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Gene Regulatory Networks

  • 1.
    Feigin C, Li S, Moreno J, Mallarino R. The GRN concept as a guide for evolutionary developmental biology. Journal of experimental zoology. Part B, Molecular and developmental evolution. 2023;340(2):92–104. PMCID: PMC9515236
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  • 1.
    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
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  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    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.
    Aedo S, Gelderman G, Brynildsen M. Tackling host-circuit give and take. Nat Microbiol. 2017;2(12):1584–1585. PMID: 29176699
    Reference Link
  • 1.
    Hristov B, Singh M. Network-Based Coverage of Mutational Profiles Reveals Cancer Genes. Cell Syst. 2017;5(3):221–229.e4. PMCID: PMC5997485
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    Schüpbach T. The Complexities and Unexpected Insights of Developmental Genetic Analysis. Curr Top Dev Biol. 2016;117:319–30. PMID: 26969986
    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.
    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
    Reference Link
  • 1.
    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
    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.
    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
    Reference Link
  • 1.
    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
    Reference Link

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