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Noncovalent inhibitors reveal BTK gatekeeper and auto-inhibitory residues that control its transforming activity.

Wang S, Mondal S, Zhao C, Berishaj M, Ghanakota P, Batlevi CL, Dogan A, Seshan VE, Abel R, Green MR, Younes A, Wendel HG.

JCI Insight. 2019 Jun 20;4(12). pii: 127566. doi: 10.1172/jci.insight.127566. eCollection 2019 Jun 20.


Testing Clonal Relatedness of Two Tumors from the Same Patient based on their Mutational Profiles: update of the Clonality R Package.

Mauguen A, Seshan VE, Begg CB, Ostrovnaya I.

Bioinformatics. 2019 Jun 14. pii: btz486. doi: 10.1093/bioinformatics/btz486. [Epub ahead of print]


Identification of prognostic molecular biomarkers in 157 HPV-positive and HPV-negative squamous cell carcinomas of the oropharynx.

Dogan S, Xu B, Middha S, Vanderbilt CM, Bowman AS, Migliacci J, Morris LGT, Seshan VE, Ganly I.

Int J Cancer. 2019 Dec 1;145(11):3152-3162. doi: 10.1002/ijc.32412. Epub 2019 May 30.


Harnessing Clinical Sequencing Data for Survival Stratification of Patients with Metastatic Lung Adenocarcinomas.

Shen R, Martin A, Ni A, Hellmann M, Arbour KC, Jordan E, Arora A, Ptashkin R, Zehir A, Kris MG, Rudin CM, Berger MF, Solit DB, Seshan VE, Arcila M, Ladanyi M, Riely GJ.

JCO Precis Oncol. 2019;3. doi: 10.1200/PO.18.00307. Epub 2019 Mar 28.


Author Correction: The Rho GTPase Rnd1 suppresses mammary tumorigenesis and EMT by restraining Ras-MAPK signalling.

Okada T, Sinha S, Esposito I, Schiavon G, López-Lago MA, Su W, Pratilas CA, Abele C, Hernandez JM, Ohara M, Okada M, Viale A, Heguy A, Socci ND, Sapino A, Seshan VE, Long S, Inghirami G, Rosen N, Giancotti FG.

Nat Cell Biol. 2019 Apr;21(4):534. doi: 10.1038/s41556-019-0288-3.


NOXA genetic amplification or pharmacologic induction primes lymphoma cells to BCL2 inhibitor-induced cell death.

Liu Y, Mondello P, Erazo T, Tannan NB, Asgari Z, de Stanchina E, Nanjangud G, Seshan VE, Wang S, Wendel HG, Younes A.

Proc Natl Acad Sci U S A. 2018 Nov 20;115(47):12034-12039. doi: 10.1073/pnas.1806928115. Epub 2018 Nov 7.


HSP90-incorporating chaperome networks as biosensor for disease-related pathways in patient-specific midbrain dopamine neurons.

Kishinevsky S, Wang T, Rodina A, Chung SY, Xu C, Philip J, Taldone T, Joshi S, Alpaugh ML, Bolaender A, Gutbier S, Sandhu D, Fattahi F, Zimmer B, Shah SK, Chang E, Inda C, Koren J 3rd, Saurat NG, Leist M, Gross SS, Seshan VE, Klein C, Tomishima MJ, Erdjument-Bromage H, Neubert TA, Henrickson RC, Chiosis G, Studer L.

Nat Commun. 2018 Oct 19;9(1):4345. doi: 10.1038/s41467-018-06486-6.


PTEN Expression, Not Mutation Status in TSC1, TSC2, or mTOR, Correlates with the Outcome on Everolimus in Patients with Renal Cell Carcinoma Treated on the Randomized RECORD-3 Trial.

Voss MH, Chen D, Reising A, Marker M, Shi J, Xu J, Ostrovnaya I, Seshan VE, Redzematovic A, Chen YB, Patel P, Han X, Hsieh JJ, Hakimi AA, Motzer RJ.

Clin Cancer Res. 2019 Jan 15;25(2):506-514. doi: 10.1158/1078-0432.CCR-18-1833. Epub 2018 Oct 16.


Vemurafenib Redifferentiation of BRAF Mutant, RAI-Refractory Thyroid Cancers.

Dunn LA, Sherman EJ, Baxi SS, Tchekmedyian V, Grewal RK, Larson SM, Pentlow KS, Haque S, Tuttle RM, Sabra MM, Fish S, Boucai L, Walters J, Ghossein RA, Seshan VE, Ni A, Li D, Knauf JA, Pfister DG, Fagin JA, Ho AL.

