Yang, D., H. Cho, Z. Tayyebi, A. Shukla, R. Luo, G. Dixon, V. Ursu, S. Stransky, D. M. Tremmel, S. D. Sackett, R. Koche, S. J. Kaplan, Q. V. Li, J. Park, Z. Zhu, B. P. Rosen, J. Pulecio, Z. D. Shi, Y. Bram, R. E. Schwartz, J. S. Odorico, S. Sidoli, C. V. Wright, C. S. Leslie and D. Huangfu (2022). CRISPR screening uncovers a central requirement for HHEX in pancreatic lineage commitment and plasticity restriction. Nat Cell Biol, 24(7), 1064-1076.

Yan, J., Y. Chen, A. J. Patel, S. Warda, C. J. Lee, B. G. Nixon, E. W. Wong, M. A. Miranda-Román, N. Yang, Y. Wang, M. R. Pachai, J. Sher, E. Giff, F. Tang, E. Khurana, S. Singer, Y. Liu, P. M. Galbo, Jr., J. L. Maag, R. P. Koche, D. Zheng, C. Antonescu, L. Deng, M. Li and P. Chi (2022). Tumor-intrinsic PRC2 inactivation drives a context-dependent immune-desert microenvironment and is sensitized by immunogenic therapeutic viruses. J Clin Invest, 132(17):e153437.

Weiss, J. M., M. V. Hunter, N. M. Cruz, A. Baggiolini, M. Tagore, Y. Ma, S. Misale, M. Marasco, T. Simon-Vermot, N. R. Campbell, F. Newell, J. S. Wilmott, P. A. Johansson, J. F. Thompson, G. V. Long, J. V. Pearson, G. J. Mann, R. A. Scolyer, N. Waddell, E. D. Montal, T. H. Huang, P. Jonsson, M. T. A. Donoghue, C. C. Harris, B. S. Taylor, T. Xu, R. Chaligné, P. V. Shliaha, R. Hendrickson, A. A. Jungbluth, C. Lezcano, R. Koche, L. Studer, C. E. Ariyan, D. B. Solit, J. D. Wolchok, T. Merghoub, N. Rosen, N. K. Hayward and R. M. White (2022). Anatomic position determines oncogenic specificity in melanoma. Nature, 604(7905), 354-361.

Quintanal-Villalonga, A., H. Taniguchi, Y. Hao, A. Chow, Y. A. Zhan, S. S. Chavan, F. Uddin, V. Allaj, P. Manoj, N. S. Shah, J. M. Chan, M. Offin, M. Ciampricotti, J. Ray-Kirton, J. Egger, U. Bhanot, I. Linkov, M. Asher, M. H. Roehrl, J. Qiu, E. de Stanchina, T. J. Hollmann, R. P. Koche, T. Sen, J. T. Poirier and C. M. Rudin (2022). Inhibition of XPO1 Sensitizes Small Cell Lung Cancer to First- and Second-Line Chemotherapy. Cancer Res, 82(3), 472-483.

Patel, A. J., S. Warda, J. L. V. Maag, R. Misra, M. A. Miranda-Roman, M. R. Pachai, C. J. Lee, D. Li, N. Wang, G. Bayshtok, E. Fishinevich, Y. Meng, E. W. P. Wong, J. Yan, E. Giff, M. B. Pappalardi, M. T. McCabe, J. A. Fletcher, C. M. Rudin, S. Chandarlapaty, J. M. Scandura, R. P. Koche, J. L. Glass, C. R. Antonescu, D. Zheng, Y. Chen and P. Chi (2022). PRC2 Inactivating Mutations in Cancer Enhance Cytotoxic Response to DNMT1 Targeted Therapy via Enhanced Viral Mimicry. Cancer Discov, 12(9), 2120-2139.

Baggiolini A, Callahan SJ, Montal E, Weiss JM, Trieu T, Tagore MM, Tischfield SE, Walsh RM, Suresh S, Fan Y, Campbell NR, Perlee SC, Saurat N, Hunter MV, Simon-Vermot T, Huang TH, Ma Y, Hollmann T, Tickoo SK, Taylor BS, Khurana E, Koche RP, Studer L, White RM. (2021) Developmental chromatin programs determine oncogenic competence in melanoma. Science, 373(6559):eabc1048.

Wolfe AL, Zhou Q, Toska E, Galeas J, Ku AA, Koche RP, Bandyopadhyay S, Scaltriti M, Lebrilla CB, McCormick F, Kim SE. (2021) UDP-glucose pyrophosphorylase 2, a regulator of glycogen synthesis and glycosylation, is critical for pancreatic cancer growth. Proc Natl Acad Sci USA. 118(31):e2103592118.

