Samir Amin
Associate Research Scientist
Research & Publications
Biography
Locations
Coauthors
Selected Publications
- Comparative Molecular Life History of Spontaneous Canine and Human GliomasAmin S, Anderson K, Boudreau C, Martinez-Ledesma E, Kocakavuk E, Johnson K, Barthel F, Varn F, Kassab C, Ling X, Kim H, Barter M, Lau C, Ngan C, Chapman M, Koehler J, Long J, Miller A, Miller C, Porter B, Rissi D, Mazcko C, LeBlanc A, Dickinson P, Packer R, Taylor A, Rossmeisl J, Woolard K, Heimberger A, Levine J, Verhaak R. Comparative Molecular Life History of Spontaneous Canine and Human Gliomas. Cancer Cell 2020, 37: 243-257.e7. PMID: 32049048, PMCID: PMC7132629, DOI: 10.1016/j.ccell.2020.01.004.
- Analyses of non-coding somatic drivers in 2,658 cancer whole genomesRheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen J, Getz G. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature 2020, 578: 102-111. PMID: 32025015, PMCID: PMC7054214, DOI: 10.1038/s41586-020-1965-x.
- Systematic analysis of telomere length and somatic alterations in 31 cancer typesBarthel F, Wei W, Tang M, Martinez-Ledesma E, Hu X, Amin S, Akdemir K, Seth S, Song X, Wang Q, Lichtenberg T, Hu J, Zhang J, Zheng S, Verhaak R. Systematic analysis of telomere length and somatic alterations in 31 cancer types. Nature Genetics 2017, 49: 349-357. PMID: 28135248, PMCID: PMC5571729, DOI: 10.1038/ng.3781.
- Truncating PREX2 mutations activate its GEF activity and alter gene expression regulation in NRAS-mutant melanomaLissanu Deribe Y, Shi Y, Rai K, Nezi L, Amin S, Wu C, Akdemir K, Mahdavi M, Peng Q, Chang Q, Hornigold K, Arold S, Welch H, Garraway L, Chin L. Truncating PREX2 mutations activate its GEF activity and alter gene expression regulation in NRAS-mutant melanoma. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: e1296-e1305. PMID: 26884185, PMCID: PMC4780599, DOI: 10.1073/pnas.1513801113.
- The Cancer Genome Atlas Pan-Cancer analysis projectChang K, Creighton C, Davis C, Donehower L, Drummond J, Wheeler D, Ally A, Balasundaram M, Birol I, Butterfield Y, Chu A, Chuah E, Chun H, Dhalla N, Guin R, Hirst M, Hirst C, Holt R, Jones S, Lee D, Li H, Marra M, Mayo M, Moore R, Mungall A, Robertson A, Schein J, Sipahimalani P, Tam A, Thiessen N, Varhol R, Beroukhim R, Bhatt A, Brooks A, Cherniack A, Freeman S, Gabriel S, Helman E, Jung J, Meyerson M, Ojesina A, Pedamallu C, Saksena G, Schumacher S, Tabak B, Zack T, Lander E, Bristow C, Hadjipanayis A, Haseley P, Kucherlapati R, Lee S, Lee E, Luquette L, Mahadeshwar H, Pantazi A, Parfenov M, Park P, Protopopov A, Ren X, Santoso N, Seidman J, Seth S, Song X, Tang J, Xi R, Xu A, Yang L, Zeng D, Auman J, Balu S, Buda E, Fan C, Hoadley K, Jones C, Meng S, Mieczkowski P, Parker J, Perou C, Roach J, Shi Y, Silva G, Tan D, Veluvolu U, Waring S, Wilkerson M, Wu J, Zhao W, Bodenheimer T, Hayes D, Hoyle A, Jeffreys S, Mose L, Simons J, Soloway M, Baylin S, Berman B, Bootwalla M, Danilova L, Herman J, Hinoue T, Laird P, Rhie S, Shen H, Triche T, Weisenberger D, Carter S, Cibulskis K, Chin L, Zhang J, Getz G, Sougnez C, Wang M, Saksena G, Carter S, Cibulskis K, Chin L, Zhang J, Getz G, Dinh H, Doddapaneni H, Gibbs R, Gunaratne P, Han Y, Kalra D, Kovar C, Lewis L, Morgan M, Morton D, Muzny D, Reid J, Xi L, Cho J, DiCara D, Frazer S, Gehlenborg N, Heiman D, Kim J, Lawrence M, Lin P, Liu Y, Noble M, Stojanov P, Voet D, Zhang H, Zou L, Stewart C, Bernard B, Bressler R, Eakin A, Iype L, Knijnenburg T, Kramer R, Kreisberg R, Leinonen K, Lin J, Liu Y, Miller M, Reynolds S, Rovira H, Shmulevich I, Thorsson V, Yang D, Zhang W, Amin S, Wu C, Wu C, Akbani R, Aldape K, Baggerly K, Broom B, Casasent T, Cleland J, Creighton C, Dodda D, Edgerton M, Han L, Herbrich S, Ju Z, Kim H, Lerner S, Li J, Liang H, Liu W, Lorenzi P, Lu Y, Melott J, Mills G, Nguyen L, Su X, Verhaak R, Wang W, Weinstein J, Wong A, Yang Y, Yao J, Yao R, Yoshihara K, Yuan Y, Yung A, Zhang N, Zheng S, Ryan M, Kane D, Aksoy B, Ciriello G, Dresdner G, Gao J, Gross B, Jacobsen A, Kahles A, Ladanyi M, Lee W, Lehmann K, Miller M, Ramirez R, Rätsch G, Reva B, Sander C, Schultz N, Senbabaoglu Y, Shen R, Sinha R, Sumer S, Sun Y, Taylor B, Weinhold N, Fei S, Spellman P, Benz C, Carlin D, Cline M, Craft B, Ellrott K, Goldman M, Haussler D, Ma S, Ng S, Paull E, Radenbaugh A, Salama S, Sokolov A, Stuart J, Swatloski T, Uzunangelov V, Waltman P, Yau C, Zhu J, Hamilton S, Getz G, Sougnez C, Abbott S, Abbott R, Dees N, Delehaunty K, Ding L, Dooling