [DOI]
Canzler, S. ; Stadler, P. F. and J. Hertel:
Evolution of fungal U3 snoRNAs : structural variation and introns.
Non-coding RNA,
3 (2017) 1, 3 [DOI]
Domin, G. ; Findeiß, S. ; Wachsmuth, M. ; Will, S. ; Stadler, P. F. and M. Mörl:
Applicability of a computational design approach for synthetic riboswitches.
Nucleic acids research,
45 (2017) 7, p. 4108-4119 [DOI] [FREELINK]
Findeiß, S. ; Etzel, M. ; Will, S. ; Mörl, M. and P. F. Stadler:
Design of artificial riboswitches as biosensors.
Sensors,
17 (2017) 9, 1990 [DOI]
Grüning, B. A. ; Fallmann, J. ; Yusuf, D. ; Will, S. ; Erxleben, A. ; Eggenhofer, F. ; Houwaart, T. ; Batut, B. ; Videm, P. ; Bagnacani, A. ; Wolfien, M. ; Lott, S. C. ; Hoogstrate, Y. ; Hess, W. R. ; Wolkenhauer, O. ; Hoffmann, S. ; Akalin, A. ; Ohler, U. ; Stadler, P. F. and R. Backofen:
The RNA workbench : best practices for RNA and high-throughput sequencing bioinformatics
in Galaxy.
Nucleic acids research,
45 (2017) W1, p. 560-566 [DOI]
Hellmuth, M. ; Stadler, P. F. and N. Wieseke:
The mathematics of xenology : di-cographs, symbolic ultrametrics, 2-structures and
tree-representable systems of binary relations.
Journal of mathematical biology,
75 (2017) 1, p. 199-237 [DOI] [ARXIV]
Indrischek, H. ; Prohaska, S. J. ; Gurevich, V. V. ; Gurevich, E. V. and P. F. Stadler:
Uncovering missing pieces : duplication and deletion history of arrestins in deuterostomes.
BMC evolutionary biology,
17 (2017), 163 [DOI]
Kolora, S. R.
; Faria, R. ; Weigert, A. ; Schaffer, S. ; Grimm-Seyfarth, A. ; Henle, K. ; Sahyoun, A. H. ; Stadler, P. F. ; Nowick, K. ; Bleidorn, C. and M. Schlegel:
The complete mitochondrial genome of Lacerta bilineata and comparison with its closely
related congener L. Viridis.
Mitochondrial DNA / Part A,
28 (2017) 1, p. 116-118 [DOI]
Kühnl, F. ; Stadler, P. F. and S. Will:
Tractable RNA-ligand interaction kinetics.
BMC bioinformatics,
18 (2017) Suppl. 12, 424 [DOI]
Llanos, E. J. ; Leal, W. ; Restrepo, G. and P. F. Stadler:
Computational approach to the history of chemical reactivity : exploring reaxys database.
254th ACS national meeting of the American Chemical Society Society, 2017[FREELINK]
Machné, R. ; Murray, D. B. and P. F. Stadler:
Similarity-based segmentation of multi-dimensional signals.
Scientific reports,
7 (2017), 12355 [DOI]
Nøjgaard, N. ; Geiß, M. ; Stadler, P. F. ; Merkle, D. ; Wieseke, N. and M. Hellmuth:
Forbidden time travel : characterization of time-consistent tree reconciliation maps.
17th international workshop on algorithms in bioinformatics : WABI 2017, August 21-23,
2017, Boston, MA, USA / R.
Schwartz... (eds.). Schloss Dagstuhl : Leibniz-Zentrum für Informatik, 2017 [DOI] [ARXIV]
Nitsche, A. and P. F. Stadler:
Evolutionary clues in lncRNAs.
Wiley interdisciplinary reviews / RNA,
8 (2017) 1, e1376 [DOI]
Parikesit, A. A.
; Stadler, P. F. and S. J. Prohaska:
Large-scale evolutionary patterns of protein domain distributions in eukaryotes.
[ARXIV]
Richards, C. L. ; Alonso, C. ; Becker, C. ; Bossdorf, O. ; Bucher, E. ; Colomé-Tatché, M. ; Durka, W. ; Engelhardt, J. ; Gaspar, B. ; Gogol-Döring, A. ; Grosse, I. ; van Gurp, T. P. ; Heer, K. ; Kronholm, I. ; Lampei, C. ; Latzel, V. ; Mirouze, M. ; Opgenoorth, L. ; Paun, O. ; Prohaska, S. J. ; Rensing, S. A. ; Stadler, P. F. ; Trucchi, E. ; Ullrich, K. and K. J. F. Verhoeven:
Ecological plant epigenetics : evidence from model and non-model species, and the
way forward.
Ecology letters,
20 (2017) 12, p. 1576-1590 [DOI] [ARXIV]
Saker, H. S. ; Stadler, P. F. and A. M. Shahin:
Multidimensional segmentation of heterogeneous data.
2017 fourth international conference on advances in biomedical engineering (ICABME)
: took place 19-21 October 2017 in Beirut, Lebanon IEEE, 2017. - P. 1-4 [DOI]
Sen, R. ; Doose, G. and P. F. Stadler:
Rare splice variants in long non-coding RNAs.
Non-coding RNA,
3 (2017) 3, 23 [DOI]
Stadler, B. M. R. and P. F. Stadler:
Oriented components and their separations.
Applied general topology,
18 (2017) 2, p. 255-275 [DOI]
Valach, M. ; Moreira, S. ; Hoffmann, S. ; Stadler, P. F. and G. Burger:
Keeping it complicated : mitochondrial genome plasticity across diplonemids.
Scientific reports,
7 (2017), 14166 [DOI]
Yazbeck, A. M. ; Tout, K. R. ; Stadler, P. F. and J. Hertel:
Towards a consistent, quantitative evaluation of microRNA evolution.
Journal of integrative bioinformatics,
14 (2017) 1, 20160013 [DOI]
Andersen, J. L. ; Flamm, C. ; Merkle, D. and P. F. Stadler:
A software package for chemically inspired graph transformation.
Graph transformation : 9th International Conference, ICGT 2016, in Memory of Hartmut
Ehrig, Held as Part of STAF 2016, Vienna, Austria, July 5-6, 2016, Proceedings / R.
Echahed... (eds.). Springer, 2016. - P. 73-88
(Lecture notes in computer science ; 9761)
[DOI] [ARXIV]
Bernhart, S. H. ; Kretzmer, H. ; Holdt, L. M. ; Jühling, F. ; Ammerpohl, O. ; Bergmann, A. K. ; Northoff, B. H. ; Doose, G. ; Siebert, R. ; Stadler, P. F. and S. Hoffmann:
Changes of bivalent chromatin coincide with increased expression of developmental
genes in cancer.
Scientific reports,
6 (2016), 37393 [DOI]
Bhattacharya, D. P.
; Canzler, S. ; Kehr, S. ; Hertel, J. ; Grosse, I. and P. F. Stadler:
Phylogenetic distribution of plant snoRNA families.
BMC genomics,
17 (2016), 969 [DOI]
Blasi, D. E. ; Wichmann, S. ; Hammarström, H. ; Stadler, P. F. and M. H. Christiansen:
Sound-meaning association biases evidenced across thousands of languages.
Proceedings of the National Academy of Sciences of the United States of America,
113 (2016) 39, p. 10818-10823 [DOI] [FREELINK]
Canzler, S. ; Stadler, P. F. and J. Hertel:
U6 snRNA intron insertion occurred multiple times during fungi evolution.
RNA biology,
13 (2016) 2, p. 119-127 [DOI] [FREELINK]
Flamm, C. ; Merkle, D. ; Stadler, P. F. and U. Thorsen:
Automatic inference of graph transformation rules using the cyclic nature of chemical
reactions.
Graph transformation : 9th International Conference, ICGT 2016, in Memory of Hartmut
Ehrig, Held as Part of STAF 2016, Vienna, Austria, July 5-6, 2016, Proceedings / R.
Echahed... (eds.). Springer, 2016. - P. 206-222
(Lecture notes in computer science ; 9761)
[DOI] [ARXIV]
Gu, J. ; Jost, J. ; Liu, S. and P. F. Stadler:
Spectral classes of regular, random, and empirical graphs.
Linear algebra and its applications,
489 (2016), p. 30-49 [DOI] [ARXIV]
Hammack, R. H. ; Hellmuth, M. ; Ostermeier, L. and P. F. Stadler:
Associativity and non-associativity of some hypergraph products.
Mathematics in computer science,
10 (2016) 3, p. 403-408 [DOI] [ARXIV]
Hecker, N. ; Kahlscheuer, M. L. ; Kerpedjiev, P. ; Stadler, P. F. ; Gorodkin, J. ; Hofacker, I. L. ; Walter, N. G. and J. Qin:
FRETtranslator : translating FRET traces into RNA structural pathways.
[ARXIV]
Hezaveh, K. ; Kloetgen, A. ; Bernhart, S. H. ; Das Mahapatra, K. ; Lenze, D. ; Richter, J. ; Haake, A. ; Bergmann, A. K. ; Brors, B. ; Burkhardt, B. ; Claviez, A. ; Drexler, H. G. ; Eils, R. ; Haas, S. ; Hoffmann, S. ; Karsch, D. ; Klapper, W. ; Kleinheinz, K. ; Korbel, J. O. ; Kretzmer, H. ; Kreuz, M. ; Küppers, R. ; Lawerenz, C. ; Leich, E. ; Loeffler, M. ; Mantovani-Loeffler, L. ; López, C. ; McHardy, A. C. ; Moeller, P. ; Rohde, M. ; Rosenstiel, P. ; Rosenwald, A. ; Schilhabel, M. ; Schlesner, M. ; Scholz, I. ; Stadler, P. F. ; Stilgenbauer, S. ; Sungalee, S. ; Szczepanowski, M. ; Trümper, L. ; Weniger, M. A. ; Siebert, R. ; Borkhardt, A. ; Hummel, M. and J. I. Hoell:
Alterations of microRNA and microRNA-regulated messenger RNA expression in germinal
center B-cell lymphomas determined by integrative sequencing analysis.
Haematologica,
101 (2016) 11, p. 1380-1389 [DOI]
Hoffmann, S. and P. F. Stadler:
Read mapping.
Information technology : it,
58 (2016) 3, p. 119-125 [DOI]
Indrischek, H. ; Wieseke, N. ; Stadler, P. F. and S. J. Prohaska:
The paralog-to-contig assignment problem : high quality gene models from fragmented
assemblies.
Algorithms for molecular biology,
11 (2016) 1, p. 1-14 [DOI]
Jorjani, H. ; Kehr, S. ; Jedlinski, D. J. ; Gumienny, R. ; Hertel, J. ; Stadler, P. F. ; Zavolan, M. and A. R. Gruber:
An updated human snoRNAome.
Nucleic acids research,
44 (2016) 11, p. 5068-5082 [DOI]
Jühling, F. ; Kretzmer, H. ; Bernhart, S. H. ; Otto, C. ; Stadler, P. F. and S. Hoffmann:
Metilene : fast and sensitive calling of differentially methylated regions from bisulfite
sequencing data.
