[Google Scholar Profile]


S. Ghaffari, E. Saleh, A. G. Schwing, Y. Wang, M. D. Burke, S. Sinha. Robust Model-Based Optimization for Challenging Fitness Landscapes. ICLR 2024.


Dubinkina V, Bhogale S, Hsieh PH, Dibaeinia P, Nambiar A, Maslov S, Yoshikuni Y, Sinha S. A transcriptomic atlas of acute stress response to low pH in multiple Issatchenkia orientalis strains. Microbiology Spectrum. 2023 Nov 29:e02536-23.

S Ghaffari, KJ Bouchonville, E Saleh, RE Schmidt, SM Offer, S Sinha (2023). BEDwARS: a robust Bayesian approach to bulk gene expression deconvolution with noisy reference signatures. Genome biology. 2023. 24 (1), 178.

Hao, Qinyu, et al. Monoallelically-expressed Noncoding RNAs form nucleolar territories on NOR-containing chromosomes and regulate rRNA expression. Elife 13 (2024): e80684.

Tabe-Bordbar S, Sinha S. Integrative modeling of lncRNA-chromatin interaction maps reveals diverse mechanisms of nuclear retention. BMC genomics. 2023 Jul 13;24(1):395.

Traniello IM, Bukhari SA, Dibaeinia P, Serrano G, Avalos A, Ahmed AC, Sankey AL, Hernaez M, Sinha S, Zhao SD, Catchen J, Robinson GE. Single-cell dissection of aggression in honeybee colonies. Nature Ecology & Evolution. 2023 Jun 1:1-3.

Dibaeinia P, Sinha S. CIMLA: Interpretable AI for inference of differential causal networks. arXiv preprint arXiv:2304.12523. 2023 Apr 25.

Nora, E. P., Aerts, S., Wittkopp, P. J., Bussemaker, H. J., Bulyk, M., Sinha, S., ... & Bass, J. I. F. (2023). Emerging questions in transcriptional regulation. Cell Systems, 14(4), 247-251. 


CH Seward, MC Saul, JM Troy, P Dibaeinia, H Zhang, S Sinha, LJ Stubbs (2022). An epigenomic shift in amygdala marks the transition to maternal behaviors in alloparenting virgin female mice. Plos one 17 (2), e0263632

Ma, Liqian, et al. (2022) The liver x receptor is selectively modulated to differentially alter female mammary metastasis-associated myeloid cells. Endocrinology 163.7 (2022): bqac072.

S Bhogale, S Sinha (2022). Thermodynamics-based modeling reveals regulatory effects of indirect transcription factor-DNA binding. Iscience 25 (5), 104152


P Dibaeinia, S Sinha (2021). Deciphering enhancer sequence using thermodynamics-based models and convolutional neural networks. Nucleic acids research 49 (18), 10309-10327

X. Xie, M. Kendzior, X. Ge, L.S. Mainzer, S. Sinha (2021). VarSAn: Associating pathways with a set of genomic variants using network analysis. Nucleic acids research 49 (15), 8471-8487

S You, EJ Chaney, H Tu, Y Sun, S Sinha, SA Boppart (2021). Label-free deep profiling of the tumor microenvironment. Cancer research 81 (9), 2534-2544

Emad, A., Sinha, S (2021). Inference of phenotype-relevant transcriptional regulatory networks elucidates cancer type-specific regulatory mechanisms in a pan-cancer study. npj Systems Biology and Appl. 7 (1), 1-14.

S. Ghaffari, C. Hanson, R.E. Schmidt, K.J. Bouchonville, S.M. Offer, S. Sinha (2021). An integrated multi-omics approach to identify regulatory mechanisms in cancer metastatic processes. Genome Biology 22(1):19.


P. Dibaeinia, S. Sinha (2020). SERGIO: a single-cell expression simulator guided by gene regulatory networks. Cell Systems 11 (3), 252-271. e11. [Full text] 

S. Sinha*, B.M. Jones, I.M. Traniello, S.A. Bukhari, M.S. Halfon, H.A. Hofmann, S. Huang, P.S. Katz, J. Keagy, V.J. Lynch, M.B. Sokolowski, L.J. Stubbs, S. Tabe-Bordbar, M.F. Wolfner, G.E Robinson* (2020). Behavior-related gene regulatory networks: A new level of organization in the brain. Proceedings of the National Academy of Sciences 117 (38), 23270-23279. [Full text]  *Corresponding authors.

