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Broad Institute of MIT & Harvard 's Articles

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QuantTB – a method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data

Authors: Christine Anyansi, Arlin Keo, Bruce J. Walker, Timothy J. Straub, Abigail L. Manson, Ashlee M. Earl and Thomas Abeel

Citation: BMC Genomics 2020 21:80

Content type: Research article

Published on: 28 January 2020
Is ‘likely pathogenic’ really 90% likely? Reclassification data in ClinVar

Authors: Steven M. Harrison and Heidi L. Rehm

Citation: Genome Medicine 2019 11:72

Content type: Comment

Published on: 21 November 2019
Application of CRISPR genetic screens to investigate neurological diseases

Authors: Raphaella W. L. So, Sai Wai Chung, Heather H. C. Lau, Jeremy J. Watts, Erin Gaudette, Zaid A. M. Al-Azzawi, Jossana Bishay, Lilian Tsai-Wei Lin, Julia Joung, Xinzhu Wang and Gerold Schmitt-Ulms

Citation: Molecular Neurodegeneration 2019 14:41

Content type: Review

Published on: 14 November 2019
Scaling computational genomics to millions of individuals with GPUs

Authors: Amaro Taylor-Weiner, François Aguet, Nicholas J. Haradhvala, Sager Gosai, Shankara Anand, Jaegil Kim, Kristin Ardlie, Eliezer M. Van Allen and Gad Getz

Citation: Genome Biology 2019 20:228

Content type: Short Report

Published on: 1 November 2019
Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods

Authors: Brian J. Haas, Alexander Dobin, Bo Li, Nicolas Stransky, Nathalie Pochet and Aviv Regev

Citation: Genome Biology 2019 20:213

Content type: Research

Published on: 21 October 2019
Risk versus reward: host dependent parasite mortality rates and phenotypes in the facultative generalist Triphysaria versicolor

Authors: Loren A. Honaas, Sam Jones, Nina Farrell, William Kamerow, Huiting Zhang, Kathryn Vescio, Naomi S. Altman, John I. Yoder and Claude W. dePamphilis

Citation: BMC Plant Biology 2019 19:334

Content type: Research article

Published on: 1 August 2019
Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges

Authors: Keira A. Cohen, Abigail L. Manson, Christopher A. Desjardins, Thomas Abeel and Ashlee M. Earl

Citation: Genome Medicine 2019 11:45

Content type: Review

Published on: 25 July 2019
L1TD1 - a prognostic marker for colon cancer

Authors: Deepankar Chakroborty, Maheswara Reddy Emani, Riku Klén, Camilla Böckelman, Jaana Hagström, Caj Haglund, Ari Ristimäki, Riitta Lahesmaa and Laura L. Elo

Citation: BMC Cancer 2019 19:727

Content type: Research article

Published on: 23 July 2019
GEMINI: a variational Bayesian approach to identify genetic interactions from combinatorial CRISPR screens

Authors: Mahdi Zamanighomi, Sidharth S. Jain, Takahiro Ito, Debjani Pal, Timothy P. Daley and William R. Sellers

Citation: Genome Biology 2019 20:137

Content type: Method

Published on: 12 July 2019
Emerging technologies towards enhancing privacy in genomic data sharing

Authors: Bonnie Berger and Hyunghoon Cho

Citation: Genome Biology 2019 20:128

Content type: Editorial

Published on: 2 July 2019
Detection of low-density Plasmodium falciparum infections using amplicon deep sequencing

Authors: Angela M. Early, Rachel F. Daniels, Timothy M. Farrell, Jonna Grimsby, Sarah K. Volkman, Dyann F. Wirth, Bronwyn L. MacInnis and Daniel E. Neafsey

Citation: Malaria Journal 2019 18:219

Content type: Methodology

Published on: 1 July 2019
Impact of the rumen microbiome on milk fatty acid composition of Holstein cattle

Authors: Bart Buitenhuis, Jan Lassen, Samantha Joan Noel, Damian R. Plichta, Peter Sørensen, Gareth F. Difford and Nina A. Poulsen

Citation: Genetics Selection Evolution 2019 51:23

Content type: Research Article

Published on: 29 May 2019
Mutations in ATP13A2 (PARK9) are associated with an amyotrophic lateral sclerosis-like phenotype, implicating this locus in further phenotypic expansion

Authors: Rossella Spataro, Maria Kousi, Sali M. K. Farhan, Jason R. Willer, Jay P. Ross, Patrick A. Dion, Guy A. Rouleau, Mark J. Daly, Benjamin M. Neale, Vincenzo La Bella and Nicholas Katsanis