Genome research,
26 (2016) 2, p. 256-262 [DOI]
Krakauer, D. C. ; Müller, L. ; Prohaska, S. J. and P. F. Stadler:
Design specifications for cellular regulation.
Theory in biosciences,
135 (2016) 4, p. 231-240 [DOI] [ARXIV]
Kucharík, M. ; Hofacker, I. L. ; Stadler, P. F. and J. Qin:
Pseudoknots in RNA folding landscapes.
Bioinformatics,
32 (2016) 2, p. 187-194 [DOI]
Kuhnl, F. ; Stadler, P. F. and S. Will:
Tractable kinetics of RNA-ligand interaction.
Bioinformatics research and applications : 12th international symposium, ISBRA 2016,
Minsk, Belarus, June 5-8, 2016, proceedings / A.
Bourgeois... (eds.). Springer, 2016. - P. 337-338
(Lecture notes in computer science ; 9683)
[DOI]
Lorenz, R. ; Hofacker, I. L. and P. F. Stadler:
RNA folding with hard and soft constraints.
Algorithms for molecular biology,
11 (2016), 8 [DOI]
Lorenz, R. ; Luntzer, D. ; Hofacker, I. L. ; Stadler, P. F. and M. T. Wolfinger:
SHAPE directed RNA folding.
Bioinformatics,
32 (2016) 1, p. 145-147 [DOI] [ARXIV]
Oliveira, J. V.
; Costa, F. ; Backofen, R. ; Stadler, P. F. ; Walter, M. Emilia M. T. and J. Hertel:
SnoReport 2.0 : new features and a refined Support Vector Machine to improve snoRNA
identification [Proceedings of X-meeting 2015 : 11th international conference of the
AB3C + Brazilian symposium on bioinformatics].
BMC bioinformatics,
17 (2016) Supplement 18, 464 [DOI]
Restrepo, G. and P. F. Stadler:
Assessing greenness of chemical reactions and synthesis plans through posetic landscapes.
ACS sustainable chemistry and engineering,
4 (2016) 4, p. 2191-2199 [DOI]
Riechert, M. ; Siederdissen, C. H.
and P. F. Stadler:
Algebraic dynamic programming for multiple context-free grammars.
Theoretical computer science,
639 (2016), p. 91-109 [DOI]
Righetti, F. ; Nuss, A. M. ; Twittenhoff, C. ; Beele, S. ; Urban, K. ; Will, S. ; Bernhart, S. H. ; Stadler, P. F. ; Dersch, P. and F. Narberhaus:
Temperature-responsive in vitro RNA structurome of Yersinia pseudotuberculosis.
Proceedings of the National Academy of Sciences of the United States of America,
113 (2016) 26, p. 7237-7242 [DOI]
Shostak, A. ; Ruppert, B. ; Ha, N. ; Bruns, P. ; Toprak, U. H. ; Lawerenz, C. ; Lichter, P. ; Radlwimmer, B. ; Eils, J. ; Brors, B. ; Radomski, S. ; Scholz, I. ; Richter, G. ; Siebert, R. ; Wagner, S. ; Haake, A. ; Richter, J. ; Aukema, S. M. ; Ammerpohl, O. ; López, C. ; Nagel, I. ; Vater, I. ; Wagner, R. ; Borst, C. ; Haas, S. ; Rohde, M. ; Burkhardt, B. ; Lisfeld, J. ; Claviez, A. ; Dreyling, M. ; Eberth, S. ; Trümper, L. ; Kube, D. ; Stadler, C. ; Einsele, H. ; Frickhofen, N. ; Hansmann, M.-L. ; Karsch, D. ; Kneba, M. ; Mantovani-Loeffler, L. ; Staib, P. ; Stilgenbauer, S. ; Ott, G. ; Küppers, R. ; Weniger, M. A. ; Hummel, M. ; Lenze, D. ; Szczepanowski, M. ; Klapper, W. ; Kostezka, U. ; Moeller, P. ; Rosenwald, A. ; Leich, E. ; Pischimariov, J. ; Binder, V. ; Borkhardt, A. ; Hezaveh, K. ; Hoell, J. I. ; Rosenstiel, P. ; Schilhabel, M. ; Schreiber, S. ; Bernhart, S. H. ; Doose, G. ; Hoffmann, S. ; Kretzmer, H. ; Langenberger, D. ; Binder, H. ; Hopp, L. ; Kreuz, M. ; Loeffler, M. ; Rosolowski, M. ; Korbel, J. O. ; Sungalee, S. ; Stadler, P. F. ; Zenz, T. ; Eils, R. ; Schlesner, M. ; Diernfellner, A. and M. Brunner:
MYC/MIZ1-dependent gene repression inversely coordinates the circadian clock with
cell cycle and proliferation.
Nature communications,
7 (2016), 11807 [DOI]
Stadler, P. F.:
Evolution of RNA-based networks.
Quasispecies : from theory to experimental systems / E.
Domingo... (eds.). Springer, 2016. - P. 43-59
(Current Topics in Microbiology and Immunology ; 392)
[DOI]
Stadler, P. F.:
Monsters in the RNA zoo : evolution of non-coding RNAs.
[FREELINK]
Velandia-Huerto, C. A. ; Berkemer, S. ; Hoffmann, A. ; Retzlaff, N. ; Romero Marroquín, L. C. ; Hernández Rosales, M. ; Stadler, P. F. and C. I. Bermúdez-Santana:
Orthologs, turn-over, and remolding of tRNAs in primates and fruit flies.
BMC genomics,
17 (2016), 617 [DOI] [FREELINK]
Velandia-Huerto, C. A. ; Gittenberger, A. A. ; Brown, F. D. ; Stadler, P. F. and C. I. Bermúdez-Santana:
Automated detection of ncRNAs in the draft genome sequence of a colonial tunicate
: the carpet sea squirt Didemnum vexillum.
BMC genomics,
17 (2016), 691 [DOI]
Westermann, A. J. ; Förstner, K. U. ; Amman, F. ; Barquist, L. ; Chao, Y. ; Schulte, L. N. ; Müller, L. ; Reinhardt, R. ; Stadler, P. F. and J. Vogel:
Dual RNA-seq unveils noncoding RNA functions in host-pathogen interactions.
Nature,
529 (2016) 7587, p. 496-501 [DOI]
Andersen, J. L. ; Flamm, C. ; Merkle, D. and P. F. Stadler:
In silico support for Eschenmoser's glyoxylate scenario.
Israel journal of chemistry,
55 (2015) 8, p. 919-933 [DOI] [ARXIV]
Angrisani, A. ; Tafer, H. ; Stadler, P. F. and M. Furia:
Unusual novel SnoRNA-like RNAs in Drosophila melanogaster.
Non-coding RNA,
1 (2015) 2, p. 139-150 [DOI]
Banzhaf, W. ; Flamm, C. ; Merkle, D. and P. F. Stadler:
Algorithmic cheminformatics : Dagstuhl Seminar 14452.
Dagstuhl reports,
4 (2015) 11, p. 22-39 [DOI]
Berkemer, S. ; Chaves, R. R.C. ; Fritz, A. ; Hellmuth, M. ; Hernández Rosales, M. and P. F. Stadler:
Spiders can be recognized by counting their legs.
Mathematics in computer science,
9 (2015) 4, p. 437-441 [DOI] [ARXIV]
Berkemer, S. ; Siederdissen, C. H.
; Amman, F. ; Wintsche, A. ; Will, S. ; Hofacker, I. L. ; Prohaska, S. J. and P. F. Stadler:
Processed small RNAs in Archaea and BHB elements.
Genomics and computational biology,
1 (2015) 1, e18[FREELINK]
Bernhart, S. H. ; Kretzmer, H. ; Jühling, F. ; Stadler, P. F. and S. Hoffmann:
Disturbance of poised chromatin coincides with increased expression of developmental
genes in cancer.
[ARXIV]
Betat, H. ; Mede, T. ; Tretbar, S. ; Steiner, L. ; Stadler, P. F. ; Mörl, M. and S. J. Prohaska:
The ancestor of modern Holozoa acquired the CCA-adding enzyme from Alphaproteobacteria
by horizontal gene transfer.
Nucleic acids research,
43 (2015) 14, p. 6739-6746 [DOI]
Dingemanse, M. ; Blasi, D. E. ; Lupyan, G. ; Christiansen, M. H. and P. Monaghan:
Arbitrariness, iconicity, and systematicity in language.
Trends in cognitive sciences,
19 (2015) 10, p. 603-615 [DOI] [FREELINK]
Doose, G. ; Haake, A. ; Bernhart, S. H. ; López, C. ; Duggimpudi, S. ; Wojciech, F. ; Bergmann, A. K. ; Borkhardt, A. ; Burkhardt, B. ; Claviez, A. ; Dimitrova, L. ; Haas, S. ; Hoell, J. I. ; Hummel, M. ; Karsch, D. ; Klapper, W. ; Kleo, K. ; Kretzmer, H. ; Kreuz, M. ; Küppers, R. ; Lawerenz, C. ; Lenze, D. ; Loeffler, M. ; Mantovani-Loeffler, L. ; Moeller, P. ; Ott, G. ; Richter, J. ; Rohde, M. ; Rosenstiel, P. ; Rosenwald, A. ; Schilhabel, M. ; Schneider, M. ; Scholz, I. ; Stilgenbauer, S. ; Stunnenberg, H. G. ; Szczepanowski, M. ; Trümper, L. ; Weniger, M. A. ; Richter, G. ; Wagner, S. ; Eils, R. ; Radomski, S. ; Borst, C. ; Dreyling, M. ; Eberth, S. ; Einsele, H. ; Frickhofen, N. ; Hansmann, M.-L. ; Kneba, M. ; Lisfeld, J. ; Stadler, C. ; Staib, P. ; Zenz, T. ; Kube, D. ; Kostezka, U. ; Ammerpohl, O. ; Aukema, S. M. ; Binder, V. ; Hezaveh, K. ; Leich, E. ; Lichter, P. ; Nagel, I. ; Pischimariov, J. ; Radlwimmer, B. ; Schreiber, S. ; Vater, I. ; Wagner, R. ; Brors, B. ; Eils, J. ; Hopp, L. ; Korbel, J. O. ; Langenberger, D. ; Rosolowski, M. ; Schlesner, M. ; Stadler, P. F. ; Sungalee, S. ; Hoffmann, S. ; Siebert, R. and I. Iaccarino:
MINCR is a MYC-induced lncRNA able to modulate MYC's transcriptional network in Burkitt
lymphoma cells.
Proceedings of the National Academy of Sciences of the United States of America,
112 (2015) 38, p. E5261-E5270 [DOI]
Engelhardt, J. and P. F. Stadler:
Evolution of the unspliced transcriptome.
BMC evolutionary biology,
15 (2015), 166 [DOI]
Everett, C. ; Blasi, D. E. and S. G. Roberts:
Climate, vocal folds, and tonal languages : connecting the physiological and geographic
dots.
Proceedings of the National Academy of Sciences of the United States of America,
112 (2015) 5, p. 1322-1327 [DOI] [FREELINK]
Findeiß, S. ; Wachsmuth, M. ; Mörl, M. and P. F. Stadler:
Chapter one : design of transcription regulating riboswitches.
