Learning and Inference
Head:
Sayan Mukherjee
Phone:
+49 (0) 341 - 9959 - 50
Fax:
+49 (0) 341 - 9959 - 658
Address:
Inselstr. 22
04103 Leipzig
Publications Sayan Mukherjee
Journal Articles 
S. I. Berchuck ; M. Janko ; F. A. Medeiros ; W. Pan and S. Mukherjee:
Bayesian non-parametric factor analysis for longitudinal spatial surfaces.
Bayesian analysis,
17 (2022) 2, p. 435-464 Bibtex [DOI] [ARXIV] Journal Open Access
K. McGoff ; S. Mukherjee and A. Nobel:
Gibbs posterior convergence and the thermodynamic formalism.
The annals of applied probability,
32 (2022) 1, p. 461-496 Bibtex [DOI] [ARXIV] Repository Open Access
J. D. Silverman ; K. Roche ; Z. C. Holmes ; L. A. David and S. Mukherjee:
Bayesian multinomial logistic normal models through Marginally Latent Matrix-T processes.
Journal of machine learning research,
23 (2022) 7, p. 1-42 Bibtex [ARXIV] [FREELINK] [CODELINK] Journal Open Access
B. St. Thomas ; L. Lin ; L.-H. Lim and S. Mukherjee:
Learning subspaces of different dimensions.
Journal of computational and graphical statistics,
31 (2022) 2, p. 337-350 Bibtex [DOI] [ARXIV] [CODELINK] Repository Open Access
J. Bryan ; A. Mandan ; G. Kamat ; W. K.
Gottschalk ; A. Badea ; K. J. Adams ; J. W.
Thompson ; C. A. Colton ; S. Mukherjee and M. W. Lutz:
Likelihood ratio statistics for gene set enrichment in Alzheimer's disease pathways.
Alzheimer's and dementia,
17 (2021) 4, p. 561-573 Bibtex [DOI] [CODELINK]
T. Gao ; J. Brodzki and S. Mukherjee:
The geometry of synchronization problems and learning group actions.
Discrete and computational geometry,
65 (2021) 1, p. 150-211 Bibtex [DOI] [ARXIV] [CODELINK] Repository Open Access
R. A. Johnston ; P. Vullioud ; J. Thorley ; H. Kirveslahti ; L. Shen ; S. Mukherjee ; C. M. Karner ; T. Clutton-Brock and J. Tung:
Morphological and genomic shifts in mole-rat 'queens' increase fecundity but reduce
skeletal integrity.
eLife,
10 (2021), e65760 Bibtex [DOI] [ARXIV] Journal Open Access
W. Li ; J. Hannig and S. Mukherjee:
Subspace clustering through sub-clusters.
Journal of machine learning research,
22 (2021), 53 Bibtex [ARXIV] [FREELINK] Journal Open Access
B. Wang ; T. Sudijono ; H. Kirveslahti ; T. Gao ; D. M. Boyer ; S. Mukherjee and L. Crawford:
A statistical pipeline for identifying physical features that differentiate classes
of 3D shapes.
The annals of applied statistics :,
15 (2021) 2, p. 638-661 Bibtex [DOI] [ARXIV] Journal Open Access
L. Crawford ; A. Monod ; A. X. Chen ; S. Mukherjee and R. Rabadán:
Predicting clinical outcomes in glioblastoma : an application of topological and functional
data analysis.
Journal of the American Statistical Association,
115 (2020) 531, p. 1139-1150 Bibtex [DOI] [ARXIV] [CODELINK] Repository Open Access
J. D. Silverman ; K. Roche ; S. Mukherjee and L. A. David:
Naught all zeros in sequence count data are the same.
Computational and structural biotechnology journal,
18 (2020), p. 2789-2798 Bibtex [DOI] [ARXIV] Journal Open Access
S. I. Berchuck ; S. Mukherjee and F. A. Medeiros:
Estimating rates of progression and predicting future visual fields in glaucoma using
a deep variational autoencoder.
Scientific reports,
9 (2019), 18113 Bibtex [DOI] [ARXIV] Journal Open Access
M. Cakir ; S. Mukherjee and K. C. Wood:
Label propagation defines signaling networks associated with recurrently mutated cancer
genes.
Scientific reports,
9 (2019), 9401 Bibtex [DOI] [ARXIV] Journal Open Access
T. Vilgalys ; J. Rogers ; C. J. Jolly ; S. Mukherjee and J. Tung:
Evolution of DNA methylation in Papio baboons.
Molecular biology and evolution,
36 (2019) 3, p. 527-540 Bibtex [DOI] [ARXIV] Journal Open Access
A. D. Washburne ; J. D. Silverman ; J. T. Morton ; D. Becker ; D. Crowley ; S. Mukherjee ; L. A. David and R. K. Plowright:
Phylofactorization : a graph partitioning algorithm to identify phylogenetic scales
of ecological data.
Ecological monographs,
89 (2019) 2, e01353 Bibtex [DOI] [ARXIV] [CODELINK] Repository Open Access
F. Wu ; A. J. Lopatkin ; D. A. Needs ; C. T. Lee ; S. Mukherjee and L. You:
A unifying framework for interpreting and predicting mutualistic systems.
Nature communications,
10 (2019), 242 Bibtex [DOI] Journal Open Access
S. Barish ; S. Nuss ; I. Strunilin ; S. Bao ; S. Mukherjee ; C. D. Jones and P. C. Volkan:
Combinations of DIPs and Dprs control organization of olfactory receptor neuron terminals
in Drosophila.
PloS genetics,
14 (2018) 8, e1007560 Bibtex [DOI] [ARXIV] Journal Open Access
L. Crawford ; K. C. Wood ; X. Zhou and S. Mukherjee:
Bayesian approximate kernel regression with variable selection.
Journal of the American Statistical Association,
113 (2018) 524, p. 1710-1721 Bibtex [DOI] [ARXIV] [CODELINK] Repository Open Access
T. Gao ; G. S. Yapuncich ; I. Daubechies ; S. Mukherjee and D. M. Boyer:
Development and assessment of fully automated and globally transitive geometric morphometric
methods, with application to a biological comparative dataset with high interspecific
variation.
