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Items: 29

1.

Genomic landscape of allelic imbalance in premalignant atypical adenomatous hyperplasias of the lung.

Sivakumar S, San Lucas FA, Jakubek YA, McDowell TL, Lang W, Kallsen N, Peyton S, Davies GE, Fukuoka J, Yatabe Y, Zhang J, Futreal PA, Fowler J, Fujimoto J, Ehli EA, Hawk ET, Wistuba II, Kadara H, Scheet P.

EBioMedicine. 2019 Apr;42:296-303. doi: 10.1016/j.ebiom.2019.03.020. Epub 2019 Mar 21.

2.

Driver Mutations in Normal Airway Epithelium Elucidate Spatiotemporal Resolution of Lung Cancer.

Kadara H, Sivakumar S, Jakubek Y, San Lucas FA, Lang W, McDowell T, Weber Z, Behrens C, Davies GE, Kalhor N, Moran C, El-Zein R, Mehran R, Swisher SG, Wang J, Zhang J, Fujimoto J, Fowler J, Heymach JV, Dubinett S, Spira AE, Ehli EA, Wistuba II, Scheet P.

Am J Respir Crit Care Med. 2019 Mar 21. doi: 10.1164/rccm.201806-1178OC. [Epub ahead of print]

PMID:
30896962
3.

Classifying mild traumatic brain injuries with functional network analysis.

San Lucas FA, Redell J, Pramod D, Liu Y.

BMC Syst Biol. 2018 Dec 21;12(Suppl 8):131. doi: 10.1186/s12918-018-0645-z.

4.

System for Quality-Assured Data Analysis: Flexible, reproducible scientific workflows.

Fowler J, San Lucas FA, Scheet P.

Genet Epidemiol. 2019 Mar;43(2):227-237. doi: 10.1002/gepi.22178. Epub 2018 Dec 18.

5.

Directional allelic imbalance profiling and visualization from multi-sample data with RECUR.

Jakubek YA, San Lucas FA, Scheet P.

Bioinformatics. 2018 Nov 21. doi: 10.1093/bioinformatics/bty885. [Epub ahead of print]

PMID:
30462146
6.

Colorectal premalignancy is associated with consensus molecular subtypes 1 and 2.

Chang K, Willis JA, Reumers J, Taggart MW, San Lucas FA, Thirumurthi S, Kanth P, Delker DA, Hagedorn CH, Lynch PM, Ellis LM, Hawk ET, Scheet PA, Kopetz S, Arts J, Guinney J, Dienstmann R, Vilar E.

Ann Oncol. 2018 Oct 1;29(10):2061-2067. doi: 10.1093/annonc/mdy337.

PMID:
30412224
7.

Single-Cell Transcriptomics of Pancreatic Cancer Precursors Demonstrates Epithelial and Microenvironmental Heterogeneity as an Early Event in Neoplastic Progression.

Bernard V, Semaan A, Huang J, San Lucas FA, Mulu FC, Stephens BM, Guerrero PA, Huang Y, Zhao J, Kamyabi N, Sen S, Scheet PA, Taniguchi CM, Kim MP, Tzeng CW, Katz MH, Singhi AD, Maitra A, Alvarez HA.

Clin Cancer Res. 2019 Apr 1;25(7):2194-2205. doi: 10.1158/1078-0432.CCR-18-1955. Epub 2018 Nov 1.

PMID:
30385653
8.

DNA Sequencing of Small Bowel Adenocarcinomas Identifies Targetable Recurrent Mutations in the ERBB2 Signaling Pathway.

Adam L, San Lucas FA, Fowler R, Yu Y, Wu W, Liu Y, Wang H, Menter D, Tetzlaff MT, Ensor J Jr, Manyam G, Arold ST, Huff C, Kopetz S, Scheet P, Overman MJ.

Clin Cancer Res. 2019 Jan 15;25(2):641-651. doi: 10.1158/1078-0432.CCR-18-1480. Epub 2018 Oct 23.

PMID:
30352910
9.

Circulating Nucleic Acids Are Associated With Outcomes of Patients With Pancreatic Cancer.

