Publications by authors named "Malachi Griffith"

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Gastroenterology 2020 02 16;158(3):793-794. Epub 2019 Nov 16.

McDonnell Genome Institute, and Department of Genetics, and Division of Oncology, Department of Medicine, and Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri.

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http://dx.doi.org/10.1053/j.gastro.2019.11.023DOI Listing
February 2020

Best practices for bioinformatic characterization of neoantigens for clinical utility.

Genome Med 2019 08 28;11(1):56. Epub 2019 Aug 28.

Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.

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http://dx.doi.org/10.1186/s13073-019-0666-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6714459PMC
August 2019

A Spontaneous Aggressive ERα+ Mammary Tumor Model Is Driven by Kras Activation.

Cell Rep 2019 08;28(6):1526-1537.e4

McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63108, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.06.098DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6713291PMC
August 2019

Noninvasive Detection of High-Risk Adenomas Using Stool-Derived Eukaryotic RNA Sequences as Biomarkers.

Gastroenterology 2019 09 30;157(3):884-887.e3. Epub 2019 May 30.

McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri; Department of Genetics, Washington University School of Medicine, St Louis, Missouri; Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, Missouri; Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri. Electronic address:

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http://dx.doi.org/10.1053/j.gastro.2019.05.058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6707888PMC
September 2019

Oral Cavity Squamous Cell Carcinoma Xenografts Retain Complex Genotypes and Intertumor Molecular Heterogeneity.

Cell Rep 2018 08;24(8):2167-2178

McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Division of Medical Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63108, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S22111247183116
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http://dx.doi.org/10.1016/j.celrep.2018.07.058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417872PMC
August 2018

DGIdb 3.0: a redesign and expansion of the drug-gene interaction database.

Nucleic Acids Res 2018 01;46(D1):D1068-D1073

McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO 63108, USA.

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http://dx.doi.org/10.1093/nar/gkx1143DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5888642PMC
January 2018

Clinical implications of neoepitope landscapes for adult and pediatric cancers.

Genome Med 2017 08 31;9(1):77. Epub 2017 Aug 31.

McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.

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http://dx.doi.org/10.1186/s13073-017-0470-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5577778PMC
August 2017

Comprehensive discovery of noncoding RNAs in acute myeloid leukemia cell transcriptomes.

Exp Hematol 2017 11 28;55:19-33. Epub 2017 Jul 28.

The McDonnell Genome Institute, Washington University, St. Louis, MO; Department of Medicine, Washington University, St. Louis, MO; Siteman Cancer Center, Washington University, St. Louis, MO; Department of Biomedical Engineering, Washington University, St. Louis, MO. Electronic address:

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http://dx.doi.org/10.1016/j.exphem.2017.07.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5772960PMC
November 2017

Melorheostosis: Exome sequencing of an associated dermatosis implicates postzygotic mosaicism of mutated KRAS.

Bone 2017 Aug 21;101:145-155. Epub 2017 Apr 21.

McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Division of Genomics and Bioinformatics, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA. Electronic address:

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http://dx.doi.org/10.1016/j.bone.2017.04.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5518630PMC
August 2017

Cancer Immunogenomics: Computational Neoantigen Identification and Vaccine Design.

Cold Spring Harb Symp Quant Biol 2016 7;81:105-111. Epub 2017 Apr 7.

Nationwide Children's Hospital, Institute for Genomic Medicine, Columbus, Ohio 43205.

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http://dx.doi.org/10.1101/sqb.2016.81.030726DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5702270PMC
February 2018

Neoantigens in immunotherapy and personalized vaccines: Implications for head and neck squamous cell carcinoma.

Oral Oncol 2017 08 14;71:169-176. Epub 2016 Oct 14.

Department of Otolaryngology, Washington University School of Medicine, St. Louis, United States; Brigham and Women's Hospital and Dana-Farber Cancer Institute, Boston, MA, United States. Electronic address:

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http://dx.doi.org/10.1016/j.oraloncology.2016.09.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5423853PMC
August 2017

Truncating Prolactin Receptor Mutations Promote Tumor Growth in Murine Estrogen Receptor-Alpha Mammary Carcinomas.

Cell Rep 2016 09;17(1):249-260

McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Ave., St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, 660 S Euclid Ave., St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University School of Medicine, 4921 Parkview Pl., St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, 660 S Euclid Ave., St. Louis, MO 63110, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.08.076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5557050PMC
September 2016

GenVisR: Genomic Visualizations in R.

Bioinformatics 2016 10 10;32(19):3012-4. Epub 2016 Jun 10.

McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA Siteman Cancer Center Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw325DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5039916PMC
October 2016

A common founding clone with TP53 and PTEN mutations gives rise to a concurrent germ cell tumor and acute megakaryoblastic leukemia.