The anatomical record : advances in integrative anatomy and evolutionary biology,
301 (2018) 4, p. 636-658 Bibtex [DOI] [ARXIV] Repository Open Access
J. D. Silverman ; H. K. Durand ; R. J. Bloom ; S. Mukherjee and L. A. David:
Dynamic linear models guide design and analysis of microbiota studies within artificial
human guts.
Microbiome,
6 (2018), 202 Bibtex [DOI] [ARXIV] [CODELINK] Journal Open Access
S. Zhao ; B. E. Engelhardt ; S. Mukherjee and D. B. Dunson:
Fast moment estimation for generalized latent Dirichlet models.
Journal of the American Statistical Association,
113 (2018) 524, p. 1528-1540 Bibtex [DOI] [ARXIV] [CODELINK] Repository Open Access
O. Bobrowski ; S. Mukherjee and J. E. Taylor:
Topological consistency via kernel estimation.
Bernoulli,
23 (2017) 1, p. 288-328 Bibtex [DOI] [ARXIV] Repository Open Access
L. Crawford ; S. Mukherjee ; S. Mukherjee and X. Zhou:
Detecting epistasis with the marginal epistasis test in genetic mapping studies of
quantitative traits.
PloS genetics,
13 (2017) 7, e1006869 Bibtex [DOI] [ARXIV] [CODELINK] Journal Open Access
G. Darnell ; S. Georgiew ; S. Mukherjee and B. E. Engelhardt:
Adaptive randomized dimension reduction on massive data.
Journal of machine learning research,
18 (2017), 140 Bibtex [ARXIV] [FREELINK] [CODELINK] Journal Open Access
S. Lunagómez ; S. Mukherjee ; R. L. Wolpert and E. M. Airoldi:
Geometric representations of random hypergraphs.
Journal of the American Statistical Association,
112 (2017) 517, p. 363-383 Bibtex [DOI] [ARXIV] Repository Open Access
J. Lynch ; K. Tang ; S. Priya ; J. Sands ; M. Sands ; E. Tang ; S. Mukherjee ; D. Knights and R. Blekhaman:
HOMINID : a framework for identifying associations between host genetic variation
and microbiome composition.
GigaScience,
6 (2017) 12, gix107 Bibtex [DOI] [ARXIV] [CODELINK] Journal Open Access
J. D. Silverman ; A. D. Washburne ; S. Mukherjee and L. A. David:
A phylogenetic transform enhances analysis of compositional microbiota data.
eLife,
6 (2017), e21887 Bibtex [DOI] [ARXIV] [FREELINK] [CODELINK] Journal Open Access
K. R. Singleton ; L. Crawford ; E. Tsui ; H. E. Manchester ; O. Maertens ; X. Liu ; M. Liberti ; A. N. Magpusao ; D. J. Adams ; J. W. Locasale ; K. Cichowski ; S. Mukherjee and K. C. Wood:
Melanoma therapeutic strategies that select against resistance by exploiting MYC-driven
evolutionary convergence.
Cell reports,
21 (2017) 10, p. 2796-2812 Bibtex [DOI] Journal Open Access
S. Sun ; M. Hood ; L. Scott ; Q. Peng ; S. Mukherjee ; J. Tung and X. Zhou:
Differential expression analysis for RNAseq using Poisson mixed models.
Nucleic acids research,
45 (2017) 11, e106 Bibtex [DOI] [ARXIV] Journal Open Access
A. D. Washburne ; J. D. Silverman ; J. W. Leff ; D. J. Bennett ; J. L. Darcy ; S. Mukherjee ; N. Fierer and L. A. David:
Phylogenetic factorization of compositional data yields lineage-level associations
in microbiome datasets.
PeerJ,
5 (2017), e2969 Bibtex [DOI] [ARXIV] [CODELINK] Journal Open Access
K. J. Galinsky ; G. Bhatia ; P.-R. Loh ; S. Georgiew ; S. Mukherjee ; N. J. Patterson and A. L. Price:
Fast principal-component analysis reveals convergent evolution of ADH1B in Europe
and East Asia.
American journal of human genetics : AJHG,
93 (2016) 3, p. 456-472 Bibtex [DOI] [ARXIV] [CODELINK] Repository Open Access
S. Mukherjee and J. Steenbergen:
Random walks on simplicial complexes and harmonics.
Random structures and algorithms,
49 (2016) 2, p. 379-405 Bibtex [DOI] [ARXIV] Journal Open Access
N. Snyder-Mackler ; W. H. Majoros ; M. L. Yuan ; A. O. Shaver ; J. B. Gordon ; G. H. Kopp ; S. A. Schlebusch ; J. D. Wall ; S. C. Alberts ; S. Mukherjee ; X. Zhou and J. Tung:
Efficient genome-wide sequencing and low-coverage pedigree analysis from noninvasively
collected samples.
Genetics,
203 (2016) 2, p. 699-714 Bibtex [DOI] [ARXIV] [CODELINK] Repository Open Access
S. Zhao ; C. Gao ; S. Mukherjee and B. E. Engelhardt:
Bayesian group factor analysis with structured sparsity.
Journal of machine learning research,
17 (2016), 196 Bibtex [ARXIV] [FREELINK] [CODELINK] Journal Open Access
O. Bobrowski and S. Mukherjee:
The topology of probability distributions on manifolds.
Probability theory and related fields,
161 (2015) 3/4, p. 651-686 Bibtex [DOI] [ARXIV] Repository Open Access
D. M. Boyer ; J. Puente ; J. T. Gladman ; C. Glynn ; S. Mukherjee ; G. S. Yapuncich and I. Daubechies:
A new fully automated approach for aligning and comparing shapes.
The anatomical record : advances in integrative anatomy and evolutionary biology,
298 (2015) 1, p. 249-276 Bibtex [DOI] [FREELINK] [CODELINK] Repository Open Access
K. McGoff ; S. Mukherjee ; A. Nobel and N. Pillai:
Consistency of maximum likelihood estimation for some dynamical systems.
The annals of statistics,
43 (2015) 1, p. 1-29 Bibtex [DOI] [ARXIV] Repository Open Access
K. McGoff ; S. Mukherjee and N. Pillai:
Statistical inference for dynamical systems : a review.