Riboswitches as targets and tools / D.
H. Burke-Aguero (ed.). Academic press, 2015. - P. 1-22
(Methods in enzymology ; 550)
[DOI]
Flamm, C. ; Stadler, B. M. R. and P. F. Stadler:
Generalized topologies : hypergraphs, chemical reactions, and biological evolution.
Advances in mathematical chemistry and applications : volume 2 / S.
C. Basak... (eds.). Bentham Science, 2015. - P. 300-328 [DOI]
Gardner, P. P. ; Fasold, M. ; Burge, S. W. ; Ninova, M. ; Hertel, J. ; Kehr, S. ; Steeves, T. E. ; Griffiths-Jones, S. and P. F. Stadler:
Conservation and losses of non-coding RNAs in avian genomes.
PLOS ONE,
10 (2015) 3, e0121797 [DOI] [ARXIV]
Gu, J. ; Hua, B. and S. Liu:
Spectral distances on graphs.
Discrete applied mathematics,
190-191 (2015), p. 56-74 MIS-Preprint: 31/2014 [DOI] [ARXIV]
Hecker, N. ; Christensen-Dalsgaard, M. ; Seemann, S. E. ; Havgaard, J. H.
; Stadler, P. F. ; Hofacker, I. L. ; Nielsen, H. and J. Gorodkin:
Optimizing RNA structures by sequence extensions using RNAcop.
Nucleic acids research,
43 (2015) 17, p. 8135-8145 [DOI]
Hellmuth, M. ; Fritz, A. ; Wieseke, N. and P. F. Stadler:
Techniques for the cograph editing problem : module merge is equivalent to editing
P4s.
[ARXIV]
Hellmuth, M. ; Marc, T. ; Ostermeier, L. and P. F. Stadler:
The relaxed square property.
The Australasian Journal of Combinatorics,
62 (2015) 3, p. 240-270[ARXIV] [FREELINK]
Hellmuth, M. ; Wieseke, N. ; Lechner, M. ; Lenhof, H.-P. ; Middendorf, M. and P. F. Stadler:
Phylogenetics from paralogs.
Proceedings of the National Academy of Sciences of the United States of America,
112 (2015) 7, p. 2058-2063 [DOI] [ARXIV]
Hellmuth, M. ; Wieseke, N. ; Lechner, M. ; Lenhof, H.-P. ; Middendorf, M. and P. F. Stadler:
Phylogenomics with paralogs.
Proceedings of the National Academy of Sciences of the United States of America,
112 (2015) 7, p. 2058-2063 [DOI] [ARXIV]
Hertel, J. and P. F. Stadler:
The expansion of animal microRNA families revisited.
Life : open access journal,
5 (2015) 1, p. 905-920 [DOI]
Hoffmann, S. ; Stadler, P. F. and K. Strimmer:
A simple data-adaptive probabilistic variant calling model.
Algorithms for molecular biology,
10 (2015), 10 [DOI]
Kretzmer, H. ; Bernhart, S. H. ; Wang, W. ; Haake, A. ; Weniger, M. A. ; Bergmann, A. K. ; Betts, M. J. ; Carrillo-de-Santa-Pau, E. ; Doose, G. ; Gutwein, J. ; Richter, J. ; Hovestadt, V. ; Huang, B. ; Rico, D. ; Jühling, F. ; Kolarova, J. ; Lu, Q. ; Otto, C. ; Wagener, R. ; Arnolds, J. ; Burkhardt, B. ; Claviez, A. ; Drexler, H. G. ; Eberth, S. ; Eils, R. ; Flicek, P. ; Haas, S. ; Hummel, M. ; Karsch, D. ; Kerstens, H. H. D. ; Klapper, W. ; Kreuz, M. ; Lawerenz, C. ; Lenze, D. ; Loeffler, M. ; López, C. ; MacLeod, R. A. F. ; Martens, J. H. A. ; Kulis, M. ; Martín-Subero, J. I.
; Moeller, P. ; Nagel, I. ; Picelli, S. ; Vater, I. ; Rohde, M. ; Rosenstiel, P. ; Rosolowski, M. ; Russell, R. B. ; Schilhabel, M. ; Schlesner, M. ; Stadler, P. F. ; Szczepanowski, M. ; Trümper, L. ; Stunnenberg, H. G. ; Küppers, R. ; Ammerpohl, O. ; Lichter, P. ; Siebert, R. ; Hoffmann, S. and B. Radlwimmer:
DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially
methylated regions linked to somatic mutation and transcriptional control.
Nature genetics,
47 (2015) 11, p. 1316-1325 [DOI]
Laubichler, M. D. ; Stadler, P. F. ; Prohaska, S. J. and K. Nowick:
The relativity of biological function.
Theory in biosciences,
134 (2015) 3-4, p. 143-147 [DOI]
Nitsche, A. ; Rose, D. ; Fasold, M. ; Reiche, K. and P. F. Stadler:
Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well
conserved.
RNA,
21 (2015), p. 801-812 [DOI]
Ostermeier, L.:
(Relaxed) product structures of graphs and hypergraphs.
Dissertation, Universität Leipzig, 2015[FREELINK]
Ostermeier, L. and P. F. Stadler:
The grid property and product-like hypergraphs.
Graphs and combinatorics,
31 (2015) 3, p. 757-770 [DOI] [FREELINK]
Sahyoun, A. H. ; Hölzer, M. ; Jühling, F. ; Siederdissen, C. H.
; Al-Arab, M. ; Tout, K. R. ; Marz, M. ; Middendorf, M. ; Stadler, P. F. and M. Bernt:
Towards a comprehensive picture of alloacceptor tRNA remolding in metazoan mitochondrial
genomes.
Nucleic acids research,
43 (2015) 16, p. 8044-8056 [DOI]
Siederdissen, C. H.
; Hofacker, I. L. and P. F. Stadler:
Product grammars for alignment and folding.
IEEE ACM transactions on computational biology and bioinformatics,
12 (2015) 3, p. 507-519 [DOI] [FREELINK]
Siederdissen, C. H.
; Prohaska, S. J. and P. F. Stadler:
Algebraic dynamic programming over general data structures.
BMC bioinformatics,
16 (2015) Supplement 19, S2 [DOI] [FREELINK]
Stadler, B. M. R. and P. F. Stadler:
Connectivity spaces.
Mathematics in computer science,
9 (2015) 4, p. 409-436 [DOI]
Stadler, P. F. and C. H.
Siederdissen:
Dynamic programming for lazy bastards.
[FREELINK]
Wachsmuth, M. ; Domin, G. ; Lorenz, R. ; Serfling, R. ; Findeiß, S. ; Stadler, P. F. and M. Mörl:
Design criteria for synthetic riboswitches acting on transcription.
RNA biology,
12 (2015) 2, p. 221-231 [DOI] [FREELINK]
Amman, F. ; Wolfinger, M. T. ; Lorenz, R. ; Hofacker, I. L. ; Stadler, P. F. and S. Findeiß:
TSSAR : TSS annotation regime for dRNA-seq data.
BMC bioinformatics,
15 (2014), 89 [DOI]
Andersen, J. L. ; Flamm, C. ; Merkle, D. and P. F. Stadler:
50 shades of rule composition : from chemical reactions to higher levels of abstraction.
Formal methods in macro-biology : first international conference, FMMB 2014, Nouméa,
New Caledonia, September 22-24, 2014. Proceedings / F.
Fages... (eds.). Springer, 2014. - P. 117-135
(Lecture notes in computer science ; 8738)
[DOI]
Andersen, J. L. ; Flamm, C. ; Merkle, D. and P. F. Stadler:
Generic strategies for chemical space exploration.
International journal of computational biology and drug design,
7 (2014) 2-3, p. 225-258 [DOI] [ARXIV]
Backofen, R. ; Amman, F. ; Costa, F. ; Findeiß, S. ; Richter, A. S. and P. F. Stadler:
Bioinformatics of prokaryotic RNAs.
RNA biology,
11 (2014) 5, p. 470-483 [DOI]
Bernt, M. ; Merkle, D. ; Middendorf, M. ; Schierwater, B. ; Schlegel, M. and P. F. Stadler:
Computational methods for the analysis of mitochondrial genome rearrangements.
Deep metazoan phylogeny : the backbone of the tree of life / J.
W.
Wägele... (eds.). de Gruyter, 2014. - P. 515-530 [DOI]
Blasi, D. E. ; Christiansen, M. H. ; Wichmann, S. ; Hammarström, H. and P. F. Stadler:
Sound symbolism and the origins of language.
The evolution of language : proceedings of the 10th international conference (EVOLANG10),
Vienna, Austria, 14-17 April 2014 / E.
A. Cartmill... (eds.). World scientific, 2014. - P. 391-392 [DOI]
Donath, A. and P. F. Stadler:
Molecular morphology : higher order characters derivable from sequence information.
Deep metazoan phylogeny : the backbone of the tree of life / J.
W.
Wägele... (eds.). de Gruyter, 2014. - P. 549-562 [DOI]
Fiala, J. ; Hubicka, J. and Y. Long:
Universality of intervals of line graph order.
European journal of combinatorics,
41 (2014), p. 221-231 MIS-Preprint: 30/2014 [DOI] [ARXIV]
Gu, J.:
The spectral distance based on the normalized Laplacian and applications to large
networks.
Dissertation, Universität Leipzig, 2014
Hackermüller, J. ; Reiche, K. ; Otto, C. ; Hösler, N. ; Blumert, C. ; Brocke-Heidrich, K. ; Böhlig, L. ; Nietsche, A. ; Kasack, K. ; Ahnert, P. ; Krupp, W. ; Engeland, K. ; Stadler, P. F. and F. Horn:
Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro
non-protein-coding RNAs.
Genome biology,
15 (2014) 3, UNSP R48 [DOI]
Hellmuth, M. ; Leydold, J. and P. F. Stadler:
Convex cycle bases.
Ars mathematica contemporanea,
7 (2014) 1, p. 123-140[FREELINK]
Hellmuth, M. ; Noll, M. and L. Ostermeier:
Strong products of hypergraphs: Unique prime factorization theorems and algorithms.
Discrete applied mathematics,
171 (2014), p. 60-71 [DOI] [ARXIV]
Hellmuth, M. ; Ostermeier, L. and P. F. Stadler:
Unique square property, equitable partitions, and product-like graphs.
Discrete mathematics,
320 (2014), p. 92-103 [DOI] [ARXIV]
Hernández Rosales, M. ; Wieseke, N. ; Hellmuth, M. and P. F. Stadler:
Simulation of gene family histories.
BMC bioinformatics,
15 (2014) Suppl. 3, A8 [DOI]
Hertel, J. ; Langenberger, D. and P. F. Stadler:
Computational prediction of microRNA genes.
RNA sequence, structure, and function : computational and bioinformatic methods / J.
Gorodkin... (eds.). Humana press, 2014. - P. 437-456
(Methods in molecular biology ; 1097)
[DOI]
Hoffmann, S. ; Otto, C. ; Doose, G. ; Tanzer, A. ; Langenberger, D. ; Christ, S. ; Kunz, M. ; Holdt, L. M. ; Teupser, D. ; Hackermüller, J. and P. F. Stadler:
A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion
detection.