Quintanal-Villalonga A, Taniguchi H, Zhan YA, Hasan MM, Chavan SS, Meng F, Uddin F, Manoj P, Donoghue MTA, Won HH, Chan JM, Ciampricotti M, Chow A, Offin M, Chang JC, Ray-Kirton J, Tischfield SE, Egger J, Bhanot UK, Linkov I, Asher M, Sinha S, Silber J, Iacobuzio-Donahue CA, Roehrl MH, Hollmann TJ, Yu HA, Qiu J, de Stanchina E, Baine MK, Rekhtman N, Poirier JT, Loomis B, Koche RP, Rudin CM, Sen T. (2021) Multi-omic analysis of lung tumors defines pathways activated in neuroendocrine transformation. Cancer Discov. 11(12), 3028-3047

Li R, Grimm SA, Wade PA. (2021) Low-input ATAC&mRNA-Seq: a simple and robust method for simultaneous dual-omics profiling with low cell number. Cell Rep Methods 1(3), 100041.

Sahin M, Wong W, Zhan Y, Van Deynze K, Koche R, Leslie CS. (2021) HiC-DC+ enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP. Nat Commun. 12(1), 3366.

Müller I, Moroni AS, Shlyueva D, Sahadevan S, Schoof EM, Radzisheuskaya A, Højfeldt JW, Tatar T, Koche RP, Huang C, Helin K. (2021) MPP8 is essential for sustaining self-renewal of ground-state pluripotent stem cells. Nat Commun. 12(1), 3034

Radzisheuskaya A, Shliaha PV, Grinev VV, Shlyueva D, Damhofer H, Koche R, Gorshkov V, Kovalchuk S, Zhan Y, Rodriguez KL, Johnstone AL, Keogh MC, Hendrickson RC, Jensen ON, Helin K. (2021) Complex-dependent histone acetyltransferase activity of KAT8 determines its role in transcription and cellular homeostasis. Mol Cell. 81(8), 1749-1765.

Marinaccio C, Suraneni P, Celik H, Volk A, Wen QJ, Ling T, Bulic M, Lasho T, Koche RP, Famulare CA, Farnoud N, Stein B, Schieber M, Gurbuxani S, Root DE, Younger ST, Hoffman R, Gangat N, Ntziachristos P, Chandel NS, Levine RL, Rampal RK, Challen GA, Tefferi A, Crispino JD. (2021) LKB1/ STK11 Is a Tumor Suppressor in the Progression of Myeloproliferative Neoplasms. Cancer Discov. 11(6), 1398-1410.

Alonso-Curbelo D, Ho YJ, Burdziak C, Maag JLV, Morris JP 4th, Chandwani R, Chen HA, Tsanov KM, Barriga FM, Luan W, Tasdemir N, Livshits G, Azizi E, Chun J, Wilkinson JE, Mazutis L, Leach SD, Koche R, Pe’er D, Lowe SW. (2021) A gene-environment-induced epigenetic program initiates tumorigenesis. Nature. 590(7847), 642-648.

Takao S, Forbes L, Uni M, Cheng S, Pineda JMB, Tarumoto Y, Cifani P, Minuesa G, Chen C, Kharas MG, Bradley RK, Vakoc CR, Koche RP, Kentsis A. (2021) Convergent organization of aberrant MYB complex controls oncogenic gene expression in acute myeloid leukemia. Elife. 10:e65905

Saqcena M, Leandro-Garcia LJ, Maag JLV, Tchekmedyian V, Krishnamoorthy GP, Tamarapu PP, Tiedje V, Reuter V, Knauf JA, de Stanchina E, Xu B, Liao XH, Refetoff S, Ghossein R, Chi P, Ho AL, Koche RP, Fagin JA. (2021) SWI/SNF Complex Mutations Promote Thyroid Tumor Progression and Insensitivity to Redifferentiation Therapies. Cancer Discov. 11(5), 1158-1175.

Helmsauer K, Valieva ME, Ali S, Chamorro González R, Schöpflin R, Röefzaad C, Bei Y, Dorado Garcia H, Rodriguez-Fos E, Puiggròs M, Kasack K, Haase K, Keskeny C, Chen CY, Kuschel LP, Euskirchen P, Heinrich V, Robson MI, Rosswog C, Toedling J, Szymansky A, Hertwig F, Fischer M, Torrents D, Eggert A, Schulte JH, Mundlos S, Henssen AG, Koche RP. (2020) Enhancer hijacking determines extrachromosomal circular MYCN amplicon architecture in neuroblastoma. Nat Commun. 11(1), 5823.