Statistics surveys,
9 (2015), p. 209-252 Bibtex [DOI] [ARXIV] Journal Open Access
E. Munch ; K. Turner ; P. Bendich ; S. Mukherjee ; J. C. Mattingly and J. Harer:
Probabilistic Fréchet means for time varying persistence diagrams.
Electronic journal of statistics,
9 (2015) 1, p. 1173-1204 Bibtex [DOI] [ARXIV] Journal Open Access
G. Raskutti and S. Mukherjee:
The information geometry of mirror descent.
IEEE transactions on information theory,
61 (2015) 3, p. 1451-1457 Bibtex [DOI] [ARXIV] Repository Open Access
L. Stewart ; E. L. MacLean ; D. Ivy ; V. Woods ; E. Cohen ; K. Rodriguez ; M. McIntyre ; S. Mukherjee ; J. Call ; J. Kaminski ; M. Adáms ; R. W. Wrangham and B. Hare:
Citizen science as a new tool in dog cognition research.
PLOS ONE,
10 (2015) 9, e0135176 Bibtex [DOI] Journal Open Access
D. Fusco ; T. J. Barnum ; A. E. Bruno ; J. R. Luft ; E. H. Snell ; S. Mukherjee and P. Charbonneau:
Statistical analysis of crystallization database links protein physico-chemical features
with crystallization mechanism.
PLOS ONE,
9 (2014) 7, e101123 Bibtex [DOI] Journal Open Access
B. Huang ; N. W. D. Jarrett ; S. Babu ; S. Mukherjee and J. Yang:
Cumulon : cloud-based statistical analysis from users perspective.
Bulletin of the Technical Committee on Data Engineering,
37 (2014) 3, p. 77-89 Bibtex [FREELINK] Journal Open Access
A. Kapur ; J. A. Schneider ; D. Heard ; S. Mukherjee ; P. Schumm ; G. Oruganti and E. O. Laumann:
A digital network approach to infer sex behavior in emerging HIV epidemics.
PLOS ONE,
9 (2014) 7, e101416 Bibtex [DOI] Journal Open Access
J. Steenbergen ; C. Klivans and S. Mukherjee:
A Cheeger-type inequality on simplicial complexes.
Advances in applied mathematics,
56 (2014), p. 56-77 Bibtex [DOI] [ARXIV] Repository Open Access
K. Turner ; Y. Mileyko ; S. Mukherjee and J. Harer:
Fréchet means for distributions of persistence diagrams.
Discrete and computational geometry,
52 (2014) 1, p. 44-70 Bibtex [DOI] [ARXIV] Repository Open Access
K. Turner ; S. Mukherjee and D. M. Boyer:
Persistent homology transform for modeling shapes and surfaces.
Information and inference,
3 (2014) 4, p. 310-344 Bibtex [DOI] [ARXIV] Repository Open Access
M. Weiser ; S. Mukherjee and T. S. Furey:
Novel distal eQTL analysis demonstrates effect of population genetic architecture
on detecting and interpreting associations.
Genetics,
198 (2014) 3, p. 879-893 Bibtex [DOI] [CODELINK] Repository Open Access
O. Whitney ; A. R. Pfenning ; J. T. Howard ; C. A. Blatti ; F. Liu ; J. M. Ward ; R. Wang ; J.-N. Audet ; M. Kellis ; S. Mukherjee ; S. Sinha ; A. J. Hartemink ; A. E. West and E. D. Jarvis:
Core and region-enriched networks of behaviorally regulated genes and the singing
genome.
Science,
346 (2014) 6215, 1256780 Bibtex [DOI]
Q. Xiong ; S. Mukherjee and T. S. Furey:
GSAASeqSP : a toolset for gene set association analysis of RNA-seq data.
Scientific reports,
4 (2014), 6347 Bibtex [DOI] Journal Open Access
B. D. Bennett ; Q. Xiong ; S. Mukherjee and T. S. Furey:
Correction [update acknowledgement]: 'A predictive framework for integrating disparate
genomic data types using sample-specific gene set enrichment analysis and multi-task
learning' [In: PLOS ONE, 7 (2012) 9 , e44635].
PLOS ONE,
8 (2013) 9, p. 1-1 Bibtex [DOI] Journal Open Access
J. M. Blum ; L. Ano ; Z. Li ; D. Van Mater ; B. D. Bennett ; M. Sachdeva ; I. Lagutina ; M. Zhang ; J. K. Mito ; C. Lepper ; C. M. Linardic ; S. Mukherjee ; G. C. Grosveld ; C.-M. Fan and D. G. Kirsch:
Distinct and overlapping sarcoma subtypes initiated from muscle stem and progenitor
cells.
Cell reports,
5 (2013) 4, p. 933-940 Bibtex [DOI] Journal Open Access
D. Hafez ; T. Ni ; S. Mukherjee ; J. Zhu and U. Ohler:
Genome-wide identification and predictive modeling of tissue-specific alternative
polyadenylation.
Bioinformatics,
29 (2013) 13, p. i108-i116 Bibtex [DOI] Journal Open Access
P. R.
Hahn ; C. M. Carvalho and S. Mukherjee:
Partial factor modeling : predictor-dependent shrinkage for linear regression.
Journal of the American Statistical Association,
108 (2013) 503, p. 999-1008 Bibtex [DOI] [ARXIV] [CODELINK] Repository Open Access
M. Megraw ; S. Mukherjee and U. Ohler:
Sustained-input switches for transcription factors and microRNAs are central building
blocks of eukaryotic gene circuits.
Genome biology,
14 (2013), R85 Bibtex [DOI] Journal Open Access
B. A. Perez ; A. P.
Ghafoori ; C.-L. Lee ; S. M. Johnston ; Y. Li ; J. G. Moroshek ; Y. Ma ; S. Mukherjee ; Y. Kim ; C. T. Badea and D. G. Kirsch:
Assessing the radiation response of lung cancer with different gene mutations using
genetically engineered mice.
Frontiers in oncology,
3 (2013), 72 Bibtex [DOI] Journal Open Access
D. E. Runcie and S. Mukherjee:
Dissecting high-dimensional phenotypes with Bayesian sparse factor analysis of genetic
covariance matrices.