Cold Spring Harb Mol Case Stud 2016 Jan;2(1):a000687

McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63110, USA;; Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA;

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http://dx.doi.org/10.1101/mcs.a000687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4849848PMC
January 2016

pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens.

Genome Med 2016 Jan 29;8(1):11. Epub 2016 Jan 29.

McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.

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http://dx.doi.org/10.1186/s13073-016-0264-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4733280PMC
January 2016

Optimizing cancer genome sequencing and analysis.

Cell Syst 2015 Sep;1(3):210-223

The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108 ; Department of Genetics, Washington University, St. Louis, MO, USA, 63108 ; Siteman Cancer Center, Washington University, St. Louis, MO, USA, 63108 ; Department of Medicine, Washington University, St. Louis, MO, USA, 63108.

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http://dx.doi.org/10.1016/j.cels.2015.08.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4669575PMC
September 2015

ORegAnno 3.0: a community-driven resource for curated regulatory annotation.

Nucleic Acids Res 2016 Jan 17;44(D1):D126-32. Epub 2015 Nov 17.

McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO 63110, USA

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http://dx.doi.org/10.1093/nar/gkv1203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702855PMC
January 2016

DGIdb 2.0: mining clinically relevant drug-gene interactions.

Nucleic Acids Res 2016 Jan 3;44(D1):D1036-44. Epub 2015 Nov 3.

McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA

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http://dx.doi.org/10.1093/nar/gkv1165DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702839PMC
January 2016

Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud.

PLoS Comput Biol 2015 Aug 6;11(8):e1004393. Epub 2015 Aug 6.

McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America; Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, United States of America; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America; Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004393DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4527835PMC
August 2015

Genome Modeling System: A Knowledge Management Platform for Genomics.

PLoS Comput Biol 2015 Jul 9;11(7):e1004274. Epub 2015 Jul 9.

The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America; Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America; Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, United States of America; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004274DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4497734PMC
July 2015

Hippo signaling influences HNF4A and FOXA2 enhancer switching during hepatocyte differentiation.

Cell Rep 2014 Oct 25;9(1):261-271. Epub 2014 Sep 25.

Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z4H4, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.08.046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4612615PMC
October 2014

SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution.

PLoS Comput Biol 2014 Aug 7;10(8):e1003665. Epub 2014 Aug 7.

The Genome Institute, Washington University, St. Louis, Missouri, United States of America; Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America; Department of Genetics, Washington University, St. Louis, Missouri, United States of America; Siteman Cancer Center, Barnes-Jewish Hospital, Washington University School of Medicine, St. Louis, Missouri, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003665DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4125065PMC
August 2014

cDNA hybrid capture improves transcriptome analysis on low-input and archived samples.

J Mol Diagn 2014 Jul 9;16(4):440-51. Epub 2014 May 9.

The Genome Institute, Washington University School of Medicine, St. Louis, Missouri; Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri; Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri; Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, Missouri. Electronic address:

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http://dx.doi.org/10.1016/j.jmoldx.2014.03.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4078367PMC
July 2014

Functional heterogeneity of genetically defined subclones in acute myeloid leukemia.

Cancer Cell 2014 Mar 6;25(3):379-92. Epub 2014 Mar 6.

The Genome Institute, Washington University, St. Louis, MO 63110, USA; Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccr.2014.01.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3983786PMC
March 2014

Single exon-resolution targeted chromosomal microarray analysis of known and candidate intellectual disability genes.

Eur J Hum Genet 2014 Jun 20;22(6):792-800. Epub 2013 Nov 20.

1] Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada [2] Child & Family Research Institute, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1038/ejhg.2013.248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4023222PMC
June 2014

DGIdb: mining the druggable genome.

Nat Methods 2013 Dec 13;10(12):1209-10. Epub 2013 Oct 13.

1] The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA. [2] Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA. [3].

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http://dx.doi.org/10.1038/nmeth.2689DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3851581PMC
December 2013

Extensive relationship between antisense transcription and alternative splicing in the human genome.

Genome Res 2011 Aug 30;21(8):1203-12. Epub 2011 Jun 30.

British Columbia Cancer Agency, Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada.

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http://dx.doi.org/10.1101/gr.113431.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3149488PMC
August 2011

The completion of the Mammalian Gene Collection (MGC).

