BEDTools: a flexible suite of utilities for comparing genomic features

por Quinlan, Aaron R., Hall, Ira M.
Publicado 2010

YAHA: fast and flexible long-read alignment with optimal breakpoint detection

por Faust, Gregory G., Hall, Ira M.
Publicado 2012

SAMBLASTER: fast duplicate marking and structural variant read extraction

por Faust, Gregory G., Hall, Ira M.
Publicado 2014

SVScore: an impact prediction tool for structural variation

por Ganel, Liron, Abel, Haley J, Hall, Ira M
Publicado 2017

Structural variants are a major source of gene expression differences in humans and often affect multiple nearby genes

por Scott, Alexandra J., Chiang, Colby, Hall, Ira M.
Publicado 2021

Defining the DNA uptake specificity of naturally competent Haemophilus influenzae cells

por Mell, Joshua Chang, Hall, Ira M., Redfield, Rosemary J.
Publicado 2012

Chromosomal structural variations during progression of a prostate epithelial cell line to a malignant metastatic state inactivate the NF2, NIPSNAP1, UGT2B17, and LPIN2 genes

por Malhotra, Ankit, Shibata, Yoshiyuki, Hall, Ira M, Dutta, Anindya
Publicado 2013

Population-based structural variation discovery with Hydra-Multi

por Lindberg, Michael R., Hall, Ira M., Quinlan, Aaron R.
Publicado 2015

Transformation of Natural Genetic Variation into Haemophilus Influenzae Genomes

por Mell, Joshua Chang, Shumilina, Svetlana, Hall, Ira M., Redfield, Rosemary J.
Publicado 2011

LUMPY: a probabilistic framework for structural variant discovery

por Layer, Ryan M, Chiang, Colby, Quinlan, Aaron R, Hall, Ira M
Publicado 2014

Ploidy-Seq: inferring mutational chronology by sequencing polyploid tumor subpopulations

por Malhotra, Ankit, Wang, Yong, Waters, Jill, Chen, Ken, Meric-Bernstam, Funda, Hall, Ira M, Navin, Nicholas E
Publicado 2015

Evidence for two independent associations with type 1 diabetes at the 12q13 locus

por Keene, Keith L., Quinlan, Aaron R., Hou, Xuanlin, Hall, Ira M., Mychaleckyj, Josyf C., Onengut-Gumuscu, Suna, Concannon, Patrick
Publicado 2011

svtools: population-scale analysis of structural variation

por Larson, David E, Abel, Haley J, Chiang, Colby, Badve, Abhijit, Das, Indraniel, Eldred, James M, Layer, Ryan M, Hall, Ira M
Publicado 2019

Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms

por Malhotra, Ankit, Lindberg, Michael, Faust, Gregory G., Leibowitz, Mitchell L., Clark, Royden A., Layer, Ryan M., Quinlan, Aaron R., Hall, Ira M.
Publicado 2013

SpeedSeq: Ultra-fast personal genome analysis and interpretation

por Chiang, Colby, Layer, Ryan M., Faust, Gregory G., Lindberg, Michael R., Rose, David B., Garrison, Erik P., Marth, Gabor T., Quinlan, Aaron R., Hall, Ira M.
Publicado 2015

Identification of Drivers of Aneuploidy in Breast Tumors

por Pfister, Katherine, Pipka, Justyna L., Chiang, Colby, Liu, Yunxian, Clark, Royden A., Keller, Ray, Skoglund, Paul, Guertin, Michael J., Hall, Ira M., Stukenberg, P. Todd
Publicado 2018

The impact of structural variation on human gene expression

por Chiang, Colby, Scott, Alexandra J., Davis, Joe R., Tsang, Emily K., Li, Xin, Kim, Yungil, Hadzic, Tarik, Damani, Farhan N., Ganel, Liron, Montgomery, Stephen B., Battle, Alexis, Conrad, Donald F., Hall, Ira M.
Publicado 2017

The impact of rare variation on gene expression across tissues

por Li, Xin, Kim, Yungil, Tsang, Emily K., Davis, Joe R., Damani, Farhan N., Chiang, Colby, Hess, Gaelen T., Zappala, Zachary, Strober, Benjamin J., Scott, Alexandra J., Li, Amy, Ganna, Andrea, Bassik, Michael C., Merker, Jason D., Hall, Ira M., Battle, Alexis, Montgomery, Stephen B.
Publicado 2017

Polygenic burden has broader impact on health, cognition, and socioeconomic outcomes than most rare and high-risk copy number variants

por Saarentaus, Elmo Christian, Havulinna, Aki Samuli, Mars, Nina, Ahola-Olli, Ari, Kiiskinen, Tuomo Tapio Johannes, Partanen, Juulia, Ruotsalainen, Sanni, Kurki, Mitja, Urpa, Lea Martta, Chen, Lei, Perola, Markus, Salomaa, Veikko, Veijola, Juha, Männikkö, Minna, Hall, Ira M., Pietiläinen, Olli, Kaprio, Jaakko, Ripatti, Samuli, Daly, Mark, Palotie, Aarno
Publicado 2021

Mapping and characterization of structural variation in 17,795 human genomes

por Abel, Haley J., Larson, David E., Regier, Allison A., Chiang, Colby, Das, Indraniel, Kanchi, Krishna L., Layer, Ryan M., Neale, Benjamin M., Salerno, William J., Reeves, Catherine, Buyske, Steven, Matise, Tara C., Muzny, Donna M., Zody, Michael C., Lander, Eric S., Dutcher, Susan K., Stitziel, Nathan O., Hall, Ira M.
Publicado 2020