D, Eldred J, Fronick C, Fulton R, Fulton L, Kalicki-Veizer J, Kanchi K, Kandoth C, Koboldt D, Larson D, Ley T, Lin L, Lu C, Magrini V, Mardis E, McLellan M, McMichael J, Miller C, O'Laughlin M, Pohl C, Schmidt H, Smith S, Walker J, Wallis J, Wendl M, Wilson R, Wylie T, Zhang Q, Burton R, Jensen M, Kahn A, Pihl T, Pot D, Wan Y, Levine D, Black A, Bowen J, Frick J, Gastier-Foster J, Harper H, Helsel C, Leraas K, Lichtenberg T, McAllister C, Ramirez N, Sharpe S, Wise L, Zmuda E, Chanock S, Davidsen T, Demchok J, Eley G, Felau I, Ozenberger B, Sheth M, Sofia H, Staudt L, Tarnuzzer R, Wang Z, Yang L, Zhang J, Omberg L, Margolin A, Raphael B, Vandin F, Wu H, Leiserson M, Benz S, Vaske C, Noushmehr H, Knijnenburg T, Wolf D, Veer L, Collisson E, Anastassiou D, Yang T, Lopez-Bigas N, Gonzalez-Perez A, Tamborero D, Xia Z, Li W, Cho D, Przytycka T, Hamilton M, McGuire S, Nelander S, Johansson P, Jörnsten R, Kling T, Sanchez J. The Cancer Genome Atlas Pan-Cancer analysis project. Nature Genetics 2013, 45: 1113-1120. PMID: 24071849, PMCID: PMC3919969, DOI: 10.1038/ng.2764.
- Integrating Gene and Mir Expression Profiles and Regulatory Network Structures to Define Aberrent Feed Forward Loops with Functional and Clinical Implications in Myeloma.Fulciniti M, Li Y, Wang X, Samur M, Yan Z, Amin S, Li C, Anderson K, Munshi N. Integrating Gene and Mir Expression Profiles and Regulatory Network Structures to Define Aberrent Feed Forward Loops with Functional and Clinical Implications in Myeloma. Blood 2012, 120: 2386. DOI: 10.1182/blood.v120.21.2386.2386.
- Gene expression profile alone is inadequate in predicting complete response in multiple myelomaAmin S, Yip W, Minvielle S, Broyl A, Li Y, Hanlon B, Swanson D, Shah P, Moreau P, van der Holt B, van Duin M, Magrangeas F, Pieter Sonneveld P, Anderson K, Li C, Avet-Loiseau H, Munshi N. Gene expression profile alone is inadequate in predicting complete response in multiple myeloma. Leukemia 2014, 28: 2229-2234. PMID: 24732597, PMCID: PMC4198516, DOI: 10.1038/leu.2014.140.
- Abstract 3106: Identifying drivers in the converging syntenic aneuploidies of spontaneous canine and pediatric high-grade glioma using imaging-based an arrayed CRISPR-Cas9 phenotypic screenAmin S, Gujar A, Yi E, Kang W, Costa M, Sjogren G, Gabriel P, Maher L, Dickinson P, Packer R, Courtois E, Robson P, Lee C, Verhaak R. Abstract 3106: Identifying drivers in the converging syntenic aneuploidies of spontaneous canine and pediatric high-grade glioma using imaging-based an arrayed CRISPR-Cas9 phenotypic screen. Cancer Research 2022, 82: 3106-3106. DOI: 10.1158/1538-7445.am2022-3106.
- Glioma progression is shaped by genetic evolution and microenvironment interactionsVarn F, Johnson K, Martinek J, Huse J, Nasrallah M, Wesseling P, Cooper L, Malta T, Wade T, Sabedot T, Brat D, Gould P, Wöehrer A, Aldape K, Ismail A, Sivajothi S, Barthel F, Kim H, Kocakavuk E, Ahmed N, White K, Datta I, Moon H, Pollock S, Goldfarb C, Lee G, Garofano L, Anderson K, Nehar-Belaid D, Barnholtz-Sloan J, Bakas S, Byrne A, D’Angelo F, Gan H, Khasraw M, Migliozzi S, Ormond D, Paek S, Van Meir E, Walenkamp A, Watts C, Weiss T, Weller M, Palucka K, Stead L, Poisson L, Noushmehr H, Iavarone A, Verhaak R, Consortium T, Varn F, Johnson K, Martinek J, Huse J, Nasrallah M, Wesseling P, Cooper L, Malta T, Wade T, Sabedot T, Brat D, Gould P, Wöehrer A, Aldape K, Ismail A, Sivajothi S, Barthel F, Kim H, Kocakavuk E, Ahmed N, White K, Datta I, Moon H, Pollock S, Goldfarb C, Lee G, Garofano L, Anderson K, Nehar-Belaid D, Barnholtz-Sloan J, Bakas S, Byrne A, D’Angelo F, Gan H, Khasraw M, Migliozzi S, Ormond D, Paek S, Van Meir E, Walenkamp A, Watts C, Weiss T, Weller M, Alfaro K, Amin S, Ashley D, Bock C, Brodbelt A, Bulsara K, Castro A, Connelly J, Costello J, de Groot J, Finocchiaro G, French P, Golebiewska A, Hau A, Hong C, Horbinski C, Kannan K, Kouwenhoven M, Lasorella A, LaViolette P, Ligon K, Lowman A, Mehta S, Miletic H, Molinaro A, Ng H, Niclou S, Niers J, Phillips J, Rabadan R, Rao G, Reifenberger G, Sanai N, Short S, Smitt P, Sloan A, Smits M, Snyder J, Suzuki H, Tabatabai G, Tanner G, Tomaszewski W, Wells M, Westerman B, Wheeler H, Xie J, Yung W, Zadeh G, Zhao J, Palucka K, Stead L, Poisson L, Noushmehr H, Iavarone A, Verhaak R. Glioma progression is shaped by genetic evolution and microenvironment interactions. Cell 2022, 185: 2184-2199.e16. PMID: 35649412, PMCID: PMC9189056, DOI: 10.1016/j.cell.2022.04.038.
