Repeat expansions confer WRN dependence in microsatellite-unstable cancers
van Wietmarschen, Niek, Sridharan, Sriram, Nathan, William J., Tubbs, Anthony, Chan, Edmond M., Callen, Elsa, Wu, Wei, Belinky, Frida, Tripathi, Veenu, Wong, Nancy, Foster, Kyla, Noorbakhsh, Javad, Garimella, Kiran, Cruz-Migoni, Abimael, Sommers, Joshua A., Huang, Yongqing, Borah, Ashir A., Smith, Jonathan T., Kalfon, Jeremie, Kesten, Nikolas, Fugger, Kasper, Walker, Robert L., Dolzhenko, Egor, Eberle, Michael A., Hayward, Bruce E., Usdin, Karen, Freudenreich, Catherine H., Brosh, Robert M., West, Stephen C., McHugh, Peter J., Meltzer, Paul S., Bass, Adam J., Nussenzweig, André
Published in Nature (London) (08.10.2020)
Published in Nature (London) (08.10.2020)
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Journal Article
Mapping the landscape of genetic dependencies in chordoma
Sharifnia, Tanaz, Wawer, Mathias J., Goodale, Amy, Lee, Yenarae, Kazachkova, Mariya, Dempster, Joshua M., Muller, Sandrine, Levy, Joan, Freed, Daniel M., Sommer, Josh, Kalfon, Jérémie, Vazquez, Francisca, Hahn, William C., Root, David E., Clemons, Paul A., Schreiber, Stuart L.
Published in Nature communications (06.04.2023)
Published in Nature communications (06.04.2023)
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Journal Article
Synthetic Lethal Interaction between the ESCRT Paralog Enzymes VPS4A and VPS4B in Cancers Harboring Loss of Chromosome 18q or 16q
Neggers, Jasper E., Paolella, Brenton R., Asfaw, Adhana, Rothberg, Michael V., Skipper, Thomas A., Yang, Annan, Kalekar, Radha L., Krill-Burger, John M., Dharia, Neekesh V., Kugener, Guillaume, Kalfon, Jérémie, Yuan, Chen, Dumont, Nancy, Gonzalez, Alfredo, Abdusamad, Mai, Li, Yvonne Y., Spurr, Liam F., Wu, Westley W., Durbin, Adam D., Wolpin, Brian M., Piccioni, Federica, Root, David E., Boehm, Jesse S., Cherniack, Andrew D., Tsherniak, Aviad, Hong, Andrew L., Hahn, William C., Stegmaier, Kimberly, Golub, Todd R., Vazquez, Francisca, Aguirre, Andrew J.
Published in Cell reports (Cambridge) (15.12.2020)
Published in Cell reports (Cambridge) (15.12.2020)
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Journal Article
Germline variation contributes to false negatives in CRISPR-based experiments with varying burden across ancestries
Misek, Sean A., Fultineer, Aaron, Kalfon, Jeremie, Noorbakhsh, Javad, Boyle, Isabella, Roy, Priyanka, Dempster, Joshua, Petronio, Lia, Huang, Katherine, Saadat, Alham, Green, Thomas, Brown, Adam, Doench, John G., Root, David E., McFarland, James M., Beroukhim, Rameen, Boehm, Jesse S.
