Saurabh Sinha

Director, Mayo Clinic & Illinois Alliance for Technology-based Healthcare

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Research Output

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2020

Global shape of Toll activation is determined by wntD enhancer properties

Rahimi, N., Carmon, S., Averbukh, I., Khajouei, F., Sinha, S., Schejter, E. D., Barkai, N. & Shilo, B. Z., Jan 21 2020, In : Proceedings of the National Academy of Sciences of the United States of America. 117, 3, p. 1552-1558 7 p.

Research output: Contribution to journalArticle

Knowledge-guided analysis of "omics" data using the KnowEnG cloud platform

Blatti, C., Emad, A., Berry, M. J., Gatzke, L., Epstein, M., Lanier, D., Rizal, P., Ge, J., Liao, X., Sobh, O., Lambert, M., Post, C. S., Xiao, J., Groves, P., Epstein, A. T., Chen, X., Srinivasan, S., Lehnert, E., Kalari, K. R., Wang, L. & 8 others, Weinshilboum, R. M., Song, J. S., Jongeneel, C. V., Han, J., Ravaioli, U., Sobh, N., Bushell, C. B. & Sinha, S., 2020, In : PLoS biology. 18, 1, e3000583.

Research output: Contribution to journalArticle

Open Access

Superior breast cancer metastasis risk stratification using an epithelial-mesenchymal-amoeboid transition gene signature

Emad, A., Ray, T., Jensen, T. W., Parat, M., Natrajan, R., Sinha, S. & Ray, P. S., Jul 8 2020, In : Breast cancer research : BCR. 22, 1, 1 p.

Research output: Contribution to journalArticle

Open Access

Tissue-guided LASSO for prediction of clinical drug response using preclinical samples

Huang, E. W., Bhope, A., Lim, J., Sinha, S. & Emad, A., Jan 1 2020, In : PLoS computational biology. 16, 1, e1007607.

Research output: Contribution to journalArticle

Open Access
2019

A subtype of oral, laryngeal, esophageal, and lung, squamous cell carcinoma with high levels of TrkB-T1 neurotrophin receptor mRNA

Zhou, Y., Sinha, S., Schwartz, J. L. & Adami, G. R., Jun 20 2019, In : BMC Cancer. 19, 1, 607.

Research output: Contribution to journalArticle

Open Access

Cross-species systems analysis of evolutionary toolkits of neurogenomic response to social challenge

Saul, M. C., Blatti, C., Yang, W., Bukhari, S. A., Shpigler, H. Y., Troy, J. M., Seward, C. H., Sloofman, L., Chandrasekaran, S., Bell, A. M., Stubbs, L., Robinson, G. E., Zhao, S. D. & Sinha, S., Jan 2019, In : Genes, Brain and Behavior. 18, 1, p. e12502 e12502.

Research output: Contribution to journalArticle

Global analysis of osteosarcoma lipidomes reveal altered lipid profiles in metastatic versus nonmetastatic cells

Roy, J., Dibaeinia, P., Fan, T. M., Sinha, S. & Das, A., Jan 1 2019, In : Journal of Lipid Research. 60, 2, p. 375-387 13 p.

Research output: Contribution to journalArticle

Identification of pathways associated with chemosensitivity through network embedding

Wang, S., Huang, E., Cairns, J., Peng, J., Wang, L. & Sinha, S., Mar 2019, In : PLoS computational biology. 15, 3, e1006864.

Research output: Contribution to journalArticle

Open Access

Label-free visualization and characterization of extracellular vesicles in breast cancer

You, S., Barkalifa, R., Chaney, E. J., Tu, H., Park, J., Sorrells, J. E., Sun, Y., Liu, Y. Z., Yang, L., Chen, D. Z., Marjanovic, M., Sinha, S. & Boppart, S. A., Nov 26 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 48, p. 24012-24018 7 p.

Research output: Contribution to journalArticle

Mechanistic interpretation of non-coding variants for discovering transcriptional regulators of drug response

Xie, X., Hanson, C. & Sinha, S., Jul 30 2019, In : BMC biology. 17, 1, 62.

Research output: Contribution to journalArticle

Open Access

Real-time intraoperative diagnosis by deep neural network driven multiphoton virtual histology

You, S., Sun, Y., Yang, L., Park, J., Tu, H., Marjanovic, M., Sinha, S. & Boppart, S. A., Dec 17 2019, In : npj Precision Oncology. 3, 1, 33.