Genome biology,
15 (2014) 2, R34 [DOI]
Kehr, S. ; Bartschat, S. ; Tafer, H. ; Stadler, P. F. and J. Hertel:
Matching of soulmates : coevolution of snoRNAs and their targets.
Molecular biology and evolution,
31 (2014) 2, p. 455-467 [DOI]
Klemm, K. ; Qin, J. and P. F. Stadler:
Geometry and coarse-grained representations of landscapes.
Recent advances in the theory and application of fitness landscapes / H.
Richter... (eds.). Springer, 2014. - P. 153-176
(Emergence, complexity, and computation ; 6)
[DOI]
Klemm, K. and P. F. Stadler:
Rugged and elementary landscapes.
Theory and principled methods for the design of metaheuristics / Y.
Borenstein... (eds.). Springer, 2014. - P. 41-61
(Natural computing series)
[DOI]
Kucharík, M. ; Hofacker, I. L. ; Stadler, P. F. and J. Qin:
Basin hopping graph : a computational framework to characterize RNA folding landscapes.
Bioinformatics,
30 (2014) 14, p. 2009-2017 [DOI]
Lechner, M. ; Hernández Rosales, M. ; Doerr, D. ; Wieseke, N. ; Thévenin, A. ; Stoye, J. ; Hartmann, R. K. ; Prohaska, S. J. and P. F. Stadler:
Orthology detection combining clustering and synteny for very large datasets.
PLOS ONE,
9 (2014) 8, e105015 [DOI]
Lehmann, J. ; Eisenhardt, C. ; Krauss, V. and P. F. Stadler:
Intron positions and near intron pairs.
Deep metazoan phylogeny : the backbone of the tree of life / J.
W.
Wägele... (eds.). de Gruyter, 2014. - P. 539-548 [DOI]
Li, W. ; Gu, J. ; Liu, S. ; Zhu, Y. ; Deng, S. ; Zhao, L. ; Han, J. and X. Cai:
Optimal transport in worldwide metro networks.
[ARXIV]
Long, Y.:
Graph relations and constrained homomorphism partial orders.
Dissertation, Universität Leipzig, 2014[FREELINK]
Mann, M. ; Nahar, F. ; Schnorr, N. ; Backofen, R. ; Stadler, P. F. and C. Flamm:
Atom mapping with constraint programming.
Algorithms for molecular biology,
9 (2014), 23 [DOI]
Marz, M. ; Beerenwinkel, N. ; Drosten, C. ; Fricke, M. ; Frishman, D. ; Hofacker, I. L. ; Hoffmann, D. ; Middendorf, M. ; Rattei, T. ; Stadler, P. F. and A. Toepfer:
Challenges in RNA virus bioinformatics.
Bioinformatics,
30 (2014) 13, p. 1793-1799 [DOI]
Misof, B. ; Meusemann, K. ; von Reumont, B. ; Kuck, P. ; Prohaska, S. J. and P. F. Stadler:
A priori assessment of data quality in molecular phylogenetics.
Algorithms for molecular biology,
9 (2014), UNSP 22 [DOI]
Müller, G. A. ; Wintsche, A. ; Stangner, K. ; Prohaska, S. J. ; Stadler, P. F. and K. Engeland:
The CHR site : definition and genome-wide identification of a cell cycle transcriptional
element.
Nucleic acids research,
42 (2014) 16, p. 10331-10350 [DOI]
Nitsche, A. ; Doose, G. ; Tafer, H. ; Robinson, M. ; Saha, N. R.
; Gerdol, M. ; Canapa, A. ; Hoffmann, S. ; Amemiya, C. T. and P. F. Stadler:
Atypical RNAs in the coelacanth transcriptome.
Journal of experimental zoology / B,
322 (2014) 6, p. 342-351 [DOI]
Otto, C. ; Stadler, P. F. and S. Hoffmann:
Lacking alignments? The next-generation sequencing mapper segemehl revisited.
Bioinformatics,
30 (2014) 13, p. 1837-1843 [DOI]
Parikesit, A. A.
; Steiner, L. ; Stadler, P. F. and S. J. Prohaska:
Pitfalls of ascertainment biases in genome annotations : computing comparable protein
domain distributions in eukarya.
Malaysian journal of fundamental and applied sciences,
10 (2014) 2, p. 64-73 [DOI]
Patra, D. ; Fasold, M. ; Langenberger, D. ; Steger, G. ; Grosse, I. and P. F. Stadler:
plantDARIO : web based quantitative and qualitative analysis of small RNA-seq data
in plants.
Frontiers in plant science,
5 (2014), 708 [DOI]
Qin, J. ; Fricke, M. ; Marz, M. ; Stadler, P. F. and R. Backofen:
Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures.
Algorithms for molecular biology,
9 (2014), 19 [DOI]
Rivarola-Duarte, L. ; Otto, C. ; Jühling, F. ; Schreiber, S. ; Bedulina, D. ; Jakob, L. ; Gurkov, A. ; Axenov-Gribanov, D. ; Sahyoun, A. H. ; Lucassen, M. ; Hackermüller, J. ; Hoffmann, S. ; Sartoris, F. ; Pörtner, H.-O. ; Timofeyev, M. ; Luckenbach, T. and P. F. Stadler:
A first Glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus.
Journal of experimental zoology / B,
322 (2014) 3, p. 177-189 [DOI]
Sahyoun, A. H. ; Bernt, M. ; Stadler, P. F. and K. R. Tout:
GC skew and mitochondrial origins of replication.
Mitochondrion,
17 (2014), p. 56-66 [DOI]
Schlegel, M. ; Weidhase, M. and P. F. Stadler:
Deuterostome phylogeny : a molecular perspective.
Deep metazoan phylogeny : the backbone of the tree of life / J.
W.
Wägele... (eds.). de Gruyter, 2014. - P. 413-424 [DOI]
Schneider, H. W. ; Bartschat, S. ; Doose, G. ; Maciel, L. ; Pizani, E. ; Bassani, M. ; Torres, F. A.
; Will, S. ; Raiol, T. ; Brigido, M. M. ; Walter, M. Emilia M. T. and P. F. Stadler:
Genome-wide identification of non-coding RNAs in Komagatella pastoris str. GS115.
Advances in bioinformatics and computational biology : 9th Brazilian Symposium on
Bioinformatics, BSB 2014, Belo Horizonte, Brazil, October 28-30, 2014, Proceedings / S.
Campos (ed.). Springer, 2014. - P. 115-122
(Lecture notes in computer science ; 8826)
[DOI]
Siederdissen, C. H.
; Berkemer, S. ; Amman, F. ; Wintsche, A. ; Will, S. ; Prohaska, S. J. and P. F. Stadler:
Comparative detection of processed small RNAs in Archaea.
Proceedings IWBBIO 2014 : 2nd International Work-Conference on Bioinformatics and
Biomedical Engineering ; Granada, Spain / F. Ortuno... (eds.). Copicentro Granada, 2014. - P. 286-297[FREELINK]
Stadler, P. F.:
Class-specific prediction of ncRNAs.
RNA sequence, structure, and function : computational and bioinformatic methods / J.
Gorodkin... (eds.). Humana press, 2014. - P. 199-213
(Methods in molecular biology ; 1097)
[DOI]
Stadler, P. F.:
Computational RNA design.
[FREELINK]
Stocsits, R. R. ; Letsch, H. ; Meusemann, K. ; Reumont, B. M. von ; Misof, B. ; Hertel, J. ; Tafer, H. and P. F. Stadler:
RNA in phylogenetic reconstruction.
Deep metazoan phylogeny : the backbone of the tree of life / J.
W.
Wägele... (eds.). de Gruyter, 2014. - P. 531-538 [DOI]
Sun, C. ; Zhao, M. and Y. Long:
Learning concepts and taxonomic relations by metric learning for regression.
Communications in statistics : theory and methods,
43 (2014) 14, p. 2938-2950 [DOI]
Wende, S. ; Platzer, E. G. ; Juhling, F. ; Pütz, J. ; Florentz, C. ; Stadler, P. F. and M. Mörl:
Biological evidence for the world's smallest tRNAs.
Biochimie,
100 (2014), p. 151-158 [DOI]
Will, S. and P. F. Stadler:
A common framework for linear and cyclic multiple sequence alignment problems.
Algorithms in bioinformatics : 14th International Workshop, WABI 2014, Wroclaw, Poland,
September 8-10, 2014 ; Proceedings / D.
Brown... (eds.). Springer, 2014. - P. 135-147
(Lecture notes in computer science ; 8701)
[DOI]
Amman, F. ; Bernhart, S. H. ; Doose, G. ; Hofacker, I. L. ; Qin, J. ; Stadler, P. F. and S. Will:
The trouble with long-range base pairs in RNA folding.
Advances in bioinformatics and computational biology : 8th Brazilian Symposium on
Bioinformatics, BSB 2013, Recife, Brazil, November 3-7, 2013 ; proceedings / J.
C. Setubal... (eds.). Springer, 2013. - P. 1-11
(Lecture notes in computer science ; 8213)
[DOI]
Andersen, J. L. ; Andersen, T. ; Flamm, C. ; Hanczyc, M. ; Merkle, D. and P. F. Stadler:
Navigating the chemical space of HCN polymerization and hydrolysis : guiding graph
grammars by mass spectrometry data.
Entropy,
15 (2013) 10, p. 4066-4083 [DOI]
Andersen, J. L. ; Flamm, C. ; Merkle, D. and P. F. Stadler:
Inferring chemical reaction patterns using rule composition in graph grammars.
Journal of systems chemistry,
4 (2013), 4 [DOI] [ARXIV]
Arnold, C. ; Stadler, P. F. and S. J. Prohaska:
Chromatin computation : epigenetic inheritance as a pattern reconstruction problem.
Journal of theoretical biology,
336 (2013), p. 61-74 [DOI] [FREELINK]
Backofen, R. ; Fricke, M. ; Marz, M. ; Qin, J. and P. F. Stadler:
Distribution of graph-distances in Boltzmann ensembles of RNA secondary structures.
Algorithms in bioinformatics : 13th International Workshop ; WABI 2013 ; Sophia Antipolis,
France ; September 2-4, 2013 ; Proceedings / A.
Darling... (eds.). Springer, 2013. - P. 112-125
(Lecture notes in computer science ; 8126)
[DOI] [ARXIV]
Bernt, M. ; Bleidorn, C. ; Braband, A. ; Dambach, J. ; Donath, A. ; Fritzsch, G. ; Golombek, A. ; Hadrys, H. ; Jühling, F. ; Meusemann, K. ; Middendorf, M. ; Misof, B. ; Perseke, M. ; Podsiadlowski, L. ; von Reumont, B. ; Schierwater, B. ; Schlegel, M. ; Schrödl, M. ; Simon, S. ; Stadler, P. F. ; Stöger, I. and T. H. Struck:
A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny.
Molecular phylogenetics and evolution,
69 (2013) 2, p. 352-364 [DOI]
Bernt, M. ; Braband, A. ; Middendorf, M. ; Misof, B. ; Rota-Stabelli, O. and P. F. Stadler:
Bioinformatics methods for the comparative analysis of metazoan mitochondrial genome
sequences.