Published in Nature communications (07.06.2024)
Published in Nature communications (07.06.2024)
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A distinct core regulatory module enforces oncogene expression in KMT2A-rearranged leukemia
Harada, Taku, Heshmati, Yaser, Kalfon, Jérémie, Perez, Monika W, Xavier Ferrucio, Juliana, Ewers, Jazmin, Hubbell Engler, Benjamin, Kossenkov, Andrew, Ellegast, Jana M, Yi, Joanna S, Bowker, Allyson, Zhu, Qian, Eagle, Kenneth, Liu, Tianxin, Kai, Yan, Dempster, Joshua M, Kugener, Guillaume, Wickramasinghe, Jayamanna, Herbert, Zachary T, Li, Charles H, Vrabič Koren, Jošt, Weinstock, David M, Paralkar, Vikram R, Nabet, Behnam, Lin, Charles Y, Dharia, Neekesh V, Stegmaier, Kimberly, Orkin, Stuart H, Pimkin, Maxim
Published in Genes & development (01.03.2022)
Published in Genes & development (01.03.2022)
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Hypoxic, glycolytic metabolism is a vulnerability of B-acute lymphoblastic leukemia-initiating cells
Morris, Vivian, Wang, Dahai, Li, Zhiheng, Marion, William, Hughes, Travis, Sousa, Patricia, Harada, Taku, Sui, Shannan Ho, Naumenko, Sergey, Kalfon, Jérémie, Sensharma, Prerana, Falchetti, Marcelo, Vinicius da Silva, Renan, Candelli, Tito, Schneider, Pauline, Margaritis, Thanasis, Holstege, Frank C.P., Pikman, Yana, Harris, Marian, Stam, Ronald W., Orkin, Stuart H., Koehler, Angela N., Shalek, Alex K., North, Trista E., Pimkin, Maxim, Daley, George Q., Lummertz da Rocha, Edroaldo, Rowe, R. Grant
Published in Cell reports (Cambridge) (26.04.2022)
Published in Cell reports (Cambridge) (26.04.2022)
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Journal Article
Synthetic Lethal Interaction between the ESCRT Paralog Enzymes VPS4A and VPS4B in Cancers Harboring Loss of Chromosome 18q or 16q
Neggers, Jasper E., Paolella, Brenton R., Asfaw, Adhana, Rothberg, Michael V., Skipper, Thomas A., Yang, Annan, Kalekar, Radha L., Krill-Burger, John M., Dharia, Neekesh V., Kugener, Guillaume, Kalfon, Jérémie, Yuan, Chen, Dumont, Nancy, Gonzalez, Alfredo, Abdusamad, Mai, Li, Yvonne Y., Spurr, Liam F., Wu, Westley W., Durbin, Adam D., Wolpin, Brian M., Piccioni, Federica, Root, David E., Boehm, Jesse S., Cherniack, Andrew D., Tsherniak, Aviad, Hong, Andrew L., Hahn, William C., Stegmaier, Kimberly, Golub, Todd R., Vazquez, Francisca, Aguirre, Andrew J.
Published in Cell reports (Cambridge) (13.07.2021)
Published in Cell reports (Cambridge) (13.07.2021)
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Journal Article
Transcriptional Plasticity Drives Leukemia Immune Escape
Eagle, Kenneth, Harada, Taku, Kalfon, Jérémie, Perez, Monika W, Heshmati, Yaser, Ewers, Jazmin, Koren, Jošt Vrabič, Dempster, Joshua M, Kugener, Guillaume, Paralkar, Vikram R, Lin, Charles Y, Dharia, Neekesh V, Stegmaier, Kimberly, Orkin, Stuart H, Pimkin, Maxim
Published in Blood cancer discovery (06.09.2022)
Published in Blood cancer discovery (06.09.2022)
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Journal Article
CaImAn an open source tool for scalable calcium imaging data analysis
Giovannucci, Andrea, Friedrich, Johannes, Gunn, Pat, Kalfon, Jérémie, Brown, Brandon L, Koay, Sue Ann, Taxidis, Jiannis, Najafi, Farzaneh, Gauthier, Jeffrey L, Zhou, Pengcheng, Khakh, Baljit S, Tank, David W, Chklovskii, Dmitri B, Pnevmatikakis, Eftychios A
Published in eLife (17.01.2019)
Published in eLife (17.01.2019)
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Hidden patterns of codon usage bias across kingdoms
Deng, Yun, de Lima Hedayioglu, Fabio, Kalfon, Jeremie, Chu, Dominique, von der Haar, Tobias
Published in Journal of the Royal Society interface (01.02.2020)
Published in Journal of the Royal Society interface (01.02.2020)
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Journal Article
Transcriptional Immunoediting of AML Cells after Allogeneic Hematopoietic Stem Cell Transplantation
Eagle, Kenneth, Harada, Taku, Kalfon, Jeremie, Perez, Monika, Heshmati, Yaser, Ewers, Jazmin, Stegmaier, Kimberly, Orkin, Stuart H., Pimkin, Maxim
Published in Blood (23.11.2021)
Published in Blood (23.11.2021)
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Journal Article
Abstract NG01: Synthetic lethal interaction between the ESCRT paralog enzymes VPS4A and VPS4B in cancers harboring loss of chromosome 18q or 16q
Neggers, Jasper E., Paolella, Brenton, Asfaw, Adhana, Rothberg, Michael V., Skipper, Tom A., Kalekar, Radha, Burger, Michael, Dharia, Neekesh, Kugener, Guillaume, Kalfon, Jeremie, Dumont, Nancy, Li, Yvonne, Spurr, Liam, Yang, Annan, Wu, Wenbo, Durbin, AndrewAdam, Wolpin, Brian M., Root, David E., Boehm, Jesse, Cherniack, Andrew D., Tsherniak, Aviad, Hong, Andrew L., Hahn, William C., Stegmaier, Kimberly, Golub, Todd, Vazquez, Francisca, Aguirre, Andrew J.
