Seyboldt R, Lavoie J, Henry A, Vanaret J, Petkova M, Gregor T, François P. Latent space of a small genetic network: Geometry of dynamics and information. Proc Natl Acad Sci U S A. 2022;119(26):e2113651119. PMCID: PMC9245618

McNamara H, Ramm B, Toettcher J. Synthetic developmental biology: New tools to deconstruct and rebuild developmental systems. Semin Cell Dev Biol. 2023;141:33–42. PMID: 35484026

Keenan S, Avdeeva M, Yang L, Alber D, Wieschaus E, Shvartsman S. Dynamics of endoderm specification. Proc Natl Acad Sci U S A. 2022;119(15):e2112892119. PMCID: PMC9169638

Feigin C, Li S, Moreno J, Mallarino R. The GRN concept as a guide for evolutionary developmental biology. J Exp Zool B Mol Dev Evol. 2023;340(2):92–104. PMCID: PMC9515236

Chacha P, Horie R, Kusakabe T, Sasakura Y, Singh M, Horie T, Levine M. Neuronal identities derived by misexpression of the POU IV sensory determinant in a protovertebrate. Proc Natl Acad Sci U S A. 2022;119(4). PMCID: PMC8794889

Bauer M, Petkova M, Gregor T, Wieschaus E, Bialek W. Trading bits in the readout from a genetic network. Proc Natl Acad Sci U S A. 2021;118(46). PMCID: PMC8609648

Ravindran P, McFann S, Thornton R, Toettcher J. A synthetic gene circuit for imaging-free detection of signaling pulses. Cell Syst. 2022;13(2):131–142.e13. PMCID: PMC8857027

Wong A, Sealfon R, Theesfeld C, Troyanskaya O. Decoding disease: from genomes to networks to phenotypes. Nat Rev Genet. 2021;22(12):774–790. PMCID: 6786975

Ruf-Zamojski F, Zhang Z, Zamojski M, Smith G, Mendelev N, Liu H, Nudelman G, Moriwaki M, Pincas H, Castanon R, Nair V, Seenarine N, Amper M, Zhou X, Ongaro L, Toufaily C, Schang G, Nery J, Bartlett A, Aldridge A, Jain N, Childs G, Troyanskaya O, Ecker J, Turgeon J, Welt C, Bernard D, Sealfon S. Single nucleus multi-omics regulatory landscape of the murine pituitary. Nat Commun. 2021;12(1):2677. PMCID: PMC8113460

Chen X, Zhou J, Zhang R, Wong A, Park C, Theesfeld C, Troyanskaya O. Tissue-specific enhancer functional networks for associating distal regulatory regions to disease. Cell Syst. 2021;12(4):353–362.e6. PMID: 33689683

Posfai E, Schell J, Janiszewski A, Rovic I, Murray A, Bradshaw B, Yamakawa T, Pardon T, Bakkali M, Talon I, De Geest N, Kumar P, To S, Petropoulos S, Jurisicova A, Pasque V, Lanner F, Rossant J. Evaluating totipotency using criteria of increasing stringency. Nat Cell Biol. 2021;23(1):49–60. PMCID: 2846056

Menon R, Otto E, Sealfon R, Nair V, Wong A, Theesfeld C, Chen X, Wang Y, Boppana A, Luo J, Yang Y, Kasson P, Schaub J, Berthier C, Eddy S, Lienczewski C, Godfrey B, Dagenais S, Sohaney R, Hartman J, Fermin D, Subramanian L, Looker H, Harder J, Mariani L, Hodgin J, Sexton J, Wobus C, Naik A, Nelson R, Troyanskaya O, Kretzler M. SARS-CoV-2 receptor networks in diabetic and COVID-19-associated kidney disease. Kidney Int. 2020;98(6):1502–1518. PMCID: PMC7543950

Ledo J, Zhang R, Mesin L, Mourão-Sá D, Azevedo E, Troyanskaya O, Bustos V, Greengard P. Lack of a site-specific phosphorylation of Presenilin 1 disrupts microglial gene networks and progenitors during development. PLoS One. 2020;15(8):e0237773. PMCID: PMC7444478

Hristov B, Chazelle B, Singh M. uKIN Combines New and Prior Information with Guided Network Propagation to Accurately Identify Disease Genes. Cell Syst. 2020;10(6):470–479.e3. PMCID: PMC7821437

