https://www.mskilab.org/publicationsnew daily 0.75 2025-07-01 https://www.mskilab.org/publicationsnew/blog-post-title-one-lzkff monthly 0.5 2025-07-01 https://www.mskilab.org/publicationsnew/blog-post-title-two-plxy2 monthly 0.5 2020-05-19 https://www.mskilab.org/publicationsnew/blog-post-title-three-wpm87 monthly 0.5 2020-05-19 https://www.mskilab.org/publicationsnew/blog-post-title-four-b66zd monthly 0.5 2020-05-19 https://www.mskilab.org/software daily 0.75 2026-10-13 https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1550177992157-I9PUCZL8KK57HJ08625L/image.png GitHub - GxG The GxG package provides a flexible, queriable R interface to genome matrices (i.e. matrices of genomic ranges), such as those used to represent maps of 3D chromatin contacts or linked-read barcode sharing. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524108903443-1RUNU0HBO9LTAQGGY6BN/JaBbA.png GitHub - JaBbA MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524579974910-DG0UIAJDP6AQNDGA98HB/SvAbA.png GitHub - SvAbA Glocal streaming assembly for somatic and germline structural variant detection. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1528415278483-MHU703M20OK38FL3QZDH/FishHook.png GitHub - fishHook R package for applying Gamma-Poisson regression to identify statistical enrichment of somatic mutations in regions after correcting for genomic covariates. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524109182126-KRV8Q5HUSEE6OH07ROT6/gTrack.png GitHub - gTrack R package for visualizing complex and multi-track 1D and 2D genomic data in GenomicRanges framework https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524109314535-PR0KEMWWBGN3YG0IRYDW/gGnome.png GitHub - gGnome R API for building, manipulating, querying, and mining reference-aligned genome graphs within GenomicRanges framework. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524109609702-LCE40TVQL1YQG6W4KQZP/gGnome.js.png GitHub - gGnome.js D3.js-based dynamic visualization framework of reference-aligned genome graphs and assemblies https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524109555789-1ICS8GI4UFE7PQJ1ZKYM/gUtils.png GitHub - gUtils Syntactic sugar for GenomicRanges ninjas. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524109498455-0TMJSO6XOS3H2T4CSW68/Flow.png GitHub - Flow Lightweight R-based genomics workflow management for SGE, UGER, and LSF https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524109391006-7D2IPETPCE74KU1XZ49H/ffTrack.png GitHub - ffTrack GenomicRanges based R class for fast, out-of-core memory access and storage of numeric and character data that is a function of genomic position. https://www.mskilab.org/join-us daily 0.75 2025-07-01 https://www.mskilab.org/new-page-2-1 daily 0.75 2022-12-21 https://www.mskilab.org/selected-2 daily 0.75 2025-05-07 https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1730838729605-JD0M6KEAZ70LW06NYOUV/Screenshot+2024-10-29+at+3.43.45%E2%80%AFPM.png Selected 2 - Long-molecule scars of backup DNA repair in BRCA1- and BRCA2-deficient cancers (Copy) Long-molecule scars of backup DNA repair in BRCA1- and BRCA2-deficient cancers Jeremy Setton, Kevin Hadi, Zi-Ning Choo, Katherine S. Kuchin, Huasong Tian, Arnaud Da Cruz Paula, Joel Rosiene, Pier Selenica, Julie Behr, Xiaotong Yao, Aditya Deshpande, Michael Sigouros, Jyothi Manohar, Jones T. Nauseef, Juan-Miguel Mosquera, Olivier Elemento, Britta Weigelt, Nadeem Riaz, Jorge S. Reis-Filho, Simon N. Powell & Marcin Imieliński Nature 621, 129–137 (2023) https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1730841094408-ZZINDS2N0HWEBUA1R0NI/Screenshot+2024-11-05+at+4.11.28%E2%80%AFPM.png Selected 2 - Most large structural variants in cancer genomes can be detected without long reads (Copy) Most large structural variants in cancer genomes can be detected without long reads Zi-Ning Choo, Julie M. Behr, Aditya Deshpande, Kevin Hadi, Xiaotong Yao, Huasong Tian, Kaori Takai, George Zakusilo, Joel Rosiene, Arnaud Da Cruz Paula, Britta Weigelt, Jeremy Setton, Nadeem Riaz, Simon N. Powell, Klaus Busam, Alexander N. Shoushtari, Charlotte Ariyan, Jorge Reis-Filho, Titia de Lange & Marcin Imieliński