Authors:
Gary Temple Daniela S Gerhard Rebekah Rasooly Elise A Feingold Peter J Good Cristen Robinson Allison Mandich Jeffrey G Derge Jeanne Lewis Debonny Shoaf Francis S Collins Wonhee Jang Lukas Wagner Carolyn M Shenmen Leonie Misquitta Carl F Schaefer Kenneth H Buetow Tom I Bonner Linda Yankie Ming Ward Lon Phan Alex Astashyn Garth Brown Catherine Farrell Jennifer Hart Melissa Landrum Bonnie L Maidak Michael Murphy Terence Murphy Bhanu Rajput Lillian Riddick David Webb Janet Weber Wendy Wu Kim D Pruitt Donna Maglott Adam Siepel Brona Brejova Mark Diekhans Rachel Harte Robert Baertsch Jim Kent David Haussler Michael Brent Laura Langton Charles L G Comstock Michael Stevens Chaochun Wei Marijke J van Baren Kourosh Salehi-Ashtiani Ryan R Murray Lila Ghamsari Elizabeth Mello Chenwei Lin Christa Pennacchio Kirsten Schreiber Nicole Shapiro Amber Marsh Elizabeth Pardes Troy Moore Anita Lebeau Mike Muratet Blake Simmons David Kloske Stephanie Sieja James Hudson Praveen Sethupathy Michael Brownstein Narayan Bhat Joseph Lazar Howard Jacob Chris E Gruber Mark R Smith John McPherson Angela M Garcia Preethi H Gunaratne Jiaqian Wu Donna Muzny Richard A Gibbs Alice C Young Gerard G Bouffard Robert W Blakesley Jim Mullikin Eric D Green Mark C Dickson Alex C Rodriguez Jane Grimwood Jeremy Schmutz Richard M Myers Martin Hirst Thomas Zeng Kane Tse Michelle Moksa Merinda Deng Kevin Ma Diana Mah Johnson Pang Greg Taylor Eric Chuah Athena Deng Keith Fichter Anne Go Stephanie Lee Jing Wang Malachi Griffith Ryan Morin Richard A Moore Michael Mayo Sarah Munro Susan Wagner Steven J M Jones Robert A Holt Marco A Marra Sun Lu Shuwei Yang James Hartigan Marcus Graf Ralf Wagner Stanley Letovksy Jacqueline C Pulido Keith Robison Dominic Esposito James Hartley Vanessa E Wall Ralph F Hopkins Osamu Ohara Stefan Wiemann

The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

Authors:
Daniela S Gerhard Lukas Wagner Elise A Feingold Carolyn M Shenmen Lynette H Grouse Greg Schuler Steven L Klein Susan Old Rebekah Rasooly Peter Good Mark Guyer Allison M Peck Jeffery G Derge David Lipman Francis S Collins Wonhee Jang Steven Sherry Mike Feolo Leonie Misquitta Eduardo Lee Kirill Rotmistrovsky Susan F Greenhut Carl F Schaefer Kenneth Buetow Tom I Bonner David Haussler Jim Kent Mark Kiekhaus Terry Furey Michael Brent Christa Prange Kirsten Schreiber Nicole Shapiro Narayan K Bhat Ralph F Hopkins Florence Hsie Tom Driscoll M Bento Soares Tom L Casavant Todd E Scheetz Michael J Brown-stein Ted B Usdin Shiraki Toshiyuki Piero Carninci Yulan Piao Dawood B Dudekula Minoru S H Ko Koichi Kawakami Yutaka Suzuki Sumio Sugano C E Gruber M R Smith Blake Simmons Troy Moore Richard Waterman Stephen L Johnson Yijun Ruan Chia Lin Wei S Mathavan Preethi H Gunaratne Jiaqian Wu Angela M Garcia Stephen W Hulyk Edwin Fuh Ye Yuan Anna Sneed Carla Kowis Anne Hodgson Donna M Muzny John McPherson Richard A Gibbs Jessica Fahey Erin Helton Mark Ketteman Anuradha Madan Stephanie Rodrigues Amy Sanchez Michelle Whiting Anup Madari Alice C Young Keith D Wetherby Steven J Granite Peggy N Kwong Charles P Brinkley Russell L Pearson Gerard G Bouffard Robert W Blakesly Eric D Green Mark C Dickson Alex C Rodriguez Jane Grimwood Jeremy Schmutz Richard M Myers Yaron S N Butterfield Malachi Griffith Obi L Griffith Martin I Krzywinski Nancy Liao Ryan Morin Ryan Morrin Diana Palmquist Anca S Petrescu Ursula Skalska Duane E Smailus Jeff M Stott Angelique Schnerch Jacqueline E Schein Steven J M Jones Robert A Holt Agnes Baross Marco A Marra Sandra Clifton Kathryn A Makowski Stephanie Bosak Joel Malek

Genome Res 2004 Oct;14(10B):2121-7

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http://dx.doi.org/10.1101/gr.2596504DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC528928PMC
October 2004

Escherichia coli endA deletion strain for use in two-hybrid shuttle vector selection.

Biotechniques 2003 Aug;35(2):272-4, 276, 278

University of Manitoba, Winnipeg, MB, Canada.

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http://dx.doi.org/10.2144/03352bm05DOI Listing
August 2003