J Clin Endocrinol Metab. 2019 May 1;104(5):1417-1428. doi: 10.1210/jc.2018-01478.


BET Inhibition-Induced GSK3β Feedback Enhances Lymphoma Vulnerability to PI3K Inhibitors.

Derenzini E, Mondello P, Erazo T, Portelinha A, Liu Y, Scallion M, Asgari Z, Philip J, Hilden P, Valli D, Rossi A, Djaballah H, Ouerfelli O, de Stanchina E, Seshan VE, Hendrickson RC, Younes A.

Cell Rep. 2018 Aug 21;24(8):2155-2166. doi: 10.1016/j.celrep.2018.07.055.


Targeted delivery of a PD-1-blocking scFv by CAR-T cells enhances anti-tumor efficacy in vivo.

Rafiq S, Yeku OO, Jackson HJ, Purdon TJ, van Leeuwen DG, Drakes DJ, Song M, Miele MM, Li Z, Wang P, Yan S, Xiang J, Ma X, Seshan VE, Hendrickson RC, Liu C, Brentjens RJ.

Nat Biotechnol. 2018 Oct;36(9):847-856. doi: 10.1038/nbt.4195. Epub 2018 Aug 13.


Integrated DNA/RNA targeted genomic profiling of diffuse large B-cell lymphoma using a clinical assay.

Intlekofer AM, Joffe E, Batlevi CL, Hilden P, He J, Seshan VE, Zelenetz AD, Palomba ML, Moskowitz CH, Portlock C, Straus DJ, Noy A, Horwitz SM, Gerecitano JF, Moskowitz A, Hamlin P, Matasar MJ, Kumar A, van den Brink MR, Knapp KM, Pichardo JD, Nahas MK, Trabucco SE, Mughal T, Copeland AR, Papaemmanuil E, Moarii M, Levine RL, Dogan A, Miller VA, Younes A.

Blood Cancer J. 2018 Jun 12;8(6):60. doi: 10.1038/s41408-018-0089-0.



Begg CB, Seshan VE, Zabor EC.

Am J Epidemiol. 2018 May 1;187(5):1129-1130. doi: 10.1093/aje/kwy032. No abstract available.


Small-Cell Carcinomas of the Bladder and Lung Are Characterized by a Convergent but Distinct Pathogenesis.

Chang MT, Penson A, Desai NB, Socci ND, Shen R, Seshan VE, Kundra R, Abeshouse A, Viale A, Cha EK, Hao X, Reuter VE, Rudin CM, Bochner BH, Rosenberg JE, Bajorin DF, Schultz N, Berger MF, Iyer G, Solit DB, Al-Ahmadie HA, Taylor BS.

Clin Cancer Res. 2018 Apr 15;24(8):1965-1973. doi: 10.1158/1078-0432.CCR-17-2655. Epub 2017 Nov 27.


Contralateral breast cancers: Independent cancers or metastases?

Begg CB, Ostrovnaya I, Geyer FC, Papanastasiou AD, Ng CKY, Sakr RA, Bernstein JL, Burke KA, King TA, Piscuoglio S, Mauguen A, Orlow I, Weigelt B, Seshan VE, Morrow M, Reis-Filho JS.

Int J Cancer. 2018 Jan 15;142(2):347-356. doi: 10.1002/ijc.31051. Epub 2017 Sep 28.


Genomic landscape and evolution of metastatic chromophobe renal cell carcinoma.

Casuscelli J, Weinhold N, Gundem G, Wang L, Zabor EC, Drill E, Wang PI, Nanjangud GJ, Redzematovic A, Nargund AM, Manley BJ, Arcila ME, Donin NM, Cheville JC, Thompson RH, Pantuck AJ, Russo P, Cheng EH, Lee W, Tickoo SK, Ostrovnaya I, Creighton CJ, Papaemmanuil E, Seshan VE, Hakimi AA, Hsieh JJ.

JCI Insight. 2017 Jun 15;2(12). pii: 92688. doi: 10.1172/jci.insight.92688. eCollection 2017 Jun 15.


Defining Cancer Subtypes With Distinctive Etiologic Profiles: An Application to the Epidemiology of Melanoma.

Mauguen A, Zabor EC, Thomas NE, Berwick M, Seshan VE, Begg CB.

J Am Stat Assoc. 2017;112(517):54-63. doi: 10.1080/01621459.2016.1191499. Epub 2017 May 3.