Nat Genet 55, 2139–2148 (2023) https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1730844291647-6MSB3MLGSTCUWHNSVX30/Screenshot+2024-11-05+at+5.02.58%E2%80%AFPM.png Selected 2 - Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing (Copy) Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing Aditya S. Deshpande, Netha Ulahannan, Matthew Pendleton, Xiaoguang Dai, Lynn Ly, Julie M. Behr, Stefan Schwenk, Will Liao, Michael A. Augello, Carly Tyer, Priyesh Rughani, Sarah Kudman, Huasong Tian, Hannah G. Otis, Emily Adney, David Wilkes, Juan Miguel Mosquera, Christopher E. Barbieri, Ari Melnick, David Stoddart, Daniel J. Turner, Sissel Juul, Eoghan Harrington & Marcin Imieliński Biotechnol 40, 1488–1499 (2022) https://www.mskilab.org/research-1 daily 1.0 2025-10-08 https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524000873055-DGX79TLAX6ST7VA6Z2AX/evolution_shattered.png research - evolution of complex DNA rearrangements in cancer (Copy) evolution of complex DNA rearrangements in cancer A key challenge in analyzing cancer DNA rearrangements from short reads is defining what is an "event". However, with DNA rearrangements there is a fundamental ambiguity regarding the structure or history of a mutated region. In contrast, when we study a DNA substitution, we know both what the mutated locus looks like and how it arrived at its current state. Answering one question can help us answer the other, which is why we are using long-range sequencing technology, multi-biopsy sample sets, and computational modeling to characterize the structure and evolution of complex variants in cancer. This approach can be particularly useful in understanding large-scale rearrangement events, such as chromothripsis (chromosome shattering). https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524006155396-W2ZE4RP0D0OZZZ4JIKNL/genomic+footprints+of+cancer+cell-of-origin+new.png research - genomic footprints of cancer cell-of-origin (Copy) genomic footprints of cancer cell-of-origin Work from our group and others have demonstrated footprints of the lineage history of cancer cells in their DNA, through correlation of mutation patterns with the transcriptomic and epigenetic features of the healthy tissue from which that cancer arose. Though these correlations preliminary have been drawn from transcriptomic and chromatin profiles of bulk healthy tissue, we are working to extend these correlations to other variant types and cell type specific epigenetic profiles. These patterns may provide an orthogonal piece of evidence to link cancer types to their presumed cell-of-origin. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524001923569-YB8JNHQQYMBN1QMMM5N5/long+range+sequencing+and+cancer+genome+assembly+edited.png research - long range sequencing and cancer genome assembly (Copy) long range sequencing and cancer genome assembly Short read (<300bp) sequences leave considerable ambiguity about the long-range structure or "phase" of altered loci. Phase is often essential for diagnosing the functional outcome of a given variant, and for inferring how that variant evolved. Such information is especially important in cancer genomes affected by complex clustered variants such as chromothripsis (chromosome shattering), kataegis (mutational showers), and chromoplexy (chains of balanced rearrangements). Using novel technologies, such as linked-read sequencing (10X genomics), we can computationally reconstruct the long range structure of variant loci in cancer, and infer novel event types. Analysis of these data requires development of novel algorithms, data formats, and visualization approaches, which the lab is actively engaged in. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524000766442-TIS9KKUHPX2Y2ZYQBJ5S/DNA+signatures+of+somatic+mutation+processes+and+genome+integrity+defects.png research - DNA signatures of somatic mutation processes and genome integrity defects (Copy) DNA signatures of somatic mutation processes and genome integrity defects Every cancer genome provides a readout of mutational processes or DNA repair defects that are active in tumor cells or their healthy predecessors. Such phenomena have been extensively characterized for somatic SNV, but are less well known for indels and DNA rearrangements. The lab is actively pursuing novel analytic approaches in human cancer and engineered systems to study these processes and to infer their genetic or chemical determinants. Better understanding of these processes and repair defects can inform treatment choice for targeted therapy as well as classic chemotherapy and immunotherapy. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1484960463087-IUPOVCK435KX6XO5DV2Y/epigenetic+consequences+of+somatic+DNA+variants.fuck.png research - epigenetic consequences of somatic DNA variants (Copy) epigenetic consequences of somatic DNA variants Somatic DNA variants that land outside of coding regions can alter how genes are transcribed and chromatin is organized in the nucleus. Unlike SNVs and indels, DNA rearrangements likely induce severe perturbations to the regulatory landscape of cells, though the nature of this impact is only beginning to be understood. We seek to characterize the impact of DNA rearrangements on the tumor epigenome through long-range sequencing and chromatin profiling of rearranged tumors. We hope this analysis will yield novel noncoding driver candidates in tumor subtypes where no known coding driver alteration has been discovered. https://www.mskilab.org/previous-1 daily 0.75 2025-05-07 https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524103050822-LN80CMRTXZIIN9DJ5GLR/Imielinski+JCI+2014.png previous - Oncogenic and sorafenib-sensitive ARAF mutations in lung adenocarcinoma. (Copy) 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 https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524103462771-QLEFJZTCQCK2F84J4KBH/Berger+Oncogene+2014.png previous - Oncogenic RIT1 mutations in lung adenocarcinoma. (Copy) 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 https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524103224440-LTT2YQTMN76F3FKB226J/Imielinski+Cell+2012.png previous - Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. (Copy) 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. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524103360067-M92ZZCE8AUL3AEXKHIXZ/Imielinski+2012+MCP.png previous - Integrated proteomic, transcriptomic, and biological network analysis of breast carcinoma reveals molecular features of tumorigenesis and clinical relapse. (Copy) 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. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524103541854-T6WUUZ3JIOTEIU6VEGEX/Imielinski+Nat+Gen+2009.jpg previous - Common variants at five new loci associated with early-onset inflammatory bowel disease. (Copy) 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. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524113748430-KGMOMDTNK4NK2QLFJXKJ/Imielinski+Belta+2010.png previous - Deep epistasis in human metabolism. (Copy) Deep epistasis in human metabolism. Imielinski M, Belta C. Chaos 2010 Jun;20(2):026104. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1644964668679-YNJG0WJ9X42CC6JZQSPK/Imielinski+Belta+BMC+systems+biology.png previous - Exploiting the pathway structure of metabolism to reveal high-order epistasis. (Copy) Exploiting the pathway structure of metabolism to reveal high-order epistasis. Imielinski M, Belta C. BMC Systems Biology 2008 Apr 30;2(1):40. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524107237967-6FOD78U5IZPZQAOESW7D/Imielinski+Biophysj+2006.png previous - Systematic analysis of conservation relations in Escherichia coli genome-scale metabolic network reveals novel growth media. (Copy) Systematic analysis of conservation relations in Escherichia coli genome-scale metabolic network reveals novel growth media. Imielinski M, Belta C, Rubin H, Halász A. Biophysical Journal 2006 Apr 15;90(8):2659–72. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1644955826604-DYHAZ5WTF78I5JG8BK3H/image-asset.png previous - Investigating metabolite essentiality through genome-scale analysis of Escherichia coli production capabilities. (Copy) Investigating metabolite essentiality through genome-scale analysis of Escherichia coli production capabilities. Imieliński M, Belta C, Halász A, Rubin H. Bioinformatics. 