Genetics,
194 (2013) 3, p. 753-767 Bibtex [DOI] [ARXIV] [CODELINK] Repository Open Access
L. A. Simmons Kovacs ; M. B. Mayhew ; D. A. Orlando ; Y. Jin ; Q. Li ; C. Huang ; S. I. Reed ; S. Mukherjee and S. B. Haase:
Erratum: 'Cyclin-dependent kinases are regulators and effectors of oscillations driven
by a transcription factor network' [In: Molecular cell, 45 (2012) 5, p. 669-679].
Molecular cell,
49 (2013) 6, p. 1177-1179 Bibtex [DOI]
P. Stifanelli ; T. M. Creanza ; R. Anglani ; V. C. Liuzzi ; S. Mukherjee ; F. P. Schena and N. Ancona:
A comparative study of covariance selection models for the inference of gene regulatory
networks.
Journal of biomedical informatics,
46 (2013) 5, p. 894-904 Bibtex [DOI] Journal Open Access
D. R. Winter ; L. Song ; S. Mukherjee ; T. S. Furey and G. E. Crawford:
DNase-seq predicts regions of rotational nucleosome stability across diverse human
cell types.
Genome research,
23 (2013) 7, p. 1118-1129 Bibtex [DOI] [FREELINK] Repository Open Access
Q. Wu ; F. Liang and S. Mukherjee:
Kernel sliced inverse regression : regularization and consistency.
Abstract and applied analysis,
2013 (2013), 540725 Bibtex [DOI] [CODELINK] Journal Open Access
B. D. Bennett ; Q. Xiong ; S. Mukherjee and T. S. Furey:
A predictive framework for integrating disparate genomic data types using sample-specific
gene set enrichment analysis and multi-task learning.
PLOS ONE,
7 (2012) 9, e44635 Bibtex [DOI] Journal Open Access
D. E. Runcie ; D. A. Garfield ; C. C. Babbitt ; J. A. Wygoda ; S. Mukherjee and G. A. Wray:
Genetics of gene expression responses to temperature stress in a sea urchin gene network.
Molecular ecology,
21 (2012) 18, p. 4547-4562 Bibtex [DOI]
L. A. Simmons Kovacs ; M. B. Mayhew ; D. A. Orlando ; Y. Jin ; Q. Li ; C. Huang ; S. I. Reed ; S. Mukherjee and S. B. Haase:
Cyclin-dependent kinases are regulators and effectors of oscillations driven by a
transcription factor network.
Molecular cell,
45 (2012) 5, p. 669-679 Bibtex [DOI]
J. Tung ; M. J. E. Charpentier ; S. Mukherjee ; J. Altmann and S. C. Alberts:
Genetic effects on mating success and partner choice in a social mammal.
The American naturalist,
180 (2012) 1, p. 113-129 Bibtex [DOI] [FREELINK] Repository Open Access
Q. Xiong ; N. Ancona ; E. R. Hauser ; S. Mukherjee and T. S. Furey:
Integrating genetic and gene expression evidence into genome-wide association analysis
of gene sets.
Genome research,
22 (2012) 2, p. 386-397 Bibtex [DOI] [FREELINK] Journal Open Access
A. D'Addabbo ; O. Palmieri ; A. Latiano ; V. Annese ; S. Mukherjee and N. Ancona:
RS-SNP : a random-set method for genome-wide association studies.
BMC genomics,
12 (2011), 166 Bibtex [DOI] Journal Open Access
A. D'Addabbo ; O. Palmieri ; R. Maglietta ; A. Latiano ; S. Mukherjee ; V. Annese and N. Ancona:
Discovering genetic variants in Crohn's disease by exploring genomic regions enriched
of weak association signals.
Digestive and liver disease,
43 (2011) 8, p. 623-631 Bibtex [DOI]
J. Guinney ; Q. Wu and S. Mukherjee:
Estimating variable structure and dependence in multitask learning via gradients.
Machine learning,
83 (2011) 3, p. 265-287 Bibtex [DOI] Journal Open Access
Y. Mileyko ; S. Mukherjee and J. Harer:
Probability measures on the space of persistence diagrams.
Inverse problems,
27 (2011) 12, 124007 Bibtex [DOI] [FREELINK] Repository Open Access
S. Mukherjee:
Book reviw: 'Inference and prediction in large dimensions' by Dennis Bosq and Delphine
Blanke, Wiley, 2007.
Journal of the American Statistical Association,
106 (2011) 496, p. 1642-1643 Bibtex [DOI]
S. Georgiew ; A. P. Boyle ; K. Jayasurya ; X. Ding ; S. Mukherjee and U. Ohler:
Evidence-ranked motif identification.
Genome biology,
11 (2010), R19 Bibtex [DOI] [CODELINK] Journal Open Access
R. Maglietta ; A. Distaso ; A. Piepoli ; O. Palumbo ; M. Carella ; A. D'Addabbo ; S. Mukherjee and N. Ancona:
On the reproducibility of results of pathway analysis in genome-wide expression studies
of colorectal cancers.
Journal of biomedical informatics,
43 (2010) 3, p. 397-406 Bibtex [DOI]
S. Mukherjee:
Book reviw: 'Computational intelligence and feature selection: rough and fuzzy approaches'
by Richard Jensen and Qiang Shen, Wiley, 2008.
Journal of the American Statistical Association,
105 (2010) 489, p. 438-438 Bibtex [DOI]
S. Mukherjee ; Q. Wu and D.-X. Zhou:
Learning gradients on manifolds.
Bernoulli,
16 (2010) 1, p. 181-207 Bibtex [DOI] [ARXIV] Repository Open Access
Q. Wu ; J. Guinney ; M. Maggioni and S. Mukherjee:
Learning gradients : predictive models that infer geometry and dependence.
Journal of machine learning research,
11 (2010), p. 2175-2198 Bibtex [FREELINK] Journal Open Access
Q. Wu ; F. Liang and S. Mukherjee:
Localized sliced inverse regression.
Journal of computational and graphical statistics,
19 (2010) 4, p. 843-860 Bibtex [DOI] [FREELINK] [CODELINK] Repository Open Access
L. Abatangelo ; R. Maglietta ; A. Distaso ; A. D'Addabbo ; T. M.
Creanza ; S. Mukherjee and N. Ancona:
Comparative study of gene set enrichment methods.