- Live-Cell Imaging Shows Uneven Segregation of Extrachromosomal DNA Elements and Transcriptionally Active Extrachromosomal DNA Hubs in CancerYi E, Gujar A, Guthrie M, Kim H, Zhao D, Johnson K, Amin S, Costa M, Yu Q, Das S, Jillette N, Clow P, Cheng A, Verhaak R. Live-Cell Imaging Shows Uneven Segregation of Extrachromosomal DNA Elements and Transcriptionally Active Extrachromosomal DNA Hubs in Cancer. Cancer Discovery 2022, 12: 468-483. PMID: 34819316, PMCID: PMC8831456, DOI: 10.1158/2159-8290.cd-21-1376.
- Reprogramming of bivalent chromatin states in NRAS mutant melanoma suggests PRC2 inhibition as a therapeutic strategyTerranova C, Tang M, Maitituoheti M, Raman A, Ghosh A, Schulz J, Amin S, Orouji E, Tomczak K, Sarkar S, Oba J, Creasy C, Wu C, Khan S, Lazcano R, Wani K, Singh A, Barrodia P, Zhao D, Chen K, Haydu L, Wang W, Lazar A, Woodman S, Bernatchez C, Rai K. Reprogramming of bivalent chromatin states in NRAS mutant melanoma suggests PRC2 inhibition as a therapeutic strategy. Cell Reports 2021, 36: 109410. PMID: 34289358, PMCID: PMC8369408, DOI: 10.1016/j.celrep.2021.109410.
- Radiotherapy is associated with a deletion signature that contributes to poor outcomes in patients with cancerKocakavuk E, Anderson K, Varn F, Johnson K, Amin S, Sulman E, Lolkema M, Barthel F, Verhaak R. Radiotherapy is associated with a deletion signature that contributes to poor outcomes in patients with cancer. Nature Genetics 2021, 53: 1088-1096. PMID: 34045764, PMCID: PMC8483261, DOI: 10.1038/s41588-021-00874-3.
- Machine Learning Approaches Pertinent to Glioma ClassificationAmin S. Machine Learning Approaches Pertinent to Glioma Classification. 2021, 55-66. DOI: 10.1007/978-3-030-69170-7_4.
- Somatic mutation distributions in cancer genomes vary with three-dimensional chromatin structureAkdemir K, Le V, Kim J, Killcoyne S, King D, Lin Y, Tian Y, Inoue A, Amin S, Robinson F, Nimmakayalu M, Herrera R, Lynn E, Chan K, Seth S, Klimczak L, Gerstung M, Gordenin D, O’Brien J, Li L, Deribe Y, Verhaak R, Campbell P, Fitzgerald R, Morrison A, Dixon J, Andrew Futreal P. Somatic mutation distributions in cancer genomes vary with three-dimensional chromatin structure. Nature Genetics 2020, 52: 1178-1188. PMID: 33020667, PMCID: PMC8350746, DOI: 10.1038/s41588-020-0708-0.
- Enhancer Reprogramming Confers Dependence on Glycolysis and IGF Signaling in KMT2D Mutant MelanomaMaitituoheti M, Keung E, Tang M, Yan L, Alam H, Han G, Singh A, Raman A, Terranova C, Sarkar S, Orouji E, Amin S, Sharma S, Williams M, Samant N, Dhamdhere M, Zheng N, Shah T, Shah A, Axelrad J, Anvar N, Lin Y, Jiang S, Chang E, Ingram D, Wang W, Lazar A, Lee M, Muller F, Wang L, Ying H, Rai K. Enhancer Reprogramming Confers Dependence on Glycolysis and IGF Signaling in KMT2D Mutant Melanoma. Cell Reports 2020, 33: 108293. PMID: 33086062, PMCID: PMC7649750, DOI: 10.1016/j.celrep.2020.108293.
- Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancersKim H, Nguyen N, Turner K, Wu S, Gujar A, Luebeck J, Liu J, Deshpande V, Rajkumar U, Namburi S, Amin S, Yi E, Menghi F, Schulte J, Henssen A, Chang H, Beck C, Mischel P, Bafna V, Verhaak R. Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers. Nature Genetics 2020, 52: 891-897. PMID: 32807987, PMCID: PMC7484012, DOI: 10.1038/s41588-020-0678-2.