C. Blatti, A. Emad, M. J. Berry, L. Gatzke, M. Epstein, D. Lanier, P. Rizal, J. Ge, X. Liao, O. Sobh, M. Lambert, C. S. Post, J. Xiao, P. Groves, A. T. Epstein, X. Chen, S. Srinivasan, E. Lehnert, K. R. Kalari, L. Wang, R. M. Weinshilboum, J. S. Song, C. V. Jongeneel, J. Han, U. Ravaioli, N. Sobh, C. B. Bushell, S. Sinha (2020). Knowledge-guided analysis of ‘omics’ data using the KnowEnG cloud platform. PLoS Biology, 18 (1), e3000583. [Full text] 

A. Emad, T. Ray, T.W. Jensen, M. Parat, R. Natrajan, S. Sinha*, P.S. Ray* (2020). Superior breast cancer metastasis risk stratification using an epithelial-mesenchymal-amoeboid transition gene signature. Breast Cancer Research 22 (1), 1-13. [Full text] *Corresponding authors.

E.W. Huang, A. Bhope, J. Lim, S. Sinha*, A. Emad* (2020). Tissue-guided LASSO for prediction of clinical drug response using preclinical samples. PLoS computational biology 16 (1), e1007607. [Full text] *Corresponding authors.

B.M. Jones, V.D. Rao, T. Gernat, T. Jagla, A.C. Cash-Ahmed, B.E.R. Rubin, T.J. Comi, S. Bhogale, S.S. Husain, C. Blatti, M. Middendorf, S. Sinha, S. Chandrasekaran, G.E. Robinson. Individual differences in honey bee behavior enabled by plasticity in brain gene regulatory networks. Elife 9, e62850. [Full text] 

N. Rahimi, S. Carmon, I. Averbukh, F. Khajouei, S. Sinha, E.D. Schejter, N. Barkai, B. Shilo. Global shape of Toll activation is determined by wntD enhancer properties. Proceedings of the National Academy of Sciences 117 (3), 1552-1558. [Full text] 

S. Huang, C. Blatti, S. Sinha, A. Parameswaran (2020). Uncovering Effective Explanations for Interactive Genomic Data Analysis. Patterns, 1 (6), 100093. [Full text] 


S. You, Y. Sun, L. Yang, J. Park, H. Tu, M. Marjanovic, S. Sinha*, S. A. Boppart* (2019). Real-time intraoperative diagnosis by deep neural network driven multiphoton virtual histology. npj Precision Oncology, 3 (1), 1-8. * Corresponding authors.

X. Xie, C. Hanson, S. Sinha (2019). Mechanistic interpretation of non-coding variants for discovering transcriptional regulators of drug response. BMC biology 17 (1), 62. [Free full text]

Y. Zhou, S. Sinha, J. L. Schwartz, G. R. Adami (2019). A subtype of oral, laryngeal, esophageal, and lung, squamous cell carcinoma with high levels of TrkB-T1 neurotrophin receptor mRNA. BMC cancer 19 (1), 607. [Free full text]

S. You, R. Barkalifa, E. J. Chaney, H. Tu, J. Park, J. E. Sorrells, Y. Sun, Y. Liu, L. Yang, D. Z. Chen, M. Marjanovic, S. Sinha, S. A. Boppart (2019). Label-free visualization and characterization of extracellular vesicles in breast cancer. Proc Natl Acad Sci U S A. 2019 Nov 15. pii: 201909243.

M. HamediRad, R. Chao, S. Weisberg, J. Lian, S. Sinha*, H. Zhao* (2019). Towards a fully automated algorithm driven platform for biosystems design. Nature Communications, 10 (1), 1-10. * Corresponding authors. [Free full text]

J. Roy, P. Dibaeinia, T.M. Fan, S. Sinha, A. Das (2019). Global analysis of osteosarcoma lipidomes reveal altered lipid profiles in metastatic versus nonmetastatic cells. Journal of lipid research 60 (2), 375-387.

P.C. Peng, P. Khoueiry, C. Girardot, J.P. Reddington, D.A. Garfield, E.E.M. Furlong, S. Sinha (2019). The Role of Chromatin Accessibility in cis-Regulatory Evolution.  Genome biology and evolution, 11 (7), 1813-1828. [Free full text]

S. Wang, E. Huang, J. Cairns, J. Peng, L. Wang, S. Sinha (2019). Identification of Pathways Associated with Chemosensitivity through Network Embedding. PLoS Computational Biology, 15 (3), e1006864. [Free full text]


Khajoeui, F., Sinha, S. (2018). An information theoretic treatment of sequence-to-expression modeling. PLoS Comput. Biol. 14(9): e1006459. [Free full text

