Bingshan Li

Bingshan Li

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Bingshan Li

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Insight into the Etiology of Undifferentiated Soft Tissue Sarcomas from a Novel Mouse Model.

Mol Cancer Res 2019 May 25;17(5):1024-1035. Epub 2019 Jan 25.

Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee.

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http://dx.doi.org/10.1158/1541-7786.MCR-18-0117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6497566PMC
May 2019

A Bayesian framework that integrates multi-omics data and gene networks predicts risk genes from schizophrenia GWAS data.

Nat Neurosci 2019 05 15;22(5):691-699. Epub 2019 Apr 15.

Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.

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http://dx.doi.org/10.1038/s41593-019-0382-7DOI Listing
May 2019

Transcriptome-Wide Association Study Identifies Susceptibility Loci and Genes for Age at Natural Menopause.

Reprod Sci 2019 04 30;26(4):496-502. Epub 2018 May 30.

1 Department of Medicine, Vanderbilt Epidemiology Center and Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, TN, USA.

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http://dx.doi.org/10.1177/1933719118776788DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6421625PMC
April 2019

Methods for the Analysis and Interpretation for Rare Variants Associated with Complex Traits.

Curr Protoc Hum Genet 2019 04 8;101(1):e83. Epub 2019 Mar 8.

Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania.

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http://doi.wiley.com/10.1002/cphg.83
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http://dx.doi.org/10.1002/cphg.83DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6455968PMC
April 2019

Genetic Data from Nearly 63,000 Women of European Descent Predicts DNA Methylation Biomarkers and Epithelial Ovarian Cancer Risk.

Authors:
Yaohua Yang Lang Wu Xiang Shu Yingchang Lu Xiao-Ou Shu Qiuyin Cai Alicia Beeghly-Fadiel Bingshan Li Fei Ye Andrew Berchuck Hoda Anton-Culver Susana Banerjee Javier Benitez Line Bjørge James D Brenton Ralf Butzow Ian G Campbell Jenny Chang-Claude Kexin Chen Linda S Cook Daniel W Cramer Anna deFazio Joe Dennis Jennifer A Doherty Thilo Dörk Diana M Eccles Digna Velez Edwards Peter A Fasching Renée T Fortner Simon A Gayther Graham G Giles Rosalind M Glasspool Ellen L Goode Marc T Goodman Jacek Gronwald Holly R Harris Florian Heitz Michelle A Hildebrandt Estrid Høgdall Claus K Høgdall David G Huntsman Siddhartha P Kar Beth Y Karlan Linda E Kelemen Lambertus A Kiemeney Susanne K Kjaer Anita Koushik Diether Lambrechts Nhu D Le Douglas A Levine Leon F Massuger Keitaro Matsuo Taymaa May Iain A McNeish Usha Menon Francesmary Modugno Alvaro N Monteiro Patricia G Moorman Kirsten B Moysich Roberta B Ness Heli Nevanlinna Håkan Olsson N Charlotte Onland-Moret Sue K Park James Paul Celeste L Pearce Tanja Pejovic Catherine M Phelan Malcolm C Pike Susan J Ramus Elio Riboli Cristina Rodriguez-Antona Isabelle Romieu Dale P Sandler Joellen M Schildkraut Veronica W Setiawan Kang Shan Nadeem Siddiqui Weiva Sieh Meir J Stampfer Rebecca Sutphen Anthony J Swerdlow Lukasz M Szafron Soo Hwang Teo Shelley S Tworoger Jonathan P Tyrer Penelope M Webb Nicolas Wentzensen Emily White Walter C Willett Alicja Wolk Yin Ling Woo Anna H Wu Li Yan Drakoulis Yannoukakos Georgia Chenevix-Trench Thomas A Sellers Paul D P Pharoah Wei Zheng Jirong Long

Cancer Res 2019 02 17;79(3):505-517. Epub 2018 Dec 17.

Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee.

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http://cancerres.aacrjournals.org/lookup/doi/10.1158/0008-54
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http://dx.doi.org/10.1158/0008-5472.CAN-18-2726DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6359948PMC
February 2019

Multi-regional sequencing reveals intratumor heterogeneity and positive selection of somatic mtDNA mutations in hepatocellular carcinoma and colorectal cancer.

Int J Cancer 2018 09 16;143(5):1143-1152. Epub 2018 Apr 16.

State Key Laboratory of Cancer Biology and Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, Xi'an, 710032, China.

