Research output per year
Research output per year
- 1 - 50 out of 127 results
Search results
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2024
A transcriptomic atlas of acute stress response to low pH in multiple Issatchenkia orientalis strains
Dubinkina, V., Bhogale, S., Hsieh, P. H., Dibaeinia, P., Nambiar, A., Maslov, S., Yoshikuni, Y. & Sinha, S., Jan 2024, In: Microbiology Spectrum. 12, 1Research output: Contribution to journal › Article › peer-review
Open Access -
Monoallelically expressed noncoding RNAs form nucleolar territories on NOR-containing chromosomes and regulate rRNA expression
Hao, Q., Liu, M., Daulatabad, S. V., Gaffari, S., Song, Y. J., Srivastava, R., Bhaskar, S., Moitra, A., Mangan, H., Tseng, E., Gilmore, R. B., Frier, S. M., Chen, X., Wang, C., Huang, S., Chamberlain, S., Jin, H., Korlach, J., McStay, B. & Sinha, S. & 3 others, , Feb 8 2024, In: eLife. 13, e80684.Research output: Contribution to journal › Article › peer-review
Open Access -
2023
BEDwARS: a robust Bayesian approach to bulk gene expression deconvolution with noisy reference signatures
Ghaffari, S., Bouchonville, K. J., Saleh, E., Schmidt, R. E., Offer, S. M. & Sinha, S., Dec 2023, In: Genome biology. 24, 1, 178.Research output: Contribution to journal › Article › peer-review
Open Access -
Influenza A virus infection disrupts oligodendrocyte homeostasis and alters the myelin lipidome in the adult mouse
Louie, A. Y., Kim, J. S., Drnevich, J., Dibaeinia, P., Koito, H., Sinha, S., McKim, D. B., Soto-Diaz, K., Nowak, R. A., Das, A. & Steelman, A. J., Dec 2023, In: Journal of neuroinflammation. 20, 1, 190.Research output: Contribution to journal › Article › peer-review
Open Access -
Integrative modeling of lncRNA-chromatin interaction maps reveals diverse mechanisms of nuclear retention
Tabe-Bordbar, S. & Sinha, S., Dec 2023, In: BMC genomics. 24, 1, 395.Research output: Contribution to journal › Article › peer-review
Open Access -
Single-cell dissection of aggression in honeybee colonies
Traniello, I. M., Bukhari, S. A., Dibaeinia, P., Serrano, G., Avalos, A., Ahmed, A. C., Sankey, A. L., Hernaez, M., Sinha, S., Zhao, S. D., Catchen, J. & Robinson, G. E., Aug 2023, In: Nature Ecology and Evolution. 7, 8, p. 1232-1244 13 p.Research output: Contribution to journal › Article › peer-review
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2022
An epigenomic shift in amygdala marks the transition to maternal behaviors in alloparenting virgin female mice
Seward, C. H., Saul, M. C., Troy, J. M., Dibaeinia, P., Zhang, H., Sinha, S. & Stubbs, L. J., Feb 2022, In: PloS one. 17, 2 February, e0263632.Research output: Contribution to journal › Article › peer-review
Open Access -
The Liver X Receptor Is Selectively Modulated to Differentially Alter Female Mammary Metastasis-associated Myeloid Cells
Ma, L., Vidana Gamage, H. E., Tiwari, S., Han, C., Henn, M. A., Krawczynska, N., Dibaeinia, P., Koelwyn, G. J., Das Gupta, A., Bautista Rivas, R. O., Wright, C. L., Xu, F., Moore, K. J., Sinha, S. & Nelson, E. R., Jul 1 2022, In: Endocrinology (United States). 163, 7, bqac072.Research output: Contribution to journal › Article › peer-review
Open Access -
Thermodynamics-based modeling reveals regulatory effects of indirect transcription factor-DNA binding
Bhogale, S. & Sinha, S., May 20 2022, In: iScience. 25, 5, 104152.Research output: Contribution to journal › Article › peer-review
Open Access -
2021
An integrated multi-omics approach to identify regulatory mechanisms in cancer metastatic processes
Ghaffari, S., Hanson, C., Schmidt, R. E., Bouchonville, K. J., Offer, S. M. & Sinha, S., Dec 2021, In: Genome biology. 22, 1, 19.Research output: Contribution to journal › Article › peer-review
Open Access -
Deciphering enhancer sequence using thermodynamics-based models and convolutional neural networks
Dibaeinia, P. & Sinha, S., Oct 11 2021, In: Nucleic acids research. 49, 18, p. 10309-10327 19 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Inference of phenotype-relevant transcriptional regulatory networks elucidates cancer type-specific regulatory mechanisms in a pan-cancer study
Emad, A. & Sinha, S., Dec 2021, In: npj Systems Biology and Applications. 7, 1, 9.Research output: Contribution to journal › Article › peer-review
Open Access -
Label-free deep profiling of the tumor microenvironment
You, S., Chaney, E. J., Tu, H., Sun, Y., Sinha, S. & Boppart, S. A., May 1 2021, In: Cancer Research. 81, 9, p. 2534-2544 11 p.Research output: Contribution to journal › Article › peer-review
Open Access -
VarSAn: Associating Pathways with a Set of Genomic Variants Using Network Analysis
Xie, X., Kendzior, M. C., Ge, X., Mainzer, L. S. & Sinha, S., Sep 7 2021, In: Nucleic acids research. 49, 15, p. 8471-8487 17 p.Research output: Contribution to journal › Article › peer-review
Open Access -
2020
Behavior-related gene regulatory networks: A new level of organization in the brain
Sinha, S., Jones, B. M., Traniello, I. M., Bukhari, S. A., Halfon, M. S., Hofmann, H. A., Huang, S., Katz, P. S., Keagy, J., Lynch, V. J., Sokolowski, M. B., Stubbs, L. J., Tabe-Bordbar, S., Wolfner, M. F. & Robinson, G. E., Sep 22 2020, In: Proceedings of the National Academy of Sciences of the United States of America. 117, 38, p. 23270-23279 10 p.Research output: Contribution to journal › Review article › peer-review
Open Access -
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 journal › Article › peer-review
Open Access -