Adami, G. R., Tangney, C. C., Tang, J. L., Zhou, Y., Ghaffari, S., Naqib, A., . . . Schwartz, J. L. (2018). Effects of green tea on miRNA and microbiome of oral epithelium. Sci Rep, 8(1), 5873. doi:10.1038/s41598-018-22994-3. [Free full text]

Hanson, C., Cairns, J., Wang, L., & Sinha, S. (2018). Principled multi-omic analysis reveals gene regulatory mechanisms of phenotype variation. Genome Research, 28(8), 1207-1216. doi:10.1101/gr.227066.117. [Free full text]

Saul, M. C., Blatti, C., Yang, W., Bukhari, S. A., Shpigler, H. Y., Troy, J. M., . . . Sinha, S. (2018). Cross-species systems analysis of evolutionary toolkits of neurogenomic response to social challenge. Genes Brain Behav, e12502. doi:10.1111/gbb.12502. [Abstract]

Shen, J., Xiao, J., Zhang, Y., Yang, C., Shang, J., Han, J., ... & Han, J. (2018). SetSearch+: Entity-Set-Aware Search and Mining for Scientific Literature. Proceedings of KDD 2018. [Free full text] [System]

Shen, J., Xiao, J., He, X., Shang, J., Sinha, S., & Han, J. (2018). Entity Set Search of Scientific Literature: An Unsupervised Ranking Approach. Proceedings of SIGIR 2018. doi: 10.1145/3209978.3210055. [Free full text]

Tabe-Bordbar, S., Emad, A., Zhao, S. D., & Sinha, S. (2018). A closer look at cross-validation for assessing the accuracy of gene regulatory networks and models. Sci Rep, 8(1), 6620. doi:10.1038/s41598-018-24937-4. [Free full text]

Xiao, J., Blatti, C., & Sinha, S. (2018). SigMat: a classification scheme for gene signature matching. Bioinformatics, 34(13), i547-i554. doi:10.1093/bioinformatics/bty251. [Free full text]

You, S., Tu, H., Chaney, E. J., Sun, Y., Zhao, Y., Bower, A. J., . . . Boppart, S. A. (2018). Intravital imaging by simultaneous label-free autofluorescence-multiharmonic microscopy. Nat Commun, 9(1), 2125. doi:10.1038/s41467-018-04470-8. [Free full text]


P. Kordjamshidi, S. Singh, D. Khashabi, C. Christodoulopoulos, M. Sammons, S. Sinha, D. Roth (2017). "Relational Learning and Feature Extraction by Querying over Heterogeneous Information Networks", Seventh International Workshop on Statistical Relational AI, 2017. 

P. Khoueiry, C. Girardot, L. Ciglar, P. Peng, E. H. Gustafson, S. Sinha, E. E. M. Furlong (2017). "Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity", eLife, 6. 

M.A.H. Samee, T. Lydiard-Martin, K.M. Biette, B.J. Vincent, S. Sinha*, A.H. DePace* (2017). "Quantitative measurement and thermodynamic modeling of fused enhancers supports a two-tiered mechanism for interpreting regulatory DNA", Cell Reports, 21 (1), 236-245. * Co-corresponding authors.

A. Emad, J. Cairns, K. R. Kalari, L. Wang*, S. Sinha* (2017). "Knowledge-guided gene prioritization reveals new insights into the mechanisms of chemoresistance", Genome Biology, 18 (1), 153. * Co-corresponding authors.

M. C. Saul, C. H. Seward, J. M. Troy, H. Zhang, L. G. Sloofman, X. Lu, P. A. Weisner, D. Caetano-Anolles, H. Sun, S. D. Zhao, S. Chandrasekaran, S. Sinha, L. Stubbs (2017). "Transcriptional regulatory dynamics drive coordinated metabolic and neural response to social challenge in mice", Genome Research, 27(8).

H. Y. Shpigler, M. C. Saul, E. E. Murdoch, A. C. Cash‐Ahmed, C. H. Seward, L. Sloofman, S. Chandrasekaran, S. Sinha, L. J. Stubbs, G. E. Robinson (2017). "Behavioral, transcriptomic and epigenetic responses to social challenge in honey bees", Genes, Brain and Behavior, 16(6): 579-591.

X Ren, J Shen, M Qu, X Wang, Z Wu, Q Zhu, M Jiang, F Tao, S Sinha, D Liem, P Ping, R Weinshilboum, J Han (2017). "Life-iNet: A Structured Network-Based Knowledge Exploration and Analytics System for Life Sciences", Proceedings of ACL 2017, System Demonstrations.