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http://dx.doi.org/10.1002/ijc.31395DOI Listing
September 2018

A Transcriptome-Wide Association Study Among 97,898 Women to Identify Candidate Susceptibility Genes for Epithelial Ovarian Cancer Risk.

Authors:
Yingchang Lu Alicia Beeghly-Fadiel Lang Wu Xingyi Guo Bingshan Li Joellen M Schildkraut Hae Kyung Im Yian A Chen Jennifer B Permuth Brett M Reid Jamie K Teer Kirsten B Moysich Irene L Andrulis Hoda Anton-Culver Banu K Arun Elisa V Bandera Rosa B Barkardottir Daniel R Barnes Javier Benitez Line Bjorge James Brenton Ralf Butzow Trinidad Caldes Maria A Caligo Ian Campbell Jenny Chang-Claude Kathleen B M Claes Fergus J Couch Daniel W Cramer Mary B Daly Anna deFazio Joe Dennis Orland Diez Susan M Domchek Thilo Dörk Douglas F Easton Diana M Eccles Peter A Fasching Renée T Fortner George Fountzilas Eitan Friedman Patricia A Ganz Judy Garber Graham G Giles Andrew K Godwin David E Goldgar Marc T Goodman Mark H Greene Jacek Gronwald Ute Hamann Florian Heitz Michelle A T Hildebrandt Claus K Høgdall Antoinette Hollestelle Peter J Hulick David G Huntsman Evgeny N Imyanitov Claudine Isaacs Anna Jakubowska Paul James Beth Y Karlan Linda E Kelemen Lambertus A Kiemeney Susanne K Kjaer Ava Kwong Nhu D Le Goska Leslie Fabienne Lesueur Douglas A Levine Amalia Mattiello Taymaa May Lesley McGuffog Iain A McNeish Melissa A Merritt Francesmary Modugno Marco Montagna Susan L Neuhausen Heli Nevanlinna Finn C Nielsen Liene Nikitina-Zake Robert L Nussbaum Kenneth Offit Edith Olah Olufunmilayo I Olopade Sara H Olson Håkan Olsson Ana Osorio Sue K Park Michael T Parsons Petra H M Peeters Tanja Pejovic Paolo Peterlongo Catherine M Phelan Miquel Angel Pujana Susan J Ramus Gad Rennert Harvey Risch Gustavo C Rodriguez Cristina Rodríguez-Antona Isabelle Romieu Matti A Rookus Mary Anne Rossing Iwona K Rzepecka Dale P Sandler Rita K Schmutzler Veronica W Setiawan Priyanka Sharma Weiva Sieh Jacques Simard Christian F Singer Honglin Song Melissa C Southey Amanda B Spurdle Rebecca Sutphen Anthony J Swerdlow Manuel R Teixeira Soo H Teo Mads Thomassen Marc Tischkowitz Amanda E Toland Antonia Trichopoulou Nadine Tung Shelley S Tworoger Elizabeth J van Rensburg Adriaan Vanderstichele Ana Vega Digna Velez Edwards Penelope M Webb Jeffrey N Weitzel Nicolas Wentzensen Emily White Alicja Wolk Anna H Wu Drakoulis Yannoukakos Kristin K Zorn Simon A Gayther Antonis C Antoniou Andrew Berchuck Ellen L Goode Georgia Chenevix-Trench Thomas A Sellers Paul D P Pharoah Wei Zheng Jirong Long

Cancer Res 2018 Sep 27;78(18):5419-5430. Epub 2018 Jul 27.

Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee.

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http://dx.doi.org/10.1158/0008-5472.CAN-18-0951DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6139053PMC
September 2018

A transcriptome-wide association study of 229,000 women identifies new candidate susceptibility genes for breast cancer.