Estimating the probability of clonal relatedness of pairs of tumors in cancer patients.

Mauguen A, Seshan VE, Ostrovnaya I, Begg CB.

Biometrics. 2018 Mar;74(1):321-330. doi: 10.1111/biom.12710. Epub 2017 May 8.


International Working Group consensus response evaluation criteria in lymphoma (RECIL 2017).

Younes A, Hilden P, Coiffier B, Hagenbeek A, Salles G, Wilson W, Seymour JF, Kelly K, Gribben J, Pfreunschuh M, Morschhauser F, Schoder H, Zelenetz AD, Rademaker J, Advani R, Valente N, Fortpied C, Witzig TE, Sehn LH, Engert A, Fisher RI, Zinzani PL, Federico M, Hutchings M, Bollard C, Trneny M, Elsayed YA, Tobinai K, Abramson JS, Fowler N, Goy A, Smith M, Ansell S, Kuruvilla J, Dreyling M, Thieblemont C, Little RF, Aurer I, Van Oers MHJ, Takeshita K, Gopal A, Rule S, de Vos S, Kloos I, Kaminski MS, Meignan M, Schwartz LH, Leonard JP, Schuster SJ, Seshan VE.

Ann Oncol. 2017 Jul 1;28(7):1436-1447. doi: 10.1093/annonc/mdx097. Review.


Asynchronous fate decisions by single cells collectively ensure consistent lineage composition in the mouse blastocyst.

Saiz N, Williams KM, Seshan VE, Hadjantonakis AK.

Nat Commun. 2016 Nov 18;7:13463. doi: 10.1038/ncomms13463.


Inference for the difference in the area under the ROC curve derived from nested binary regression models.

Heller G, Seshan VE, Moskowitz CS, Gönen M.

Biostatistics. 2017 Apr 1;18(2):260-274. doi: 10.1093/biostatistics/kxw045.


Clonal relationships between lobular carcinoma in situ and other breast malignancies.

Begg CB, Ostrovnaya I, Carniello JV, Sakr RA, Giri D, Towers R, Schizas M, De Brot M, Andrade VP, Mauguen A, Seshan VE, King TA.

Breast Cancer Res. 2016 Jun 23;18(1):66. doi: 10.1186/s13058-016-0727-z.


FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing.

Shen R, Seshan VE.

Nucleic Acids Res. 2016 Sep 19;44(16):e131. doi: 10.1093/nar/gkw520. Epub 2016 Jun 7.


TNF is a key cytokine mediating neutrophil cytotoxic activity in breast cancer patients.

Comen E, Wojnarowicz P, Seshan VE, Shah R, Coker C, Norton L, Benezra R.

NPJ Breast Cancer. 2016 Apr 20;2:16009. doi: 10.1038/npjbcancer.2016.9. eCollection 2016.


Mitochondrial DNA copy number variation across human cancers.

Reznik E, Miller ML, Şenbabaoğlu Y, Riaz N, Sarungbam J, Tickoo SK, Al-Ahmadie HA, Lee W, Seshan VE, Hakimi AA, Sander C.

Elife. 2016 Feb 22;5. pii: e10769. doi: 10.7554/eLife.10769.



Ostrovnaya I, Seshan VE, Begg CB.

Ann Appl Stat. 2015 Sep;9(3):1533-1548. Epub 2015 Nov 2.


Identifying Etiologically Distinct Sub-Types of Cancer: A Demonstration Project Involving Breast Cancer.

Begg CB, Orlow I, Zabor EC, Arora A, Sharma A, Seshan VE, Bernstein JL.

Cancer Med. 2015 Sep;4(9):1432-9. doi: 10.1002/cam4.456. Epub 2015 May 13.


False discovery rates for rare variants from sequenced data.

Capanu M, Seshan VE.

Genet Epidemiol. 2015 Feb;39(2):65-76. doi: 10.1002/gepi.21880. Epub 2014 Dec 30.


Genomic investigation of etiologic heterogeneity: methodologic challenges.

Begg CB, Seshan VE, Zabor EC, Furberg H, Arora A, Shen R, Maranchie JK, Nielsen ME, Rathmell WK, Signoretti S, Tamboli P, Karam JA, Choueiri TK, Hakimi AA, Hsieh JJ.

BMC Med Res Methodol. 2014 Dec 22;14:138. doi: 10.1186/1471-2288-14-138.


The Rho GTPase Rnd1 suppresses mammary tumorigenesis and EMT by restraining Ras-MAPK signalling.

