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Selected Publications

Featured

Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs

Hadi K, Yao X, Behr JM, Deshpande A, Xanthopoulakis C, Tian H, Kudman S, Rosiene J, Darmofal M, DeRose J, Mortensen R, Adney EM, Shaiber A, Gajic Z, Sigouros M, Eng K, Wala JA, Wrzeszczyński KO, Arora K, Shah M, Emde AK, Felice V, Frank MO, Darnell RB, Ghandi M, Huang F, Dewhurst S, Maciejowski J, de Lange T, Setton J, Riaz N, Reis-Filho JS, Powell S, Knowles DA, Reznik E, Mishra B, Beroukhim R, Zody MC, Robine N, Oman KM, Sanchez CA, Kuhner MK, Smith LP, Galipeau PC, Paulson TG, Reid BJ, Li X, Wilkes D, Sboner A, Mosquera JM, Elemento O, Imielinski M.
Cell. 2020 Oct 1;183(1):197-210.e32.

Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway.

Carrot-Zhang J†, Yao X†, Devarakonda S†, Deshpande A, Damrauer JS, Silva TC, Wong CK, Choi HY, Felau I, Robertson AG, Castro MAA, Bao L, Rheinbay E, Liu EM, Trieu T, Haan D, Yau C, Hinoue T, Liu Y, Shapira O, Kumar K, Mungall KL, Zhang H, June-Koo Lee J, Berger A, Gao GF, Zhitomirsky B, Liang WW, Zhou M, Moorthi S, Berger AH, Collisson EA, Zody MC, Ding L, Cherniack AD, Getz G, Elemento O, Benz CC, Stuart J, Zenklusen JC, Beroukhim R, Chang JC, Campbell JD, Hayes DN, Yang L, Laird PW, Weinstein JN, Kwiatkowski DJ, Tsao MS, Travis WD, Khurana E, Berman BP, Hoadley KA, Robine N; TCGA Research Network, Meyerson M*, Govindan R*, Imielinski M*.
Cell Rep. 2021 Feb 23;34(8):108784.

Structural variant evolution after telomere crisis.

Dewhurst SM†, Yao X†, Rosiene J, Tian H, Behr J, Bosco N, Takai KK, de Lange T*, Imieliński M*.

Nat Commun. 2021 Apr 7;12(1):2093.

Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions.

Butler D†, Mozsary C†, Meydan C†, Foox J†, Rosiene J†, Shaiber A†, Danko D†, Afshinnekoo E, MacKay M, Sedlazeck FJ, Ivanov NA, Sierra M, Pohle D, Zietz M, Gisladottir U, Ramlall V, Sholle ET, Schenck EJ, Westover CD, Hassan C, Ryon K, Young B, Bhattacharya C, Ng DL, Granados AC, Santos YA, Servellita V, Federman S, Ruggiero P, Fungtammasan A, Chin CS, Pearson NM, Langhorst BW, Tanner NA, Kim Y, Reeves JW, Hether TD, Warren SE, Bailey M, Gawrys J, Meleshko D, Xu D, Couto-Rodriguez M, Nagy-Szakal D, Barrows J, Wells H, O'Hara NB, Rosenfeld JA, Chen Y, Steel PAD, Shemesh AJ, Xiang J, Thierry-Mieg J, Thierry-Mieg D, Iftner A, Bezdan D, Sanchez E, Campion TR Jr, Sipley J, Cong L, Craney A, Velu P, Melnick AM, Shapira S, Hajirasouliha I, Borczuk A, Iftner T, Salvatore M, Loda M, Westblade LF, Cushing M, Wu S, Levy S, Chiu C, Schwartz RE, Tatonetti N*, Rennert H*, Imielinski M*, Mason CE*.
Nat Commun. 2021 Mar 12;12(1):1660

Loose ends in cancer genome structure

Julie M. Behr, Xiaotong Yao, Kevin Hadi, Huasong Tian, Aditya Deshpande, Joel Rosiene, Titia de Lange, Marcin Imieliński

bioRxiv 2021.05.26.445837; doi: https://doi.org/10.1101/2021.05.26.445837

Impact of Lineage Plasticity to and from a Neuroendocrine Phenotype on Progression and Response in Prostate and Lung Cancers

Rubin MA, Bristow RG, Thienger PD, Dive C, Imielinski M.
Molecular Cell. 2020 Nov 19;80(4):562-577.

Patterns of somatic structural variation in human cancer genomes.

Li Y, Roberts ND, Wala JA, Shapira O, Schumacher SE, Kumar K, Khurana E, Waszak S, Korbel JO, Haber JE, Imielinski M; PCAWG Structural Variation Working Group, Weischenfeldt J, Beroukhim R, Campbell PJ; PCAWG Consortium.
Nature. 2020 Feb;578(7793):112-121. doi: 10.1038/s41586-019-1913-9.