- KMT2D Deficiency Impairs Super-Enhancers to Confer a Glycolytic Vulnerability in Lung CancerAlam H, Tang M, Maitituoheti M, Dhar S, Kumar M, Han C, Ambati C, Amin S, Gu B, Chen T, Lin Y, Chen J, Muller F, Putluri N, Flores E, DeMayo F, Baseler L, Rai K, Lee M. KMT2D Deficiency Impairs Super-Enhancers to Confer a Glycolytic Vulnerability in Lung Cancer. Cancer Cell 2020, 37: 599-617.e7. PMID: 32243837, PMCID: PMC7178078, DOI: 10.1016/j.ccell.2020.03.005.
- Molecular and clonal evolution in recurrent metastatic gliosarcomaAnderson K, Tan A, Parkinson J, Back M, Kastelan M, Newey A, Brewer J, Wheeler H, Hudson A, Amin S, Johnson K, Barthel F, Verhaak R, Khasraw M. Molecular and clonal evolution in recurrent metastatic gliosarcoma. Molecular Case Studies 2020, 6: a004671. PMID: 31896544, PMCID: PMC6996521, DOI: 10.1101/mcs.a004671.
- Longitudinal molecular trajectories of diffuse glioma in adultsBarthel FP, Johnson KC, Varn FS, Moskalik AD, Tanner G, Kocakavuk E, Anderson KJ, Abiola O, Aldape K, Alfaro KD, Alpar D, Amin SB, Ashley DM, Bandopadhayay P, Barnholtz-Sloan JS, Beroukhim R, Bock C, Brastianos PK, Brat DJ, Brodbelt AR, Bruns AF, Bulsara KR, Chakrabarty A, Chakravarti A, Chuang JH, Claus EB, Cochran EJ, Connelly J, Costello JF, Finocchiaro G, Fletcher MN, French PJ, Gan HK, Gilbert MR, Gould PV, Grimmer MR, Iavarone A, Ismail A, Jenkinson MD, Khasraw M, Kim H, Kouwenhoven MCM, LaViolette PS, Li M, Lichter P, Ligon KL, Lowman AK, Malta TM, Mazor T, McDonald KL, Molinaro AM, Nam DH, Nayyar N, Ng HK, Ngan CY, Niclou SP, Niers JM, Noushmehr H, Noorbakhsh J, Ormond DR, Park CK, Poisson LM, Rabadan R, Radlwimmer B, Rao G, Reifenberger G, Sa JK, Schuster M, Shaw BL, Short SC, Smitt PAS, Sloan AE, Smits M, Suzuki H, Tabatabai G, Van Meir EG, Watts C, Weller M, Wesseling P, Westerman BA, Widhalm G, Woehrer A, Yung WKA, Zadeh G, Huse JT, De Groot JF, Stead LF, Verhaak RGW. Longitudinal molecular trajectories of diffuse glioma in adults. Nature 2019, 576: 112-120. PMID: 31748746, PMCID: PMC6897368, DOI: 10.1038/s41586-019-1775-1.
- The effects of MicroRNA deregulation on pre-RNA processing network in multiple myelomaAdamia S, Abiatari I, Amin S, Fulciniti M, Minvielle S, Li C, Moreau P, Avet-Loiseau H, Munshi N, Anderson K. The effects of MicroRNA deregulation on pre-RNA processing network in multiple myeloma. Leukemia 2019, 34: 167-179. PMID: 31182781, PMCID: PMC6901818, DOI: 10.1038/s41375-019-0498-5.
- p53 Is a Master Regulator of Proteostasis in SMARCB1-Deficient Malignant Rhabdoid TumorsCarugo A, Minelli R, Sapio L, Soeung M, Carbone F, Robinson F, Tepper J, Chen Z, Lovisa S, Svelto M, Amin S, Srinivasan S, Del Poggetto E, Loponte S, Puca F, Dey P, Malouf G, Su X, Li L, Lopez-Terrada D, Rakheja D, Lazar A, Netto G, Rao P, Sgambato A, Maitra A, Tripathi D, Walker C, Karam J, Heffernan T, Viale A, Roberts C, Msaouel P, Tannir N, Draetta G, Genovese G. p53 Is a Master Regulator of Proteostasis in SMARCB1-Deficient Malignant Rhabdoid Tumors. Cancer Cell 2019, 35: 204-220.e9. PMID: 30753823, PMCID: PMC7876656, DOI: 10.1016/j.ccell.2019.01.006.
- An in vivo screen identifies PYGO2 as a driver for metastatic prostate cancerLu X, Pan X, Wu C, Zhao D, Feng S, Zang Y, Lee R, Khadka S, Amin S, Jin E, Shang X, Deng P, Luo Y, Morgenlander W, Weinrich J, Lu X, Jiang S, Chang Q, Navone N, Troncoso P, DePinho R, Wang Y. An in vivo screen identifies PYGO2 as a driver for metastatic prostate cancer. Cancer Research 2018, 78: canres.3564.2017. PMID: 29769196, PMCID: PMC6381393, DOI: 10.1158/0008-5472.can-17-3564.
- An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor TissuesTerranova C, Tang M, Orouji E, Maitituoheti M, Raman A, Amin S, Liu Z, Rai K. An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues. Journal Of Visualized Experiments 2018 DOI: 10.3791/56972-v.