Authors:
Lang Wu Wei Shi Jirong Long Xingyi Guo Kyriaki Michailidou Jonathan Beesley Manjeet K Bolla Xiao-Ou Shu Yingchang Lu Qiuyin Cai Fares Al-Ejeh Esdy Rozali Qin Wang Joe Dennis Bingshan Li Chenjie Zeng Helian Feng Alexander Gusev Richard T Barfield Irene L Andrulis Hoda Anton-Culver Volker Arndt Kristan J Aronson Paul L Auer Myrto Barrdahl Caroline Baynes Matthias W Beckmann Javier Benitez Marina Bermisheva Carl Blomqvist Natalia V Bogdanova Stig E Bojesen Hiltrud Brauch Hermann Brenner Louise Brinton Per Broberg Sara Y Brucker Barbara Burwinkel Trinidad Caldés Federico Canzian Brian D Carter J Esteban Castelao Jenny Chang-Claude Xiaoqing Chen Ting-Yuan David Cheng Hans Christiansen Christine L Clarke Margriet Collée Sten Cornelissen Fergus J Couch David Cox Angela Cox Simon S Cross Julie M Cunningham Kamila Czene Mary B Daly Peter Devilee Kimberly F Doheny Thilo Dörk Isabel Dos-Santos-Silva Martine Dumont Miriam Dwek Diana M Eccles Ursula Eilber A Heather Eliassen Christoph Engel Mikael Eriksson Laura Fachal Peter A Fasching Jonine Figueroa Dieter Flesch-Janys Olivia Fletcher Henrik Flyger Lin Fritschi Marike Gabrielson Manuela Gago-Dominguez Susan M Gapstur Montserrat García-Closas Mia M Gaudet Maya Ghoussaini Graham G Giles Mark S Goldberg David E Goldgar Anna González-Neira Pascal Guénel Eric Hahnen Christopher A Haiman Niclas Håkansson Per Hall Emily Hallberg Ute Hamann Patricia Harrington Alexander Hein Belynda Hicks Peter Hillemanns Antoinette Hollestelle Robert N Hoover John L Hopper Guanmengqian Huang Keith Humphreys David J Hunter Anna Jakubowska Wolfgang Janni Esther M John Nichola Johnson Kristine Jones Michael E Jones Audrey Jung Rudolf Kaaks Michael J Kerin Elza Khusnutdinova Veli-Matti Kosma Vessela N Kristensen Diether Lambrechts Loic Le Marchand Jingmei Li Sara Lindström Jolanta Lissowska Wing-Yee Lo Sibylle Loibl Jan Lubinski Craig Luccarini Michael P Lux Robert J MacInnis Tom Maishman Ivana Maleva Kostovska Arto Mannermaa JoAnn E Manson Sara Margolin Dimitrios Mavroudis Hanne Meijers-Heijboer Alfons Meindl Usha Menon Jeffery Meyer Anna Marie Mulligan Susan L Neuhausen Heli Nevanlinna Patrick Neven Sune F Nielsen Børge G Nordestgaard Olufunmilayo I Olopade Janet E Olson Håkan Olsson Paolo Peterlongo Julian Peto Dijana Plaseska-Karanfilska Ross Prentice Nadege Presneau Katri Pylkäs Brigitte Rack Paolo Radice Nazneen Rahman Gad Rennert Hedy S Rennert Valerie Rhenius Atocha Romero Jane Romm Anja Rudolph Emmanouil Saloustros Dale P Sandler Elinor J Sawyer Marjanka K Schmidt Rita K Schmutzler Andreas Schneeweiss Rodney J Scott Christopher G Scott Sheila Seal Mitul Shah Martha J Shrubsole Ann Smeets Melissa C Southey John J Spinelli Jennifer Stone Harald Surowy Anthony J Swerdlow Rulla M Tamimi William Tapper Jack A Taylor Mary Beth Terry Daniel C Tessier Abigail Thomas Kathrin Thöne Rob A E M Tollenaar Diana Torres Thérèse Truong Michael Untch Celine Vachon David Van Den Berg Daniel Vincent Quinten Waisfisz Clarice R Weinberg Camilla Wendt Alice S Whittemore Hans Wildiers Walter C Willett Robert Winqvist Alicja Wolk Lucy Xia Xiaohong R Yang Argyrios Ziogas Elad Ziv Alison M Dunning Paul D P Pharoah Jacques Simard Roger L Milne Stacey L Edwards Peter Kraft Douglas F Easton Georgia Chenevix-Trench Wei Zheng

Nat Genet 2018 07 18;50(7):968-978. Epub 2018 Jun 18.

Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA.

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http://dx.doi.org/10.1038/s41588-018-0132-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6314198PMC
July 2018

A Comprehensive cis-eQTL Analysis Revealed Target Genes in Breast Cancer Susceptibility Loci Identified in Genome-wide Association Studies.

Am J Hum Genet 2018 05;102(5):890-903

Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA.

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http://dx.doi.org/10.1016/j.ajhg.2018.03.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5986971PMC
May 2018

Learning Opportunities for Drug Repositioning via GWAS and PheWAS Findings.