Nanopore sequencing of DNA concatemers reveals higher-order features of chromatin structure

Netha Ulahannan†, Matthew Pendleton†, Aditya Deshpande†, Stefan Schwenk, Julie M. Behr, Xiaoguang Dai, Carly Tyer, Priyesh Rughani, Sarah Kudman, Emily Adney, Huasong Tian, David Wilkes, Juan Miguel Mosquera, David Stoddart, Daniel J. Turner, Sissel Juul, Eoghan Harrington*, Marcin Imielinski*

bioRxiv 833590; doi: https://doi.org/10.1101/833590

Robust foreground detection in somatic copy number data

Aditya Deshpande, Trent Walradt, Ya Hu, Amnon Koren, Marcin Imielinski
bioRxiv 847681; doi: https://doi.org/10.1101/847681

Prostate cancer: Clinical hallmarks in whole cancer genomes.

Imielinski M, Rubin MA.

Nature Reviews Clinical Oncology 2017 May;14(5):265–6.

SvABA: genome-wide detection of structural variants and indels by local assembly.

Wala JA, Bandopadhayay P, Greenwald NF, O'Rourke R, Sharpe T, Stewart C, Schumacher S, Li Y, Weischenfeldt J, Yao X, Nusbaum C, Campbell P, Getz G, Meyerson M, Zhang C-Z*, Imielinski M*, Beroukhim R*.

Genome Research 2018 Apr;28(4):581–91.

Insertions and Deletions Target Lineage-Defining Genes in Human Cancers

Imielinski M*, Guo G, Meyerson M*.

Cell 2017 Jan 26;168(3):460–472.e14.

Modeling cancer rearrangement landscapes.

Maciejowski J, Imielinski M.

Current Opinion in Systems Biology 2017 Feb;1:54–61.

Previous work

Featured

Oncogenic and sorafenib-sensitive ARAF mutations in lung adenocarcinoma.

Imielinski M†, Greulich H†, Kaplan B, Araujo L, Amann J, Horn L, Schiller J, Villalona-Calero MA, Meyerson M*, Carbone DP*.

Journal of Clinical Investigation 2014 Apr;124(4):1582–6. PMCID: PMC3973082

Oncogenic RIT1 mutations in lung adenocarcinoma.

Berger AH, Imielinski M, Duke F, Wala J, Kaplan N, Shi G-X, Andres DA, Meyerson M.

Oncogene 2014 Aug 28;33(35):4418–23. PMCID: PMC4150988

Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing.

Imielinski M, Berger AH, Hammerman PS, Hernandez B, Pugh TJ, Hodis E, Cho J, Suh J, Capelletti M, Sivachenko A, Sougnez C, Auclair D, Lawrence MS, Stojanov P, Cibulskis K, Choi K, de Waal L, Sharifnia T, Brooks A, Greulich H, Banerji S, Zander T, Seidel D, Leenders F, Ansén S, Ludwig C, Engel-Riedel W, Stoelben E, Wolf J, Goparju C, Thompson K, Winckler W, Kwiatkowski D, Johnson BE, Jänne PA, Miller VA, Pao W, Travis WD, Pass HI, Gabriel SB, Lander ES, Thomas RK, Garraway LA, Getz G, Meyerson M.

Cell 2012 Sep 14;150(6):1107–20.

Integrated proteomic, transcriptomic, and biological network analysis of breast carcinoma reveals molecular features of tumorigenesis and clinical relapse.

Imielinski M, Cha S, Rejtar T, Richardson EA, Karger BL, Sgroi DC.

Molecular Cellular Proteomics 2012 Jun;11(6):M111.014910.

Common variants at five new loci associated with early-onset inflammatory bowel disease.

Imielinski M, Baldassano RN, Griffiths A, Russell RK, Annese V, Dubinsky M, Kugathasan S, Bradfield JP, Walters TD, Sleiman P, Kim CE, Muise A, Wang K, Glessner JT, Saeed S, Zhang H, Frackelton EC, Hou C, Flory JH, Otieno G, Chiavacci RM, Grundmeier R, Castro M, Latiano A, Dallapiccola B, Stempak J, Abrams DJ, Taylor K, McGovern D, Western Regional Alliance for Pediatric IBD, Silber G, Wrobel I, Quiros A, International IBD Genetics Consortium, Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, Rioux JD, Brant SR, Silverberg MS, Taylor KD, Barmuda MM, Bitton A, Dassopoulos T, Datta LW, Green T, Griffiths AM, Kistner EO, et al.

Nature Genetics 2009 Dec;41(12):1335–40.