C. Hanson, J. Cairns, L. Wang, S. Sinha (2016). "Computational discovery of transcription factors associated with drug response", The pharmacogenomics journal. [Free full text]

W. Yang, S. Sinha (2016). "A novel method for predicting activity of cis-regulatory modules, based on a diverse training set", Bioinformatics, 3(1):1-7.

K Suryamohan, C Hanson, E Andrews, S Sinha, MD Scheel, MS Halfon. "Redeployment of a conserved gene regulatory network during Aedes aegypti development", Developmental Biology 416 (2), 402-413.

PC Peng, S Sinha (2016). "Quantitative modeling of gene expression using DNA shape features of binding sites", Nucleic acids research, 44(13):e120. doi: 10.1093/nar/gkw446. [Free full text]

JT Kwak, SM Hewitt, AA Kajdacsy-Balla, S Sinha, R Bhargava (2016). "Automated prostate tissue referencing for cancer detection and diagnosis", BMC bioinformatics 17 (1), 1. [Free full text]

C. Blatti, S. Sinha (2016). "Characterizing Gene Sets using Discriminative Random Walks with Restart on Heterogeneous Biological Networks", Bioinformatics 10.1093/bioinformatics/btw151. [Free full text


M.A.H. Samee, B. Lim, N. Samper, H. Lu, C.A. Rushlow, G. Jiménez, S.Y. Shvartsman, S. Sinha (2015) "A Systematic Ensemble Approach to Thermodynamic Modeling of Gene Expression from Sequence Data", Cell Systems, 1(6):396-407. [Full text]. Previewed by Dresch & Arnosti.

Z. D. Stephens, S. Y. Lee, F. Faghri, R. H. Campbell, C. Zhai, M. J. Efron, R. Iyer, M. C. Schatz*, S. Sinha*, G. E. Robinson* (2015). *Co-corresponding authors. "Big Data: Astronomical or Genomical?", PLoS Biology, 13(7):e1002195. [Free full text]. News coverage: Forbes magazine, Nature, Science News, GenomeWeb magazine, Washington Post

S Sinha, J Song, R Weinshilboum, V Jongeneel, J Han (2015). "KnowEnG: a knowledge engine for genomics", Journal of the American Medical Informatics Association 22 (6), 1115-1119.

K. M Kapheim, H. Pan, C. Li, S. L. Salzberg, ..., C. Blatti, S. Sinha, J.S. Johnston, S. J. Hanrahan, S. D. Kocher, J. Wang, G. E. Robinson, G. Zhang (2015). (52 authors) "Genomic signatures of evolutionary transitions from solitary to group living", Science, 348(6239):1139-43. [Abstract]

T Duque, S Sinha (2015). "What does it take to evolve an enhancer? A simulation-based study of factors influencing the emergence of combinatorial regulation", Genome biology and evolution, evv080. [Free full text]

C.A. Blatti, M. Kazemian, S. Wolfe, M. Brodsky, S. Sinha (2015). "Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism", Nucleic acids research, 43 (8), 3998-4012. [Free full text] "Breakthrough article" designation.

J.T. Kwak, A. Kajdacsy-Balla, V. Macias, M. Walsh, S. Sinha, R. Bhargava (2015). "Improving Prediction of Prostate Cancer Recurrence using Chemical Imaging", Scientific reports 5, Article number: 8758.[Free full text]

P. Peng, M.A.H. Samee, S. Sinha (2014). "Incorporating Chromatin Accessibility Data into Sequence-to-Expression Modeling", Biophysical Journal, 108 (5), 1257-1267. [Free full text


O. Whitney, A. R. Pfenning, J. T. Howard, C. A Blatti, F. Liu, J. M. Ward, R. Wang, J. Audet, M. Kellis, S. Mukherjee, S. Sinha, A. J. Hartemink, A. E. West, E. D. Jarvis (2014). Core and region-enriched networks of behaviorally regulated genes and the singing genome. Science 346 (6215), 1256780 [DOI:10.1126/science.1256780].

C.C. Rittschof, S.A. Bukhari, L.G. Sloofman, J.M. Troy, D. Caetano-Anollés, A. Cash-Ahmed, M/ Kent, X. Lu, Y. O. Sanogo, P. A. Weisner, H. Zhang, A. M. Bell, J. Ma, S. Sinha, G. E. Robinson, and L. Stubbs (2014). Neuromolecular responses to social challenge: mechanisms across mouse, stickleback fish, and honey bee. PNAS 111 (50), 17929-17934. [Free Full Text].