Koche RP, Rodriguez-Fos E, Helmsauer K, Burkert M, MacArthur IC, Maag J, Chamorro R, Munoz-Perez N, Puiggròs M, Dorado Garcia H, Bei Y, Röefzaad C, Bardinet V, Szymansky A, Winkler A, Thole T, Timme N, Kasack K, Fuchs S, Klironomos F, Thiessen N, Blanc E, Schmelz K, Künkele A, Hundsdörfer P, Rosswog C, Theissen J, Beule D, Deubzer H, Sauer S, Toedling J, Fischer M, Hertwig F, Schwarz RF, Eggert A, Torrents D, Schulte JH, Henssen AG. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma. Nat Genet. 2020 Jan;52(1):29-34.

Ganesh K, Basnet H, Laughney AM, Kaygusuz Y, He L, O’Rourke KP, Reuter V, Huang Y-H, Er EE, Masilionis I, Weiser MR, Saltz LB, Garcia-Aguilar J, Koche R, Lowe SW, Pe’er D, Shia J, Massagué J. L1CAM defines the regenerative origin of metastasis initiating cells in colorectal cancer. Nature Cancer. 2020 Jan;1:28-45.

Morris JP 4th, Yashinskie JJ, Koche R, Chandwani R, Tian S, Chen CC, Baslan T, Marinkovic ZS, Sánchez-Rivera FJ, Leach SD, Carmona-Fontaine C, Thompson CB, Finley LWS, Lowe SW. α-Ketoglutarate links p53 to cell fate during tumour suppression. Nature. 2019 Sep;573(7775):595-599.

Viny AD, Bowman RL, Liu Y, Lavallée VP, Eisman SE, Xiao W, Durham BH, Navitski A, Park J, Braunstein S, Alija B, Karzai A, Csete IS, Witkin M, Azizi E, Baslan T, Ott CJ, Pe’er D, Dekker J, Koche R, Levine RL. Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation. Cell Stem Cell. 2019 Aug 30. pii: S1934-5909(19)30338-8.

Schvartzman JM, Reuter VP, Koche RP, Thompson CB. 2-hydroxyglutarate inhibits MyoD-mediated differentiation by preventing H3K9 demethylation. Proc Natl Acad Sci U S A. 2019 Jun 25;116(26):12851-12856.

Zhan YA, Wray CG, Namburi S, Glantz ST, Laubenbacher R, Chuang JH. Fostering bioinformatics education through skill development of professors: Big Genomic Data Skills Training for Professors. PLoS Comput Biol. 2019 Jun 13;15(6):e1007026.

Finley LWS, Vardhana SA, Carey BW, Alonso-Curbelo D, Koche R, Chen Y, Wen D, King B, Radler MR, Rafii S, Lowe SW, Allis CD, Thompson CB. Pluripotency transcription factors and Tet1/2 maintain Brd4-independent stem cell identity. Nat Cell Biol. 2018 May;20(5):565-574.

Hoshii T, Cifani P, Feng Z, Huang CH, Koche R, Chen CW, Delaney CD, Lowe SW, Kentsis A, Armstrong SA. A Non-catalytic Function of SETD1A Regulates Cyclin K and the DNA Damage Response. Cell. 2018 Feb 22;172(5):1007-1021.

Kleppe M, Koche R, Zou L, van Galen P, Hill CE, Dong L, De Groote S, Papalexi E, Hanasoge Somasundara AV, Cordner K, Keller M, Farnoud N, Medina J, McGovern E, Reyes J, Roberts J, Witkin M, Rapaport F, Teruya-Feldstein J, Qi J, Rampal R, Bernstein BE, Bradner JE, Levine RL. Dual Targeting of Oncogenic Activation and Inflammatory Signaling Increases Therapeutic Efficacy in Myeloproliferative Neoplasms. Cancer Cell. 2018 Jan 8;33(1):29-43.

Ramaswamy K, Forbes L, Minuesa G, Gindin T, Brown F, Kharas MG, Krivtsov AV, Armstrong SA, Still E, de Stanchina E, Knoechel B, Koche R, Kentsis A. Peptidomimetic blockade of MYB in acute myeloid leukemia. Nat Commun. 2018 Jan 9;9(1):110.