Individual differences in honey bee behavior enabled by plasticity in brain gene regulatory networks
Jones, B. M., Rao, V. D., Gernat, T., Jagla, T., Cash-ahmed, A. C., Rubin, B. E., Comi, T. J., Bhogale, S., Husain, S. S., Blatti, C., Middendorf, M., Sinha, S., Chandrasekaran, S. & Robinson, G. E., Dec 22 2020, In: eLife. 9, p. 1-28 28 p., e62850.Research output: Contribution to journal › Article › peer-review
Open Access -
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, , 2020, In: PLoS biology. 18, 1, e3000583.Research output: Contribution to journal › Article › peer-review
Open Access -
SERGIO: A Single-Cell Expression Simulator Guided by Gene Regulatory Networks
Dibaeinia, P. & Sinha, S., Sep 23 2020, In: Cell Systems. 11, 3, p. 252-271.e11Research output: Contribution to journal › Article › peer-review
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. 22, 1, 1304.Research output: Contribution to journal › Article › peer-review
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., 2020, In: PLoS computational biology. 16, 1, e1007607.Research output: Contribution to journal › Article › peer-review
Open Access -
Uncovering Effective Explanations for Interactive Genomic Data Analysis
Huang, S., Blatti, C., Sinha, S. & Parameswaran, A., Sep 11 2020, In: Patterns. 1, 6, 100093.Research output: Contribution to journal › Article › peer-review
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 journal › Article › peer-review
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 journal › Article › peer-review
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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., 2019, In: Journal of Lipid Research. 60, 2, p. 375-387 13 p.Research output: Contribution to journal › Article › peer-review
Open Access -
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 journal › Article › peer-review
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 journal › Article › peer-review
Open Access -
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 journal › Article › peer-review
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 journal › Article › peer-review
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 journal › Article › peer-review
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 journal › Article › peer-review
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 journal › Article › peer-review
Open Access -
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 journal › Article › peer-review
Open Access -
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 journal › Article › peer-review
Open Access -
Entity set search of scientific literature: An unsupervised ranking approach
Shen, J., Xiao, J., He, X., Shang, J., Sinha, S. & Han, J., Jun 27 2018, 41st International ACM SIGIR Conference on Research and Development in Information Retrieval, SIGIR 2018. Association for Computing Machinery, p. 565-574 10 p. (41st International ACM SIGIR Conference on Research and Development in Information Retrieval, SIGIR 2018).Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
Open Access -
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 journal › Article › peer-review
Open Access -
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 journal › Article › peer-review
Open Access -
SigMat: A classification scheme for gene signature matching
Xiao, J., Blatti, C. & Sinha, S., Jul 1 2018, In: Bioinformatics. 34, 13, p. i547-i554Research output: Contribution to journal › Article › peer-review
Open Access -
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 journal › Article › peer-review
Open Access -
Automated prostate tissue referencing for cancer detection and diagnosis
Sinha, S. (Inventor), Kwak, J. T. (Inventor) & Bhargava, R. (Inventor), Oct 3 2017, U.S. Patent No. 9779283Research output: Patent
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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 journal › Article › peer-review
Open Access -
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 journal › Article › peer-review
Open Access -
Life-iNet: A structured network-based knowledge exploration and analytics system for life sciences
Ren, X., Shen, J., Qu, M., Wang, X., Wu, Z., Zhu, Q., Jiang, M., Tao, F., Sinha, S., Liem, D., Ping, P., Weinshilboum, R. & Han, J., 2017, ACL 2017 - 55th Annual Meeting of the Association for Computational Linguistics, Proceedings of System Demonstrations. Association for Computational Linguistics (ACL), p. 55-60 6 p. (ACL 2017 - 55th Annual Meeting of the Association for Computational Linguistics, Proceedings of System Demonstrations).Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
Open Access -
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 journal › Article › peer-review
Open Access -
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 journal › Article › peer-review
Open Access -
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 journal › Article › peer-review
Open Access -
2016
Automated prostate tissue referencing for cancer detection and diagnosis
Sinha, S. (Inventor), Kwak, J. T. (Inventor) & Bhargava, R. (Inventor), Jan 5 2016, U.S. Patent No. 9230063Research output: Patent
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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 journal › Article › peer-review
Open Access -
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 journal › Article › peer-review
Open Access -
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 journal › Article › peer-review
Open Access