- Glioma through the looking GLASS: molecular evolution of diffuse gliomas and the Glioma Longitudinal Analysis ConsortiumAldape K, Amin SB, Ashley DM, Barnholtz-Sloan JS, Bates AJ, Beroukhim R, Bock C, Brat DJ, Claus EB, Costello JF, de Groot JF, Finocchiaro G, French PJ, Gan HK, Griffith B, Herold-Mende CC, Horbinski C, Iavarone A, Kalkanis SN, Karabatsou K, Kim H, Kouwenhoven MCM, McDonald KL, Miletic H, Nam DH, Ng HK, Niclou SP, Noushmehr H, Ormond D, Poisson LM, Reifenberger G, Roncaroli F, Sa JK, Smitt P, Smits M, Souza CF, Tabatabai G, Van Meir EG, Verhaak RGW, Watts C, Wesseling P, Woehrer A, Yung WKA, Jungk C, Hau AC, van Dyck E, Westerman BA, Yin J, Abiola O, Zeps N, Grimmond S, Buckland M, Khasraw M, Sulman EP, Muscat AM, Stead L. Glioma through the looking GLASS: molecular evolution of diffuse gliomas and the Glioma Longitudinal Analysis Consortium. Neuro-Oncology 2018, 20: 873-884. PMID: 29432615, PMCID: PMC6280138, DOI: 10.1093/neuonc/noy020.
- TumorFusions: an integrative resource for cancer-associated transcript fusionsHu X, Wang Q, Tang M, Barthel F, Amin S, Yoshihara K, Lang F, Martinez-Ledesma E, Lee S, Zheng S, Verhaak R. TumorFusions: an integrative resource for cancer-associated transcript fusions. Nucleic Acids Research 2017, 46: gkx1018-. PMID: 29099951, PMCID: PMC5753333, DOI: 10.1093/nar/gkx1018.
- Navigating the Cancer Transcriptome by Decoding Divergent Oncogenic StatesAmin S, Verhaak R. Navigating the Cancer Transcriptome by Decoding Divergent Oncogenic States. Cell Systems 2017, 5: 90-92. PMID: 28837814, DOI: 10.1016/j.cels.2017.08.006.
- Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma ProgressionFiziev P, Akdemir K, Miller J, Keung E, Samant N, Sharma S, Natale C, Terranova C, Maitituoheti M, Amin S, Martinez-Ledesma E, Dhamdhere M, Axelrad J, Shah A, Cheng C, Mahadeshwar H, Seth S, Barton M, Protopopov A, Tsai K, Davies M, Garcia B, Amit I, Chin L, Ernst J, Rai K. Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression. Cell Reports 2017, 19: 875-889. PMID: 28445736, PMCID: PMC5473172, DOI: 10.1016/j.celrep.2017.03.078.
- Synthetic vulnerabilities of mesenchymal subpopulations in pancreatic cancerGenovese G, Carugo A, Tepper J, Robinson F, Li L, Svelto M, Nezi L, Corti D, Minelli R, Pettazzoni P, Gutschner T, Wu C, Seth S, Akdemir K, Leo E, Amin S, Molin M, Ying H, Kwong L, Colla S, Takahashi K, Ghosh P, Giuliani V, Muller F, Dey P, Jiang S, Garvey J, Liu C, Zhang J, Heffernan T, Toniatti C, Fleming J, Goggins M, Wood L, Sgambato A, Agaimy A, Maitra A, Roberts C, Wang H, Viale A, DePinho R, Draetta G, Chin L. Synthetic vulnerabilities of mesenchymal subpopulations in pancreatic cancer. Nature 2017, 542: 362-366. PMID: 28178232, PMCID: PMC7609022, DOI: 10.1038/nature21064.
- Histone demethylase JARID1C inactivation triggers genomic instability in sporadic renal cancerRondinelli B, Rosano D, Antonini E, Frenquelli M, Montanini L, Huang D, Segalla S, Yoshihara K, Amin S, Lazarevic D, The B, Verhaak R, Futreal P, Di Croce L, Chin L, Cittaro D, Tonon G. Histone demethylase JARID1C inactivation triggers genomic instability in sporadic renal cancer. Journal Of Clinical Investigation 2016, 126: 4387-4387. PMID: 27801678, PMCID: PMC5096900, DOI: 10.1172/jci91191.
- miR-182-5p Induced by STAT3 Activation Promotes Glioma TumorigenesisXue J, Zhou A, Wu Y, Morris S, Lin K, Amin S, Verhaak R, Fuller G, Xie K, Heimberger A, Huang S. miR-182-5p Induced by STAT3 Activation Promotes Glioma Tumorigenesis. Cancer Research 2016, 76: 4293-4304. PMID: 27246830, PMCID: PMC5033679, DOI: 10.1158/0008-5472.can-15-3073.
