Publications by authors named "Sumit Middha"

76Publications

Somatic HNF1A mutations in the malignant transformation of hepatocellular adenomas: a retrospective analysis of data from MSK-IMPACT and TCGA.

Hum Pathol 2019 01 17;83:1-6. Epub 2018 Aug 17.

Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology, Weill Cornell Medical College, New York, NY 10065, USA. Electronic address:

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http://dx.doi.org/10.1016/j.humpath.2018.08.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6365190PMC
January 2019

Clinical Sequencing Defines the Genomic Landscape of Metastatic Colorectal Cancer.

Cancer Cell 2018 01;33(1):125-136.e3

Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Departments of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2017.12.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5765991PMC
January 2018

Erratum: Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients.

Authors:
Ahmet Zehir Ryma Benayed Ronak H Shah Aijazuddin Syed Sumit Middha Hyunjae R Kim Preethi Srinivasan Jianjiong Gao Debyani Chakravarty Sean M Devlin Matthew D Hellmann David A Barron Alison M Schram Meera Hameed Snjezana Dogan Dara S Ross Jaclyn F Hechtman Deborah F DeLair JinJuan Yao Diana L Mandelker Donavan T Cheng Raghu Chandramohan Abhinita S Mohanty Ryan N Ptashkin Gowtham Jayakumaran Meera Prasad Mustafa H Syed Anoop Balakrishnan Rema Zhen Y Liu Khedoudja Nafa Laetitia Borsu Justyna Sadowska Jacklyn Casanova Ruben Bacares Iwona J Kiecka Anna Razumova Julie B Son Lisa Stewart Tessara Baldi Kerry A Mullaney Hikmat Al-Ahmadie Efsevia Vakiani Adam A Abeshouse Alexander V Penson Philip Jonsson Niedzica Camacho Matthew T Chang Helen H Won Benjamin E Gross Ritika Kundra Zachary J Heins Hsiao-Wei Chen Sarah Phillips Hongxin Zhang Jiaojiao Wang Angelica Ochoa Jonathan Wills Michael Eubank Stacy B Thomas Stuart M Gardos Dalicia N Reales Jesse Galle Robert Durany Roy Cambria Wassim Abida Andrea Cercek Darren R Feldman Mrinal M Gounder A Ari Hakimi James J Harding Gopa Iyer Yelena Y Janjigian Emmet J Jordan Ciara M Kelly Maeve A Lowery Luc G T Morris Antonio M Omuro Nitya Raj Pedram Razavi Alexander N Shoushtari Neerav Shukla Tara E Soumerai Anna M Varghese Rona Yaeger Jonathan Coleman Bernard Bochner Gregory J Riely Leonard B Saltz Howard I Scher Paul J Sabbatini Mark E Robson David S Klimstra Barry S Taylor Jose Baselga Nikolaus Schultz David M Hyman Maria E Arcila David B Solit Marc Ladanyi Michael F Berger

Nat Med 2017 08;23(8):1004

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http://dx.doi.org/10.1038/nm0817-1004cDOI Listing
August 2017

The genetic landscape of endometrial clear cell carcinomas.

J Pathol 2017 10 5;243(2):230-241. Epub 2017 Sep 5.

Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

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http://dx.doi.org/10.1002/path.4947DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5708127PMC
October 2017

Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients.

Authors:
Ahmet Zehir Ryma Benayed Ronak H Shah Aijazuddin Syed Sumit Middha Hyunjae R Kim Preethi Srinivasan Jianjiong Gao Debyani Chakravarty Sean M Devlin Matthew D Hellmann David A Barron Alison M Schram Meera Hameed Snjezana Dogan Dara S Ross Jaclyn F Hechtman Deborah F DeLair JinJuan Yao Diana L Mandelker Donavan T Cheng Raghu Chandramohan Abhinita S Mohanty Ryan N Ptashkin Gowtham Jayakumaran Meera Prasad Mustafa H Syed Anoop Balakrishnan Rema Zhen Y Liu Khedoudja Nafa Laetitia Borsu Justyna Sadowska Jacklyn Casanova Ruben Bacares Iwona J Kiecka Anna Razumova Julie B Son Lisa Stewart Tessara Baldi Kerry A Mullaney Hikmat Al-Ahmadie Efsevia Vakiani Adam A Abeshouse Alexander V Penson Philip Jonsson Niedzica Camacho Matthew T Chang Helen H Won Benjamin E Gross Ritika Kundra Zachary J Heins Hsiao-Wei Chen Sarah Phillips Hongxin Zhang Jiaojiao Wang Angelica Ochoa Jonathan Wills Michael Eubank Stacy B Thomas Stuart M Gardos Dalicia N Reales Jesse Galle Robert Durany Roy Cambria Wassim Abida Andrea Cercek Darren R Feldman Mrinal M Gounder A Ari Hakimi James J Harding Gopa Iyer Yelena Y Janjigian Emmet J Jordan Ciara M Kelly Maeve A Lowery Luc G T Morris Antonio M Omuro Nitya Raj Pedram Razavi Alexander N Shoushtari Neerav Shukla Tara E Soumerai Anna M Varghese Rona Yaeger Jonathan Coleman Bernard Bochner Gregory J Riely Leonard B Saltz Howard I Scher Paul J Sabbatini Mark E Robson David S Klimstra Barry S Taylor Jose Baselga Nikolaus Schultz David M Hyman Maria E Arcila David B Solit Marc Ladanyi Michael F Berger