AMIA Jt Summits Transl Sci Proc 2018 18;2017:237-246. Epub 2018 May 18.

Vanderbilt University, Nashville, TN.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5961790PMC
May 2018

Site-specific selection reveals selective constraints and functionality of tumor somatic mtDNA mutations.

J Exp Clin Cancer Res 2017 11 28;36(1):168. Epub 2017 Nov 28.

State Key Laboratory of Cancer Biology and Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, 169 Changle West Road, Xi'an, 710032, China.

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http://dx.doi.org/10.1186/s13046-017-0638-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5704541PMC
November 2017

Cancer driver gene discovery through an integrative genomics approach in a non-parametric Bayesian framework.

Bioinformatics 2017 02;33(4):483-490

Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw662DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6075201PMC
February 2017

Longitudinally collected CTCs and CTC-clusters and clinical outcomes of metastatic breast cancer.

Breast Cancer Res Treat 2017 01 22;161(1):83-94. Epub 2016 Oct 22.

Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA.

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http://dx.doi.org/10.1007/s10549-016-4026-2DOI Listing
January 2017

The impact of genotype calling errors on family-based studies.

Sci Rep 2016 06 22;6:28323. Epub 2016 Jun 22.

Division of Pulmonary Medicine, Allergy and Immunology; Department of Pediatrics, Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh, Pittsburgh, PA 15224, USA.

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http://dx.doi.org/10.1038/srep28323DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4916415PMC
June 2016

Effects of Cancer Stage and Treatment Differences on Racial Disparities in Survival From Colon Cancer: A United States Population-Based Study.

Gastroenterology 2016 05 2;150(5):1135-1146. Epub 2016 Feb 2.

Division of Population Science, Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania. Electronic address:

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http://dx.doi.org/10.1053/j.gastro.2016.01.030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4842115PMC
May 2016

RVTESTS: an efficient and comprehensive tool for rare variant association analysis using sequence data.

Bioinformatics 2016 05 15;32(9):1423-6. Epub 2016 Feb 15.

Division of Biostatistics and Bioinformatics, Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA 17033, USA and Institute for Personalized Medicine, Penn State College of Medicine, Hershey, PA 17033, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4848408PMC
May 2016

Joint detection of copy number variations in parent-offspring trios.

Bioinformatics 2016 04 7;32(8):1130-7. Epub 2015 Dec 7.

School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, China.

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http://dx.doi.org/10.1093/bioinformatics/btv707DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4907378PMC
April 2016

Cell-free circulating mitochondrial DNA content and risk of hepatocellular carcinoma in patients with chronic HBV infection.

Sci Rep 2016 Apr 11;6:23992. Epub 2016 Apr 11.

Division of Population Science, Department of Medical Oncology, Thomas Jefferson University, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1038/srep23992DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4827061PMC
April 2016

A computational method for genotype calling in family-based sequencing data.

BMC Bioinformatics 2016 Jan 16;17:37. Epub 2016 Jan 16.

Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA.

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http://dx.doi.org/10.1186/s12859-016-0880-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4715317PMC
January 2016

Prospective assessment of the prognostic value of circulating tumor cells and their clusters in patients with advanced-stage breast cancer.

Breast Cancer Res Treat 2015 Dec 16;154(3):563-71. Epub 2015 Nov 16.

Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA.

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http://dx.doi.org/10.1007/s10549-015-3636-4DOI Listing
December 2015

Genetic and chromosomal alterations in Kenyan Wilms Tumor.

Genes Chromosomes Cancer 2015 Nov 14;54(11):702-15. Epub 2015 Aug 14.

Department of Pediatric Surgery, Vanderbilt University School of Medicine, Nashville, TN.

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http://dx.doi.org/10.1002/gcc.22281DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4567398PMC
November 2015

Screening of cannabinoids in industrial-grade hemp using two-dimensional liquid chromatography coupled with acidic potassium permanganate chemiluminescence detection.

J Sep Sci 2015 Jun 7;38(12):2024-32. Epub 2015 May 7.

Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia.

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http://doi.wiley.com/10.1002/jssc.201500088
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http://dx.doi.org/10.1002/jssc.201500088DOI Listing
June 2015

Leveraging Identity-by-Descent for Accurate Genotype Inference in Family Sequencing Data.

PLoS Genet 2015 Jun 4;11(6):e1005271. Epub 2015 Jun 4.

Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America; Institute of Computational Biology, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1005271DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4456389PMC
June 2015

Improved variant calling accuracy by merging replicates in whole-exome sequencing studies.

Biomed Res Int 2014 4;2014:319534. Epub 2014 Aug 4.

Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA.

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http://downloads.hindawi.com/journals/bmri/2014/319534.pdf
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http://www.hindawi.com/journals/bmri/2014/319534/
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http://dx.doi.org/10.1155/2014/319534DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4137624PMC
May 2015

A Bayesian framework for de novo mutation calling in parents-offspring trios.

Bioinformatics 2015 May 21;31(9):1375-81. Epub 2014 Dec 21.

Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, Nashville, TN, USA,Center for Human Genetic Variation, Duke University, Durham, NC, USA, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, Nashville, TN, USA,Center for Human Genetic Variation, Duke University, Durham, NC, USA, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA.

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http://bioinformatics.oxfordjournals.org/content/early/2014/
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http://bioinformatics.oxfordjournals.org/content/early/2015/
Web Search
http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/btu839DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410659PMC
May 2015

A haplotype-based framework for group-wise transmission/disequilibrium tests for rare variant association analysis.

Bioinformatics 2015 May 6;31(9):1452-9. Epub 2015 Jan 6.

Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu860DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410665PMC
May 2015

Modeling the overall survival of patients with advanced-stage non-small cell lung cancer using data of routine laboratory tests.

Int J Cancer 2015 Jan 5;136(2):382-91. Epub 2014 Jun 5.

Division of Population Science, Department of Medical Oncology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA; College of Life Sciences, Northwest University, Xi'an, China.

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http://dx.doi.org/10.1002/ijc.28995DOI Listing
January 2015

Racial disparity in breast cancer survival: the impact of pre-treatment hematologic variables.

Cancer Causes Control 2015 Jan 31;26(1):45-56. Epub 2014 Oct 31.

Division of Population Science, Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA.

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http://dx.doi.org/10.1007/s10552-014-0481-4DOI Listing
January 2015

Erythropoiesis stimulating agents and clinical outcomes of invasive breast cancer patients receiving cytotoxic chemotherapy.

Breast Cancer Res Treat 2014 Nov 27;148(1):175-85. Epub 2014 Sep 27.

Division of Population Science, Department of Medical Oncology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA.

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http://link.springer.com/10.1007/s10549-014-3152-y
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http://dx.doi.org/10.1007/s10549-014-3152-yDOI Listing
November 2014

Transcriptome analysis of psoriasis in a large case-control sample: RNA-seq provides insights into disease mechanisms.

J Invest Dermatol 2014 Jul 17;134(7):1828-1838. Epub 2014 Jan 17.

Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA; Ann Arbor Veterans Affairs Hospital, University of Michigan, Ann Arbor, Michigan, USA. Electronic address:

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http://dx.doi.org/10.1038/jid.2014.28DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4057954PMC
July 2014

A gradient-boosting approach for filtering de novo mutations in parent-offspring trios.

Bioinformatics 2014 Jul 10;30(13):1830-6. Epub 2014 Mar 10.

School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, China, Center for Human Genome Variation, Duke University, Durham, NC 27708 and Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37235, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu141DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4071207PMC
July 2014

QPLOT: a quality assessment tool for next generation sequencing data.

Biomed Res Int 2013 11;2013:865181. Epub 2013 Nov 11.

Department of Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232, USA.

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http://www.hindawi.com/journals/bmri/2013/865181/
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http://dx.doi.org/10.1155/2013/865181DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3844194PMC
June 2014

Rare coding variants and breast cancer risk: evaluation of susceptibility Loci identified in genome-wide association studies.

Cancer Epidemiol Biomarkers Prev 2014 Apr 27;23(4):622-8. Epub 2014 Jan 27.

Authors' Affiliations: Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center; Department of Biostatistics; Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University School of Medicine, Nashville, Tennessee; Shanghai Center for Disease Control and Prevention; and Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China.

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http://dx.doi.org/10.1158/1055-9965.EPI-13-1043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3976694PMC
April 2014

Recurrent tissue-specific mtDNA mutations are common in humans.

PLoS Genet 2013 Nov 7;9(11):e1003929. Epub 2013 Nov 7.

Center for Human Genetics Research, Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1003929DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820769PMC
November 2013

Preoperative platelet count associates with survival and distant metastasis in surgically resected colorectal cancer patients.