Published in Cancer research (Chicago, Ill.) (01.07.2021)
Published in Cancer research (Chicago, Ill.) (01.07.2021)
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Abstract 2710: Associations between structural variant signatures and drug sensitivity in cell lines
Dalin, Simona, Dubois, Frank, Zhang, Shu, Crane, Alexander, Kalfon, Jeremie, Noorbakhsh, Javad, Beroukhim, Rameen
Published in Cancer research (Chicago, Ill.) (15.06.2022)
Published in Cancer research (Chicago, Ill.) (15.06.2022)
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Journal Article
Abstract 5749: Core transcriptional regulatory circuitry in AML
Harada, Taku, Perez, Monika, Kalfon, Jeremie, Eagle, Kenneth, Braes, Flora Dievenich, Batley, Rashad, Stegmaier, Kimberly, Orkin, Stuart, Pimkin, Maxim
Published in Cancer research (Chicago, Ill.) (04.04.2023)
Published in Cancer research (Chicago, Ill.) (04.04.2023)
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Journal Article
2001 – PLASTICITY OF B-LYMPHOBLASTIC LEUKEMIA STEM CELLS
Rowe, Grant, Morris, Vivian, Wang, Dahai, Marion, William, Hughes, Travis, Sousa, Patricia, Harada, Taku, Sui, Shannan Ho, Naumenko, Sergey, Kalfon, Jeremie, Sensharma, Prerana, da Silva, Renan Vinicius, Pikman, Yana, Harris, Marian, Pimkin, Maxim, Shalek, Alex, North, Trista, Daley, George, da Rocha, Edroaldo Lummertz
Published in Experimental hematology (01.08.2021)
Published in Experimental hematology (01.08.2021)
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Journal Article
Abstract LB-053: VPS4A is a synthetic lethal target in VPS4B -deficient cancers due to co-deletion with SMAD4
Neggers, Jasper E., Paolella, Brenton R., Asfaw, Adhana, Rothberg, Michael V., Skipper, Thomas A., Kalekar, Radha L., Krill-Burger, John M., Hong, Andrew L., Kugener, Guillaume, Kalfon, Jeremie, Yang, Annan, Yuan, Chen, Dumont, Nancy, Gonzalez, Alfredo, Abdusamad, Mai, Li, Yvonne Y., Spurr, Liam F., Wu, Westley W., Piccioni, Federica, Wolpin, Brian M., Root, David E., Boehm, Jesse S., Cherniack, Andrew D., Tsherniak, Aviad, Golub, Todd R., Vazquez, Francisca, Aguirre, Andrew J.
Published in Cancer research (Chicago, Ill.) (15.08.2020)
Published in Cancer research (Chicago, Ill.) (15.08.2020)
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Journal Article
Abstract 2173: Ancestry bias in CRISPR guide design impedes discovery of genetic dependencies
Misek, Sean Alexander, Fultineer, Aaron, Kalfon, Jeremie, Noorbakhsh, Javad, Boyle, Isabella, Dempster, Joshua, Petronio, Lia, Huang, Katherine, McFarland, James, Beroukhim, Rameen, Boehm, Jesse
Published in Cancer research (Chicago, Ill.) (15.06.2022)
Published in Cancer research (Chicago, Ill.) (15.06.2022)
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Journal Article
CaImAn: An open source tool for scalable Calcium Imaging data Analysis
Giovannucci, Andrea, Friedrich, Johannes, Gunn, Pat, Kalfon, Jeremie, Koay, Sue Ann, Taxidis, Jiannis, Najafi, Farzaneh, Gauthier, Jeffrey L, Zhou, Pengcheng, Tank, David W, Chklovskii, Dmitri B, Pnevmatikakis, Eftychios A
Published in bioRxiv (05.06.2018)
Published in bioRxiv (05.06.2018)
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Paper
Germline variation contributes to false negatives in CRISPR-based experiments with varying burden across ancestries
Misek, Sean A, Fultineer, Aaron, Kalfon, Jeremie, Noorbakhsh, Javad, Boyle, Isabella, Dempster, Joshua, Petronio, Lia, Huang, Katherine, Saadat, Alham, Green, Thomas, Brown, Adam, Doench, John G, Root, David E, Mcfarland, James, Beroukhim, Rameen, Boehm, Jesse S
Published in bioRxiv (19.11.2022)
Published in bioRxiv (19.11.2022)
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