M. Kazemian, K. Suryamohan, J. Chen, Y. Zhang, M. A. H. Samee, M. S. Halfon, and S. Sinha (2014). Evidence for Deep Regulatory Similarities in Early Developmental Programs across Highly Diverged Insects. Genome Biology and Evolution. 6 (9): 2301-2320. doi: 10.1093/gbe/evu184. [Free Full Text]

C. Blatti and S. Sinha (2014). Motif Enrichment Tool. Nucleic Acids Research. 2014 gku456 [Free Full Text]

M.A.H. Samee, S. Sinha (2014). Quantitative modeling of a gene's expression from its intergenic sequence. PLoS Computational Biology. 2014 10 (3), e1003467. [Free Full Text]

T. Duque, M. A. H. Samee, M. Kazemian, H. N. Pham, M. H. Brodsky, S. Sinha (2013). Simulations of enhancer evolution provide mechanistic insights into gene regulation. Molecular Biology and Evolution. 2014; 31 (1), 184-200 [Free Full Text]


M. Kazemian, H. Pham, S.A. Wolfe, M.H. Brodsky, S. Sinha (2013). Widespread evidence of cooperative DNA-binding by transcription factors in Drosophila development. Nucleic Acids Research. 2013 Jul 11. PMID: 23847101. [Free Full Text]

Y. Suleimenov, A. Ay, M. Samee, J. M. Dresch, S. Sinha, and D. N. Arnosti (2013). Global parameter estimation for thermodynamic models of transcriptional regulation. Elsevier Methods. 2013 Jul 15;62(1):99-108. [Publisher Site]

Q. Cheng, M. Kazemian, H. Pham, C. Blatti, S. E. Celniker, S. A. Wolfe, M. H. Brodsky, S. Sinha (2013). Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy. PLoS Genetics. 2013 Aug;9(8):e1003571. [Free Full Text]

M. S. Enuameh, Y. Asriyan, A. Richards, R. G. Christensen, V. L. Hall, M. Kazemian, C. Zhu, H. Pham, Q. Cheng, C. Blatti, J. A. Brasefield, M. D. Basciotta, J. Ou, J. C. McNulty, L. J. Zhu, S. E. Celniker, S. Sinha, G. D. Stormo, M. H. Brodsky, and S. Wolfe (2013). Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants. Genome Research. 2013 Jun;23(6):928-40. [PUBMED]

M. Samee and S. Sinha (2013). Evaluating Thermodynamic Models of Enhancer Activity on Cellular Resolution Gene Expression Data. Elsevier Methods. 2013 Jul 15;62(1):79-90. [Publisher Site]


Y.O Sanogo, M. Band, C. Blatti, S. Sinha, A. M Bell (2012). Transcriptional regulation of brain gene expression in response to a territorial intrusion.  Proc Biol Sci. 2012 Oct 24. [Epub ahead of print] [Full text] Open Access article.

S. A. Ament, C. A. Blatti, C. Alaux, M. M. Wheeler, A. L. Toth, Y. Le Conte, G. J. Hunt, E. Guzmán-Novoa, G. Degrandi-Hoffman, J. L. Uribe-Rubio, G. V. Amdam, R. E. Page Jr, S. L. Rodriguez-Zas, G. E. Robinson, S. Sinha (2012). New meta-analysis tools reveal common transcriptional regulatory basis for multiple determinants of behavior. Proc Natl Acad Sci U S A. 2012 Jun 12. [Epub ahead of print] [PUBMED] [Supplementary Materials] [Software downloadOpen Access article. 

S. A. Ament, Y. Wang, C. Chen, C. A. Blatti, F. Hong, Z. S. Liang, N. Negre, K. P. White, S. L. Rodriguez-Zas, C. A. Mizzen, S. Sinha, S. Zhong, G. E. Robinson (2012). The Transcription Factor Ultraspiracle Influences Honey Bee Social Behavior and Behavior-Related Gene Expression. PLoS Genetics 8(3):e1002596. Epub 2012 Mar 29. PMID 22479195.  [Full text]

X. He, T. S. P. C. Duque, and S. Sinha (2012). Evolutionary Origins of Transcription Factor Binding Site Clusters. Mol Bio Evol  2012 Mar;29(3):1059-70. Epub 2011 Nov 10.  doi:10.1093/molbev/msr277. [Free Full Text] [Free PDF]


J. T. Kwak, R. Reddy, S. Sinha, R. Bhargava (2011). Analysis of Variance in Spectroscopic Imaging Data from Human Tissues. Analytical Chemistry [Abstract]