Molecular phylogenetics and evolution,
69 (2013) 2, p. 320-327 [DOI] [FREELINK]
Bernt, M. ; Braband, A. ; Schierwater, B. and P. F. Stadler:
Genetic aspects of mitochondrial genome evolution.
Molecular phylogenetics and evolution,
69 (2013) 2, p. 328-338 [DOI] [FREELINK]
Bernt, M. ; Donath, A. ; Jühling, F. ; Externbrink, F. ; Florentz, C. ; Fritzsch, G. ; Pütz, J. ; Middendorf, M. and P. F. Stadler:
MITOS : improved de novo metazoan mitochondrial genome annotation.
Molecular phylogenetics and evolution,
69 (2013) 2, p. 313-319 [DOI] [FREELINK]
Dieterich, C. and P. F. Stadler:
Computational biology of RNA interactions.
Wiley interdisciplinary reviews / RNA,
4 (2013) 1, p. 107-120 [DOI]
Doose, G. ; Alexis, M. ; Kirsch, R. ; Findeiß, S. ; Langenberger, D. ; Machné, R. ; Morl, M. ; Hoffmann, S. and P. F. Stadler:
Mapping the RNA-Seq trash bin unusual transcripts in prokaryotic transcriptome sequencing
data.
RNA biology,
10 (2013) 7, p. 1204-1210 [DOI]
Fagerberg, R. ; Flamm, C. ; Merkle, D. ; Peters, P. and P. F. Stadler:
On the complexity of reconstructing chemical reaction networks.
Mathematics in computer science,
7 (2013) 3, p. 275-292 [DOI] [ARXIV]
Guo, L. ; Gu, J. and Z. Luo:
How much information is needed to be the majority during the binary-state opinion
formation?.
Physica / A,
392 (2013) 19, p. 4373-4379 [DOI]
Hellmuth, M. ; Hernández Rosales, M. ; Huber, K. T. ; Moulton, V. ; Stadler, P. F. and N. Wieseke:
Orthology relations, symbolic ultrametrics, and cographs.
Journal of mathematical biology,
66 (2013) 1/2, p. 399-420 [DOI]
Hernández Rosales, M.:
The orthology road : theory and methods in orthology analysis.
Dissertation, Universität Leipzig, 2013[FREELINK]
Holdt, L. M. ; Hoffmann, S. ; Sass, K. ; Langenberger, D. ; Scholz, M. ; Krohn, K. ; Finstermeier, K. ; Stahringer, A. ; Wilfert, W. ; Beutner, F. ; Gielen, S. ; Schuler, G. ; Gäbel, G. ; Bergert, H. ; Bechmann, I. ; Stadler, P. F. ; Thiery, J. and D. Teupser:
Alu elements in ANRIL non-coding RNA at chromosome 9p21 modulate atherogenic cell
functions through trans-regulation of gene networks.
PloS genetics,
9 (2013) 7, e1003588 [DOI]
Hubicka, J. ; Jost, J. ; Long, Y. ; Stadler, P. F. and L. Yang:
Relations between graphs.
Ars mathematica contemporanea,
6 (2013) 2, p. 323-350 MIS-Preprint: 28/2011 [DOI] [ARXIV]
Langenberger, D. ; Cakir, M. V.
; Hoffmann, S. and P. F. Stadler:
Dicer-processed small RNAs : rules and exceptions.
Journal of experimental zoology / B,
320 (2013) 1, p. 35-46 [DOI]
Lechner, M. ; Marz, M. ; Ihling, C. ; Sinz, A. ; Stadler, P. F. and V. Krauss:
The correlation of genome size and DNA methylation rate in metazoans.
Theory in biosciences,
132 (2013) 1, p. 47-60 [DOI]
Lehmann, J. ; Stadler, P. F. and V. Krauss:
Near intron pairs and the metazoan tree.
Molecular phylogenetics and evolution,
66 (2013) 3, p. 811-823 [DOI]
Lorenz, R. ; Bernhart, S. H. ; Qin, J. ; Siederdissen, C. H.
; Amman, F. ; Tanzer, A. ; Amman, F. ; Hofacker, I. L. and P. F. Stadler:
2D meets 4G : G-quadruplexes in RNA secondary structure prediction.
IEEE ACM transactions on computational biology and bioinformatics,
10 (2013) 4, p. 832-844 [DOI]
Müller, S. A. ; Findeiß, S. ; Pernitzsch, S. R. ; Wissenbach, D. K. ; Stadler, P. F. ; Hofacker, I. L. ; von Bergen, M. and S. Kalkhof:
Identification of new protein coding sequences and signal peptidase cleavage sites
of Helicobacter pylori strain 26695 by proteogenomics.
Journal of proteomics,
86 (2013), p. 27-42 [DOI]
Qi, X. ; Li, Y. ; Honda, S. ; Hoffmann, S. ; Marz, M. ; Mosig, A. ; Podlevsky, J. D. ; Stadler, P. F. ; Selker, E. U. and J. J. -L.-L. Chen:
The common ancestral core of vertebrate and fungal telomerase RNAs.
Nucleic acids research,
41 (2013) 1, p. 450-462 [DOI]
Qin, J. and C. M. Reidys:
On topological RNA interaction structures.
Journal of computational biology,
20 (2013) 7, p. 495-513 [DOI]
Sabarinathan, R. ; Tafer, H. ; Seemann, S. E. ; Hofacker, I. L. ; Stadler, P. F. and J. Gorodkin:
RNAsnp : efficient detection of local RNA secondary structure changes induced by SNPs.
Human mutation,
34 (2013) 4, p. 546-556 [DOI]
Sabarinathan, R. ; Tafer, H. ; Seemann, S. E. ; Hofacker, I. L. ; Stadler, P. F. and J. Gorodkin:
The RNAsnp web server : predicting SNP effects on local RNA secondary structure.
Nucleic acids research,
41 (2013) W1, p. W475-W479 [DOI]
Sabarinathan, R. ; Tafer, H. ; Seemann, S. E. ; Hofacker, I. L. ; Stadler, P. F. and J. Gorodkin:
Erratum: 'RNAsnp : efficient detection of local RNA secondary structure changes induced
by SNPs' [In: Human mutation 34(2013)4,546-556].
Human mutation,
34 (2013) 6, p. 925-925 [DOI]
Siederdissen, C. H.
; Hammer, S. ; Abfalter, I. ; Hofacker, I. L. ; Flamm, C. and P. F. Stadler:
Computational design of RNAs with complex energy landscapes.
Biopolymers,
99 (2013) 12, p. 1124-1136 [DOI]
Siederdissen, C. H.
; Hofacker, I. L. and P. F. Stadler:
How to multiply dynamic programming algorithms.
Advances in bioinformatics and computational biology : 8th Brazilian Symposium on
Bioinformatics, BSB 2013, Recife, Brazil, November 3-7, 2013 ; proceedings / J.
C. Setubal... (eds.). Springer, 2013. - P. 82-93
(Lecture notes in computer science ; 8213)
[DOI]
Smith, M. A. ; Gesell, T. ; Stadler, P. F. and J. S. Mattick:
Widespread purifying selection on RNA structure in mammals.
Nucleic acids research,
41 (2013) 17, p. 8220-8236 [DOI]
Stadler, P. F.:
An integrated tool to assess the functional impact of SNPs.
[FREELINK]
Wachsmuth, M. ; Findeiß, S. ; Weissheimer, N. ; Stadler, P. F. and M. Mörl:
De novo design of a synthetic riboswitch that regulates transcription termination.
Nucleic acids research,
41 (2013) 4, p. 2541-2551 [DOI]
Will, S. ; Siebauer, M. F. ; Heyne, S. ; Engelhardt, J. ; Stadler, P. F. ; Reiche, K. and R. Backofen:
LocARNAscan : incorporating thermodynamic stability in sequence and structure-based
RNA homology search.
Algorithms for molecular biology,
8 (2013), 14 [DOI]
Andersen, J. L. ; Flamm, C. ; Merkle, D. and P. F. Stadler:
Maximizing output and recognizing autocatalysis in chemical reaction networks is NP-Complete.
Journal of systems chemistry,
3 (2012) 1, 1 [DOI] [ARXIV]
Engelhardt, J. and P. F. Stadler:
Hidden treasures in unspliced EST data.
Theory in biosciences,
131 (2012) 1, p. 49-57 [DOI]
Gao, Z.-M. ; Gu, J. and W. Li:
Epidemic spreading in a multi-compartment system.
Chinese physics letters,
29 (2012) 2, 028902 [DOI]
Hellmuth, M. ; Ostermeier, L. and P. F. Stadler:
Diagonalized Cartesian products of S-prime graphs are S-prime.
Discrete mathematics,
312 (2012) 1, p. 74-80 [DOI]
Hellmuth, M. ; Ostermeier, L. and P. F. Stadler:
A survey on hypergraph products.
Mathematics in computer science,
6 (2012) 1, p. 1-32 [DOI] [ARXIV]
Hellmuth, M. ; Ostermeier, P.-J. and P. F. Stadler:
Minimum cycle bases of lexicographic products.
Ars mathematica contemporanea,
5 (2012) 2, p. 223-234[FREELINK]
Helm, M. ; Mörl, M. ; Stadler, P. F. and S. Hoffmann:
Biochemie 2011 : RNA - deep sequencing.
Nachrichten aus der Chemie,
60 (2012) 3, p. 300-307 [DOI]
Hernández Rosales, M. ; Hellmuth, M. ; Wieseke, N. ; Huber, K. T. ; Moulton, V. and P. F. Stadler:
From event-labeled gene trees to species trees.
BMC bioinformatics,
13 (2012) Supplement 19, S6 [DOI]
Hertel, J. ; Bartschat, S. ; Wintsche, A. ; Otto, C. and P. F. Stadler:
Evolution of the let-7 microRNA family.
RNA biology,
9 (2012) 3, p. 231-241 [DOI] [FREELINK]
Hofacker, I. L. ; Reidys, C. M. and P. F. Stadler:
Symmetric circular matchings and RNA folding.
Discrete mathematics,
312 (2012) 1, p. 100-112 [DOI]
Jühling, F. ; Pütz, J. ; Bernt, M. ; Donath, A. ; Middendorf, M. ; Florentz, C. and P. F. Stadler:
Improved systematic tRNA gene annotation allows new insights into the evolution of
mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements.
Nucleic acids research,
40 (2012) 7, p. 2833-2845 [DOI] [FREELINK]
Jühling, F. ; Pütz, J. ; Florentz, C. and P. F. Stadler:
Armless mitochondrial tRNAs in Enoplea (Nematoda).
RNA biology,
9 (2012) 9, p. 1161-1166 [DOI]
Klemm, K. ; Mehta, A. and P. F. Stadler:
Landscape encodings enhance optimization.
PLOS ONE,
7 (2012) 4, e34780 [DOI] [ARXIV]
Langenberger, D. ; Pundhir, S. ; Ekstrøem, C. T. ; Stadler, P. F. ; Hoffmann, S. and J. Gorodkin:
deepBlockAlign : a tool for aligning RNA-seq profiles of read block patterns.
