1.Juarez R, Jiang Y, Tremblay M, Shao Q, Link J, Yang Z. LassoHTP: A High-Throughput Computational Tool for Lasso Peptide Structure Construction and Modeling. J Chem Inf Model. 2023;63(2):522–530. PMID: 36594886 Reference Link
1.Pisano T, Hoag A, Dhanerawala Z, Guariglia S, Jung C, Boele H-J, Seagraves K, Verpeut J, Wang S. Automated high-throughput mouse transsynaptic viral tracing using iDISCO+ tissue clearing, light-sheet microscopy, and BrainPipe. STAR Protoc. 2022;3(2):101289. PMCID: PMC9038781 Reference Link
1.Covington B, Seyedsayamdost M. MetEx, a Metabolomics Explorer Application for Natural Product Discovery. ACS Chem Biol. 2021;16(12):2825–2833. PMCID: PMC9090437 Reference Link
1.Zhou J, Troyanskaya O. An analytical framework for interpretable and generalizable single-cell data analysis. Nat Methods. 2021;18(11):1317–1321. PMCID: PMC8959118 Reference Link
1.Sohrabi S, Moore R, Murphy C. CeAid: a smartphone application for logging and plotting Caenorhabditis elegans assays. G3 (Bethesda). 2021;11(10). PMCID: PMC8473968 Reference Link
1.Johnson A, Stadlmeier M, Wühr M. TMTpro Complementary Ion Quantification Increases Plexing and Sensitivity for Accurate Multiplexed Proteomics at the MS2 Level. J Proteome Res. 2021;20(6):3043–3052. PMCID: PMC8330405 Reference Link
1.Bass A, Storey J. The optimal discovery procedure for significance analysis of general gene expression studies. Bioinformatics. 2021;37(3):367–374. PMCID: PMC8058779 Reference Link
1.Giovannucci A, Friedrich J, Gunn P, Kalfon J, Brown B, Koay S, Taxidis J, Najafi F, Gauthier J, Zhou P, Khakh B, Tank D, Chklovskii D, Pnevmatikakis E. CaImAn an open source tool for scalable calcium imaging data analysis. Elife. 2019;8. PMCID: PMC6342523 Reference Link
1.Chen K, Cofer E, Zhou J, Troyanskaya O. Selene: a PyTorch-based deep learning library for sequence data. Nat Methods. 2019;16(4):315–318. PMCID: PMC7148117 Reference Link
1.Wong A, Krishnan A, Troyanskaya O. GIANT 2.0: genome-scale integrated analysis of gene networks in tissues. Nucleic Acids Res. 2018;46(W1):W65-W70. PMCID: PMC6030827 Reference Link
1.Przytycki P, Singh M. Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes. Genome Med. 2017;9(1):79. PMCID: PMC5574113 Reference Link
1.Hao W, Song M, Storey J. Probabilistic models of genetic variation in structured populations applied to global human studies. Bioinformatics. 2016;32(5):713–21. PMCID: PMC4795615 Reference Link
1.Ochoa A, Singh M. Domain prediction with probabilistic directional context. Bioinformatics. 2017;33(16):2471–2478. PMCID: PMC5870623 Reference Link
1.Roberts A, Wong A, Fisk I, Troyanskaya O. GIANT API: an application programming interface for functional genomics. Nucleic Acids Res. 2016;44(W1):W587–92. PMCID: PMC4987882 Reference Link
1.Holt M, David Y, Pollock S, Tang Z, Jeon J, Kim J, Roeder R, Muir T. Identification of a functional hotspot on ubiquitin required for stimulation of methyltransferase activity on chromatin. Proc Natl Acad Sci U S A. 2015;112(33):10365–70. PMCID: PMC4547310 Reference Link
1.Goya J, Wong A, Yao V, Krishnan A, Homilius M, Troyanskaya O. FNTM: a server for predicting functional networks of tissues in mouse. Nucleic Acids Res. 2015;43(W1):W182–7. PMCID: PMC4489275 Reference Link
1.Chung N, Storey J. Statistical significance of variables driving systematic variation in high-dimensional data. Bioinformatics. 2015;31(4):545–54. PMCID: PMC4325543 Reference Link
1.Robinson D, Storey J. subSeq: determining appropriate sequencing depth through efficient read subsampling. Bioinformatics. 2014;30(23):3424–6. PMCID: PMC4296149 Reference Link
1.Ghersi D, Singh M. molBLOCKS: decomposing small molecule sets and uncovering enriched fragments. Bioinformatics. 2014;30(14):2081–3. PMCID: PMC4080744 Reference Link
1.Levario T, Zhao C, Rouse T, Shvartsman S, Lu H. An integrated platform for large-scale data collection and precise perturbation of live Drosophila embryos. Sci Rep. 2016;6:21366. PMCID: PMC4750044 Reference Link