BEDTools: a flexible suite of utilities for comparing genomic features

Por Quinlan, Aaron R., Hall, Ira M.
Publicado em 2010

Characterizing complex structural variation in germline and somatic genomes

Por Quinlan, Aaron R., Hall, Ira M.
Publicado em 2011

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

Por Faust, Gregory G., Hall, Ira M.
Publicado em 2012

SAMBLASTER: fast duplicate marking and structural variant read extraction

Por Faust, Gregory G., Hall, Ira M.
Publicado em 2014

RNA interference machinery regulates chromosome dynamics during mitosis and meiosis in fission yeast

Por Hall, Ira M., Noma, Ken-ichi, Grewal, Shiv I. S.
Publicado em 2003

Defining the DNA uptake specificity of naturally competent Haemophilus influenzae cells

Por Mell, Joshua Chang, Hall, Ira M., Redfield, Rosemary J.
Publicado em 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 em 2013

Population-based structural variation discovery with Hydra-Multi

Por Lindberg, Michael R., Hall, Ira M., Quinlan, Aaron R.
Publicado no Bioinformatics (2015)

Transformation of Natural Genetic Variation into Haemophilus Influenzae Genomes

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

LUMPY: a probabilistic framework for structural variant discovery

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

Binary Interval Search: a scalable algorithm for counting interval intersections

Por Layer, Ryan M., Skadron, Kevin, Robins, Gabriel, Hall, Ira M., Quinlan, Aaron R.
Publicado em 2013

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 no Genome Med (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 em 2011

Genome sequencing of mouse induced pluripotent stem cells reveals retroelement stability and infrequent DNA rearrangement during reprogramming

Por Quinlan, Aaron R., Boland, Michael J., Leibowitz, Mitchell L., Shumilina, Svetlana, Pehrson, Sidney M., Baldwin, Kristin K., Hall, Ira M.
Publicado em 2011

Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome

Por Quinlan, Aaron R., Clark, Royden A., Sokolova, Svetlana, Leibowitz, Mitchell L., Zhang, Yujun, Hurles, Matthew E., Mell, Joshua C., Hall, Ira M.
Publicado em 2010

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 em 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 no Nat Methods (2015)

Mouse genomic representational oligonucleotide microarray analysis: Detection of copy number variations in normal and tumor specimens

Por Lakshmi, B., Hall, Ira M., Egan, Christopher, Alexander, Joan, Leotta, Anthony, Healy, John, Zender, Lars, Spector, Mona S., Xue, Wen, Lowe, Scott W., Wigler, Michael, Lucito, Robert
Publicado em 2006

Mosaic Copy Number Variation in Human Neurons

Por McConnell, Michael J., Lindberg, Michael R., Brennand, Kristen J., Piper, Julia C., Voet, Thierry, Cowing-Zitron, Chris, Shumilina, Svetlana, Lasken, Roger S., Vermeesch, Joris, Hall, Ira M., Gage, Fred H.
Publicado em 2013

The complete genome sequences, unique mutational spectra and developmental potency of adult neurons revealed by cloning

Por Hazen, Jennifer L., Faust, Gregory G., Rodriguez, Alberto R., Ferguson, William C., Shumilina, Svetlana, Clark, Royden A., Boland, Michael J., Martin, Greg, Chubukov, Pavel, Tsunemoto, Rachel K., Torkamani, Ali, Kupriyanov, Sergey, Hall, Ira M., Baldwin, Kristin K.
Publicado no Neuron (2016)