J Gastrointest Cancer 2013 Sep;44(3):293-304

Division of Population Science, Department of Medical Oncology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1007/s12029-013-9491-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3748145PMC
September 2013

Identifying rare variants associated with complex traits via sequencing.

Curr Protoc Hum Genet 2013 Jul;Chapter 1:Unit 1.26

Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA.

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http://dx.doi.org/10.1002/0471142905.hg0126s78DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3830981PMC
July 2013

A likelihood-based framework for variant calling and de novo mutation detection in families.

PLoS Genet 2012 4;8(10):e1002944. Epub 2012 Oct 4.

Center for Human Genetics Research, Department of Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.

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http://dx.doi.org/10.1371/journal.pgen.1002944DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3464213PMC
March 2013

Genotype calling and haplotyping in parent-offspring trios.

Genome Res 2013 Jan 11;23(1):142-51. Epub 2012 Oct 11.

Division of Pediatric Pulmonary Medicine, Allergy and Immunology, Department of Pediatrics, Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15224, USA.

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http://dx.doi.org/10.1101/gr.142455.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530674PMC
January 2013

ASAP: an environment for automated preprocessing of sequencing data.

BMC Res Notes 2013 Jan 4;6. Epub 2013 Jan 4.

Center for Human Genetics Research, Vanderbilt University, Nashville, USA.

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http://dx.doi.org/10.1186/1756-0500-6-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3541347PMC
January 2013

Chemiluminescence detection of cannabinoids and related compounds with acidic potassium permanganate.

Drug Test Anal 2012 Jul-Aug;4(7-8):675-9. Epub 2012 Mar 29.

Centre for Biotechnology, Chemistry and Systems Biology, School of Life and Environmental Sciences, Deakin University, Victoria, Australia.

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http://dx.doi.org/10.1002/dta.1328DOI Listing
December 2012

Genetic polymorphisms in pre-microRNA genes as prognostic markers of colorectal cancer.

Cancer Epidemiol Biomarkers Prev 2012 Jan 25;21(1):217-27. Epub 2011 Oct 25.

State Key Laboratory of Cancer Biology, Cell Engineering Research Center & Department of Cell Biology, Tangdu Hospital, Fourth Military Medical University, Xi'an, China.

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http://dx.doi.org/10.1158/1055-9965.EPI-11-0624DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3253954PMC
January 2012

Discovery of rare variants via sequencing: implications for the design of complex trait association studies.

PLoS Genet 2009 May 15;5(5):e1000481. Epub 2009 May 15.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000481DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674213PMC
May 2009

Deviations from hardy-weinberg equilibrium in parental and unaffected sibling genotype data.

Hum Hered 2009 12;67(2):104-15. Epub 2008 Dec 12.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex., USA.

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http://dx.doi.org/10.1159/000179558DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2798818PMC
March 2009

Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data.

Am J Hum Genet 2008 Sep 7;83(3):311-21. Epub 2008 Aug 7.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1016/j.ajhg.2008.06.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842185PMC
September 2008

Sequence variants in host cell factor C1 are associated with Ménière's disease.

Otol Neurotol 2008 Jun;29(4):561-6

Bobby R. Alford Department of Otolaryngology-Head and Neck Surgery, Baylor College of Medicine, Houston, Texas, U.S.A.

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http://dx.doi.org/10.1097/MAO.0b013e318168d23bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2757044PMC
June 2008

Ignoring intermarker linkage disequilibrium induces false-positive evidence of linkage for consanguineous pedigrees when genotype data is missing for any pedigree member.

Hum Hered 2008 11;65(4):199-208. Epub 2007 Dec 11.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1159/000112367DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2798807PMC
February 2008

Clone-array pooled shotgun mapping and sequencing: design and analysis of experiments.

Genome Inform 2003 ;14:186-95

Département d'informatique et de recherche opérationnelle, Université de Montréal, CP 6128 succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada.

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March 2005

Genome sequence of the Brown Norway rat yields insights into mammalian evolution.