Roussarie J-P, Yao V, Rodriguez-Rodriguez P, Oughtred R, Rust J, Plautz Z, Kasturia S, Albornoz C, Wang W, Schmidt E, Dannenfelser R, Tadych A, Brichta L, Barnea-Cramer A, Heintz N, Hof P, Heiman M, Dolinski K, Flajolet M, Troyanskaya O, Greengard P. Selective Neuronal Vulnerability in Alzheimer’s Disease: A Network-Based Analysis. Neuron. 2020;107(5):821–835.e12. PMCID: PMC7580783

Gaska J, Parsons L, Balev M, Cirincione A, Wang W, Schwartz R, Ploss A. Conservation of cell-intrinsic immune responses in diverse nonhuman primate species. Life Sci Alliance. 2019;2(5). PMCID: PMC6814850

Lee Y-S, Wong A, Tadych A, Hartmann B, Park C, DeJesus V, Ramos I, Zaslavsky E, Sealfon S, Troyanskaya O. Interpretation of an individual functional genomics experiment guided by massive public data. Nat Methods. 2018;15(12):1049–1052. PMCID: PMC6941785

Petkova M, Tkačik G, Bialek W, Wieschaus E, Gregor T. Optimal Decoding of Cellular Identities in a Genetic Network. Cell. 2019;176(4):844–855.e15. PMCID: PMC6526179

Adamson B, Smogorzewska A, Sigoillot F, King R, Elledge S. 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. PMCID: PMC3290715

Horlbeck M, Xu A, Wang M, Bennett N, Park C, Bogdanoff D, Adamson B, Chow E, Kampmann M, Peterson T, Nakamura K, Fischbach M, Weissman J, Gilbert L. Mapping the Genetic Landscape of Human Cells. Cell. 2018;174(4):953–967.e22. PMCID: PMC6426455

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

Aedo S, Gelderman G, Brynildsen M. Tackling host-circuit give and take. Nat Microbiol. 2017;2(12):1584–1585. PMID: 29176699

Hristov B, Singh M. Network-Based Coverage of Mutational Profiles Reveals Cancer Genes. Cell Syst. 2017;5(3):221–229.e4. PMCID: PMC5997485

Pyrowolakis G, Veikkolainen V, Yakoby N, Shvartsman S. Gene regulation during eggshell patterning. Proc Natl Acad Sci U S A. 2017;114(23):5808–5813. PMCID: PMC5468638

Rogers W, Goyal Y, Yamaya K, Shvartsman S, Levine M. Uncoupling neurogenic gene networks in the embryo. Genes Dev. 2017;31(7):634–638. PMCID: PMC5411704

Schüpbach T. The Complexities and Unexpected Insights of Developmental Genetic Analysis. Curr Top Dev Biol. 2016;117:319–30. PMID: 26969986

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

Costanzo M, VanderSluis B, Koch E, Baryshnikova A, Pons C, Tan G, Wang W, Usaj M, Hanchard J, Lee S, Pelechano V, Styles E, Billmann M, van Leeuwen J, van Dyk N, Lin Z-Y, Kuzmin E, Nelson J, Piotrowski J, Srikumar T, Bahr S, Chen Y, Deshpande R, Kurat C, Li S, Li Z, Usaj M, Okada H, Pascoe N, San Luis B-J, Sharifpoor S, Shuteriqi E, Simpkins S, Snider J, Suresh H, Tan Y, Zhu H, Malod-Dognin N, Janjic V, Przulj N, Troyanskaya O, Stagljar I, Xia T, Ohya Y, Gingras A-C, Raught B, Boutros M, Steinmetz L, Moore C, Rosebrock A, Caudy A, Myers C, Andrews B, Boone C. A global genetic interaction network maps a wiring diagram of cellular function. Science. 2016;353(6306). PMCID: PMC5661885

Krishnan A, Zhang R, Yao V, Theesfeld C, Wong A, Tadych A, Volfovsky N, Packer A, Lash A, Troyanskaya O. Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder. Nat Neurosci. 2016;19(11):1454–1462. PMCID: PMC5803797

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

Gorenshteyn D, Zaslavsky E, Fribourg M, Park C, Wong A, Tadych A, Hartmann B, Albrecht R, García-Sastre A, Kleinstein S, Troyanskaya O, Sealfon S. Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases. Immunity. 2015;43(3):605–14. PMCID: PMC4753773

Nadimpalli S, Persikov A, Singh M. Pervasive variation of transcription factor orthologs contributes to regulatory network evolution. PLoS Genet. 2015;11(3):e1005011. PMCID: PMC4351887