Bernard V, Kim DU, San Lucas FA, Castillo J, Allenson K, Mulu FC, Stephens BM, Huang J, Semaan A, Guerrero PA, Kamyabi N, Zhao J, Hurd MW, Koay EJ, Taniguchi CM, Herman JM, Javle M, Wolff R, Katz M, Varadhachary G, Maitra A, Alvarez HA.

Gastroenterology. 2019 Jan;156(1):108-118.e4. doi: 10.1053/j.gastro.2018.09.022. Epub 2018 Sep 19.

10.

Assessing inter-component heterogeneity of biphasic uterine carcinosarcomas.

Liu Y, Weber Z, San Lucas FA, Deshpande A, Jakubek YA, Sulaiman R, Fagerness M, Flier N, Sulaiman J, Davis CM, Fowler J, Starks D, Rojas-Espaillat L, Lazar AJ, Davies GE, Ehli EA, Scheet P.

Gynecol Oncol. 2018 Nov;151(2):243-249. doi: 10.1016/j.ygyno.2018.08.043. Epub 2018 Sep 5.

PMID:
30194005
11.

Immune Profiling of Premalignant Lesions in Patients With Lynch Syndrome.

Chang K, Taggart MW, Reyes-Uribe L, Borras E, Riquelme E, Barnett RM, Leoni G, San Lucas FA, Catanese MT, Mori F, Diodoro MG, You YN, Hawk ET, Roszik J, Scheet P, Kopetz S, Nicosia A, Scarselli E, Lynch PM, McAllister F, Vilar E.

JAMA Oncol. 2018 Aug 1;4(8):1085-1092. doi: 10.1001/jamaoncol.2018.1482.

12.

Strategies for identification of somatic variants using the Ion Torrent deep targeted sequencing platform.

Deshpande A, Lang W, McDowell T, Sivakumar S, Zhang J, Wang J, San Lucas FA, Fowler J, Kadara H, Scheet P.

BMC Bioinformatics. 2018 Jan 4;19(1):5. doi: 10.1186/s12859-017-1991-3.

13.

Surfaceome profiling enables isolation of cancer-specific exosomal cargo in liquid biopsies from pancreatic cancer patients.

Castillo J, Bernard V, San Lucas FA, Allenson K, Capello M, Kim DU, Gascoyne P, Mulu FC, Stephens BM, Huang J, Wang H, Momin AA, Jacamo RO, Katz M, Wolff R, Javle M, Varadhachary G, Wistuba II, Hanash S, Maitra A, Alvarez H.

Ann Oncol. 2018 Jan 1;29(1):223-229. doi: 10.1093/annonc/mdx542.

14.

Clinicopathological characteristics, outcomes and pattern of mutations in patients with follicular lymphoma who progressed on Bruton tyrosine kinase inhibitors.

Jain P, Kanagal-Shamanna R, San Lucas FA, Nastoupil L, Romaguera J, Fayad L, Oki Y, Westin JR, Medeiros LJ, Wang M, Fowler N.

Br J Haematol. 2018 Sep;182(5):718-723. doi: 10.1111/bjh.14857. Epub 2017 Aug 2. No abstract available.

PMID:
28771675
15.

Mutational Heterogeneity in APC and KRAS Arises at the Crypt Level and Leads to Polyclonality in Early Colorectal Tumorigenesis.

Gausachs M, Borras E, Chang K, Gonzalez S, Azuara D, Delgado Amador A, Lopez-Doriga A, San Lucas FA, Sanjuan X, Paules MJ, Taggart MW, Davies GE, Ehli EA, Fowler J, Moreno V, Pineda M, You YN, Lynch PM, Lazaro C, Navin NE, Scheet PA, Hawk ET, Capella G, Vilar E.

Clin Cancer Res. 2017 Oct 1;23(19):5936-5947. doi: 10.1158/1078-0432.CCR-17-0821. Epub 2017 Jun 23.

16.

High prevalence of mutant KRAS in circulating exosome-derived DNA from early-stage pancreatic cancer patients.