Research output: Contribution to journalArticle

Open Access

The role of chromatin accessibility in cis-regulatory evolution

Peng, P. C., Khoueiry, P., Girardot, C., Reddington, J. P., Garfield, D. A., Furlong, E. E. M. & Sinha, S., May 22 2019, In : Genome biology and evolution. 11, 7, p. 1813-1828 16 p., evz103.

Research output: Contribution to journalArticle

Open Access

Towards a fully automated algorithm driven platform for biosystems design

HamediRad, M., Chao, R., Weisberg, S., Lian, J., Sinha, S. & Zhao, H., Nov 13 2019, In : Nature communications. 10, 1, 5150.

Research output: Contribution to journalArticle

Open Access
2018

A closer look at cross-validation for assessing the accuracy of gene regulatory networks and models

Tabe-Bordbar, S., Emad, A., Zhao, S. D. & Sinha, S., Dec 1 2018, In : Scientific reports. 8, 1, 6620.

Research output: Contribution to journalArticle

An information theoretic treatment of sequence-to-expression modeling

Khajouei, F. & Sinha, S., Sep 2018, In : PLoS computational biology. 14, 9, e1006459.

Research output: Contribution to journalArticle

Effects of green tea on miRNA and microbiome of oral epithelium

Adami, G. R., Tangney, C. C., Tang, J. L., Zhou, Y., Ghaffari, S., Naqib, A., Sinha, S., Green, S. J. & Schwartz, J. L., Dec 1 2018, In : Scientific reports. 8, 1, 5873.

Research output: Contribution to journalArticle

Intravital imaging by simultaneous label-free autofluorescence-multiharmonic microscopy

You, S., Tu, H., Chaney, E. J., Sun, Y., Zhao, Y., Bower, A. J., Liu, Y. Z., Marjanovic, M., Sinha, S., Pu, Y. & Boppart, S. A., Dec 1 2018, In : Nature communications. 9, 1, 2125.

Research output: Contribution to journalArticle

Principled multi-omic analysis reveals gene regulatory mechanisms of phenotype variation

Hanson, C., Cairns, J., Wang, L. & Sinha, S., Aug 2018, In : Genome Research. 28, 8, p. 1207-1216 10 p.

Research output: Contribution to journalArticle

SigMat: A classification scheme for gene signature matching

Xiao, J., Blatti, C. & Sinha, S., Jul 1 2018, In : Bioinformatics. 34, 13, p. i547-i554

Research output: Contribution to journalArticle

2017

A novel method for predicting activity of cis-regulatory modules, based on a diverse training set

Yang, W. & Sinha, S., Jan 1 2017, In : Bioinformatics. 33, 1, p. 1-7 7 p.

Research output: Contribution to journalArticle

Behavioral, transcriptomic and epigenetic responses to social challenge in honey bees

Shpigler, H. Y., Saul, M. C., Murdoch, E. E., Cash-Ahmed, A. C., Seward, C. H., Sloofman, L., Chandrasekaran, S., Sinha, S., Stubbs, L. J. & Robinson, G. E., Jul 2017, In : Genes, Brain and Behavior. 16, 6, p. 579-591 13 p.

Research output: Contribution to journalArticle

Knowledge-guided gene prioritization reveals new insights into the mechanisms of chemoresistance

Emad, A., Cairns, J., Kalari, K. R., Wang, L. & Sinha, S., Aug 11 2017, In : Genome biology. 18, 1, 153.

Research output: Contribution to journalArticle

Quantitative Measurement and Thermodynamic Modeling of Fused Enhancers Support a Two-Tiered Mechanism for Interpreting Regulatory DNA

Samee, M. A. H., Lydiard-Martin, T., Biette, K. M., Vincent, B. J., Bragdon, M. D., Eckenrode, K. B., Wunderlich, Z., Estrada, J., Sinha, S. & DePace, A. H., Oct 3 2017, In : Cell Reports. 21, 1, p. 236-245 10 p.

Research output: Contribution to journalArticle

Transcriptional regulatory dynamics drive coordinated metabolic and neural response to social challenge in mice

Saul, M. C., Seward, C. H., Troy, J. M., Zhang, H., Sloofman, L. G., Lu, X., Weisner, P. A., Caetano-Anolles, D., Sun, H., Zhao, S. D., Chandrasekaran, S., Sinha, S. & Stubbs, L., Jun 2017, In : Genome Research. 27, 6, p. 959-972 14 p.