BMC bioinformatics,
10 (2009), 275 Bibtex [DOI] Journal Open Access
D. S. Hsu ; C. R. Acharya ; B. S. Balakumaran ; R. F. Riedel ; M. K. Kim ; M. Stevenson ; S. Tuchman ; S. Mukherjee ; W. Barry ; H. K. Dressman ; J. R. Nevins ; S. Powers ; D. Mu and A. Potti:
Characterizing the developmental pathways TTF-1, NKX2-8, and PAX9 in lung cancer.
Proceedings of the National Academy of Sciences of the United States of America,
106 (2009) 13, p. 5312-5317 Bibtex [DOI] [FREELINK] Repository Open Access
J. Lesneck ; S. Mukherjee ; Z. Yurkovetsky ; M. Clyde ; J. R. Marks ; A. E. Lokshin and J. Y. Lo:
Do serum biomarkers really measure breast cancer?.
BMC cancer,
9 (2009), 164 Bibtex [DOI] Journal Open Access
J. K. Mito ; R. F. Riedel ; L. Dodd ; G. Lahat ; A. J. Lazar ; R. D. Dodd ; L. Stangenberg ; W. C. Eward ; F. J. Hornicek ; S. S. Yoon ; B. E. Brigman ; T. Jacks ; D. Lev ; S. Mukherjee and D. G. Kirsch:
Cross species genomic analysis identifies a mouse model as undifferentiated Pleomorphic
Sarcoma/Malignant Fibrous Histiocytoma.
PLOS ONE,
4 (2009) 11, e8075 Bibtex [DOI] Journal Open Access
S. Mukherjee:
Book reviw: 'The probabilistic method' by Noga Alon and Joel H. Spencer, Wiley, 3rd
ed., 2008.
Journal of the American Statistical Association,
104 (2009) 488, p. 1723-1723 Bibtex [DOI]
J. Tung ; O. Fédrigo ; R. Haygood ; S. Mukherjee and G. A. Wray:
Genomic features that predict allelic imbalance in humans suggest patterns of constraint
on gene expression variation.
Molecular biology and evolution,
26 (2009) 9, p. 2047-2059 Bibtex [DOI] Journal Open Access
E. J. Edelman ; J. Guinney ; J.-T. Chi ; P. G. Febbo and S. Mukherjee:
Modeling cancer progression via pathway dependencies.
PLoS computational biology,
4 (2008) 2, e28 Bibtex [DOI] Journal Open Access
K. H. Salter ; C. R. Acharya ; K. S. Walters ; R. Redman ; A. Anguiano ; K. S. Garman ; C. K. Anders ; S. Mukherjee ; H. K. Dressman ; W. T. Barry ; K. P. Marcom ; J. Olson ; J. R. Nevins and A. Potti:
An integrated approach to the prediction of chemotherapeutic response in patients
with breast cancer.
PLOS ONE,
3 (2008) 4, e1908 Bibtex [DOI] Journal Open Access
Z. Wang ; H. F. Willard ; S. Mukherjee and T. S. Furey:
Evidence of influence of genomic DNA sequence on human X chromosome inactivation.
PLoS computational biology,
2 (2008) 9, e113 Bibtex [DOI] Journal Open Access
J.-T. Chi ; E. H. Rodriguez ; Z. Wang ; D. S. A. Nuyten ; S. Mukherjee ; M. Van de Rijn ; M. J. Van de Vijver ; T. Hastie and P. O. Brown:
Gene expression programs of human smooth muscle cells : tissue-specific differentiation
and prognostic significance in breast cancers.
PloS genetics,
9 (2007) 3, e164 Bibtex [DOI] Journal Open Access
E. Edelman ; A. Porrello ; J. Guinney ; B. Balakumaran ; A. Bild ; P. G. Febbo and S. Mukherjee:
Analysis of sample set enrichment scores : assaying the enrichment of sets of genes
for individual samples in genome-wide expression profiles.
Bioinformatics,
22 (2007) 14, p. e108-e116 Bibtex [DOI] [FREELINK] Journal Open Access
L. Goh ; S. K. Murphy ; S. Mukherjee and T. S. Furey:
Genomic sweeping for hypermethylated genes.
Bioinformatics,
23 (2007) 3, p. 281-288 Bibtex [DOI] [FREELINK] Repository Open Access
F. Liang ; S. Mukherjee and M. West:
The use of unlabeled data in predictive modeling.
Statistical science,
22 (2007) 2, p. 189-205 Bibtex [DOI] [ARXIV] Repository Open Access
N. S. Pillai ; Q. Wu ; F. Liang ; S. Mukherjee and R. L. Wolpert:
Characterizing the function space for Bayesian kernel models.
Journal of machine learning research,
8 (2007), p. 1769-1797 Bibtex [FREELINK] Journal Open Access
S. Mukherjee ; P. Niyogi ; T. Poggio and R. Rifkin:
Learning theory : stability is sufficient for generalization and necessary and sufficient
for consistency of empirical risk minimization.
Advances in computational mathematics,
25 (2006) 1-3, p. 161-193 Bibtex [DOI] [FREELINK] Repository Open Access
S. Mukherjee and Q. Wu:
Estimation of gradients and coordinate covariation in classification.
Journal of machine learning research,
7 (2006), p. 2481-2514 Bibtex [FREELINK] Journal Open Access
S. Mukherjee and D.-X. Zhou:
Learning coordinate covariances via gradients.
Journal of machine learning research,
7 (2006), p. 519-549 Bibtex [FREELINK] Journal Open Access
D. Tropea ; G. Kreiman ; A. Lyckman ; S. Mukherjee ; H. Yu ; S. Horng and M. Sur:
Gene expression changes and molecular pathways mediating activity-dependent plasticity
in visual cortex.
Nature neuroscience,
9 (2006) 5, p. 660-668 Bibtex [DOI] [FREELINK] Repository Open Access
A. Rahkhlin ; D. Panchenko and S. Mukherjee:
Risk bounds for mixture density estimation.