Allenson K, Castillo J, San Lucas FA, Scelo G, Kim DU, Bernard V, Davis G, Kumar T, Katz M, Overman MJ, Foretova L, Fabianova E, Holcatova I, Janout V, Meric-Bernstam F, Gascoyne P, Wistuba I, Varadhachary G, Brennan P, Hanash S, Li D, Maitra A, Alvarez H.

Ann Oncol. 2017 Apr 1;28(4):741-747. doi: 10.1093/annonc/mdx004.

17.

Rapid and powerful detection of subtle allelic imbalance from exome sequencing data with hapLOHseq.

San Lucas FA, Sivakumar S, Vattathil S, Fowler J, Vilar E, Scheet P.

Bioinformatics. 2016 Oct 1;32(19):3015-7. doi: 10.1093/bioinformatics/btw340. Epub 2016 Jun 10.

18.

Genomic Landscape of Colorectal Mucosa and Adenomas.

Borras E, San Lucas FA, Chang K, Zhou R, Masand G, Fowler J, Mork ME, You YN, Taggart MW, McAllister F, Jones DA, Davies GE, Edelmann W, Ehli EA, Lynch PM, Hawk ET, Capella G, Scheet P, Vilar E.

Cancer Prev Res (Phila). 2016 Jun;9(6):417-27. doi: 10.1158/1940-6207.CAPR-16-0081. Epub 2016 May 24.

19.

Tumor microenvironment derived exosomes pleiotropically modulate cancer cell metabolism.

Zhao H, Yang L, Baddour J, Achreja A, Bernard V, Moss T, Marini JC, Tudawe T, Seviour EG, San Lucas FA, Alvarez H, Gupta S, Maiti SN, Cooper L, Peehl D, Ram PT, Maitra A, Nagrath D.

Elife. 2016 Feb 27;5:e10250. doi: 10.7554/eLife.10250.

20.

Minimally invasive genomic and transcriptomic profiling of visceral cancers by next-generation sequencing of circulating exosomes.

San Lucas FA, Allenson K, Bernard V, Castillo J, Kim DU, Ellis K, Ehli EA, Davies GE, Petersen JL, Li D, Wolff R, Katz M, Varadhachary G, Wistuba I, Maitra A, Alvarez H.

Ann Oncol. 2016 Apr;27(4):635-41. doi: 10.1093/annonc/mdv604. Epub 2015 Dec 17.

21.

Genetic risk factors for the development of osteonecrosis in children under age 10 treated for acute lymphoblastic leukemia.

Karol SE, Mattano LA Jr, Yang W, Maloney KW, Smith C, Liu C, Ramsey LB, Fernandez CA, Chang TY, Neale G, Cheng C, Mardis E, Fulton R, Scheet P, San Lucas FA, Larsen EC, Loh ML, Raetz EA, Hunger SP, Devidas M, Relling MV.

Blood. 2016 Feb 4;127(5):558-64. doi: 10.1182/blood-2015-10-673848. Epub 2015 Nov 20.

22.

Preliminary whole-exome sequencing reveals mutations that imply common tumorigenicity pathways in multiple endocrine neoplasia type 1 patients.

Romero Arenas MA, Fowler RG, San Lucas FA, Shen J, Rich TA, Grubbs EG, Lee JE, Scheet P, Perrier ND, Zhao H.

Surgery. 2014 Dec;156(6):1351-7; discussion 1357-8. doi: 10.1016/j.surg.2014.08.073. Epub 2014 Nov 11.

23.

Cancer in silico drug discovery: a systems biology tool for identifying candidate drugs to target specific molecular tumor subtypes.

San Lucas FA, Fowler J, Chang K, Kopetz S, Vilar E, Scheet P.

Mol Cancer Ther. 2014 Dec;13(12):3230-40. doi: 10.1158/1535-7163.MCT-14-0260. Epub 2014 Oct 27.

24.

Improving the sensitivity of sample clustering by leveraging gene co-expression networks in variable selection.

Wang Z, San Lucas FA, Qiu P, Liu Y.

BMC Bioinformatics. 2014 May 20;15:153. doi: 10.1186/1471-2105-15-153.

25.

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.

Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D Jr, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, de Bakker PI, Duzkale H, Dworzyński P, Fairbrother W, Francioli L, Funke BH, Giovanni MA, Handsaker RE, Lage K, Lebo MS, Lek M, Leshchiner I, MacArthur DG, McLaughlin HM, Murray MF, Pers TH, Polak PP, Raychaudhuri S, Rehm HL, Soemedi R, Stitziel NO, Vestecka S, Supper J, Gugenmus C, Klocke B, Hahn A, Schubach M, Menzel M, Biskup S, Freisinger P, Deng M, Braun M, Perner S, Smith RJ, Andorf JL, Huang J, Ryckman K, Sheffield VC, Stone EM, Bair T, Black-Ziegelbein EA, Braun TA, Darbro B, DeLuca AP, Kolbe DL, Scheetz TE, Shearer AE, Sompallae R, Wang K, Bassuk AG, Edens E, Mathews K, Moore SA, Shchelochkov OA, Trapane P, Bossler A, Campbell CA, Heusel JW, Kwitek A, Maga T, Panzer K, Wassink T, Van Daele D, Azaiez H, Booth K, Meyer N, Segal MM, Williams MS, Tromp G, White P, Corsmeier D, Fitzgerald-Butt S, Herman G, Lamb-Thrush D, McBride KL, Newsom D, Pierson CR, Rakowsky AT, Maver A, Lovrečić L, Palandačić A, Peterlin B, Torkamani A, Wedell A, Huss M, Alexeyenko A, Lindvall JM, Magnusson M, Nilsson D, Stranneheim H, Taylan F, Gilissen C, Hoischen A, van Bon B, Yntema H, Nelen M, Zhang W, Sager J, Zhang L, Blair K, Kural D, Cariaso M, Lennon GG, Javed A, Agrawal S, Ng PC, Sandhu KS, Krishna S, Veeramachaneni V, Isakov O, Halperin E, Friedman E, Shomron N, Glusman G, Roach JC, Caballero J, Cox HC, Mauldin D, Ament SA, Rowen L, Richards DR, San Lucas FA, Gonzalez-Garay ML, Caskey CT, Bai Y, Huang Y, Fang F, Zhang Y, Wang Z, Barrera J, Garcia-Lobo JM, González-Lamuño D, Llorca J, Rodriguez MC, Varela I, Reese MG, De La Vega FM, Kiruluta E, Cargill M, Hart RK, Sorenson JM, Lyon GJ, Stevenson DA, Bray BE, Moore BM, Eilbeck K, Yandell M, Zhao H, Hou L, Chen X, Yan X, Chen M, Li C, Yang C, Gunel M, Li P, Kong Y, Alexander AC, Albertyn ZI, Boycott KM, Bulman DE, Gordon PM, Innes AM, Knoppers BM, Majewski J, Marshall CR, Parboosingh JS, Sawyer SL, Samuels ME, Schwartzentruber J, Kohane IS, Margulies DM.

Genome Biol. 2014 Mar 25;15(3):R53. doi: 10.1186/gb-2014-15-3-r53.

26.

Incorporating prior knowledge into Gene Network Study.

Wang Z, Xu W, San Lucas FA, Liu Y.

Bioinformatics. 2013 Oct 15;29(20):2633-40. doi: 10.1093/bioinformatics/btt443. Epub 2013 Aug 16.

27.

An S/T-Q cluster domain census unveils new putative targets under Tel1/Mec1 control.

Cheung HC, San Lucas FA, Hicks S, Chang K, Bertuch AA, Ribes-Zamora A.

BMC Genomics. 2012 Nov 23;13:664. doi: 10.1186/1471-2164-13-664.

28.

Haploscope: a tool for the graphical display of haplotype structure in populations.

San Lucas FA, Rosenberg NA, Scheet P.

Genet Epidemiol. 2012 Jan;36(1):17-21. doi: 10.1002/gepi.20640. Epub 2011 Dec 6.

29.

Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools.

San Lucas FA, Wang G, Scheet P, Peng B.

Bioinformatics. 2012 Feb 1;28(3):421-2. doi: 10.1093/bioinformatics/btr667. Epub 2011 Dec 2.

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