Nat Med 2017 Jun 8;23(6):703-713. Epub 2017 May 8.

Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.

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http://www.nature.com/doifinder/10.1038/nm.4333
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http://dx.doi.org/10.1038/nm.4333DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5461196PMC
June 2017

Novel High-grade Endometrial Stromal Sarcoma: A Morphologic Mimicker of Myxoid Leiomyosarcoma.

Am J Surg Pathol 2017 01;41(1):12-24

*Department of Pathology, Memorial Sloan Kettering Cancer Center ‡Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, New York, NY †Department of Pathology, Cork University Hospital, Wilton, Cork, Ireland.

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http://dx.doi.org/10.1097/PAS.0000000000000721DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5630222PMC
January 2017

Reliable Detection of Mismatch Repair Deficiency in Colorectal Cancers Using Mutational Load in Next-Generation Sequencing Panels.

J Clin Oncol 2016 06 28;34(18):2141-7. Epub 2016 Mar 28.

Zsofia K. Stadler, Francesca Battaglin, Sumit Middha, Jaclyn F. Hechtman, Christina Tran, Andrea Cercek, Rona Yaeger, Neil H. Segal, Anna M. Varghese, Diane L. Reidy-Lagunes, Nancy E. Kemeny, Erin E. Salo-Mullen, Asad Ashraf, Martin R. Weiser, Julio Garcia-Aguilar, Mark E. Robson, Kenneth Offit, Maria E. Arcila, Michael F. Berger, Jinru Shia, David B. Solit, and Leonard B. Saltz, Memorial Sloan Kettering Cancer Center, New York, NY; and Francesca Battaglin, Veneto Institute of Oncology, Padua, Italy.

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http://dx.doi.org/10.1200/JCO.2015.65.1067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4962706PMC
June 2016

Identification of Targetable Kinase Alterations in Patients with Colorectal Carcinoma That are Preferentially Associated with Wild-Type RAS/RAF.

Mol Cancer Res 2016 Mar 11;14(3):296-301. Epub 2015 Dec 11.

Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York. Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.

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http://dx.doi.org/10.1158/1541-7786.MCR-15-0392-TDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4972456PMC
March 2016

Comparison of the Life Cycles of Genetically Distant Species C and Species D Human Adenoviruses Ad6 and Ad26 in Human Cells.

J Virol 2015 Dec 30;89(24):12401-17. Epub 2015 Sep 30.

Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA Department of Immunology, Mayo Clinic, Rochester, Minnesota, USA Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA

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http://dx.doi.org/10.1128/JVI.01534-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4665244PMC
December 2015

How well do whole exome sequencing results correlate with medical findings? A study of 89 Mayo Clinic Biobank samples.

Front Genet 2015 24;6:244. Epub 2015 Jul 24.

Center for Individualized Medicine, Mayo Clinic Rochester, MN, USA ; Department of Laboratory Medicine and Pathology, Mayo Clinic Rochester, MN, USA.

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http://dx.doi.org/10.3389/fgene.2015.00244DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4513238PMC
August 2015

Gene expression patterns in CD4+ peripheral blood cells in healthy subjects and stage IV melanoma patients.

Cancer Immunol Immunother 2015 Nov 6;64(11):1437-47. Epub 2015 Aug 6.

Department of Immunology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN, 55905, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5066565PMC
http://dx.doi.org/10.1007/s00262-015-1745-xDOI Listing
November 2015

Homozygous/Compound Heterozygous Triadin Mutations Associated With Autosomal-Recessive Long-QT Syndrome and Pediatric Sudden Cardiac Arrest: Elucidation of the Triadin Knockout Syndrome.

Circulation 2015 Jun 28;131(23):2051-60. Epub 2015 Apr 28.