Okada T, Sinha S, Esposito I, Schiavon G, López-Lago MA, Su W, Pratilas CA, Abele C, Hernandez JM, Ohara M, Okada M, Viale A, Heguy A, Socci ND, Sapino A, Seshan VE, Long S, Inghirami G, Rosen N, Giancotti FG.

Nat Cell Biol. 2015 Jan;17(1):81-94. doi: 10.1038/ncb3082. Epub 2014 Dec 22. Erratum in: Nat Cell Biol. 2019 Apr;21(4):534.


Frequent disruption of the RB pathway in indolent follicular lymphoma suggests a new combination therapy.

Oricchio E, Ciriello G, Jiang M, Boice MH, Schatz JH, Heguy A, Viale A, de Stanchina E, Teruya-Feldstein J, Bouska A, McKeithan T, Sander C, Tam W, Seshan VE, Chan WC, Chaganti RS, Wendel HG.

J Exp Med. 2014 Jun 30;211(7):1379-91. doi: 10.1084/jem.20132120. Epub 2014 Jun 9.


Feasibility and predictability of perioperative PET and estrogen receptor ligand in patients with invasive breast cancer.

Gemignani ML, Patil S, Seshan VE, Sampson M, Humm JL, Lewis JS, Brogi E, Larson SM, Morrow M, Pandit-Taskar N.

J Nucl Med. 2013 Oct;54(10):1697-702. doi: 10.2967/jnumed.112.113373. Epub 2013 Aug 22.


Testing the incremental predictive accuracy of new markers.

Begg CB, Gonen M, Seshan VE.

Clin Trials. 2013 Oct;10(5):690-2. doi: 10.1177/1740774513496490. Epub 2013 Jul 23.


A conceptual and methodological framework for investigating etiologic heterogeneity.

Begg CB, Zabor EC, Bernstein JL, Bernstein L, Press MF, Seshan VE.

Stat Med. 2013 Dec 20;32(29):5039-52. doi: 10.1002/sim.5902. Epub 2013 Jul 16.


Pattern discovery and cancer gene identification in integrated cancer genomic data.

Mo Q, Wang S, Seshan VE, Olshen AB, Schultz N, Sander C, Powers RS, Ladanyi M, Shen R.

Proc Natl Acad Sci U S A. 2013 Mar 12;110(11):4245-50. doi: 10.1073/pnas.1208949110. Epub 2013 Feb 21.


Comparing ROC curves derived from regression models.

Seshan VE, Gönen M, Begg CB.

Stat Med. 2013 Apr 30;32(9):1483-93. doi: 10.1002/sim.5648. Epub 2012 Oct 3.


Clonal relatedness between lobular carcinoma in situ and synchronous malignant lesions.

Andrade VP, Ostrovnaya I, Seshan VE, Morrogh M, Giri D, Olvera N, De Brot M, Morrow M, Begg CB, King TA.

Breast Cancer Res. 2012 Jul 9;14(4):R103. doi: 10.1186/bcr3222.


A CXCL1 paracrine network links cancer chemoresistance and metastasis.

Acharyya S, Oskarsson T, Vanharanta S, Malladi S, Kim J, Morris PG, Manova-Todorova K, Leversha M, Hogg N, Seshan VE, Norton L, Brogi E, Massagué J.

Cell. 2012 Jul 6;150(1):165-78. doi: 10.1016/j.cell.2012.04.042.


Detectable clonal mosaicism from birth to old age and its relationship to cancer.

Laurie CC, Laurie CA, Rice K, Doheny KF, Zelnick LR, McHugh CP, Ling H, Hetrick KN, Pugh EW, Amos C, Wei Q, Wang LE, Lee JE, Barnes KC, Hansel NN, Mathias R, Daley D, Beaty TH, Scott AF, Ruczinski I, Scharpf RB, Bierut LJ, Hartz SM, Landi MT, Freedman ND, Goldin LR, Ginsburg D, Li J, Desch KC, Strom SS, Blot WJ, Signorello LB, Ingles SA, Chanock SJ, Berndt SI, Le Marchand L, Henderson BE, Monroe KR, Heit JA, de Andrade M, Armasu SM, Regnier C, Lowe WL, Hayes MG, Marazita ML, Feingold E, Murray JC, Melbye M, Feenstra B, Kang JH, Wiggs JL, Jarvik GP, McDavid AN, Seshan VE, Mirel DB, Crenshaw A, Sharopova N, Wise A, Shen J, Crosslin DR, Levine DM, Zheng X, Udren JI, Bennett S, Nelson SC, Gogarten SM, Conomos MP, Heagerty P, Manolio T, Pasquale LR, Haiman CA, Caporaso N, Weir BS.