2005 May 1;21(9):2008-16. doi: 10.1093/bioinformatics/bti245. https://www.mskilab.org/pubs daily 0.75 2025-05-07 https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1644951610160-4JYMNEJC9U20JQBUJOJ1/image-asset.png pubs - Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs (Copy) 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. 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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. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1644952291173-XGX9EKR6MLHS8F8WS9WZ/image-asset.png pubs - Structural variant evolution after telomere crisis. (Copy) 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. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1644952509808-HF3J59GET240W0H050SA/image-asset.png pubs - Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions. (Copy) Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions. 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Turner, Sissel Juul, Eoghan Harrington*, Marcin Imielinski* bioRxiv 833590; doi: https://doi.org/10.1101/833590 https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1644954633536-QVSBP9MRIPYIXZ0WPHEX/image-asset.png pubs - Robust foreground detection in somatic copy number data (Copy) 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 https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524102738062-4LYDIJTS9SLYS9LAKBN8/Imielinski+and+Rubin+2017.png pubs - Prostate cancer: Clinical hallmarks in whole cancer genomes. (Copy) Prostate cancer: Clinical hallmarks in whole cancer genomes. Imielinski M, Rubin MA. Nature Reviews Clinical Oncology 2017 May;14(5):265–6. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524102252157-W97609RAQKCO2VWJWY58/Wala+Genome+Research+2018.png pubs - SvABA: genome-wide detection of structural variants and indels by local assembly. (Copy) 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. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524102036903-XMYFTR46OCRINP3DQLEM/Imielinski+Cell+2017.jpg pubs - Insertions and Deletions Target Lineage-Defining Genes in Human Cancers (Copy) 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. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524102688449-0VFZSL61JZNWD9ETZ6VL/Imielinski+and+Maciejowski.png pubs - Modeling cancer rearrangement landscapes. (Copy) Modeling cancer rearrangement landscapes. Maciejowski J, Imielinski M. Current Opinion in Systems Biology 2017 Feb;1:54–61. https://www.mskilab.org/our-team daily 0.75 2026-10-13 https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/ecbe55e4-918f-43f7-82fe-ceb9544b2d54/Screenshot+2026-10-05+at+10.32.53%E2%80%AFAM.png https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/9cefe841-5058-412e-9ef8-d16224788ad4/narcissism_1024.jpg https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/6aed00c7-cbd8-4627-8e73-ea3b5d3067a4/360_F_602503659_0LbDrdzqysTGbKcKKxRo3vKuLhxkwahL.jpg https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/5383c7bc-7da3-41d9-9443-f7eea6d20931/IMG_0149.jpeg https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/b0619297-b2fb-4213-89f9-bb192bbf66c8/360_F_602503659_0LbDrdzqysTGbKcKKxRo3vKuLhxkwahL.jpg https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/c6f4cd11-7177-45e4-9102-d46908cdad8b/IMG_2838.jpg https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/62b95530-b553-44a8-8c3f-3f03c72aa42d/Image+from+iOS+%281%29.jpg https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/b0619297-b2fb-4213-89f9-bb192bbf66c8/360_F_602503659_0LbDrdzqysTGbKcKKxRo3vKuLhxkwahL.jpg https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/b0619297-b2fb-4213-89f9-bb192bbf66c8/360_F_602503659_0LbDrdzqysTGbKcKKxRo3vKuLhxkwahL.jpg https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/d192ac8f-0ea3-442f-b081-2e6998bcd7fc/IMG_4907.jpeg https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/b0619297-b2fb-4213-89f9-bb192bbf66c8/360_F_602503659_0LbDrdzqysTGbKcKKxRo3vKuLhxkwahL.jpg https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/b0619297-b2fb-4213-89f9-bb192bbf66c8/360_F_602503659_0LbDrdzqysTGbKcKKxRo3vKuLhxkwahL.jpg