From Department of Molecular Pharmacology & Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory (H.M.A., D.J.T., M.L.W., M.J.A.), Department of Medicine/Division of Cardiovascular Diseases (D.J.T., M.L.W., M.J.A.), Medical Genome Facility (B.W.E.), and Department of Pediatrics/Division of Pediatric Cardiology (M.J.A.), Mayo Clinic, Rochester, MN; and Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo College of Medicine, Rochester, MN (S.M., J.M.E.).

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http://dx.doi.org/10.1161/CIRCULATIONAHA.115.015397DOI Listing
June 2015

Characterizing genetic variation of adrenergic signalling pathways in Takotsubo (stress) cardiomyopathy exomes.

Eur J Heart Fail 2014 Sep 8;16(9):942-9. Epub 2014 Aug 8.

Mayo Medical School, Mayo Clinic, Rochester, MN, USA.

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http://dx.doi.org/10.1002/ejhf.145DOI Listing
September 2014

HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data.

BMC Bioinformatics 2014 Aug 15;15:280. Epub 2014 Aug 15.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, 200 1st St SW, Rochester, MN 55905, USA.

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http://dx.doi.org/10.1186/1471-2105-15-280DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4152589PMC
August 2014

Mutational landscape of candidate genes in familial prostate cancer.

Prostate 2014 Oct 11;74(14):1371-8. Epub 2014 Aug 11.

Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan.

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http://dx.doi.org/10.1002/pros.22849DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4142071PMC
October 2014

TNNI3K mutation in familial syndrome of conduction system disease, atrial tachyarrhythmia and dilated cardiomyopathy.

Hum Mol Genet 2014 Nov 11;23(21):5793-804. Epub 2014 Jun 11.

Cardiovascular Genetics Research Laboratory, Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine,

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http://dx.doi.org/10.1093/hmg/ddu297DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4189907PMC
November 2014

CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data.

BMC Genomics 2014 Jun 3;15:423. Epub 2014 Jun 3.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA.

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http://dx.doi.org/10.1186/1471-2164-15-423DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4070549PMC
June 2014

From days to hours: reporting clinically actionable variants from whole genome sequencing.

PLoS One 2014 5;9(2):e86803. Epub 2014 Feb 5.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0086803PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3914798PMC
November 2014

Ubiquitin ligase defect by DCAF8 mutation causes HMSN2 with giant axons.

Neurology 2014 Mar 5;82(10):873-8. Epub 2014 Feb 5.

From the Peripheral Nerve Laboratory (C.J.K., X.D., P.J.D.), Laboratory Medicine and Pathology (Y.W.), Department of Biochemistry and Molecular Biology (M.-V.B., G.M.), and Biomedical Statistics and Informatics (S.M., E.J.A.), Mayo Clinic, Rochester, MN; Department of Neurology (P.V.), St. Georg Hospital, Hamburg, Germany; Department of Neuropathology (H.H.G.), Charité-Universitätsmedizin, Berlin, Germany; and Neurogenetics Branch (C.B., K.Z.), National Institute of Neurological Disorders and Stroke, Bethesda, MD.

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http://www.neurology.org/content/82/10/873.full.pdf
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http://www.neurology.org/cgi/doi/10.1212/WNL.000000000000020
Publisher Site
http://dx.doi.org/10.1212/WNL.0000000000000206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3959756PMC
March 2014

Novel TRAF1-ALK fusion identified by deep RNA sequencing of anaplastic large cell lymphoma.

Genes Chromosomes Cancer 2013 Nov 2;52(11):1097-102. Epub 2013 Sep 2.

Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN.

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http://dx.doi.org/10.1002/gcc.22104DOI Listing
November 2013

Novel late-onset Alzheimer disease loci variants associate with brain gene expression.

