• 2025
  Kalfon J, Samaran J, Peyré G, Cantini L, scPRINT: pre-training on 50 million cells allows robust gene network predictions., Nat Commun 2025 Apr; 16(1): 3607.
• 2023
  Harada T, Perez MW, Kalfon J, Braes FD, Batley R, Eagle K, Nabet B, Leifer B, Kruell J, Paralkar VR, Stegmaier K, Koehler AN, Orkin SH, Pimkin M, Rapid-kinetics degron benchmarking reveals off-target activities and mixed agonism-antagonism of MYB inhibitors., bioRxiv 2023 Apr; (): .
• 2023
  Sharifnia T, Wawer MJ, Goodale A, Lee Y, Kazachkova M, Dempster JM, Muller S, Levy J, Freed DM, Sommer J, Kalfon J, Vazquez F, Hahn WC, Root DE, Clemons PA, Schreiber SL, Mapping the landscape of genetic dependencies in chordoma., Nat Commun 2023 Apr; 14(1): 1933.
• 2023
  Harada T, Kalfon J, Perez MW, Eagle K, Braes FD, Batley R, Heshmati Y, Ferrucio JX, Ewers J, Mehta S, Kossenkov A, Ellegast JM, Bowker A, Wickramasinghe J, Nabet B, Paralkar VR, Dharia NV, Stegmaier K, Orkin SH, Pimkin M, Leukemia core transcriptional circuitry is a sparsely interconnected hierarchy stabilized by incoherent feed-forward loops., bioRxiv 2023 Mar; (): .
• 2022
  Eagle K, Harada T, Kalfon J, Perez MW, Heshmati Y, Ewers J, Koren JV, Dempster JM, Kugener G, Paralkar VR, Lin CY, Dharia NV, Stegmaier K, Orkin SH, Pimkin M, Transcriptional Plasticity Drives Leukemia Immune Escape., Blood Cancer Discov 2022 Sep; 3(5): 394-409.
• 2022
  Morris V, Wang D, Li Z, Marion W, Hughes T, Sousa P, Harada T, Sui SH, Naumenko S, Kalfon J, Sensharma P, Falchetti M, Vinicius da Silva R, Candelli T, Schneider P, Margaritis T, Holstege FCP, Pikman Y, Harris M, Stam RW, Orkin SH, Koehler AN, Shalek AK, North TE, Pimkin M, Daley GQ, Lummertz da Rocha E, Rowe RG, Hypoxic, glycolytic metabolism is a vulnerability of B-acute lymphoblastic leukemia-initiating cells., Cell Rep 2022 Apr; 39(4): 110752.
• 2022
  Harada T, Heshmati Y, Kalfon J, Perez MW, Xavier Ferrucio J, Ewers J, Hubbell Engler B, Kossenkov A, Ellegast JM, Yi JS, Bowker A, Zhu Q, Eagle K, Liu T, Kai Y, Dempster JM, Kugener G, Wickramasinghe J, Herbert ZT, Li CH, Vrabič Koren J, Weinstock DM, Paralkar VR, Nabet B, Lin CY, Dharia NV, Stegmaier K, Orkin SH, Pimkin M, A distinct core regulatory module enforces oncogene expression in KMT2A-rearranged leukemia., Genes Dev 2022 Mar; 36(5-6): 368-389.
• 2021
  Neggers JE, Paolella BR, Asfaw A, Rothberg MV, Skipper TA, Yang A, Kalekar RL, Krill-Burger JM, Dharia NV, Kugener G, Kalfon J, Yuan C, Dumont N, Gonzalez A, Abdusamad M, Li YY, Spurr LF, Wu WW, Durbin AD, Wolpin BM, Piccioni F, Root DE, Boehm JS, Cherniack AD, Tsherniak A, Hong AL, Hahn WC, Stegmaier K, Golub TR, Vazquez F, Aguirre AJ, Synthetic Lethal Interaction between the ESCRT Paralog Enzymes VPS4A and VPS4B in Cancers Harboring Loss of Chromosome 18q or 16q., Cell Rep 2021 Jul; 36(2): 109367.
• 2020
  Neggers JE, Paolella BR, Asfaw A, Rothberg MV, Skipper TA, Yang A, Kalekar RL, Krill-Burger JM, Dharia NV, Kugener G, Kalfon J, Yuan C, Dumont N, Gonzalez A, Abdusamad M, Li YY, Spurr LF, Wu WW, Durbin AD, Wolpin BM, Piccioni F, Root DE, Boehm JS, Cherniack AD, Tsherniak A, Hong AL, Hahn WC, Stegmaier K, Golub TR, Vazquez F, Aguirre AJ, Synthetic Lethal Interaction between the ESCRT Paralog Enzymes VPS4A and VPS4B in Cancers Harboring Loss of Chromosome 18q or 16q., Cell Rep 2020 Dec; 33(11): 108493.
• 2020
  van Wietmarschen N, Sridharan S, Nathan WJ, Tubbs A, Chan EM, Callen E, Wu W, Belinky F, Tripathi V, Wong N, Foster K, Noorbakhsh J, Garimella K, Cruz-Migoni A, Sommers JA, Huang Y, Borah AA, Smith JT, Kalfon J, Kesten N, Fugger K, Walker RL, Dolzhenko E, Eberle MA, Hayward BE, Usdin K, Freudenreich CH, Brosh RM, West SC, McHugh PJ, Meltzer PS, Bass AJ, Nussenzweig A, Repeat expansions confer WRN dependence in microsatellite-unstable cancers., Nature 2020 Oct; 586(7828): 292-298.
• 2020
  Deng Y, de Lima Hedayioglu F, Kalfon J, Chu D, von der Haar T, Hidden patterns of codon usage bias across kingdoms., J R Soc Interface 2020 Feb; 17(163): 20190819.
• 2019
  Giovannucci A, Friedrich J, Gunn P, Kalfon J, Brown BL, Koay SA, Taxidis J, Najafi F, Gauthier JL, Zhou P, Khakh BS, Tank DW, Chklovskii DB, Pnevmatikakis EA, CaImAn an open source tool for scalable calcium imaging data analysis., Elife 2019 Jan; 8(): .