Aaron Arvey

Publications         |         Software

Me Hiking

Contact

Aaron Arvey
Sloan Kettering Cancer Center
Zuckerman 1440
417 E 68th St.
New York, NY 10021

Email: aarvey (--*AT*--) cbio.mskcc.org

Representative Papers

map.stat <- cbind("Genic"=gene.counts, "Non-Genic"=bam.counts-gene.counts, "Unaligned"=read.counts-bam.counts) map.stat <- map.stat[grep("newparse.new.bam", rownames(map.stat)), ] rownames(map.stat) <- gsub("\\.", "__", gsub(".newparse.new.bam|Proflex|run_", "", rownames(map.stat))) map.stat First and corresponding author publications listed below. A full list of manuscripts can be found on Google Scholar or Pubmed


Machine Learning in Genomics

Sequence and chromatin determinants of cell-type specific transcription factor binding
Aaron Arvey Phaedra Agius, William Stafford Noble, Christina Leslie
Genome Research, 2012.
PDF

Target mRNA abundance dilutes microRNA and siRNA activity
Aaron Arvey, Erik Larsson, Chris Sander, Christina S Leslie and Debora S Marks
Molecular Systems Biology 6:363, April 2010
PDF Supp    ISMB Slides: (PDF) (PPT)    Keystone Slides: (PDF) (PPT)

Minimizing off-target signals in RNA fluorescent in situ hybridization
Aaron Arvey*, Anita Hermann*, Cheryl C. Hsia, Eugene Ie, Yoav Freund, and William McGinnis (* Joint first authors)
Nucleic Acids Research, February 2010.
Software PDF Supp Slides (PDF), Slides (ODP),

Detection of genomic islands via segmental genome heterogeneity.
Aaron Arvey, Rajeev Azad, Alpan Raval, and Jeffrey Lawrence.
Nucleic Acids Research, July 2009.
Software PDF Supp


Machine Learning in Immunology

Genetic and epigenetic variation in the lineage specification of regulatory T cells
Aaron Arvey Joris van der Veeken, George Plitas, Stephen S Rich, Patrick Concannon, Alexander Y Rudensky
eLife, 2015.
PDF

Inflammation-induced repression of chromatin bound by the transcription factor Foxp3 in regulatory T cells
Aaron Arvey*, Joris van der Veeken*, Robbie Samstein*, (* Joint first authors), Yong Feng, John Stamatoyannopoulos, Alexander Rudensky
Nature Immunology, 2014.
PDF

Foxp3 exploits a preexistent enhancer landscape for regulatory T cell lineage specification
Robbie Samstein*, Aaron Arvey*, Steven Josefowicz* (* Joint first authors), Alex Reynolds, Richard Sandstrom, Shane Neph, Peter Sabo, Xiao Peng, Jeong Kim, Will Liao, Ming Li, Christina Leslie, John Stamatoyannopoulos, Alexander Rudensky
Cell, 2012.
PDF


Machine Learning in Virology

GS-5734 and its parent nucleoside analog inhibit Filo-, Pneumo-, and Paramyxoviruses
Aaron Arvey, et al
Scientific Reports, 2017.
PDF

The tumor virus landscape of AIDS-related lymphomas
Aaron Arvey, Akinyemi Ojesina, Chandra Sekhar Pedamallu, Gianna Ballon, Joonil Jung, Fujiko Duke, Lorenzo Leoncini, Giulia De Falco, Eric Bressman, Wayne Tam, Amy Chadburn, Matthew Meyerson, and Ethel Cesarman
Blood, 2015.
PDF

An Atlas of the Epstein-Barr Virus Transcriptome and Epigenome Reveals Host-Virus Regulatory Interactions
Aaron Arvey, Italo Tempera, Kevin Tsai, Horng-Shen Chen, Nadezhda Tikhmyanova, Michael Klichinsky, Christina Leslie, and Paul M. Lieberman
Cell Host & Microbe, 2012.
PDF    Supp Material    EBV Portal Database   

Software

Here is software I've released. If you have any questions, don't hesitate to email me, or the appropriate mailing list.


Valid CSS! Valid HTML 4.01 Transitional