Authors:
Richard A Gibbs George M Weinstock Michael L Metzker Donna M Muzny Erica J Sodergren Steven Scherer Graham Scott David Steffen Kim C Worley Paula E Burch Geoffrey Okwuonu Sandra Hines Lora Lewis Christine DeRamo Oliver Delgado Shannon Dugan-Rocha George Miner Margaret Morgan Alicia Hawes Rachel Gill Celera Robert A Holt Mark D Adams Peter G Amanatides Holly Baden-Tillson Mary Barnstead Soo Chin Cheryl A Evans Steve Ferriera Carl Fosler Anna Glodek Zhiping Gu Don Jennings Cheryl L Kraft Trixie Nguyen Cynthia M Pfannkoch Cynthia Sitter Granger G Sutton J Craig Venter Trevor Woodage Douglas Smith Hong-Mei Lee Erik Gustafson Patrick Cahill Arnold Kana Lynn Doucette-Stamm Keith Weinstock Kim Fechtel Robert B Weiss Diane M Dunn Eric D Green Robert W Blakesley Gerard G Bouffard Pieter J De Jong Kazutoyo Osoegawa Baoli Zhu Marco Marra Jacqueline Schein Ian Bosdet Chris Fjell Steven Jones Martin Krzywinski Carrie Mathewson Asim Siddiqui Natasja Wye John McPherson Shaying Zhao Claire M Fraser Jyoti Shetty Sofiya Shatsman Keita Geer Yixin Chen Sofyia Abramzon William C Nierman Paul H Havlak Rui Chen K James Durbin Amy Egan Yanru Ren Xing-Zhi Song Bingshan Li Yue Liu Xiang Qin Simon Cawley Kim C Worley A J Cooney Lisa M D'Souza Kirt Martin Jia Qian Wu Manuel L Gonzalez-Garay Andrew R Jackson Kenneth J Kalafus Michael P McLeod Aleksandar Milosavljevic Davinder Virk Andrei Volkov David A Wheeler Zhengdong Zhang Jeffrey A Bailey Evan E Eichler Eray Tuzun Ewan Birney Emmanuel Mongin Abel Ureta-Vidal Cara Woodwark Evgeny Zdobnov Peer Bork Mikita Suyama David Torrents Marina Alexandersson Barbara J Trask Janet M Young Hui Huang Huajun Wang Heming Xing Sue Daniels Darryl Gietzen Jeanette Schmidt Kristian Stevens Ursula Vitt Jim Wingrove Francisco Camara M Mar Albà Josep F Abril Roderic Guigo Arian Smit Inna Dubchak Edward M Rubin Olivier Couronne Alexander Poliakov Norbert Hübner Detlev Ganten Claudia Goesele Oliver Hummel Thomas Kreitler Young-Ae Lee Jan Monti Herbert Schulz Heike Zimdahl Heinz Himmelbauer Hans Lehrach Howard J Jacob Susan Bromberg Jo Gullings-Handley Michael I Jensen-Seaman Anne E Kwitek Jozef Lazar Dean Pasko Peter J Tonellato Simon Twigger Chris P Ponting Jose M Duarte Stephen Rice Leo Goodstadt Scott A Beatson Richard D Emes Eitan E Winter Caleb Webber Petra Brandt Gerald Nyakatura Margaret Adetobi Francesca Chiaromonte Laura Elnitski Pallavi Eswara Ross C Hardison Minmei Hou Diana Kolbe Kateryna Makova Webb Miller Anton Nekrutenko Cathy Riemer Scott Schwartz James Taylor Shan Yang Yi Zhang Klaus Lindpaintner T Dan Andrews Mario Caccamo Michele Clamp Laura Clarke Valerie Curwen Richard Durbin Eduardo Eyras Stephen M Searle Gregory M Cooper Serafim Batzoglou Michael Brudno Arend Sidow Eric A Stone J Craig Venter Bret A Payseur Guillaume Bourque Carlos López-Otín Xose S Puente Kushal Chakrabarti Sourav Chatterji Colin Dewey Lior Pachter Nicolas Bray Von Bing Yap Anat Caspi Glenn Tesler Pavel A Pevzner David Haussler Krishna M Roskin Robert Baertsch Hiram Clawson Terrence S Furey Angie S Hinrichs Donna Karolchik William J Kent Kate R Rosenbloom Heather Trumbower Matt Weirauch David N Cooper Peter D Stenson Bin Ma Michael Brent Manimozhiyan Arumugam David Shteynberg Richard R Copley Martin S Taylor Harold Riethman Uma Mudunuri Jane Peterson Mark Guyer Adam Felsenfeld Susan Old Stephen Mockrin Francis Collins

Nature 2004 Apr;428(6982):493-521

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA. http://www.hgsc.bcm.tmc.edu

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http://dx.doi.org/10.1038/nature02426DOI Listing
April 2004