Bioinformatics,
28 (2012) 1, p. 17-24 [DOI]
Lessa, F. A. ; Raiol, T. ; Brigido, M. M. ; Martins Neto, D. S. B. ; Walter, M. Emilia M. T. and P. F. Stadler:
Clustering Rfam 10.1 : clans, families, and classes.
Genes,
3 (2012) 3, p. 378-390 [DOI]
Lorenz, R. ; Bernhart, S. H. ; Externbrink, F. ; Qin, J. ; Siederdissen, C. H.
; Amman, F. ; Hofacker, I. L. and P. F. Stadler:
RNA folding algorithms with g-quadruplexes.
Advances in bioinformatics and computational biology : 7th Brazilian Symposium on
Bioinformatics, BSB 2012, Campo Grande, Brazil, August 15-17, 2012 ; proceedings / M.
C. de Souto... (eds.). Springer, 2012. - P. 49-60
(Lecture notes in computer science ; 7409)
[DOI]
Ostermeier, L. ; Hellmuth, M. and P. F. Stadler:
The cartesian product of hypergraphs.
Journal of graph theory,
70 (2012) 2, p. 180-196 [DOI]
Otto, C. ; Stadler, P. F. and S. Hoffmann:
Fast and sensitive mapping of bisulfite-treated sequencing data.
Bioinformatics,
28 (2012) 13, p. 1698-1704 [DOI] [FREELINK]
Schmidtke, C. ; Findeiß, S. ; Sharma, C. M. ; Kuhfuss, J. ; Hoffmann, S. ; Vogel, J. ; Stadler, P. F. and U. Bonas:
Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs
with putative virulence functions.
Nucleic acids research,
40 (2012) 5, p. 2020-2031 [DOI] [FREELINK]
Tippmann, S. C. ; Ivanek, R. ; Gaidatzis, D. ; Schöler, A. ; Hoerner, L. ; Nimwegen, E. v.
; Stadler, P. F. ; Stadler, M. B. and D. Schübeler:
Chromatin measurements reveal contributions of synthesis and decay to steady-state
mRNA levels.
Molecular systems biology,
8 (2012) 1, 593 [DOI]
Washietl, S. ; Hofacker, I. L. ; Stadler, P. F. and M. Kellis:
RNA folding with soft constraints : reconciliation of probing data and thermodynamic
secondary structure prediction.
Nucleic acids research,
40 (2012) 10, p. 4261-4272 [DOI]
Will, S. ; Joshi, T. ; Hofacker, I. L. ; Stadler, P. F. and R. Backofen:
LocARNA-P : accurate boundary prediction and improved detection of structural RNAs.
RNA,
18 (2012) 5, p. 900-914 [DOI]
Eggenhofer, F. ; Tafer, H. ; Stadler, P. F. and I. L. Hofacker:
RNApredator : fast accessibility-based prediction of sRNA targets.
Nucleic acids research,
39 (2011), p. W149-W154 [DOI]
Fasold, M. ; Langenberger, D. ; Binder, H. ; Stadler, P. F. and S. Hoffmann:
DARIO : a ncRNA detection and analysis tool for next-generation sequencing experiments.
Nucleic acids research,
39 (2011), p. W112-W117 [DOI]
Findeiß, S. ; Engelhardt, J. ; Prohaska, S. J. and P. F. Stadler:
Protein-coding structured RNAs : a computational survey of conserved RNA secondary
structures overlapping coding regions in drosophilids.
Biochimie,
93 (2011) 11, p. 2019-2023 [DOI] [FREELINK]
Findeiß, S. ; Langenberger, D. ; Stadler, P. F. and S. Hoffmann:
Traces of post-transcriptional RNA modifications in deep sequencing data.
Biological chemistry,
392 (2011) 4, p. 305-313 [DOI] [FREELINK]
Gu, J. ; Gao, Z. M.
and W. Li:
Modeling of epidemic spreading with white Gaussian noise.
Chinese science bulletin,
56 (2011) 34, p. 3683-3688 [DOI]
Kehr, S. ; Bartschat, S. ; Stadler, P. F. and H. Tafer:
PLEXY : efficient target prediction for box C/D snoRNAs.
Bioinformatics,
27 (2011) 2, p. 279-280 [DOI] [FREELINK]
Krakauer, D. C. ; Collins, J. P. ; Erwin, D. ; Flack, J. C. ; Fontana, W. ; Laubichler, M. D. ; Prohaska, S. J. ; West, G. B. and P. F. Stadler:
The challenges and scope of theoretical biology.
Journal of theoretical biology,
276 (2011) 1, p. 269-276 [DOI]
Langenberger, D. ; Bartschat, S. ; Hertel, J. ; Hoffmann, S. ; Tafer, H. and P. F. Stadler:
MicroRNA or Not MicroRNA?.
Advances in bioinformatics and computational biology : 6th Brazilian Symposium on
Bioinformatics, BSB 2011, Brasilia, Brazil, August 10-12, 2011 ; proceedings / O.
N.
Souza... (eds.). Springer, 2011. - P. 1-9
(Lecture notes in computer science ; 6832)
[DOI]
Lechner, M. ; Findeiß, S. ; Steiner, L. ; Marz, M. ; Stadler, P. F. and S. J. Prohaska:
Proteinortho : detection of (Co-)orthologs in large-scale analysis.
BMC bioinformatics,
12 (2011), 124 [DOI] [FREELINK]
Li, A. X. ; Marz, M. ; Qin, J. and C. M. Reidys:
RNA-RNA interaction prediction based on multiple sequence alignments.
Bioinformatics,
27 (2011) 4, p. 456-463 [DOI] [ARXIV]
Li, W. ; Gao, Z.-M. and J. Gu:
Effects of variant rates and noise on epidemic spreading.
Chinese physics letters,
28 (2011) 5, 058903 [DOI]
Lorenz, R. ; Bernhart, S. H. ; Siederdissen, C. H.
; Tafer, H. ; Flamm, C. ; Stadler, P. F. and I. L. Hofacker:
ViennaRNA Package 2.0.
Algorithms for molecular biology,
6 (2011), 26 [DOI]
Lozada-Chávez, I. ; Stadler, P. F. and S. J. Prohaska:
'Hypothesis for the modern RNA world' : a pervasive non-coding RNA-based genetic regulation
is a prerequisite for the emergence of multicellular complexity.
Origins of life and evolution of the biosphere,
41 (2011) 6, p. 587-607 [DOI]
Marz, M. ; Gruber, A. R. ; Siederdissen, C. H.
; Amman, F. ; Badelt, S. ; Bartschat, S. ; Bernhart, S. H. ; Beyer, W. ; Kehr, S. ; Lorenz, R. ; Tanzer, A. ; Yusuf, D. ; Tafer, H. ; Hofacker, I. L. and P. F. Stadler:
Animal snoRNAs and scaRNAs with exceptional structures.
RNA biology,
8 (2011) 6, p. 938-946 [DOI]
Menzel, P. ; Stadler, P. F. and J. Gorodkin:
maxAlike : maximum likelihood-based sequence reconstruction with application to improved
primer design for unknown sequences.
Bioinformatics,
27 (2011) 3, p. 317-325 [DOI] [FREELINK]
Otto, C. ; Hoffmann, S. ; Gorodkin, J. and P. F. Stadler:
Fast local fragment chaining using sum-of-pair gap costs.
Algorithms for molecular biology,
6 (2011), 4 [DOI] [FREELINK]
Otto, W.:
Transcriptional regulatory elements : detection and evolutionary analysis.
Dissertation, Universität Leipzig, 2011[FREELINK]
Otto, W. ; Stadler, P. F. and S. J. Prohaska:
Phylogenetic footprinting and consistent sets of local aligments.
Combinatorial pattern matching : 22nd annual symposium, CPM 2011, Palermo, Italy,
June 27-29, 2011. proceedings. / R.
Giancarlo... (eds.). Springer, 2011. - P. 118-131
(Lecture notes in computer science ; 6661)
[DOI]
Parikesit, A. A.
; Stadler, P. F. and S. J. Prohaska:
Evolution and quantitative comparison of genome-wide protein domain distributions.
Genes,
2 (2011) 4, p. 912-924 [DOI]
Perseke, M. ; Hetmank, J. ; Bernt, M. ; Stadler, P. F. ; Schlegel, M. and D. Bernhard:
The enigmatic mitochondrial genome of Rhabdopleura compacta (Pterobranchia) reveals
insights into selection of an efficient tRNA system and supports monophyly of Ambulacraria.
BMC evolutionary biology,
11 (2011), 134 [DOI]
Raincrow, J. D. ; Dewar, K. ; Stocsits, C. ; Prohaska, S. J. ; Amemiya, C. T. ; Stadler, P. F. and C.-h. Chiu:
Hox clusters of the bichir (Actinopterygii, Polypterus senegalus) highlight unique
patterns of sequence evolution in Gnathostome phylogeny.
Journal of experimental zoology / B,
316 (2011) 6, p. 451-464 [DOI] [FREELINK]
Reidys, C. M. ; Huang, F. W. D. ; Andersen, J. E. ; Penner, R. C. ; Stadler, P. F. and M. E. Nebel:
Topology and prediction of RNA pseudoknots.
Bioinformatics,
27 (2011) 8, p. 1076-1085 [DOI]
Siederdissen, C. H.
; Bernhart, S. H. ; Stadler, P. F. and I. L. Hofacker:
A folding algorithm for extended RNA secondary structures.
Bioinformatics,
27 (2011) 13, p. i129-i136 [DOI]
Stadler, P. F. and D. Rose:
Molecular evolution of the non-coding eosinophil granule ontogeny transcript.
Frontiers in genetics,
2 (2011), 69 [DOI] [FREELINK]
Steiner, L. ; Stadler, P. F. and M. Dysouw:
A Pipeline for computational historical linguistics.
Language dynamics and change,
1 (2011) 1, p. 89-127 [DOI] [FREELINK]
Tafer, H. ; Amman, F. ; Eggenhofer, F. ; Stadler, P. F. and I. L. Hofacker:
Fast accessibility-based prediction of RNA-RNA interactions.
Bioinformatics,
27 (2011) 14, p. 1934-1940 [DOI]
Tramontano, A. ; Donath, A. ; Bernhart, S. H. ; Reiche, K. ; Boehmdorfer, G. ; Stadler, P. F. and A. Bachmair:
Deletion analysis of the 3 ' long terminal repeat sequence of plant retrotransposon
Tto1 identifies 125 base pairs redundancy as sufficient for first strand transfer.
Virology,
412 (2011) 1, p. 75-82 [DOI]
Ullrich, A. ; Rohrschneider, M. ; Scheuermann, G. ; Stadler, P. F. and C. Flamm:
In silico evolution of early metabolism.
Artificial life,
17 (2011) 2, p. 87-108 [DOI]
Washietl, S. ; Findeiß, S. ; Müller, S. A. ; Kalkhof, S. ; von Bergen, M. ; Hofacker, I. L. ; Stadler, P. F. and N. Goldman:
RNAcode : robust discrimination of coding and noncoding regions in comparative sequence
data.