- The Molecular Taxonomy of Primary Prostate CancerNetwork T, Abeshouse A, Ahn J, Akbani R, Ally A, Amin S, Andry C, Annala M, Aprikian A, Armenia J, Arora A, Auman J, Balasundaram M, Balu S, Barbieri C, Bauer T, Benz C, Bergeron A, Beroukhim R, Berrios M, Bivol A, Bodenheimer T, Boice L, Bootwalla M, dos Reis R, Boutros P, Bowen J, Bowlby R, Boyd J, Bradley R, Breggia A, Brimo F, Bristow C, Brooks D, Broom B, Bryce A, Bubley G, Burks E, Butterfield Y, Button M, Canes D, Carlotti C, Carlsen R, Carmel M, Carroll P, Carter S, Cartun R, Carver B, Chan J, Chang M, Chen Y, Cherniack A, Chevalier S, Chin L, Cho J, Chu A, Chuah E, Chudamani S, Cibulskis K, Ciriello G, Clarke A, Cooperberg M, Corcoran N, Costello A, Cowan J, Crain D, Curley E, David K, Demchok J, Demichelis F, Dhalla N, Dhir R, Doueik A, Drake B, Dvinge H, Dyakova N, Felau I, Ferguson M, Frazer S, Freedland S, Fu Y, Gabriel S, Gao J, Gardner J, Gastier-Foster J, Gehlenborg N, Gerken M, Gerstein M, Getz G, Godwin A, Gopalan A, Graefen M, Graim K, Gribbin T, Guin R, Gupta M, Hadjipanayis A, Haider S, Hamel L, Hayes D, Heiman D, Hess J, Hoadley K, Holbrook A, Holt R, Holway A, Hovens C, Hoyle A, Huang M, Hutter C, Ittmann M, Iype L, Jefferys S, Jones C, Jones S, Juhl H, Kahles A, Kane C, Kasaian K, Kerger M, Khurana E, Kim J, Klein R, Kucherlapati R, Lacombe L, Ladanyi M, Lai P, Laird P, Lander E, Latour M, Lawrence M, Lau K, LeBien T, Lee D, Lee S, Lehmann K, Leraas K, Leshchiner I, Leung R, Libertino J, Lichtenberg T, Lin P, Linehan W, Ling S, Lippman S, Liu J, Liu W, Lochovsky L, Loda M, Logothetis C, Lolla L, Longacre T, Lu Y, Luo J, Ma Y, Mahadeshwar H, Mallery D, Mariamidze A, Marra M, Mayo M, McCall S, McKercher G, Meng S, Mes-Masson A, Merino M, Meyerson M, Mieczkowski P, Mills G, Shaw K, Minner S, Moinzadeh A, Moore R, Morris S, Morrison C, Mose L, Mungall A, Murray B, Myers J, Naresh R, Nelson J, Nelson M, Nelson P, Newton Y, Noble M, Noushmehr H, Nykter M, Pantazi A, Parfenov M, Park P, Parker J, Paulauskis J, Penny R, Perou C, Piché A, Pihl T, Pinto P, Prandi D, Protopopov A, Ramirez N, Rao A, Rathmell W, Rätsch G, Ren X, Reuter V, Reynolds S, Rhie S, Rieger-Christ K, Roach J, Robertson A, Robinson B, Rubin M, Saad F, Sadeghi S, Saksena G, Saller C, Salner A, Sanchez-Vega F, Sander C, Sandusky G, Sauter G, Sboner A, Scardino P, Scarlata E, Schein J, Schlomm T, Schmidt L, Schultz N, Schumacher S, Seidman J, Neder L, Seth S, Sharp A, Shelton C, Shelton T, Shen H, Shen R, Sherman M, Sheth M, Shi Y, Shih J, Shmulevich I, Simko J, Simon R, Simons J, Sipahimalani P, Skelly T, Sofia H, Soloway M, Song X, Sorcini A, Sougnez C, Stepa S, Stewart C, Stewart J, Stuart J, Sullivan T, Sun C, Sun H, Tam A, Tan D, Tang J, Tarnuzzer R, Tarvin K, Taylor B, Teebagy P, Tenggara I, Têtu B, Tewari A, Thiessen N, Thompson T, Thorne L, Tirapelli D, Tomlins S, Trevisan F, Troncoso P, True L, Tsourlakis M, Tyekucheva S, Van Allen E, Van Den Berg D, Veluvolu U, Verhaak R, Vocke C, Voet D, Wan Y, Wang Q, Wang W, Wang Z, Weinhold N, Weinstein J, Weisenberger D, Wilkerson M, Wise L, Witte J, Wu C, Wu J, Wu Y, Xu A, Yadav S, Yang L, Yang L, Yau C, Ye H, Yena P, Zeng T, Zenklusen J, Zhang H, Zhang J, Zhang J, Zhang W, Zhong Y, Zhu K, Zmuda E. The Molecular Taxonomy of Primary Prostate Cancer. Cell 2015, 163: 1011-1025. PMID: 26544944, PMCID: PMC4695400, DOI: 10.1016/j.cell.2015.10.025.