ESAIM : Probability and statistics,
9 (2005), p. 220-229 Bibtex [DOI] Journal Open Access
A. Rakhlin ; S. Mukherjee and T. Poggio:
Stability results in learning theory.
Analysis and applications,
3 (2005) 4, p. 397-417 Bibtex [DOI]
A. Subramanian ; P. Tomayo ; V. K. Mootha ; S. Mukherjee ; B. L. Ebert ; M. A. Gillette ; A. Paulovich ; S. L. Pomeroy ; T. R. Golub ; E. S. Lander and J. P. Mesirov:
Gene set enrichment analysis : a knowledge-based approach for interpreting genome-wide
expression profiles.
Proceedings of the National Academy of Sciences of the United States of America,
102 (2005) 43, p. 15545-15550 Bibtex [DOI] [CODELINK]
A. Sweet-Cordero ; S. Mukherjee ; A. Subramanian ; H. You ; J. J. Roix ; C. Ladd-Acosta ; J. Mesirov ; T. R. Golub and T. Jacks:
An oncogenic KRAS2 expression signature identified by cross-species gene-expression
analysis.
Nature genetics,
37 (2005) 1, p. 48-55 Bibtex [DOI] [FREELINK] Repository Open Access
R. Berger ; P. G. Febbo ; P. K. Majumder ; J. J. Zhao ; S. Mukherjee ; S. Signoretti ; K. T.
Campbell ; W. R. Sellers ; T. M. Roberts ; M. Loda ; T. R. Golub and W. C. Hahn:
Androgen-induced differentiation and tumorigenicity of human prostate epithelial cells.
Cancer research,
64 (2004) 24, p. 8867-8875 Bibtex [DOI]
S. Mukherjee ; P. Tamayo ; S. Rogers ; R. Rifkin ; A. Engle ; C. Campbell ; T. R. Golub and J. P. Mesirov:
Estimating dataset size requirements for classifying DNA microarray data.
Journal of computational biology,
10 (2004) 2, p. 119-142 Bibtex [DOI] [FREELINK] Repository Open Access
T. Poggio ; R. Rifkin ; S. Mukherjee and P. Niyogi:
General conditions for predictivity in learning theory.
Nature,
428 (2004), p. 419-422 Bibtex [DOI] Repository Open Access
R. Rinfkin ; S. Mukherjee ; P. Tamayo ; S. Ramaswamy ; C.-H. Yeang ; M. Angelo ; M. Reich ; T. Poggio ; E. S. Lander ; T. R. Golub and J. P. Mesirov:
An analytical method for multiclass molecular cancer classification.
SIAM review,
45 (2003) 4, p. 706-723 Bibtex [DOI] [FREELINK] Repository Open Access
O. Chapelle ; V. Vapnik ; O. Bousquet and S. Mukherjee:
Choosing multiple parameters for support vector machines.
Machine learning,
46 (2002) 1-3, p. 131-159 Bibtex [DOI] [FREELINK] Repository Open Access
L. D. Miller ; P. M. Long ; L. Wong ; S. Mukherjee ; L. M. McShane and E. T. Liu:
Optimal gene expression analysis by microarrays.
Cancer cell,
2 (2002) 5, p. 353-361 Bibtex [DOI]
S. Pomeroy ; P. Tamayo ; M. Gaasenbeek ; L. M. Sturla ; M. Angelo ; M. E. McLaughlin ; J. Y. H. Kim ; L. C. Goumnerova ; P. M. Black ; C. Lau ; J. Allen ; D. Zagzag ; J. M. Olson ; T. Curran ; D. Wetmore ; J. A. Biegel ; T. Poggio ; S. Mukherjee ; R. Rifkin ; A. Califano ; G. Stolovitzky ; D. N. Louis ; J. P. Mesirov ; E. S. Lander and T. R. Golub:
Prediction of central nervous system embryonal tumour outcome based on gene expression.
Nature,
415 (2002) 6870, p. 436-442 Bibtex [DOI] [FREELINK] Repository Open Access
S. Ramaswamy ; P. Tomayo ; R. Rifkin ; S. Mukherjee ; C.-H. Yeang ; M. Angelo ; C. Ladd ; M. Reich ; E. Latulippe ; J. P. Mesirov ; T. Poggio ; W. Gerald ; M. Loda ; E. S. Lander and T. R. Golub:
Multiclass cancer diagnosis using tumor gene expression signatures.
Proceedings of the National Academy of Sciences of the United States of America,
98 (2001) 26, p. 15149-15154 Bibtex [DOI]
C.-H. Yeang ; S. Ramaswamy ; P. Tamayo ; S. Mukherjee ; R. Rifkin ; M. Angelo ; M. Reich ; E. Lander ; J. Mesirov and T. Golub:
Molecular classification of multiple tumor types.
Bioinformatics,
17 (2001) Suppl. 1, p. S316-S322 Bibtex [DOI] [FREELINK] Repository Open Access
Publications in Books and Conference Proceedings
X. Zhang ; R. Bashizade ; Y. Wang ; S. Mukherjee and A. R. Lebeck:
Statistical robustness of Markov chain Monte Carlo accelerators.
ASPLOS 2021 : Proceedings of the 26th ACM international conference on architectural
support for programming languages and operating systems ; virtual ; April 19 - 23,
2021 / T.
Sherwood (ed.). Association for Computing Machinery, 2021. - P. 959-974 Bibtex [DOI] [FREELINK] Repository Open Access
Z. Tan ; K. Roche ; X. Zhou and S. Mukherjee:
Scalable algorithms for learning high-dimensional linear mixed model.
Proceedings of the Thirty-Fourth Conference on Uncertainty in Artificial Intelligence,
{UAI} 2018, Monterey, California, USA, August 6-10, 2018 / A.
Globerson... (eds.). AUAI Press, 2018. - P. 259-268 Bibtex [ARXIV] [FREELINK] [CODELINK] Repository Open Access
Z. Tan and S. Mukherjee:
Partitioned tensor factorizations for learning mixed membership models.
Proceedings of the 34th international conference on machine learning : 6-11 August
2017, International Convention Centre, Sydney, Australia / D.