RNA,
17 (2011) 4, p. 578-594 [DOI] [FREELINK]
Amemiya, C. T. ; Powers, T. P. ; Prohaska, S. J. ; Grimwood, J. ; Schmutz, J. ; Dickson, M. ; Miyake, T. ; Schönborn, M. A. ; Myers, R. M. ; Ruddle, F. H. and P. F. Stadler:
Complete HOX cluster characterization of the coelacanth provides further evidence
for slow evolution of its genome.
Proceedings of the National Academy of Sciences of the United States of America,
107 (2010) 8, p. 3622-3627 [DOI] [FREELINK]
Arnold, C. and P. F. Stadler:
Polynomial algorithms for the Maximal Pairing Problem : efficient phylogenetic targeting
on arbitrary trees.
Algorithms for molecular biology,
5 (2010), 25 [DOI] [FREELINK]
Bermúdez-Santana, C. I. ; Attolini, C. S.
-O. ; Kirsten, T. ; Engelhardt, J. ; Prohaska, S. J. ; Steigele, S. and P. F. Stadler:
Genomic organization of eukaryotic tRNAs.
BMC genomics,
11 (2010), 270 [DOI] [FREELINK]
Boria, I. ; Gruber, A. R. ; Tanzer, A. ; Bernhart, S. H. ; Lorenz, R. ; Müller, M. M. ; Hofacker, I. L. and P. F. Stadler:
Nematode sbRNAs : homologs of vertebrate Y RNAs.
Journal of molecular evolution,
70 (2010) 4, p. 346-358 [DOI] [FREELINK]
Dalloul, R. A. ; Long, J. A. ; Zimin, A. V. ; Aslam, L. ; Beal, K. ; Blomberg, L. A.
; Bouffard, P. ; Burt, D. W. ; Crasta, O. ; Crooijmans, R. P. M. A. ; Cooper, K. ; Coulombe, R. A. ; De, S. ; Delany, M. E. ; Dodgson, J. B. ; Dong, J. J. ; Evans, C. ; Frederickson, K. M. ; Flicek, P. ; Florea, L. ; Folkerts, O. ; Groenen, M. A. M. ; Harkins, T. T. ; Herrero, J. ; Hoffmann, S. ; Megens, H.-J. ; Jiang, A. ; de Jong, P. ; Kaiser, P. ; Kim, H. ; Kim, K.-W. ; Kim, S. ; Langenberger, D. ; Lee, M.-K. ; Lee, T. ; Mane, S. ; Marcais, G. ; Marz, M. ; McElroy, A. P. ; Modise, T. ; Nefedov, M. ; Notredame, C. ; Paton, I. R. ; Payne, W. S. ; Pertea, G. ; Prickett, D. ; Puiu, D. ; Qioa, D. ; Raineri, E. ; Ruffier, M. ; Salzberg, S. L. ; Schatz, M. C. ; Scheuring, C. ; Schmidt, C. J. ; Schroeder, S. ; Searle, S. M. J. ; Smith, E. J. ; Smith, J. ; Sonstegard, T. S. ; Stadler, P. F. ; Tafer, H. ; Tu, Z. ; Van Tassell, C. P. ; Vilella, A. J. ; Williams, K. P. ; Yorke, J. A. ; Zhang, L. ; Zhang, H.-B. ; Zhang, X. ; Zhang, Y. and K. M. Reed:
Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo)
: genome assembly and analysis.
PLoS Biology,
8 (2010) 9, e1000475 [DOI]
Fasold, M. ; Stadler, P. F. and H. Binder:
G-stack modulated probe intensities on expression arrays : sequence corrections and
signal calibration.
BMC bioinformatics,
11 (2010), 207 [DOI]
Ferreira, C. E. ; Miyano, S. and P. F. Stadler (eds.):
Advances in bioinformatics and computational biology : 5th Brazilian Symposium on
Bioinformatics, BSB 2010, Rio de Janeiro, Brazil, August 31 - September 3, 2010 ;
proceedings.
Springer, 2010. - VIII, 79 p.
(Lecture notes in computer science ; 6268)
ISBN 978-3-642-15059-3 [DOI]
Findeiß, S. ; Schmidtke, C. ; Stadler, P. F. and U. Bonas:
A novel family of plasmid-transferred anti-sense ncRNAs.
RNA biology,
7 (2010) 2, p. 120-124 [DOI]
Flamm, C. ; Ullrich, A. ; Ekker, H. ; Mann, M. ; Högerl, D. ; Rohrschneider, M. ; Sauer, S. ; Scheuermann, G. ; Klemm, K. ; Hofacker, I. L. and P. F. Stadler:
Evolution of metabolic networks : a computational fame-work.
Journal of systems chemistry,
1 (2010), 4 [DOI]
Hofacker, I. L. ; Flamm, C. ; Heine, C. ; Wolfinger, M. T. ; Scheuermann, G. and P. F. Stadler:
BarMap : RNA folding on dynamic energy landscapes.
RNA,
16 (2010) 7, p. 1308-1316 [DOI]
Huang, F. W. D. ; Qin, J. ; Reidys, C. M. and P. F. Stadler:
Target prediction and a statistical sampling algorithm for RNA-RNA interaction.
Bioinformatics,
26 (2010) 2, p. 175-181 [DOI] [FREELINK]
Jin, C. and Y. Long:
On label information incorporated metric learning for regressions.
International journal of computational intelligence and applications,
9 (2010) 4, p. 339-351 [DOI]
Jänicke, S. ; Heine, C. ; Hellmuth, M. ; Stadler, P. F. and G. Scheuermann:
Visualization of graph products.
IEEE transactions on visualization and computer graphics,
16 (2010) 6, p. 1082-1089 [DOI]
Langenberger, D. ; Bermúdez-Santana, C. I. ; Stadler, P. F. and S. Hoffmann:
Identification and classification of small RNAs in transcriptome sequence data.
Pacific Symposium on Biocomputing 2010 : Kamuela, Hawaii, USA, 4 - 8 January 2010 / R.
B. Altman... (eds.). World Scientific, 2010. - P. 80-87 [DOI]
Lehmann, J. ; Eisenhardt, C. ; Stadler, P. F. and V. Krauss:
Some novel intron positions in conserved Drosophila genes are caused by intron sliding
or tandem duplication.
BMC evolutionary biology,
10 (2010), 156 [DOI] [FREELINK]
Marz, M. ; Vanzo, N. and P. F. Stadler:
Temperature-dependent structural variability of RNAs : spliced leader RNAs and their
evolutionary history.
Journal of bioinformatics and computational biology,
8 (2010) 1, p. 1-17 [DOI] [FREELINK]
Müller, S. A. ; Kohajda, T. ; Findeiß, S. ; Stadler, P. F. ; Washietl, S. ; Kellis, M. ; von Bergen, M. and S. Kalkhof:
Optimization of parameters for coverage of low molecular weight proteins.
Analytical and bioanalytical chemistry,
398 (2010) 7/8, p. 2867-2881 [DOI]
Parikesit, A. A.
; Stadler, P. F. and S. J. Prohaska:
Detection of protein domains in eukaryotic genome sequences.
Advances in bioinformatics and computational biology : 5th Brazilian Symposium on
Bioinformatics, BSB 2010, Rio de Janeiro, Brazil, August 31 - September 3, 2010 ;
proceedings / C.
E. Ferreira... (eds.). Springer, 2010. - P. 71-74
(Lecture notes in computer science ; 6268)
[DOI]
Parikesit, A. A.
; Stadler, P. F. and S. J. Prohaska:
Quantitative comparison of genomic-wide protein domain distributions.
German Conference on Bioinformatics 2010 : September 20 - 22, 2010, Technische Universität
Carolo Wilhelmina zu Braunschweig, Germany / D.
Schomburg... (eds.). Gesellschaft für Informatik, 2010. - P. 93-102
(Lecture notes in informatics ; P-173)
Prohaska, S. J. ; Stadler, P. F. and D. C. Krakauer:
Innovation in gene regulation : the case of chromatin computation.
Journal of theoretical biology,
265 (2010) 1, p. 27-44 [DOI]
Riester, M. ; Stadler, P. F. and K. Klemm:
Reconstruction of pedigrees in clonal plant populations.
Theoretical population biology,
78 (2010) 2, p. 109-117 [DOI] [FREELINK]
Sharma, C. M. ; Hoffmann, S. ; Darfeuille, F. ; Reignier, J. ; Findeiß, S. ; Sittka, A. ; Chabas, S. ; Reiche, K. ; Hackermüller, J. ; Reinhardt, R. ; Stadler, P. F. and J. Vogel:
The primary transcriptome of the major human pathogen Helicobacter pylori.
Nature,
464 (2010) 7286, p. 250-255 [DOI]
Stadler, B. M. R. and P. F. Stadler:
Combinatorial vector fields and the valley structure of fitness landscapes.
Journal of mathematical biology,
61 (2010) 6, p. 877-898 MIS-Preprint: 65/2009 [DOI]
Stadler, P. F.:
Evolution of the long non-coding RNAs MALAT1 and MENb/e.
Advances in bioinformatics and computational biology : 5th Brazilian Symposium on
Bioinformatics, BSB 2010, Rio de Janeiro, Brazil, August 31 - September 3, 2010 ;
proceedings / C.
E. Ferreira... (eds.). Springer, 2010. - P. 1-12
(Lecture notes in computer science ; 6268)
[DOI]
Tafer, H. ; Kehr, S. ; Hertel, J. ; Hofacker, I. L. and P. F. Stadler:
RNAsnoop : efficient target prediction for H/ACA snoRNAs.
Bioinformatics,
26 (2010) 5, p. 610-616 [DOI]
Ullrich, A. ; Flamm, C. ; Rohrschneider, M. and P. F. Stadler:
In silico evolution of early metabolism.
Artificial life XII : proceedings of the twelfth International Conference on the Synthesis
and Simulation of Living Systems / H.
Fellermann... (eds.). MIT Press, 2010. - P. 57-64
Yusuf, D. ; Marz, M. ; Stadler, P. F. and I. L. Hofacker:
Bcheck : a wrapper tool for detecting RNase P RNA genes.
BMC genomics,
11 (2010), 432 [DOI] [FREELINK]
Benkö, G. ; Centler, F. ; Dittrich, P. ; Flamm, C. ; Stadler, B. M. R. and P. F. Stadler:
A topological approach to chemical organizations.
Artificial life,
15 (2009) 1, p. 71-88 [DOI]
Copeland, C. C. ; Marz, M. ; Rose, D. ; Hertel, J. ; Brindley, P. J. ; Bermúdez-Santana, C. I. ; Kehr, S. ; Stephan-Otto Attolini, C. and P. F. Stadler:
Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni
and Schistosoma japonicum.
BMC genomics,
10 (2009), 464 [DOI] [FREELINK]
Dress, A. W. M. ; Karasözen, B. ; Stadler, P. F. and G.-W. Weber:
Preface [to the special issue 'Networks in computational biology'].
Discrete applied mathematics,
157 (2009) 10, p. 2217-2220 [DOI]
Hellmuth, M. ; Imrich, W. ; Kloeckl, W. and P. F. Stadler:
Local algorithms for the prime factorization of strong product graphs.
Mathematics in computer science,
2 (2009) 4, p. 653-682 [DOI] [ARXIV]
Hoffmann, S. ; Otto, C. ; Kurtz, S. ; Sharma, C. M. ; Khaitovich, P. ; Vogel, J. ; Stadler, P. F. and J. Hackermüller:
Fast mapping of short sequences with mismatches, insertions and deletions using index
structures.