Research output: Contribution to journalArticle

Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity

Khoueiry, P., Girardot, C., Ciglar, L., Peng, P. C., Hilary Gustafson, E., Sinha, S. & Furlong, E. E. M., Aug 9 2017, In : eLife. 6, e28440.

Research output: Contribution to journalArticle

2016

Automated prostate tissue referencing for cancer detection and diagnosis

Kwak, J. T., Hewitt, S. M., Kajdacsy-Balla, A. A., Sinha, S. & Bhargava, R., Jun 1 2016, In : BMC bioinformatics. 17, 1, 227.

Research output: Contribution to journalArticle

Characterizing gene sets using discriminative random walks with restart on heterogeneous biological networks

Blatti, C. & Sinha, S., Jul 15 2016, In : Bioinformatics. 32, 14, p. 2167-2175 9 p.

Research output: Contribution to journalArticle

Computational discovery of transcription factors associated with drug response

Hanson, C., Cairns, J., Wang, L. & Sinha, S., Nov 1 2016, In : Pharmacogenomics Journal. 16, 6, p. 573-582 10 p.

Research output: Contribution to journalArticle

Quantitative modeling of gene expression using DNA shape features of binding sites

Peng, P. C. & Sinha, S., Jul 27 2016, In : Nucleic acids research. 44, 13, p. e120

Research output: Contribution to journalArticle

Redeployment of a conserved gene regulatory network during Aedes aegypti development

Suryamohan, K., Hanson, C., Andrews, E., Sinha, S., Scheel, M. D. & Halfon, M. S., Aug 15 2016, In : Developmental Biology. 416, 2, p. 402-413 12 p.

Research output: Contribution to journalArticle

2015

A Systematic Ensemble Approach to Thermodynamic Modeling of Gene Expression from Sequence Data

Samee, M. A. H., Lim, B., Samper, N., Lu, H., Rushlow, C. A., Jiménez, G., Shvartsman, S. Y. & Sinha, S., Dec 23 2015, In : Cell Systems. 1, 6, p. 396-407 12 p.

Research output: Contribution to journalArticle

Big data: Astronomical or genomical?

Stephens, Z. D., Lee, S. Y., Faghri, F., Campbell, R. H., Zhai, C., Efron, M. J., Iyer, R., Schatz, M. C., Sinha, S. & Robinson, G. E., 2015, In : PLoS biology. 13, 7

Research output: Contribution to journalArticle

Genomic signatures of evolutionary transitions from solitary to group living

Kapheim, K. M., Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., Robertson, H. M., Hudson, M. E., Venkat, A., Fischman, B. J., Hernandez, A., Yandell, M., Ence, D., Holt, C., Yocum, G. D., Kemp, W. P., Bosch, J., Waterhouse, R. M., Zdobnov, E. M., Stolle, E. & 32 others, Kraus, F. B., Helbing, S., Moritz, R. F. A., Glastad, K. M., Hunt, B. G., Goodisman, M. A. D., Hauser, F., Grimmelikhuijzen, C. J. P., Pinheiro, D. G., Nunes, F. M. F., Soares, M. P. M., Tanaka, É. D., Simões, Z. L. P., Hartfelder, K., Evans, J. D., Barribeau, S. M., Johnson, R. M., Massey, J. H., Southey, B. R., Hasselmann, M., Hamacher, D., Biewer, M., Kent, C. F., Zayed, A., Blatti, C., Sinha, S., Johnston, J. S., Hanrahan, S. J., Kocher, S. D., Wang, J., Robinson, G. E. & Zhang, G., Jun 5 2015, In : Science. 348, 6239

Research output: Contribution to journalArticle

Improving prediction of prostate cancer recurrence using chemical imaging

Kwak, J. T., Kajdacsy-Balla, A., Macias, V., Walsh, M., Sinha, S. & Bhargava, R., Jan 1 2015, In : Scientific reports. 5, 8758.

Research output: Contribution to journalArticle

Incorporating chromatin accessibility data into sequence-to-expression modeling

Peng, P. C., Hassan Samee, M. A. & Sinha, S., Mar 10 2015, In : Biophysical journal. 108, 5, p. 1257-1267 11 p.

Research output: Contribution to journalArticle

Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism

Blatti, C., Kazemian, M., Wolfe, S., Brodsky, M. & Sinha, S., Feb 24 2015, In : Nucleic acids research. 43, 8, p. 3998-4012 15 p.