Authors:
Mariet Allen Fanggeng Zou High Seng Chai Curtis S Younkin Julia Crook V Shane Pankratz Minerva M Carrasquillo Christopher N Rowley Asha A Nair Sumit Middha Sooraj Maharjan Thuy Nguyen Li Ma Kimberly G Malphrus Ryan Palusak Sarah Lincoln Gina Bisceglio Constantin Georgescu Debra Schultz Fariborz Rakhshan Christopher P Kolbert Jin Jen Jonathan L Haines Richard Mayeux Margaret A Pericak-Vance Lindsay A Farrer Gerard D Schellenberg Ronald C Petersen Neill R Graff-Radford Dennis W Dickson Steven G Younkin Nilüfer Ertekin-Taner Liana G Apostolova Steven E Arnold Clinton T Baldwin Robert Barber Michael M Barmada Thomas Beach Gary W Beecham Duane Beekly David A Bennett Eileen H Bigio Thomas D Bird Deborah Blacker Bradley F Boeve James D Bowen Adam Boxer James R Burke Jacqueline Buros Joseph D Buxbaum Nigel J Cairns Laura B Cantwell Chuanhai Cao Chris S Carlson Regina M Carney Steven L Carroll Helena C Chui David G Clark Jason Corneveaux Carl W Cotman Paul K Crane Carlos Cruchaga Jeffrey L Cummings Philip L De Jager Charles DeCarli Steven T DeKosky F Yesim Demirci Ramon Diaz-Arrastia Malcolm Dick Beth A Dombroski Ranjan Duara William D Ellis Denis Evans Kelley M Faber Kenneth B Fallon Martin R Farlow Steven Ferris Tatiana M Foroud Matthew Frosch Douglas R Galasko Paul J Gallins Mary Ganguli Marla Gearing Daniel H Geschwind Bernardino Ghetti John R Gilbert Sid Gilman Bruno Giordani Jonathan D Glass Alison M Goate Robert C Green John H Growdon Hakon Hakonarson Ronald L Hamilton John Hardy Lindy E Harrell Elizabeth Head Lawrence S Honig Matthew J Huentelman Christine M Hulette Bradley T Hyman Gail P Jarvik Gregory A Jicha Lee-Way Jin Gyungah Jun M Ilyas Kamboh Jason Karlawish Anna Karydas John S K Kauwe Jeffrey A Kaye Nancy Kennedy Ronald Kim Edward H Koo Neil W Kowall Patricia Kramer Walter A Kukull James J Lah Eric B Larson Allan I Levey Andrew P Lieberman Oscar L Lopez Kathryn L Lunetta Wendy J Mack Daniel C Marson Eden R Martin Frank Martiniuk Deborah C Mash Eliezer Masliah Wayne C McCormick Susan M McCurry Andrew N McDavid Ann C McKee Marsel Mesulam Bruce L Miller Carol A Miller Joshua W Miller Thomas J Montine John C Morris Amanda J Myers Adam C Naj Petra Nowotny Joseph E Parisi Daniel P Perl Elaine Peskind Wayne W Poon Huntington Potter Joseph F Quinn Ashok Raj Ruchita A Rajbhandary Murray Raskind Eric M Reiman Barry Reisberg Christiane Reitz John M Ringman Erik D Roberson Ekaterina Rogaeva Roger N Rosenberg Mary Sano Andrew J Saykin Julie A Schneider Lon S Schneider William Seeley Michael L Shelanski Michael A Slifer Charles D Smith Joshua A Sonnen Salvatore Spina Peter St George-Hyslop Robert A Stern Rudolph E Tanzi John Q Trojanowski Juan C Troncoso Debby W Tsuang Vivianna M Van Deerlin Badri Narayan Vardarajan Harry V Vinters Jean Paul Vonsattel Li-San Wang Sandra Weintraub Kathleen A Welsh-Bohmer Jennifer Williamson Randall L Woltjer

Neurology 2012 Jul 20;79(3):221-8. Epub 2012 Jun 20.

Department of Neuroscience, Biostatistics Unit, Mayo Clinic Florida, Jacksonville, FL, USA.

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http://dx.doi.org/10.1212/WNL.0b013e3182605801DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3398432PMC
July 2012

SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing.

Bioinformatics 2012 Aug 10;28(16):2180-1. Epub 2012 Jun 10.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413387PMC
August 2012

The human gut microbiome: current knowledge, challenges, and future directions.

Transl Res 2012 Oct 7;160(4):246-57. Epub 2012 Jun 7.

Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA.

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http://dx.doi.org/10.1016/j.trsl.2012.05.003DOI Listing
October 2012

A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines.

Nucleic Acids Res 2011 Aug 27;39(15):e100. Epub 2011 May 27.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA.

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http://dx.doi.org/10.1093/nar/gkr362DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159479PMC
August 2011

Evaluation of oligonucleotide sequence capture arrays and comparison of next-generation sequencing platforms for use in molecular diagnostics.

Clin Chem 2010 Aug 18;56(8):1297-306. Epub 2010 Jun 18.

Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA.

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http://dx.doi.org/10.1373/clinchem.2010.145441DOI Listing
August 2010

3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer.

BMC Genomics 2009 Nov 16;10:531. Epub 2009 Nov 16.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA.

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http://dx.doi.org/10.1186/1471-2164-10-531DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2781828PMC
November 2009

Evolution and potential function of fibrinogen-like domains across twelve Drosophila species.

BMC Genomics 2008 May 30;9:260. Epub 2008 May 30.

Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1186/1471-2164-9-260DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2429915PMC
May 2008