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Bass AJ, Storey JD. The optimal discovery procedure for significance analysis of general gene expression studies. Bioinformatics. 2021 ;37(3):367-374.
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Chen KM, Cofer EM, Zhou J, Troyanskaya OG. Selene: a PyTorch-based deep learning library for sequence data. Nat Methods. 2019 ;16(4):315-318.
Chung NChristophe, Storey JD. Statistical significance of variables driving systematic variation in high-dimensional data. Bioinformatics. 2015 ;31(4):545-54.
Covington BC, Seyedsayamdost MR. MetEx, a Metabolomics Explorer Application for Natural Product Discovery. ACS Chem Biol. 2021 ;16(12):2825-2833.
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Ghersi D, Singh M. molBLOCKS: decomposing small molecule sets and uncovering enriched fragments. Bioinformatics. 2014 ;30(14):2081-3.
Giovannucci A, Friedrich J, Gunn P, Kalfon J, Brown BL, Koay SAnn, et al. CaImAn an open source tool for scalable calcium imaging data analysis. Elife. 2019 ;8.
Goya J, Wong AK, Yao V, Krishnan A, Homilius M, Troyanskaya OG. FNTM: a server for predicting functional networks of tissues in mouse. Nucleic Acids Res. 2015 ;43(W1):W182-7.
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Hao W, Song M, Storey JD. Probabilistic models of genetic variation in structured populations applied to global human studies. Bioinformatics. 2016 ;32(5):713-21.
Holt MT, David Y, Pollock S, Tang Z, Jeon J, Kim J, et al. 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.
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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.
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Levario TJ, Zhao C, Rouse T, Shvartsman SY, Lu H. An integrated platform for large-scale data collection and precise perturbation of live Drosophila embryos. Sci Rep. 2016 ;6:21366.
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Ochoa A, Singh M. Domain prediction with probabilistic directional context. Bioinformatics. 2017 ;33(16):2471-2478.
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Pisano TJ, Hoag AT, Dhanerawala ZM, Guariglia SR, Jung C, Boele H-J, et al. Automated high-throughput mouse transsynaptic viral tracing using iDISCO+ tissue clearing, light-sheet microscopy, and BrainPipe. STAR Protoc. 2022 ;3(2):101289.
Przytycki PF, Singh M. Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes. Genome Med. 2017 ;9(1):79.
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Roberts AM, Wong AK, Fisk I, Troyanskaya OG. GIANT API: an application programming interface for functional genomics. Nucleic Acids Res. 2016 ;44(W1):W587-92.
Robinson DG, Storey JD. subSeq: determining appropriate sequencing depth through efficient read subsampling. Bioinformatics. 2014 ;30(23):3424-6.
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Sohrabi S, Moore RS, Murphy CT. CeAid: a smartphone application for logging and plotting Caenorhabditis elegans assays. G3 (Bethesda). 2021 ;11(10).
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Wong AK, Krishnan A, Troyanskaya OG. GIANT 2.0: genome-scale integrated analysis of gene networks in tissues. Nucleic Acids Res. 2018 ;46(W1):W65-W70.
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Zhou J, Troyanskaya OG. An analytical framework for interpretable and generalizable single-cell data analysis. Nat Methods. 2021 ;18(11):1317-1321.