M. Kazemian, Q. Zhu, M. S. Halfon, S. Sinha (2011). Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison. Nucl. Acids Res doi: 10.1093/nar/gkr621. [Full Text]

M. Kazemian, M. H. Brodsky, S. Sinha (2011). Genome surveyor 2.0: cis-regulatory analysis in Drosophila. Nucl. Acids Res doi: 10.1093/nar/gkr291. [Full Text]

D. E. Janes, C. Chapus, Y. Gondo, D. F. Clayton, S. Sinha, C. A. Blatti, C. L. Organ, M. K. Fujita, C. N. Balakrishnan, and S. V. Edwards (2011). Reptiles and mammals have differentially retained long conserved non-coding sequences from the amniote ancestor. Genome Biology & Evolution 3 102-113.

J. T. Kwak, S. Sinha, R. Bhargava (2011). A new segmentation framework for Infrared Spectroscopy imaging using frequent pattern mining IEEE International Symposium on Biomedical Imaging: From Nano to Micro. Issue: March 30 2011-April 2 2011. Page 452 - 455.

J. T. Kwak, S. M. Hewitt, S. Sinha, R. Bhargava (2011). Multimodal microscopy for automated histologic analysis of prostate cancer. BMC Cancer 11:62.


X. He, M. Samee, C. Blatti, S. Sinha (2010). Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression. PLoS Computational Biology 6(9). [Full Text]

L. J. Zhu, R. G. Christensen, M. Kazemian, C. J. Hull, M. S. Enuameh, M. D. Basciotta, J. A. Brasefield, C. Zhu, Y. Asriyan, D. S. Lapointe, S. Sinha, S. A. Wolfe, and M. H. Brodsky (2010). FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system. Nucleic Acids Research (Database issue) D111-7.

G. E. Robinson, J. A. Banks, D. K. Padilla, W. W. Burggren, C. S. Cohen, C. F. Delwiche, V. Funk, H. E. Hoekstra, E. D. Jarvis, L. Johnson, M. Q. Martindale, C. Martinez del Rio, M. Medina, D. E. Salt, S. Sinha, C. Specht, K. Strange, J. E. Strassmann, B. J. Swalla, L. Tomanek (2010). Empowering 21st Century Biology. BioScience.

M. Kazemian, C. Blatti, A. Richards, M. McCutchan, N. Wakabayashi-Ito, A. Hammonds, S. Celniker, S. Kumar, S. Wolfe, M. Brodsky, and S. Sinha (2010). Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials. PLoS Biology [Full Text] [Nature Rev Gen commentary]

W.C. Warren, D.F. Clayton, … S. Sinha, C. Blatti, … R.K. Wilson (83 authors) (2010). The genome of a songbird. Nature 454: 757-62. [IN THE NEWS] [ABSTRACT]

X. He, S. Sinha. (2010). ChIPs and Regulatory Bits. Nature Biotechnology, 28, 142 - 143. [Full Text]

The Nasonia Genome Working Group: J. H. Werren, S. Richards, ... J. Kim, ... S. Sinha, ... R. A. Gibbs. (157 authors). (2010). Functional and Evolutionary Insights from the Genomes of Three Parasitoid Nasonia Species. Science. 327 (5963), pp. 343 - 348 [IN THE NEWS] [SCIENCE PODCAST] [Pubmed] [Synopsis]

J. Kim, R. Cunningham, B. James, S. Wyder, J. D. Gibson, O. Niehuis, E. M. Zdobnov, H. M. Robertson, G. E. Robinson, J. H. Werren, and S. Sinha. (2010). Functional Characterization of Transcription Factor Motifs Using Cross-species Comparison across Large Evolutionary Distances. PLoS Computational Biology, 6(1): e1000652. [Full Text]

J. Kim, S. Sinha (2010). Towards realistic benchmarks for multiple alignments of non-coding sequences. BMC Bioinformatics, 11:54. [Full Text]

S. Sinha, X. He. (2010). [Invited Book Chapter] Evolution of regulatory sequences in Drosophila species. Methods in Molecular Biology, Humana Press. Computational Biology of Transcription Factor Binding. Vol. 674, 283-296. Ed: Istvan Ladunga.


X. He, F. Hong, C. Chen, F. Fang, S. Sinha, H. Ng, S. Zhong. (2009). A Biophysical Model for Analysis of Transcription Factor Interaction and Binding Site Arrangement from Genome-Wide Binding Data. RECOMB Regulatory Genomics 2009. PloS ONE, 4(12):e8155.[Pubmed]

A. Moses and S. Sinha. (2009). [Invited Book Chapter] Regulatory Motif Analysis. Bioinformatics; Tools and Applications. Ed: David Edwards, Jason Stajich, David Hansen. Springer.