https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/6aed00c7-cbd8-4627-8e73-ea3b5d3067a4/360_F_602503659_0LbDrdzqysTGbKcKKxRo3vKuLhxkwahL.jpg https://www.mskilab.org/publications-new daily 0.75 2025-07-01 https://www.mskilab.org/join-us-1 daily 0.75 2026-10-13 https://www.mskilab.org/research daily 0.75 2026-10-13 https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1780932028.195412-GIRPQEJAAZBKCYZAHFPE/imgg-gg3p-BC-DQ-C-103a576c.png https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1780932028.295652-ZIMTFBPHNJAOEGUPULTF/imgg-gg3p-BC-DQ-F-9f708727.png https://www.mskilab.org/funding daily 0.75 2026-10-13 https://www.mskilab.org/funding/new-page-cndkx monthly 0.5 2025-04-24 https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524111809563-2ASQUX09GM5DUESEQK7S/BWF.png Funding - Funding - Burroughs Wellcome Fund https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524111856139-PSQ7B7LS4GKJYZ5VKMW5/DDCF.jpeg Funding - Funding https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524111890028-Z485UEO47MOVHCNPEIKB/Starr.jpeg Funding - Funding https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524667227274-ZL1SIO768RCKPM7V9CGN/MRA.jpg Funding - Funding https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524111924464-SFVC4Y85NO8KOMZ4HKCG/NCI.png Funding - Funding https://www.mskilab.org/publications daily 0.75 2026-10-13 https://www.mskilab.org/publications/selected-1-gxkbp monthly 0.5 2026-10-13 https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524103050822-LN80CMRTXZIIN9DJ5GLR/Imielinski+JCI+2014.png Publications - previous - 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 https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524103462771-QLEFJZTCQCK2F84J4KBH/Berger+Oncogene+2014.png Publications - previous - 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 https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524103224440-LTT2YQTMN76F3FKB226J/Imielinski+Cell+2012.png Publications - previous - 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. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524103360067-M92ZZCE8AUL3AEXKHIXZ/Imielinski+2012+MCP.png Publications - previous - 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. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524103541854-T6WUUZ3JIOTEIU6VEGEX/Imielinski+Nat+Gen+2009.jpg Publications - previous - 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. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524113748430-KGMOMDTNK4NK2QLFJXKJ/Imielinski+Belta+2010.png Publications - previous - Deep epistasis in human metabolism. Imielinski M, Belta C. Chaos 2010 Jun;20(2):026104. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1644964668679-YNJG0WJ9X42CC6JZQSPK/Imielinski+Belta+BMC+systems+biology.png Publications - previous - Exploiting the pathway structure of metabolism to reveal high-order epistasis. Imielinski M, Belta C. BMC Systems Biology 2008 Apr 30;2(1):40. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524107237967-6FOD78U5IZPZQAOESW7D/Imielinski+Biophysj+2006.png Publications - previous - Systematic analysis of conservation relations in Escherichia coli genome-scale metabolic network reveals novel growth media. Imielinski M, Belta C, Rubin H, Halász A. Biophysical Journal 2006 Apr 15;90(8):2659–72. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1644955826604-DYHAZ5WTF78I5JG8BK3H/image-asset.png Publications - previous - Investigating metabolite essentiality through genome-scale analysis of Escherichia coli production capabilities. Imieliński M, Belta C, Halász A, Rubin H. Bioinformatics. 