PLoS computational biology,
5 (2009) 9, e1000502 [DOI]
Huang, F. W. D. ; Qin, J. ; Reidys, C. M. and P. F. Stadler:
Partition function and base pairing probabilities for RNA-RNA interaction prediction.
Bioinformatics,
25 (2009) 20, p. 2646-2654 [DOI] [FREELINK]
Langenberger, D. ; Bermúdez-Santana, C. I. ; Hertel, J. ; Hoffmann, S. ; Khaitovich, P. and P. F. Stadler:
Evidence for human microRNA-offset RNAs in small RNA sequencing data.
Bioinformatics,
25 (2009) 18, p. 2298-2301 [DOI] [FREELINK]
Marz, M. ; Donath, A. ; Verstraete, N. ; Nguyen, V. T.
; Stadler, P. F. and O. Bensaude:
Evolution of 7SK RNA and its protein partners in metazoa.
Molecular biology and evolution,
26 (2009) 12, p. 2821-2830 [DOI] [FREELINK]
Marz, M. and P. F. Stadler:
Comparative analysis of eukaryotic U3 snoRNA.
RNA biology,
6 (2009) 5, p. 503-507 [DOI] [FREELINK]
Menzel, P. ; Gorodkin, J. and P. F. Stadler:
Maximum likelihood estimation of weight matrices for targeted homology search.
German Conference on Bioinformatics 2009 / I.
Grosse... (eds.). Gesellschaft für Informatik, 2009. - P. 211-220
(GI-Edition : lecture notes in informatics / Proceedings ; 157)
Menzel, P. ; Gorodkin, J. and P. F. Stadler:
The tedious task of finding homologous noncoding RNA genes.
RNA,
15 (2009) 12, p. 2075-2082 [DOI] [FREELINK]
Mosig, A. ; Biyikoglu, T. ; Prohaska, S. J. and P. F. Stadler:
Discovering cis-regulatory modules by optimizing barbecues.
Discrete applied mathematics,
157 (2009) 10, p. 2458-2468 [DOI] [FREELINK]
Munteanu, A. and P. F. Stadler:
Mutate now, die later : evolutionary dynamics with delayed selection.
Journal of theoretical biology,
260 (2009) 3, p. 412-421 [DOI]
Ostermeier, P.-J. ; Hellmuth, M. ; Leydold, J. ; Klemm, K. and P. F. Stadler:
A note on quasi-robust cycle bases.
Ars mathematica contemporanea,
2 (2009) 2, p. 231-240 [DOI]
Stadler, P. F. ; Chen, J. J. -L.-L. ; Hackermüller, J. ; Hoffmann, S. ; Horn, F. ; Khaitovich, P. ; Kretzschmar, A. K. ; Mosig, A. ; Prohaska, S. J. ; Qi, X. ; Schutt, K. and K. Ullmann:
Evolution of vault RNAs.
Molecular biology and evolution,
26 (2009) 9, p. 1975-1991 [DOI] [FREELINK]
Stadler, P. F. ; Prohaska, S. J. ; Forst, C. V. and D. C. Krakauer:
Defining genes : a computational framework.
Theory in biosciences,
128 (2009) 3, p. 165-170 [DOI]
Stocsits, R. R. ; Letsch, H. ; Hertel, J. ; Misof, B. and P. F. Stadler:
Accurate and efficient reconstruction of deep phylogenies from structured RNAs.
Nucleic acids research,
37 (2009) 18, p. 6184-6193 [DOI] [FREELINK]
Dress, A. W. M. ; Flamm, C. ; Fritzsch, G. ; Grünewald, S. ; Kruspe, M. ; Prohaska, S. J. and P. F. Stadler:
Noisy : Identification of problematic columns in multiple sequence alignments.
Algorithms for molecular biology,
3 (2008), 7 [DOI]
Gruber, A. R. ; Kilgus, C. ; Mosig, A. ; Hofacker, I. L. ; Hennig, W. and P. F. Stadler:
Arthropod 7SK RNA.
Molecular biology and evolution,
25 (2008) 9, p. 1923-1930 [DOI]
Gruber, A. R. ; Koper-Emde, D. ; Marz, M. ; Tafer, H. ; Bernhart, S. H. ; Obernosterer, G. ; Mosig, A. ; Hofacker, I. L. ; Stadler, P. F. and B.-J. Benecke:
Invertebrate 7SK snRNAs.
Journal of molecular evolution,
66 (2008) 2, p. 107-115 [DOI]
Gu, J. ; Li, W. and X. Cai:
Message spreading and forget-remember mechanism on a scale-free network.
Chinese physics letters,
25 (2008) 6, p. 2303-2306 [DOI]
Gu, J. ; Li, W. and X. Cai:
The effect of the forget-remember mechanism on spreading.
The European physical journal / B,
62 (2008) 2, p. 247-255 [DOI]
Hoffmann, S. ; Cepok, S. ; Grummel, V. ; Lehmann-Horn, K. ; Hackermüller, J. ; Stadler, P. F. ; Hartung, H.-P. ; Berthele, A. ; Deisenhammer, F. ; Wasmuth, R. and B. Hemmer:
Erratum: 'HLA-DRB1*0401 and HLA-DRB1*0408 are strongly associated with the development
of antibodies against interferon-b therapy in multiple sclerosis' [In: American journal
of human genetics 83(2008)2,219-227].
American journal of human genetics : AJHG,
83 (2008) 4, p. 541-541 [DOI]
Stadler, P. F. and B. M. R. Stadler:
Replicator dynamics in protocells.
Protocells : bridging nonliving and living matter / S. Rasmussen (ed.). MIT Press, 2008. - P. 317-336
Xie, M. ; Mosig, A. ; Qi, X. ; Li, Y. ; Stadler, P. F. and Julian J.-L. Chen:
Structure and function of the smallest vertebrate telomerase RNA from teleost fish.
The journal of biological chemistry,
283 (2008) 4, p. 2049-2059 [DOI]
Backofen, R. ; Bernhart, S. H. ; Flamm, C. ; Fried, C. ; Fritzsch, G. ; Hackermüller, J. ; Hertel, J. ; Hofacker, I. L. ; Missal, K. ; Mosig, A. ; Prohaska, S. J. ; Rose, D. ; Stadler, P. F. ; Tanzer, A. ; Washietl, S. ; Will, S. and A. F. Bompfünewerer:
RNAs everywhere : genome-wide annotation of structured RNAs.
Journal of experimental zoology / B,
308 (2007) 1, p. 1-25 [DOI]
Biyikoglu, T. ; Leydold, J. and P. F. Stadler (eds.):
Laplacian eigenvectors of graphs : Perron-Frobenius and Faber-Krahn type theorems.
Springer, 2007. - VIII, 115 p.
(Lecture notes in mathematics ; 1915)
ISBN 978-3-540-73509-0 [DOI]
Breidbach, O. ; Jost, J. and P. F. Stadler:
Towards theoretical formalisms.
Theory in biosciences,
126 (2007) 1, p. 1-2 [DOI]
Chen, Julian J.-L. ; Mosig, A. and P. F. Stadler:
Homology search with fragmented nucleic acid sequence patterns.
Algorithms in bioinformatics : 7th International Workshop ; WABI 2007 ; Philadelphia,
PA, USA ; September 8-9, 2007 ; Proceedings / R.
Giancarlo... (eds.). Springer, 2007. - P. 335-345
(Lecture notes in computer science ; 4645)
[DOI]
Flamm, C. ; Hofacker, I. L. ; Stadler, B. M. R. and P. F. Stadler:
Saddles and barrier in landscapes of generalized search operators.
Foundations of genetic algorithms : 9th international workshop, FOGA 2007, Mexico
City, Mexico, January 8 - 11, 2007, revised selected papers / C.
R. Stephens... (eds.). Springer, 2007. - P. 194-212
(Lecture notes in computer science ; 4436)
[DOI]
Marz, M. ; Mosig, A. ; Stadler, B. M. R. and P. F. Stadler:
U7 snRNAs : a computational survey.
Genomics, proteomics and bioinformatics,
5 (2007) 3/4, p. 187-195 [DOI]
Mosig, A. ; Guofeng, M. ; Stadler, B. M. R. and P. F. Stadler:
Evolution of the vertebrate Y RNA cluster.
Theory in biosciences,
126 (2007) 1, p. 9-14 [DOI]
Mosig, A. ; Stadler, P. F. and P. Menzel:
Tanimoto's best barbecue : discovering regulatory modules using Tanimoto scores.
GI-Edition / Proceedings,
115 (2007), p. 68-77
Prohaska, S. J. ; Mosig, A. and P. F. Stadler:
Regulatory signals in genomic sequences.
Networks : from biology to theory / J.
F.
Feng... (eds.). Springer, 2007. - P. S. 189-216 [DOI]
Biyikoglu, T. ; Stadler, P. F. ; Prohaska, S. J. and A. Mosig:
Detecting phylogenetic footprint clusters by optimizing barbeques.
MIS-Preprint: 32/2005
Bompfünewerer, A. F. ; Flamm, C. ; Fried, C. ; Fritzsch, G. ; Hofacker, I. L. ; Lehmann, J. ; Missal, K. ; Mosig, A. ; Müller, B. ; Prohaska, S. J. ; Stadler, B. M. R. ; Stadler, P. F. ; Tanzer, A. ; Washietl, S. and C. Witwer:
Evolutionary patterns of non-coding RNAs.
Theory in biosciences,
123 (2005) 4, p. 301-369 [DOI]
Leydold, J. ; Stadler, P. F. and T. Biyikoglu:
Nodal Domain Theorems and Bipartite Subgraphs.
The electronic journal of linear algebra,
13 (2005), p. 344-351 MIS-Preprint: 73/2005 [DOI]
Campos, P. R. A. ; deOliveira, V. M. ; Wagner, G. P. and P. F. Stadler:
Gene phylogenies and protein-protein interactions : possible artifacts resulting from
shared protein interaction partners.
Journal of theoretical biology,
231 (2004) 2, p. 197-202 [DOI]
Rasmussen, S. ; Chen, L. ; Stadler, B. M. R. and P. F. Stadler:
Proto-organism kinetics : evolutionary dynamics of lipid aggregates with genes and
metabolism.
Origins of life and evolution of the biosphere,
34 (2004) 1/2, p. 171-180 MIS-Preprint: 91/2002 [DOI]
Stadler, B. M. R. and P. F. Stadler:
The Topology of Evolutionary Biology.
Modelling in molecular biology / G.
Ciobanu (ed.). Springer, 2004. - P. 267-286
(Natural computing series)
Wolfinger, M. T. ; Svrcek-Seiler, W. A.
; Flamm, C. ; Hofacker, I. L. and P. F. Stadler:
Efficient computation of RNA folding dynamics.
Journal of physics / A,
37 (2004) 17, p. 4731-4741 [DOI]
Stadler, B. M. R. and P. F. Stadler:
Higher separation axioms in generalized closure spaces.
Annales Societatis Mathematicae Polonae / 1,
43 (2003) 2, p. 257-273