M. R. Kantorovitz, M. Kazemian, S. Kinston, D. Miranda-Saavedra, Q. Zhu, G. E. Robinson, B. Gottgens, M. S. Halfon, S. Sinha. (2009). Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse. Developmental Cell, Volume 17, Issue 4, 568-79. [IN THE NEWS][Pubmed]

C. Alaux, S. Sinha, L. Hasadsri, G. J. Hunt, E. Guzman-Novoa, G. DeGrandi-Hoffman, J. L. Uribe-Rubio, B. R. Southey, S. Rodriguez-Zas, and G. E. Robinson. (2009). Honey bee aggression supports a link between gene regulation and behavioral evolution. Proc. Natl. Acad. Sci. USA, 106, 15400-15405. [IN THE NEWS] [Pubmed]

C. Alaux, Y. Le Conte, H. Adams, S. Rodriguez-Zas, C. Grozinger, S. Sinha, G. E. Robinson. (2009). Regulation of Brain Gene Expression in Honey Bees by Brood Pheromone Genes, Brain and Behavior, 8(3):309-19. [Pubmed]

J. Kim, X. He, S. Sinha (2009). Evolution of Regulatory Sequences in 12 Drosophila Species. PLoS Genetics, 5(1):e1000330. [Pubmed]

X. He, X. Ling, S. Sinha (2009). Alignment and Prediction of cis-Regulatory Modules Based on a Probabilistic Model of Evolution. PLoS Computational Biology, 5(3):e1000299. [Pubmed]


A. Kosorukoff, S. Sinha (2008). Heart of the Matter: discovering the consensus of multiple clustering results. BIBM 08 . IEEE Intl. Conf. on Bioinformatics & Biomedicine, Philadelphia.

A. Ivan, M.S. Halfon, S. Sinha (2008). Computational discovery of cis-regulatory modules in Drosophila, without prior knowledge of motifs. Genome Biology, 9(1):R22. (Marked by journal as highly accessed.) [Pubmed]

M.B. Noyes, X. Meng, A. Wakabayashi, S. Sinha, M. H. Brodsky, S. A. Wolfe (2008). The systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Nucleic Acids Res. 36, 2547-2560. [Pubmed]

S. Sinha, A. S. Adler, Y. Field, H. Y. Chang, E. Segal (2008). Systematic Functional Characterization of cis-Regulatory Motifs in Human Core Promoters. Genome Research. 18:477-488. [Pubmed]


S. Sinha and X. He (2007). MORPH: Probabilistic alignment combined with Hidden Markov Models of cis-regulatory modules. PLoS Computational Biology. 3(11):e216. [Pubmed]

A. Adler, S. Sinha, E. Segal, H. Chang. (2007). Motif module map reveals enforcement of aging by continual NF-kB activity. Genes & Development, 21:3244-3257. Cover article. Recommended by Faculty of 1000. [Pubmed]

L. Li, Q. Zhu, X. He, S. Sinha and M. S. Halfon. (2007) Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses. Genome Biology 8, R101. (Marked by journal as highly accessed.) [Pubmed]

R. Kantorovitz, G. E. Robinson and S. Sinha (2007).  A statistical method for alignment-free comparison of regulatory sequences. ISMB 07. Bioinformatics, 23(13). (Acceptance rate: 15% in over 400.) [Pubmed]

J. Kim and S. Sinha (2007) Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment. Bioinformatics, 23(3). [Pubmed]

S. Sinha (2007). [Invited Book Chapter] PhyME: a software tool for finding motifs in sets of orthologous sequences. Methods Mol Biol.;395:309-18. [Pubmed]


S. Sinha, X. Ling, C.W. Whitfield, C. Zhai, G.E. Robinson (2006) Genome scan forcis-regulatory DNA motifs associated with social behavior in honey bees. Proc. Nat. Acad. Sci. USA, 103(44). [Pubmed]

S. Sinha (2006). On counting position weight matrix matches in a sequence, with application to discriminative motif finding. ISMB '06. Bioinformatics, 22(14).(Acceptance rate: 15% in over 400.) [Pubmed]

S. Sinha, Y. Liang, E.D. Siggia (2006). Stubb: a program for discovery and analysis of cis-regulatory modules. Nucl. Acids Res, 34 (Web server issue): W555-9. [Pubmed]

S. Sinha, M. Pearce, U. Unnerstall, J. Fak, M. Dandapani, M.D. Schroeder, E.D. Siggia, U. Gaul (2006). Evolution of transcription control in the segmentation gene network of Drosophila. Unpublished. [Download]. 