Research output: Contribution to journalArticle

KnowEnG: A knowledge engine for genomics

Sinha, S., Song, J., Weinshilboum, R., Jongeneel, V. & Han, J., Jan 1 2015, In : Journal of the American Medical Informatics Association. 22, 6, p. 1115-1119 5 p.

Research output: Contribution to journalArticle

2014

Core and region-enriched networks of behaviorally regulated genes and the singing genome

Whitney, O., Pfenning, A. R., Howard, J. T., Blatti, C. A., Liu, F., Ward, J. M., Wang, R., Audet, J. N., Kellis, M., Mukherjee, S., Sinha, S., Hartemink, A. J., West, A. E. & Jarvis, E. D., Dec 12 2014, In : Science. 346, 6215, 1256780.

Research output: Contribution to journalArticle

Evidence for deep regulatory similarities in early developmental programs across highly diverged insects

Kazemian, M., Suryamohan, K., Chen, J. Y., Zhang, Y., Samee, M. A. H., Halfon, M. S. & Sinha, S., Jan 1 2014, In : Genome biology and evolution. 6, 9, p. 2301-2320 20 p.

Research output: Contribution to journalArticle

Motif enrichment tool

Blatti, C. & Sinha, S., Jul 1 2014, In : Nucleic acids research. 42, W1, p. W20-W25

Research output: Contribution to journalArticle

Neuromolecular responses to social challenge: Common mechanisms across mouse, stickleback fish, and honey bee

Rittschof, C. C., Bukhari, S. A., Sloofman, L. G., Troy, J. M., Caetano-Anollés, D., Cash-Ahmed, A., Kent, M., Lu, X., Sanogo, Y. O., Weisner, P. A., Zhang, H., Bell, A. M., Ma, J., Sinha, S., Robinson, G. E. & Stubbs, L., Dec 16 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 50, p. 17929-17934 6 p.

Research output: Contribution to journalArticle

Quantitative Modeling of a Gene's Expression from Its Intergenic Sequence

Samee, M. A. H. & Sinha, S., Mar 2014, In : PLoS computational biology. 10, 3, e1003467.

Research output: Contribution to journalArticle

Simulations of enhancer evolution provide mechanistic insights into gene regulation

Duque, T., Samee, M. A. H., Kazemian, M., Pham, H. N., Brodsky, M. H. & Sinha, S., Jan 1 2014, In : Molecular biology and evolution. 31, 1, p. 184-200 17 p.

Research output: Contribution to journalArticle

2013

Computational Identification of Diverse Mechanisms Underlying Transcription Factor-DNA Occupancy

Cheng, Q., Kazemian, M., Pham, H., Blatti, C., Celniker, S. E., Wolfe, S. A., Brodsky, M. H. & Sinha, S., Aug 2013, In : PLoS genetics. 9, 8, e1003571.

Research output: Contribution to journalArticle

Evaluating thermodynamic models of enhancer activity on cellular resolution gene expression data

Samee, M. A. H. & Sinha, S., Jul 15 2013, In : Methods. 62, 1, p. 79-90 12 p.

Research output: Contribution to journalArticle

Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants

Enuameh, M. S., Asriyan, Y., Richards, A., Christensen, R. G., Hall, V. L., Kazemian, M., Zhu, C., Pham, H., Cheng, Q., Blatti, C., Brasefield, J. A., Basciotta, M. D., Ou, J., McNulty, J. C., Zhu, L. J., Celniker, S. E., Sinha, S., Stormo, G. D., Brodsky, M. H. & Wolfe, S. A., Jun 2013, In : Genome Research. 23, 6, p. 928-940 13 p.

Research output: Contribution to journalArticle

Global parameter estimation for thermodynamic models of transcriptional regulation

Suleimenov, Y., Ay, A., Samee, M. A. H., Dresch, J. M., Sinha, S. & Arnosti, D. N., Jul 15 2013, In : Methods. 62, 1, p. 99-108 10 p.

Research output: Contribution to journalArticle

Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development

Kazemian, M., Pham, H., Wolfe, S. A., Brodsky, M. H. & Sinha, S., Sep 2013, In : Nucleic acids research. 41, 17, p. 8237-8252 16 p.

Research output: Contribution to journalArticle

2012

Analysis of variance in spectroscopic imaging data from human tissues

Kwak, J. T., Reddy, R., Sinha, S. & Bhargava, R., Jan 17 2012, In : Analytical chemistry. 84, 2, p. 1063-1069 7 p.

Research output: Contribution to journalArticle