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Schüpbach T. The Complexities and Unexpected Insights of Developmental Genetic Analysis. Curr Top Dev Biol. 2016 ;117:319-30.
Gaska JM, Parsons L, Balev M, Cirincione A, Wang W, Schwartz RE, et al. Conservation of cell-intrinsic immune responses in diverse nonhuman primate species. Life Sci Alliance. 2019 ;2(5).
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Wong AK, Sealfon RSG, Theesfeld CL, Troyanskaya OG. Decoding disease: from genomes to networks to phenotypes. Nat Rev Genet. 2021 ;22(12):774-790.
Keenan SE, Avdeeva M, Yang L, Alber DS, Wieschaus EF, Shvartsman SY. Dynamics of endoderm specification. Proc Natl Acad Sci U S A. 2022 ;119(15):e2112892119.
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Posfai E, Schell JPaul, Janiszewski A, Rovic I, Murray A, Bradshaw B, et al. Evaluating totipotency using criteria of increasing stringency. Nat Cell Biol. 2021 ;23(1):49-60.
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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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Pyrowolakis G, Veikkolainen V, Yakoby N, Shvartsman SY. Gene regulation during eggshell patterning. Proc Natl Acad Sci U S A. 2017 ;114(23):5808-5813.
Adamson B, Smogorzewska A, Sigoillot FD, King RW, Elledge SJ. A genome-wide homologous recombination screen identifies the RNA-binding protein RBMX as a component of the DNA-damage response. Nat Cell Biol. 2012 ;14(3):318-28.
Krishnan A, Zhang R, Yao V, Theesfeld CL, Wong AK, Tadych A, et al. Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder. Nat Neurosci. 2016 ;19(11):1454-1462.
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.
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.
Costanzo M, VanderSluis B, Koch EN, Baryshnikova A, Pons C, Tan G, et al. A global genetic interaction network maps a wiring diagram of cellular function. Science. 2016 ;353(6306).
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Gorenshteyn D, Zaslavsky E, Fribourg M, Park CY, Wong AK, Tadych A, et al. Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases. Immunity. 2015 ;43(3):605-14.
Lee Y-S, Wong AK, Tadych A, Hartmann BM, Park CY, DeJesus VA, et al. Interpretation of an individual functional genomics experiment guided by massive public data. Nat Methods. 2018 ;15(12):1049-1052.
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Ledo JHenrique, Zhang R, Mesin L, Mourão-Sá D, Azevedo EP, Troyanskaya OG, et al.. Lack of a site-specific phosphorylation of Presenilin 1 disrupts microglial gene networks and progenitors during development. PLoS One. 2020 ;15(8):e0237773.
Seyboldt R, Lavoie J, Henry A, Vanaret J, Petkova MD, Gregor T, et al. Latent space of a small genetic network: Geometry of dynamics and information. Proc Natl Acad Sci U S A. 2022 ;119(26):e2113651119.
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Horlbeck MA, Xu A, Wang M, Bennett NK, Park CY, Bogdanoff D, et al. Mapping the Genetic Landscape of Human Cells. Cell. 2018 ;174(4):953-967.e22.
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Hristov BH, Singh M. Network-Based Coverage of Mutational Profiles Reveals Cancer Genes. Cell Syst. 2017 ;5(3):221-229.e4.
Chacha PPaul, Horie R, Kusakabe TG, Sasakura Y, Singh M, Horie T, et al. Neuronal identities derived by misexpression of the POU IV sensory determinant in a protovertebrate. Proc Natl Acad Sci U S A. 2022 ;119(4).
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Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. Optimal Decoding of Cellular Identities in a Genetic Network. Cell. 2019 ;176(4):844-855.e15.
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Nadimpalli S, Persikov AV, Singh M. Pervasive variation of transcription factor orthologs contributes to regulatory network evolution. PLoS Genet. 2015 ;11(3):e1005011.
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Menon R, Otto EA, Sealfon R, Nair V, Wong AK, Theesfeld CL, et al. SARS-CoV-2 receptor networks in diabetic and COVID-19-associated kidney disease. Kidney Int. 2020 ;98(6):1502-1518.
Roussarie J-P, Yao V, Rodriguez-Rodriguez P, Oughtred R, Rust J, Plautz Z, et al. Selective Neuronal Vulnerability in Alzheimer's Disease: A Network-Based Analysis. Neuron. 2020 ;107(5):821-835.e12.
Ruf-Zamojski F, Zhang Z, Zamojski M, Smith GR, Mendelev N, Liu H, et al. Single nucleus multi-omics regulatory landscape of the murine pituitary. Nat Commun. 2021 ;12(1):2677.
Ravindran PT, McFann S, Thornton RH, Toettcher JE. A synthetic gene circuit for imaging-free detection of signaling pulses. Cell Syst. 2022 ;13(2):131-142.e13.