S. Sinha and E. D. Siggia (2005). Sequence Turnover and Tandem Repeats in cis-Regulatory Modules in Drosophila. Molecular Biology and Evolution, 22(4):874-85. [Pubmed]

M. Tompa, N. Li, T. L. Bailey, G. M. Church, B. DeMoor, E. Eskin, A. V. Favorov,  M. C. Frith, Y. Fu, W. J. Kent, V. J. Makeev, A. A. Mironov, W. S. Noble, G. Pavesi, G. Pesole, M. Regnier, N. Simonis, S. Sinha, G. Thijs, J. van Helden, M. Vandenbogaert, Z. Weng, C. Workman, C. Ye, Z. Zhu (2005). An Assessment of Computational Tools for the Discovery of Transcription Factor Binding Sites. Nature Biotechnology, Vol. 23, No. 1, pp. 137 – 144. [Pubmed]


S. Sinha, M. Blanchette, and M. Tompa (2004). PhyME: A Probabilistic Algorithm for Finding Motifs in Sets of Orthologous Sequences. BMC Bioinformatics, 5(170). (Marked by journal as Research Highlight.) [Pubmed]

S. Sinha, M. Schroeder, U. Unnerstall, U. Gaul, and E. D. Siggia (2004). Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila. BMC Bioinformatics, 5(129). Cited by the Faculty of 1000. [Pubmed]

A. Prakash, M. Blanchette, S. Sinha, M. Tompa (2004). Motif Discovery in Heterogeneous Sequence Data, Pacific Symposium on Biocomputing (PSB). [Pubmed]


S. Sinha, E. van Nimwegen, and E. D. Siggia (2003). A Probabilistic Method to Detect Regulatory Modules. Bioinformatics,2003, 19(S1). (Special issue on ISMB 2003.) (Best paper award, 2nd prize.) [Pubmed]

S. Sinha (2003). Discriminative Motifs. RECOMB '02. Journal of Computational Biology, 10(3), 599-615. [Pubmed]

S. Sinha, M. Tompa (2003) YMF, a Program for Discovery of Novel Transcription Factor Binding Sites by Statistical Overrepresentation. Nucleic Acids Research, Vol. 31, No. 13, pp. 3586-358. [Pubmed]

S. Sinha, M. Tompa (2003) Performance Comparison of Algorithms for Finding Transcription Factor Binding Sites. BIBE '03. IEEE Symposium on Bioinformatics and Bioengineering (BIBE), pp. 214-220.


S. Sinha and M. Tompa (2002). Discovery of Novel Transcription Factor Binding Sites by Statistical Overrepresentation. Nucleic Acids Research, 30(24), 5549-60. [Pubmed]

Y. Chen, R. Venkatesan, M. Cary, R. Pang, S. Sinha, M. Jakubowski. (2002) Oblivious hashing:  Silent Verification of Code Execution, Fifth International Workshop on Information Hiding (IHW '02).


M. Blanchette and S. Sinha (equal authors) (2001). Separating Real Motifs from their Artifacts. ISMB 01. Bioinformatics, 17(S1).  [Pubmed]

R. Venkatesan, V. Vazirani, S. Sinha. (2001) A Graph-Theoretic Approach to Software Watermarking. Fourth International Workshop on Information Hiding (IHW '01), pp. 157-168.


M. Blanchette and S. Sinha (equal authors) (2001). Separating Real Motifs from their Artifacts. ISMB 01. Bioinformatics, 17(S1).  [Pubmed]

R. Venkatesan, V. Vazirani, S. Sinha. (2001) A Graph-Theoretic Approach to Software Watermarking. Fourth International Workshop on Information Hiding (IHW '01), pp. 157-168.

Upcoming (in review/preprints)

S. Tabe-Bordbar, Y.J. Song, B.J. Lunt, K.V. Prasanth, S. Sinha. Mechanistic analysis of enhancer sequences in the Estrogen Receptor transcriptional program. bioRxiv 

G. Linkowski, C. Blatti, K. Kalari, S. Sinha*, S. Vasudevan*. Gene Sets Analysis using Network Patterns. bioRxiv. * Corresponding authors.

F. Khajouei, N. Samper, N.J. Djabrayan, B. Lunt, G. Jiménez, S. Sinha. Model-based analysis of polymorphisms in an enhancer reveals cis-regulatory mechanisms. bioRxiv 

Lunt, B.J., Sinha, S. Regularization Improves the Robustness of Learned Sequence-to-Expression Models. biorxiv.