Citation: Human Genomics 2019 13:19

Content type: Primary research

Published on: 16 April 2019
A (fire)cloud-based DNA methylation data preprocessing and quality control platform

Authors: Divy Kangeyan, Andrew Dunford, Sowmya Iyer, Chip Stewart, Megan Hanna, Gad Getz and Martin J. Aryee

Citation: BMC Bioinformatics 2019 20:160

Content type: Software

Published on: 29 March 2019
Potential use of clinical polygenic risk scores in psychiatry – ethical implications and communicating high polygenic risk

Authors: A. C. Palk, S. Dalvie, J. de Vries, A. R. Martin and D. J. Stein

Citation: Philosophy, Ethics, and Humanities in Medicine 2019 14:4

Content type: Review

Published on: 27 February 2019
Meta-analysis of Immunochip data of four autoimmune diseases reveals novel single-disease and cross-phenotype associations

Authors: Ana Márquez, Martin Kerick, Alexandra Zhernakova, Javier Gutierrez-Achury, Wei-Min Chen, Suna Onengut-Gumuscu, Isidoro González-Álvaro, Luis Rodriguez-Rodriguez, Raquel Rios-Fernández, Miguel A. González-Gay, Maureen D. Mayes, Soumya Raychaudhuri, Stephen S. Rich, Cisca Wijmenga and Javier Martín

Citation: Genome Medicine 2018 10:97

Content type: Research

Published on: 20 December 2018
Genomics of response to immune checkpoint therapies for cancer: implications for precision medicine

Authors: Jake R. Conway, Eric Kofman, Shirley S. Mo, Haitham Elmarakeby and Eliezer Van Allen

Citation: Genome Medicine 2018 10:93

Content type: Review

Published on: 29 November 2018
Dissecting clinical outcome of porcine circovirus type 2 with in vivo derived transcriptomic signatures of host tissue responses

Authors: Nicolaas Van Renne, Ruifang Wei, Nathalie Pochet and Hans J. Nauwynck

Citation: BMC Genomics 2018 19:831

Content type: Research article

Published on: 20 November 2018
Reduced gut microbiome protects from alcohol-induced neuroinflammation and alters intestinal and brain inflammasome expression

Authors: Patrick P. Lowe, Benedek Gyongyosi, Abhishek Satishchandran, Arvin Iracheta-Vellve, Yeonhee Cho, Aditya Ambade and Gyongyi Szabo

Citation: Journal of Neuroinflammation 2018 15:298

Content type: Research

Published on: 27 October 2018
Discovering in vivo cytokine-eQTL interactions from a lupus clinical trial

Authors: Emma E. Davenport, Tiffany Amariuta, Maria Gutierrez-Arcelus, Kamil Slowikowski, Harm-Jan Westra, Yang Luo, Ciyue Shen, Deepak A. Rao, Ying Zhang, Stephen Pearson, David von Schack, Jean S. Beebe, Nan Bing, Sally John, Michael S. Vincent, Baohong Zhang…

Citation: Genome Biology 2018 19:168

Content type: Research

Published on: 19 October 2018

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Broad Institute of MIT & Harvard

Broad Institute of MIT & Harvard 's Articles

QuantTB – a method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data

Is ‘likely pathogenic’ really 90% likely? Reclassification data in ClinVar

Application of CRISPR genetic screens to investigate neurological diseases

Scaling computational genomics to millions of individuals with GPUs

Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods

Risk versus reward: host dependent parasite mortality rates and phenotypes in the facultative generalist Triphysaria versicolor

Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges

L1TD1 - a prognostic marker for colon cancer

GEMINI: a variational Bayesian approach to identify genetic interactions from combinatorial CRISPR screens

Emerging technologies towards enhancing privacy in genomic data sharing

Detection of low-density Plasmodium falciparum infections using amplicon deep sequencing

Impact of the rumen microbiome on milk fatty acid composition of Holstein cattle

Mutations in ATP13A2 (PARK9) are associated with an amyotrophic lateral sclerosis-like phenotype, implicating this locus in further phenotypic expansion

A (fire)cloud-based DNA methylation data preprocessing and quality control platform

Potential use of clinical polygenic risk scores in psychiatry – ethical implications and communicating high polygenic risk

Meta-analysis of Immunochip data of four autoimmune diseases reveals novel single-disease and cross-phenotype associations

Genomics of response to immune checkpoint therapies for cancer: implications for precision medicine

Dissecting clinical outcome of porcine circovirus type 2 with in vivo derived transcriptomic signatures of host tissue responses

Reduced gut microbiome protects from alcohol-induced neuroinflammation and alters intestinal and brain inflammasome expression

Discovering in vivo cytokine-eQTL interactions from a lupus clinical trial