Sumit Middha, PhD - MSKCC - Principal Computational Biologist

Sumit Middha

PhD

MSKCC

Principal Computational Biologist

United States

Main Specialties: Biology

Additional Specialties: next-gen sequencing NGS, bioinformatics, genomics

Sumit Middha, PhD - MSKCC - Principal Computational Biologist

Sumit Middha

PhD

Introduction

Primary Affiliation: MSKCC - United States

Specialties:

Additional Specialties:

Research Interests:

Education

Aug 2014
University of Minnesota
PhD
Biomedical Informatics
May 2005
Indiana University Bloomington
Masters
Bioinformatics

Publications

51Publications

1865Reads

-Profile Views

1155PubMed Central Citations

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
40 Reads
5 Citations
5.145 Impact Factor

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
122 Reads
36 Citations
18.430 Impact Factor

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
42 Reads
10 Citations
4.380 Impact Factor

The molecular landscape of extraskeletal osteosarcoma: A clinicopathological and molecular biomarker study.

J Pathol Clin Res 2016 Jan 29;2(1):9-20. Epub 2015 Oct 29.

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

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http://dx.doi.org/10.1002/cjp2.29DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4858130PMC
January 2016
29 Reads
2 Citations

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
5 Reads
3 Citations
4.440 Impact Factor

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
12 Reads
2 Citations
3.941 Impact Factor

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
38 Reads
2 Citations

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
16 Reads
11 Citations
14.430 Impact Factor

Whole genome analyses of a well-differentiated liposarcoma reveals novel SYT1 and DDR2 rearrangements.

PLoS One 2014 5;9(2):e87113. Epub 2014 Feb 5.

Comprehensive Cancer Center, Mayo Clinic, Scottsdale, Arizona, United States of America ; Division of Hematology/Oncology Mayo Clinic, Scottsdale, Arizona, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0087113PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3914808PMC
November 2014
35 Reads
3 Citations
3.234 Impact Factor

Application of whole exome sequencing in undiagnosed inherited polyneuropathies.

J Neurol Neurosurg Psychiatry 2014 Nov 6;85(11):1265-72. Epub 2014 Mar 6.

Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA.

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http://jnnp.bmj.com/content/early/2014/03/06/jnnp-2013-30674
Web Search
http://jnnp.bmj.com/cgi/doi/10.1136/jnnp-2013-306740
Publisher Site
http://dx.doi.org/10.1136/jnnp-2013-306740DOI Listing
November 2014
5 Reads
15 Citations
6.810 Impact Factor

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
6 Reads
3.234 Impact Factor

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
30 Reads
6 Citations
6.393 Impact Factor

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
17 Reads
8 Citations
3.565 Impact Factor

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
31 Reads
3 Citations
6.530 Impact Factor

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
32 Reads
10 Citations
2.580 Impact Factor

Comprehensive assessment of genetic variants within TCF4 in Fuchs' endothelial corneal dystrophy.

Invest Ophthalmol Vis Sci 2014 Aug 28;55(9):6101-7. Epub 2014 Aug 28.

Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, United States.

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http://dx.doi.org/10.1167/iovs.14-14958DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4179444PMC
August 2014
22 Reads
5 Citations
3.404 Impact Factor

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
29 Reads
44 Citations
3.990 Impact Factor

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
Web Search
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
9 Reads
4 Citations
8.290 Impact Factor

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
34 Reads
16 Citations
4.041 Impact Factor

Exome sequencing and systems biology converge to identify novel mutations in the L-type calcium channel, CACNA1C, linked to autosomal dominant long QT syndrome.

Circ Cardiovasc Genet 2013 Jun;6(3):279-89

Center for Translational Science Activities, Mayo Graduate School, Mayo Clinic, Rochester, MN 55905, USA.

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http://dx.doi.org/10.1161/CIRCGENETICS.113.000138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3760222PMC
June 2013
34 Reads
26 Citations
5.340 Impact Factor

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
40 Reads
41 Citations

Research resource: whole transcriptome RNA sequencing detects multiple 1α,25-dihydroxyvitamin D(3)-sensitive metabolic pathways in developing zebrafish.

Mol Endocrinol 2012 Sep 25;26(9):1630-42. Epub 2012 Jun 25.

Nephrology and Hypertension Research, Medical Sciences, Mayo Clinic, Rochester, Minnesota 55905, USA.

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http://dx.doi.org/10.1210/me.2012-1113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3434529PMC
September 2012
23 Reads
14 Citations
4.022 Impact Factor

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
28 Reads
18 Citations
4.981 Impact Factor

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
91 Reads
41 Citations
8.290 Impact Factor

TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data.

Bioinformatics 2012 Jan 15;28(2):277-8. Epub 2011 Nov 15.

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

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/btr612DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3259432PMC
January 2012
14 Reads
31 Citations
4.981 Impact Factor

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
10 Reads
49 Citations
9.112 Impact Factor

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
21 Reads
17 Citations
7.911 Impact Factor

Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function.

Genome Biol 2009 16;10(9):R97. Epub 2009 Sep 16.

School of Informatics, Indiana University, E, Tenth St, Bloomington, Indiana 47408, USA.

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http://dx.doi.org/10.1186/gb-2009-10-9-r97DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768986PMC
February 2010
26 Reads
21 Citations

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
18 Reads
73 Citations
3.990 Impact Factor

Novel splice site mutations in the gamma glutamyl carboxylase gene in a child with congenital combined deficiency of the vitamin K-dependent coagulation factors (VKCFD).

Pediatr Blood Cancer 2009 Jul;53(1):92-5

Division of Pediatric Hematology Oncology, Mayo Clinic, Rochester, Minnesota 55905, USA.

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http://dx.doi.org/10.1002/pbc.22011DOI Listing
July 2009
3 Reads
2 Citations
2.562 Impact Factor

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
11 Reads
11 Citations
3.990 Impact Factor

Top co-authors

Jean-Pierre A Kocher
Jean-Pierre A Kocher

Mayo Clinic

8
Saurabh Baheti
Saurabh Baheti

Mayo Clinic

8
Yan W Asmann
Yan W Asmann

Mayo Clinic

7
Stephen N Thibodeau
Stephen N Thibodeau

Mayo Clinic

6
Zhifu Sun
Zhifu Sun

Mayo Clinic

6
Asha A Nair
Asha A Nair

Mayo Clinic

6
Daniel J Schaid
Daniel J Schaid

Mayo Clinic

5
Bruce W Eckloff
Bruce W Eckloff

Mayo Clinic

5
Jared M Evans
Jared M Evans

Mayo Clinic

5
Eric D Wieben
Eric D Wieben

Mayo Clinic

5