Precup... (eds.). PMLR, 2017. - P. 3358-3367
(Proceedings of machine learning research ; 70)
Bibtex [ARXIV] [FREELINK] [CODELINK] Repository Open Access
S. Lunagómez ; S. Mukherjee and R. L. Wolpert:
Priors on hypergraphical models via simplicial complexes.
Current trends in Bayesian methodology with applications / S.
Upadhyay... (eds.). CRC Press, 2015. - P. 391-413 Bibtex [FREELINK]
G. Raskutti and S. Mukherjee:
The information geometry of mirror descent.
Geometric science of information : second international conference, GSI 2015, Palaiseau,
France, October 28-30, 2015, proceedings / F.
Nielsen... (eds.). Springer, 2015. - P. 359-368
(Lecture notes in computer science ; 9389)
Bibtex [DOI] [ARXIV] Repository Open Access
W. Zhang ; P. K. Agarwal and S. Mukherjee:
Contour trees of uncertain terrains.
SIGSPATIAL '15 : Proceedings of the 23rd SIGSPATIAL international conference on advances
in geographic information systems ; November 3 - 6, 2015 ; Washington, Seattle / M.
Ali... (eds.). ACM, 2015 Bibtex [DOI] Journal Open Access
P. Bendich ; B. Wang and S. Mukherjee:
Local homology transfer and stratification learning.
Proceedings of the 23rd annual ACM-SIAM symposium on discrete algorithms, SODA 2012,
Kyoto, Japan, January 17-19, 2012 Society for Industrial and Applied Mathematics, 2012. - P. 1355-1370 Bibtex [DOI] Journal Open Access
E. Edelman ; K. Garman ; A. Potti and S. Mukherjee:
Making mountains out of molehills : moving from single gene to pathway based models
of colon cancer progression.
Medical biostatistics for complex diseases / F.
Emmert-Streib... (eds.). Wiley-VCH, 2010. - P. 75-87 Bibtex [DOI]
J. Guinney ; P. Febbo ; M. Maggioni and S. Mukherjee:
Multiscale factor models for molecular networks.
JSM proceedings of the American Statistical Association : papers presented at the
joint statistical meetings 2010 ASA, 2010. - P. 4887-4901 Bibtex [FREELINK] Repository Open Access
K. Mao ; F. Liang and S. Mukherjee:
Supervised dimension reduction using Bayesian mixture modeling.
Proceedings of the thirteenth international conference on artificial intelligence
and statistics PMLR, 2010. - P. 501-508
(Proceedings of machine learning research ; 9)
Bibtex [FREELINK] [CODELINK] Repository Open Access
Q. Wu ; S. Mukherjee and F. Liang:
Localized sliced inverse regression.
Advances in neural information processing systems 21 : NIPS 2008 Neural Information Processing Systems, 2008. - P. 1785-1792 Bibtex [FREELINK] [CODELINK] Repository Open Access
P. Golland ; F. Liang ; S. Mukherjee and D. Panchenko:
Permutation tests for classification.
Learning theory.: 18th annual conference on learning theory, COLT 2005, Bertinoro,
Italy, June 27-30, 2005 ; proceedings / P.
Auer... (eds.). Springer, 2005. - P. 501-515
(Lecture notes in computer science ; 3559)
Bibtex [DOI] [FREELINK]
S. Mukherjee:
Classifying microarray data using support vector machines.
A practical approach to microarray data analysis / D.
P. Berrar... (eds.). Kluwer Academic, 2003. - P. 166-185 Bibtex [DOI]
S. Mukherjee ; R. Rifkin and P. Tomaso:
Regression and classification with regularization.
Nonlinear estimation and classification / D.
D. Denison... (eds.). Springer, 2003. - P. 111-128
(Lecture notes in statistics ; 171)
Bibtex [DOI] [FREELINK] Repository Open Access
T. Poggio ; S. Mukherjee ; R. Rifkin ; A. Rakhlin and A. Verri:
B.
Uncertainty in geometric computations / J.
Winkler... (eds.). Springer, 2002. - P. 131-141
(The Springer international series in engineering and computer science ; 704)
Bibtex [DOI]
J. Sadr ; S. Mukherjee ; K. Thoresz and P. Sinha:
The fidelity of local ordinal encoding.
Advances in neural information processing systems 14 : NIPS 2001 ; proceedings of
the 2001 neural information processing systems conference / T.
G. Dietterich... (eds.). MIT Press, 2002. - P. 1279-1286 Bibtex [FREELINK] Repository Open Access
B. Heisele ; T. Serre ; S. Mukherjee and T. Poggio:
Feature reduction and hierarchy of classifiers for fast object detection in video
images.
Proceedings of the 2001 IEEE computer society conference on computer vision and pattern
recognition : CVPR 2001 ; Dec. 8 2001 to Dec. 14 2001 ; Kauai, Hawaii ; Volume 2 IEEE, 2001. - P. 18-24 Bibtex [DOI] [FREELINK] Repository Open Access
L. Peshkin and S. Mukherjee:
Bounds on sample size for policy evaluation in Markov environments.
Computational learning theory : 14th annual conference, COLT 2001, and 5th European
conference, EuroCOLT 2001, Amsterdam, Netherlands, July 16-19, 2001 ; proceedings / D.
Helmbold... (eds.). Springer, 2001. - P. 616-629
(Lecture notes in computer science ; 2111)
Bibtex [DOI] [ARXIV] Repository Open Access
J. Weston ; S. Mukherjee ; O. Chapelle ; M. Pontil ; T. Poggio and V. Vapnik:
Feature selection for SVMs.
Advances in neural information processing systems 13 : NIPS 2000 ; proceedings of
the 2000 neural information processing systems conference / T.
K. Leen... (eds.). MIT Press, 2001. - P. 668-674 Bibtex [FREELINK] Repository Open Access
M. Pontil ; S. Mukherjee and F. Girosi:
On the noise model of support vector machines regression.
Algorithmic learning theory : 11th international conference, ALT 2000, Sydney, Australia,
December 11-13, 2000 ; proceedings / H.
Arimura... (eds.). Springer, 2000. - P. 316-324
(Lecture notes in computer science ; 1968)
Bibtex [DOI] [FREELINK] Repository Open Access
V. Vapnik and S. Mukherjee:
Support vector method for multivariate density estimation.