Nat Genet. 2012 May 6;44(6):642-50. doi: 10.1038/ng.2271.


Integrative subtype discovery in glioblastoma using iCluster.

Shen R, Mo Q, Schultz N, Seshan VE, Olshen AB, Huse J, Ladanyi M, Sander C.

PLoS One. 2012;7(4):e35236. doi: 10.1371/journal.pone.0035236. Epub 2012 Apr 23.


TALK score: Development and validation of a prognostic model for predicting larynx preservation outcome.

Sherman EJ, Fisher SG, Kraus DH, Zelefsky MJ, Seshan VE, Singh B, Shaha AR, Shah JP, Wolf GT, Pfister DG.

Laryngoscope. 2012 May;122(5):1043-50. doi: 10.1002/lary.23220. Epub 2012 Feb 28.


Multi-SNP haplotype analysis methods for association analysis.

Stram DO, Seshan VE.

Methods Mol Biol. 2012;850:423-52. doi: 10.1007/978-1-61779-555-8_23.


HDAC inhibitors and decitabine are highly synergistic and associated with unique gene-expression and epigenetic profiles in models of DLBCL.

Kalac M, Scotto L, Marchi E, Amengual J, Seshan VE, Bhagat G, Ulahannan N, Leshchenko VV, Temkin AM, Parekh S, Tycko B, O'Connor OA.

Blood. 2011 Nov 17;118(20):5506-16. doi: 10.1182/blood-2011-02-336891. Epub 2011 Jul 19.


Parent-specific copy number in paired tumor-normal studies using circular binary segmentation.

Olshen AB, Bengtsson H, Neuvial P, Spellman PT, Olshen RA, Seshan VE.

Bioinformatics. 2011 Aug 1;27(15):2038-46. doi: 10.1093/bioinformatics/btr329. Epub 2011 Jun 11.


Clonality: an R package for testing clonal relatedness of two tumors from the same patient based on their genomic profiles.

Ostrovnaya I, Seshan VE, Olshen AB, Begg CB.

Bioinformatics. 2011 Jun 15;27(12):1698-9. doi: 10.1093/bioinformatics/btr267. Epub 2011 May 5.


A critical analysis of prognostic factors in North American patients with human T-cell lymphotropic virus type-1-associated adult T-cell leukemia/lymphoma: a multicenter clinicopathologic experience and new prognostic score.

Phillips AA, Shapira I, Willim RD, Sanmugarajah J, Solomon WB, Horwitz SM, Savage DG, Bhagat G, Soff G, Zain JM, Alobeid B, Seshan VE, O'Connor OA.

Cancer. 2010 Jul 15;116(14):3438-46. doi: 10.1002/cncr.25147.


Pralatrexate is synergistic with the proteasome inhibitor bortezomib in in vitro and in vivo models of T-cell lymphoid malignancies.

Marchi E, Paoluzzi L, Scotto L, Seshan VE, Zain JM, Zinzani PL, O'Connor OA.

Clin Cancer Res. 2010 Jul 15;16(14):3648-58. doi: 10.1158/1078-0432.CCR-10-0671. Epub 2010 May 25.


A metastasis or a second independent cancer? Evaluating the clonal origin of tumors using array copy number data.

Ostrovnaya I, Olshen AB, Seshan VE, Orlow I, Albertson DG, Begg CB.

Stat Med. 2010 Jul 10;29(15):1608-21. doi: 10.1002/sim.3866.


Predictors of outcomes after surgical treatment of synchronous primary lung cancers.

Finley DJ, Yoshizawa A, Travis W, Zhou Q, Seshan VE, Bains MS, Flores RM, Rizk N, Rusch VW, Park BJ.

J Thorac Oncol. 2010 Feb;5(2):197-205. doi: 10.1097/JTO.0b013e3181c814c5. Erratum in: J Thorac Oncol. 2010 Jun;5(6):926.


Romidepsin and belinostat synergize the antineoplastic effect of bortezomib in mantle cell lymphoma.

Paoluzzi L, Scotto L, Marchi E, Zain J, Seshan VE, O'Connor OA.

Clin Cancer Res. 2010 Jan 15;16(2):554-65. doi: 10.1158/1078-0432.CCR-09-1937. Epub 2010 Jan 12.

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