- Genomic Classification of Cutaneous MelanomaNetwork T, Akbani R, Akdemir K, Aksoy B, Albert M, Ally A, Amin S, Arachchi H, Arora A, Auman J, Ayala B, Baboud J, Balasundaram M, Balu S, Barnabas N, Bartlett J, Bartlett P, Bastian B, Baylin S, Behera M, Belyaev D, Benz C, Bernard B, Beroukhim R, Bir N, Black A, Bodenheimer T, Boice L, Boland G, Bono R, Bootwalla M, Bosenberg M, Bowen J, Bowlby R, Bristow C, Brockway-Lunardi L, Brooks D, Brzezinski J, Bshara W, Buda E, Burns W, Butterfield Y, Button M, Calderone T, Cappellini G, Carter C, Carter S, Cherney L, Cherniack A, Chevalier A, Chin L, Cho J, Cho R, Choi Y, Chu A, Chudamani S, Cibulskis K, Ciriello G, Clarke A, Coons S, Cope L, Crain D, Curley E, Danilova L, D’Atri S, Davidsen T, Davies M, Delman K, Demchok J, Deng Q, Deribe Y, Dhalla N, Dhir R, DiCara D, Dinikin M, Dubina M, Ebrom J, Egea S, Eley G, Engel J, Eschbacher J, Fedosenko K, Felau I, Fennell T, Ferguson M, Fisher S, Flaherty K, Frazer S, Frick J, Fulidou V, Gabriel S, Gao J, Gardner J, Garraway L, Gastier-Foster J, Gaudioso C, Gehlenborg N, Genovese G, Gerken M, Gershenwald J, Getz G, Gomez-Fernandez C, Gribbin T, Grimsby J, Gross B, Guin R, Gutschner T, Hadjipanayis A, Halaban R, Hanf B, Haussler D, Haydu L, Hayes D, Hayward N, Heiman D, Herbert L, Herman J, Hersey P, Hoadley K, Hodis E, Holt R, Hoon D, Hoppough S, Hoyle A, Huang F, Huang M, Huang S, Hutter C, Ibbs M, Iype L, Jacobsen A, Jakrot V, Janning A, Jeck W, Jefferys S, Jensen M, Jones C, Jones S, Ju Z, Kakavand H, Kang H, Kefford R, Khuri F, Kim J, Kirkwood J, Klode J, Korkut A, Korski K, Krauthammer M, Kucherlapati R, Kwong L, Kycler W, Ladanyi M, Lai P, Laird P, Lander E, Lawrence M, Lazar A, Łaźniak R, Lee D, Lee J, Lee J, Lee K, Lee S, Lee W, Leporowska E, Leraas K, Li H, Lichtenberg T, Lichtenstein L, Lin P, Ling S, Liu J, Liu O, Liu W, Long G, Lu Y, Ma, Ma Y, Mackiewicz A, Mahadeshwar H, Malke J, Mallery D, Manikhas G, Mann G, Marra M, Matejka B, Mayo M, Mehrabi S, Meng S, Meyerson M, Mieczkowski P, Miller J, Miller M, Mills G, Moiseenko F, Moore R, Morris S, Morrison C, Morton D, Moschos S, Mose L, Muller F, Mungall A, Murawa D, Murawa P, Murray B, Nezi L, Ng S, Nicholson D, Noble M, Osunkoya A, Owonikoko T, Ozenberger B, Pagani E, Paklina O, Pantazi A, Parfenov M, Parfitt J, Park P, Park W, Parker J, Passarelli F, Penny R, Perou C, Pihl T, Potapova O, Prieto V, Protopopov A, Quinn M, Radenbaugh A, Rai K, Ramalingam S, Raman A, Ramirez N, Ramirez R, Rao U, Rathmell W, Ren X, Reynolds S, Roach J, Robertson A, Ross M, Roszik J, Russo G, Saksena G, Saller C, Samuels Y, Sander C, Sander C, Sandusky G, Santoso N, Saul M, Saw R, Schadendorf D, Schein J, Schultz N, Schumacher S, Schwallier C, Scolyer R, Seidman J, Sekhar P, Sekhon H, Senbabaoglu Y, Seth S, Shannon K, Sharpe S, Sharpless N, Shaw K, Shelton C, Shelton T, Shen R, Sheth M, Shi Y, Shiau C, Shmulevich I, Sica G, Simons J, Sinha R, Sipahimalani P, Sofia H, Soloway M, Song X, Sougnez C, Spillane A, Spychała A, Stretch J, Stuart J, Suchorska W, Sucker A, Sumer S, Sun Y, Synott M, Tabak B, Tabler T, Tam A, Tan D, Tang J, Tarnuzzer R, Tarvin K, Tatka H, Taylor B, Teresiak M, Thiessen N, Thompson J, Thorne L, Thorsson V, Trent J, Triche T, Tsai K, Tsou P, Van Den Berg D, Van Allen E, Veluvolu U, Verhaak R, Voet D, Voronina O, Walter V, Walton J, Wan Y, Wang Y, Wang Z, Waring S, Watson I, Weinhold N, Weinstein J, Weisenberger D, White P, Wilkerson M, Wilmott J, Wise L, Wiznerowicz M, Woodman S, Wu C, Wu C, Wu J, Wu Y, Xi R, Xu A, Yang D, Yang L, Yang L, Zack T, Zenklusen J, Zhang H, Zhang J, Zhang W, Zhao X, Zhu J, Zhu K, Zimmer L, Zmuda E, Zou L. Genomic Classification of Cutaneous Melanoma. Cell 2015, 161: 1681-1696. PMID: 26091043, PMCID: PMC4580370, DOI: 10.1016/j.cell.2015.05.044.
- Bone Marrow Microenvironment Regulates Alternative Splicing Events in Myeloma Cells through Downregulation of RNA Binding Protein Fox2Song W, Zhang C, Hu Y, Gkotzamanidou M, Shah P, Shan W, Yang G, Li Y, Sperling A, Rashid N, Samur M, Amin S, Tai Y, Hideshima T, Parmigiani G, Magrangeas F, Minvielle S, Avet-Loiseau H, Anderson K, Li C, Munshi N. Bone Marrow Microenvironment Regulates Alternative Splicing Events in Myeloma Cells through Downregulation of RNA Binding Protein Fox2. Blood 2014, 124: 4714. DOI: 10.1182/blood.v124.21.4714.4714.
- MicroRNA expression patterns in medullary and extramedullary plasmacytomaLin J, Mahindra A, Santo L, Amin S, Sohani A, Raje N. MicroRNA expression patterns in medullary and extramedullary plasmacytoma. Blood Cancer Journal 2014, 4: e223-e223. PMID: 24972152, PMCID: PMC4080212, DOI: 10.1038/bcj.2014.41.