2005 May 1;21(9):2008-16. doi: 10.1093/bioinformatics/bti245. https://www.mskilab.org/publications/new-page-4-9ya2d monthly 0.5 2025-07-03 https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1730838729605-JD0M6KEAZ70LW06NYOUV/Screenshot+2024-10-29+at+3.43.45%E2%80%AFPM.png Publications - Current - Long-molecule scars of backup DNA repair in BRCA1- and BRCA2-deficient cancers Jeremy Setton, Kevin Hadi, Zi-Ning Choo, Katherine S. Kuchin, Huasong Tian, Arnaud Da Cruz Paula, Joel Rosiene, Pier Selenica, Julie Behr, Xiaotong Yao, Aditya Deshpande, Michael Sigouros, Jyothi Manohar, Jones T. Nauseef, Juan-Miguel Mosquera, Olivier Elemento, Britta Weigelt, Nadeem Riaz, Jorge S. Reis-Filho, Simon N. Powell & Marcin Imieliński Nature 621, 129–137 (2023) https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1730841094408-ZZINDS2N0HWEBUA1R0NI/Screenshot+2024-11-05+at+4.11.28%E2%80%AFPM.png Publications - Current - Most large structural variants in cancer genomes can be detected without long reads Zi-Ning Choo, Julie M. Behr, Aditya Deshpande, Kevin Hadi, Xiaotong Yao, Huasong Tian, Kaori Takai, George Zakusilo, Joel Rosiene, Arnaud Da Cruz Paula, Britta Weigelt, Jeremy Setton, Nadeem Riaz, Simon N. Powell, Klaus Busam, Alexander N. Shoushtari, Charlotte Ariyan, Jorge Reis-Filho, Titia de Lange & Marcin Imieliński Nat Genet 55, 2139–2148 (2023) https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1730844291647-6MSB3MLGSTCUWHNSVX30/Screenshot+2024-11-05+at+5.02.58%E2%80%AFPM.png Publications - Current - Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing Aditya S. Deshpande, Netha Ulahannan, Matthew Pendleton, Xiaoguang Dai, Lynn Ly, Julie M. Behr, Stefan Schwenk, Will Liao, Michael A. Augello, Carly Tyer, Priyesh Rughani, Sarah Kudman, Huasong Tian, Hannah G. Otis, Emily Adney, David Wilkes, Juan Miguel Mosquera, Christopher E. Barbieri, Ari Melnick, David Stoddart, Daniel J. Turner, Sissel Juul, Eoghan Harrington & Marcin Imieliński Biotechnol 40, 1488–1499 (2022) https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1644951610160-4JYMNEJC9U20JQBUJOJ1/image-asset.png Publications - Current - 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. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1727728008420-S871Z5Q3QYVX0I8Y7LL4/Screenshot+2024-09-30+at+2.18.11%E2%80%AFPM.png Publications - Current - 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. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1644952291173-XGX9EKR6MLHS8F8WS9WZ/image-asset.png Publications - Current - 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. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1644952509808-HF3J59GET240W0H050SA/image-asset.png Publications - Current - 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 https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1644952708522-M9DFNDBKDKMZNXJF7GQS/image-asset.png Publications - Current - 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 https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1644951831323-IA7L2JO9Q1ULPXY65UIV/image-asset.png Publications - Current - 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. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524102639432-MZ8SJRRYQSTUB4YYGBEM/Li+et+al+2017.png Publications - Current - 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. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1644953020780-53DZVR7VHIWQ4EANOGLX/image-asset.png Publications - Current - 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 https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1644954633536-QVSBP9MRIPYIXZ0WPHEX/image-asset.png Publications - Current - 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 https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524102738062-4LYDIJTS9SLYS9LAKBN8/Imielinski+and+Rubin+2017.png Publications - Current - Prostate cancer: Clinical hallmarks in whole cancer genomes. Imielinski M, Rubin MA. Nature Reviews Clinical Oncology 2017 May;14(5):265–6. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524102252157-W97609RAQKCO2VWJWY58/Wala+Genome+Research+2018.png Publications - Current - 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. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524102036903-XMYFTR46OCRINP3DQLEM/Imielinski+Cell+2017.jpg Publications - Current - 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. https://images.squarespace-cdn.com/content/v1/562537a8e4b0bbf0e0b819f1/1524102688449-0VFZSL61JZNWD9ETZ6VL/Imielinski+and+Maciejowski.png Publications - Current - Modeling cancer rearrangement landscapes. Maciejowski J, Imielinski M. Current Opinion in Systems Biology 2017 Feb;1:54–61.