Advances in neural information processing systems 12 : NIPS 1999 ; proceedings of
1999 neural information processing systems conference / S.
A. Solla... (eds.). MIT Press, 2000. - P. 659-665 Bibtex [FREELINK] Repository Open Access
Preprints
S. Arya ; J. Curry and S. Mukherjee:
A sheaf-theoretic construction of shape space.
Bibtex [ARXIV] Repository Open Access
J. R. Björk ; M. R. Dasari ; K. Roche ; L. Grieneisen ; T. J. Gould ; J.-C. Grenier ; V. Yotova ; N. Gottel ; D. Jansen ; L. R. Gesquiere ; J. B. Gordon ; N. H. Learn ; T. L. Wango ; R. S. Mututua ; J. K.
Warutere ; L. Siodi ; S. Mukherjee ; L. B. Barreiro ; S. C. Alberts ; J. A. Gilbert ; J. Tung ; R. Blekhman and E. A. Archie:
Synchrony and idiosyncrasy in the gut microbiome of wild baboons.
Bibtex [ARXIV] Repository Open Access
M. Pistner Nixon ; J. Letourneau ; L. David ; S. Mukherjee and J. D. Silverman:
A statistical analysis of compositional surveys.
Bibtex [ARXIV] Repository Open Access
R. Bashizade ; X. Zhang ; S. Mukherjee and A. R. Lebeck:
Accelerating markov random field inference with uncertainty quantification.
Bibtex [ARXIV] Repository Open Access
M. Caprio ; A. Aveni and S. Mukherjee:
Concerning three classes of non-Diophantine arithmetics.
Bibtex [ARXIV] Repository Open Access
M. Caprio and S. Mukherjee:
Extended probabilities and their application to statistical inference.
Bibtex [ARXIV] Repository Open Access
H. Kirveslahti and S. Mukherjee:
Representing fields without correspondences : the lifted Euler characteristic transform.
Bibtex [ARXIV] Repository Open Access
K. E. Roche and S. Mukherjee:
The accuracy of absolute differential abundance analysis from relative count data.
Bibtex [ARXIV] Repository Open Access
L. Su and S. Mukherjee:
A large deviation approach to posterior consistency in dynamical systems.
Bibtex [ARXIV] Repository Open Access
W. S.
Tang ; G. Monteiro da Silva ; H. Kirveslahti ; E. Skeens ; B. Feng ; T. Sudijono ; K. K. Yang ; S. Mukherjee ; B. Rubenstein and L. Crawford:
A topological data analytic approach for discovering biophysical signatures in protein
dynamics.
Bibtex [ARXIV] Repository Open Access
A. K. Yanchenko ; M. Soltani ; R. J. Ravier ; S. Mukherjee and V. Tarokh:
A methodology for exploring deep convolutional features in relation to hand-crafted
features with an application to music audio modeling.
Bibtex [ARXIV] [CODELINK] Repository Open Access
M. Caprio and S. Mukherjee:
Ergodic theorems in dynamic imprecise probability kinematics.
Bibtex [ARXIV] Repository Open Access
M. Caprio and S. Mukherjee:
Finite mixture models : a bridge with stochastic geometry and Choquet theory.
Bibtex [ARXIV] Repository Open Access
Z. Ding and S. Mukherjee:
At the intersection of deep sequential model framework and state-space model framework
: study on option pricing.
Bibtex [ARXIV] Repository Open Access
N. Fraiman ; S. Mukherjee and G. Thoppe:
The bulk and the extremes of minimal spanning acycles and persistence diagrams of
random complexes.
Bibtex [ARXIV] Repository Open Access
D. Li and S. Mukherjee:
Random Lie brackets that induce torsion : a model for noisy vector fields.
Bibtex [ARXIV] Repository Open Access
A. K. Yanchenko and S. Mukherjee:
Stanza : a nonlinear state space model for probabilistic inference in non-stationary
time series.
Bibtex [ARXIV] Repository Open Access
X. Zhang ; R. Bashizade ; Y. Wang ; C. Lyu ; S. Mukherjee and A. R. Lebeck:
Beyond application end-point results : quantifying statistical robustness of MCMC
accelerators.
Bibtex [ARXIV] Repository Open Access
S. I. Berchuck ; F. A. Medeiros and S. Mukherjee:
Scalable modeling of spatiotemporal data using the variational autoencoder : an application
in glaucoma.
(The annals of applied statistics :)
Bibtex [ARXIV] Repository Open Access
J. D. Silverman ; R. J. Bloom ; S. Jiang ; H. K. Durand ; S. Mukherjee and L. A. David:
Measuring and mitigating PCR bias in microbiome data.
Bibtex [ARXIV] Repository Open Access
Z. Zou ; S. Mukherjee ; H. Antil and W. Aquino:
Adaptive particle-based approximations of the Gibbs posterior for inverse problems.
Bibtex [ARXIV] Repository Open Access
J. Curry ; S. Mukherjee and K. Turner:
How many directions determine a shape and other sufficiency results for two topological
transforms.
(Transactions of the American Mathematical Society)
Bibtex [ARXIV] Repository Open Access
J. D. Silverman ; L. Shenhav ; E. Halperin ; S. Mukherjee and L. A. David:
Statistical considerations in the design and analysis of longitudinal microbiome studies.
Bibtex [ARXIV] Repository Open Access
Z. Tan and S. Mukherjee:
Learning integral representations of Gaussian processes.
Bibtex [ARXIV] [CODELINK] Repository Open Access
M. Vejdemo-Johansson and S. Mukherjee:
Multiple testing with persistent homology.
Bibtex [ARXIV] Repository Open Access
A. Zaidi and S. Mukherjee:
Gaussian process mixtures for estimating heterogeneous treatment effects.
Bibtex [ARXIV] Repository Open Access
A. K. Yanchenko and S. Mukherjee:
Classical music composition using state space models.
Bibtex [ARXIV] [CODELINK] Repository Open Access
J. E. Johndrow ; J. C. Mattingly ; S. Mukherjee and D. B. Dunson:
Optimal approximating Markov chains for Bayesian inference.
Bibtex [ARXIV] Repository Open Access
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