- Bone Marrow Microenvironment Affects The Pathogenesis Of Multiple Myeloma Through Downregulation Of Alternative Splicing Factor Fox2 In Myeloma CellsSong W, Zhang C, Hu Y, Gkotzamanidou M, Shah P, Shan W, Yang G, Amin S, Tai Y, Li Y, Sperling A, Rashid N, Magrangeas F, Minvielle S, Avet-Loiseau H, Anderson K, Li C, Munshi N. Bone Marrow Microenvironment Affects The Pathogenesis Of Multiple Myeloma Through Downregulation Of Alternative Splicing Factor Fox2 In Myeloma Cells. Blood 2013, 122: 3085. DOI: 10.1182/blood.v122.21.3085.3085.
- Transcription factor-pathway coexpression analysis reveals cooperation between SP1 and ESR1 on dysregulating cell cycle arrest in non-hyperdiploid multiple myelomaWang X, Yan Z, Fulciniti M, Li Y, Gkotzamanidou M, Amin S, Shah P, Zhang Y, Munshi N, Li C. Transcription factor-pathway coexpression analysis reveals cooperation between SP1 and ESR1 on dysregulating cell cycle arrest in non-hyperdiploid multiple myeloma. Leukemia 2013, 28: 894-903. PMID: 23925045, PMCID: PMC4155324, DOI: 10.1038/leu.2013.233.
- Investigational agent MLN9708/2238 targets tumor-suppressor miR33b in MM cellsTian Z, Zhao J, Tai Y, Amin S, Hu Y, Berger A, Richardson P, Chauhan D, Anderson K. Investigational agent MLN9708/2238 targets tumor-suppressor miR33b in MM cells. Blood 2012, 120: 3958-3967. PMID: 22983447, PMCID: PMC3496955, DOI: 10.1182/blood-2012-01-401794.
- Integrative analysis of gene and miRNA expression profiles with transcription factor–miRNA feed-forward loops identifies regulators in human cancersYan Z, Shah P, Amin S, Samur M, Huang N, Wang X, Misra V, Ji H, Gabuzda D, Li C. Integrative analysis of gene and miRNA expression profiles with transcription factor–miRNA feed-forward loops identifies regulators in human cancers. Nucleic Acids Research 2012, 40: e135-e135. PMID: 22645320, PMCID: PMC3458521, DOI: 10.1093/nar/gks395.
- Significant Biological Role of Sp1 Transactivation in Multiple MyelomaFulciniti M, Amin S, Nanjappa P, Rodig S, Prabhala R, Li C, Minvielle S, Tai Y, Tassone P, Avet-Loiseau H, Hideshima T, Anderson K, Munshi N. Significant Biological Role of Sp1 Transactivation in Multiple Myeloma. Clinical Cancer Research 2011, 17: 6500-6509. PMID: 21856768, PMCID: PMC4318245, DOI: 10.1158/1078-0432.ccr-11-1036.
- The dChip survival analysis module for microarray dataAmin S, Shah P, Yan A, Adamia S, Minvielle S, Avet-Loiseau H, Munshi N, Li C. The dChip survival analysis module for microarray data. BMC Bioinformatics 2011, 12: 72. PMID: 21388547, PMCID: PMC3068974, DOI: 10.1186/1471-2105-12-72.
- Targeting Sp1 Transactivation In Waldenstrom's Macroglobulinemia: a Novel Therapeutic OptionFulciniti M, Amin S, Mohan V, Yang G, Nanjappa P, Tassone P, Prabhala R, Cheng L, Anderson K, Treon S, Munshi N. Targeting Sp1 Transactivation In Waldenstrom's Macroglobulinemia: a Novel Therapeutic Option. Blood 2010, 116: 120. DOI: 10.1182/blood.v116.21.120.120.
- Biology and Therapeutic Targeting of Sp1 Transactivation In MyelomaFulciniti M, Amin S, Nanjappa P, Rodig S, Hideshima T, Pal J, Mohan V, Lee K, Shammas M, Minvielle S, Prabhala R, Avet-Loiseau H, Cheng L, Anderson K, Munshi N. Biology and Therapeutic Targeting of Sp1 Transactivation In Myeloma. Blood 2010, 116: 134. DOI: 10.1182/blood.v116.21.134.134.
- Molecular Profiling of Extramedullary and Medullary Plasmacytomas Compared to Multiple MyelomaMahindra A, Amin S, Sohani A, Motyckova G, Patel K, Vallet S, Pozzi S, Santo L, Cirstea D, Toomey C, Michaelson J, Hochberg E, Dal Cin P, Rodig S, Hideshima T, Anderson K, Munshi N, Raje N. Molecular Profiling of Extramedullary and Medullary Plasmacytomas Compared to Multiple Myeloma. Blood 2010, 116: 4042. DOI: 10.1182/blood.v116.21.4042.4042.
- Elevated IL-17 produced by T h 17 cells promotes myeloma cell growth and inhibits immune function in multiple myelomaPrabhala R, Pelluru D, Fulciniti M, Prabhala H, Nanjappa P, Song W, Pai C, Amin S, Tai Y, Richardson P, Ghobrial I, Treon S, Daley J, Anderson K, Kutok J, Munshi N. Elevated IL-17 produced by T h 17 cells promotes myeloma cell growth and inhibits immune function in multiple myeloma. Blood 2010, 115: 5385-5392. PMID: 20395418, PMCID: PMC2902136, DOI: 10.1182/blood-2009-10-246660.