Aakrosh Ratan

Aakrosh Ratan

UNVERIFIED PROFILE

Are you Aakrosh Ratan?   Register this Author

Register author
Aakrosh Ratan

Aakrosh Ratan

Publications by authors named "Aakrosh Ratan"

Are you Aakrosh Ratan?   Register this Author

37Publications

866Reads

18Profile Views

Genomics of LGL leukemia and select other rare leukemia/lymphomas.

Best Pract Res Clin Haematol 2019 09 6;32(3):196-206. Epub 2019 Jun 6.

University of Virginia Cancer Center, 345 Crispell Dr, PO Box 801378, Charlottesville, VA, 22908, USA; Department of Medicine, Division of Hematology/Oncology, 345 Crispell Dr, PO Box 801378, Charlottesville, VA, 22908, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.beha.2019.06.003DOI Listing
September 2019

The Germline Variants rs61757955 and rs34988193 Are Predictive of Survival in Lower Grade Glioma Patients.

Mol Cancer Res 2019 May 16;17(5):1075-1086. Epub 2019 Jan 16.

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1158/1541-7786.MCR-18-0996DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6497557PMC
May 2019

Genomic Variants Among Threatened Corals.

G3 (Bethesda) 2019 05 7;9(5):1633-1646. Epub 2019 May 7.

208 Mueller Lab, Biology Department, The Pennsylvania State University, University Park PA 16802

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1534/g3.119.400125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6505131PMC
May 2019

Augmented Interval List: a novel data structure for efficient genomic interval search.

Bioinformatics 2019 May 31. Epub 2019 May 31.

Center for Public Health Genomics, University of Virginia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btz407DOI Listing
May 2019

SONiCS: PCR stutter noise correction in genome-scale microsatellites.

Bioinformatics 2018 12;34(23):4115-4117

Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/bty485DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6454461PMC
December 2018

Genomic analysis of DNA repair genes and androgen signaling in prostate cancer.

BMC Cancer 2018 Oct 10;18(1):960. Epub 2018 Oct 10.

Center for Cell Signaling, University of Virginia, Charlottesville, VA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12885-018-4848-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6180441PMC
October 2018

Improved molecular karyotyping in glioblastoma.

Mutat Res 2018 09 8;811:16-26. Epub 2018 Jul 8.

Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Department of Neuroscience, University of Virginia, School of Medicine, Charlottesville, VA, United States; Center for Public Health Genomics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Center for Brain Immunology and Glia, University of Virginia, School of Medicine, Charlottesville, VA, United States. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mrfmmm.2018.06.002DOI Listing
September 2018

A massively parallel strategy for STR marker development, capture, and genotyping.

Nucleic Acids Res 2017 Sep;45(15):e142

Departments of Anthropology and Biology, Pennsylvania State University, University Park, PA 16802, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkx574DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5587753PMC
September 2017

Mitogenomes reveal diversity of the European Lyme borreliosis vector Ixodes ricinus in Italy.

Mol Phylogenet Evol 2016 08 7;101:194-202. Epub 2016 May 7.

Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA; Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA, USA; Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ympev.2016.05.009DOI Listing
August 2016

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae).

Mol Phylogenet Evol 2016 06 5;99:16-33. Epub 2016 Mar 5.

Department of Biological Sciences, University at Buffalo (SUNY), Buffalo, NY 14260, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ympev.2016.02.024DOI Listing
June 2016

Elephantid Genomes Reveal the Molecular Bases of Woolly Mammoth Adaptations to the Arctic.

Cell Rep 2015 Jul 2;12(2):217-28. Epub 2015 Jul 2.

Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, 506B Wartik Lab, University Park, PA 16802, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.celrep.2015.06.027DOI Listing
July 2015

Comparative and population mitogenomic analyses of Madagascar's extinct, giant 'subfossil' lemurs.

J Hum Evol 2015 Feb 16;79:45-54. Epub 2014 Dec 16.

Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA; Department of Biology, Pennsylvania State University, University Park, PA 16802, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jhevol.2014.06.016DOI Listing
February 2015

Identification of indels in next-generation sequencing data.

BMC Bioinformatics 2015 Feb 13;16:42. Epub 2015 Feb 13.

Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, 506, Wartik Laboratory, University Park, PA, 16802, USA.

View Article

Download full-text PDF

Source
https://bmcbioinformatics.biomedcentral.com/articles/10.1186
Publisher Site
http://dx.doi.org/10.1186/s12859-015-0483-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4339746PMC
February 2015

Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history.

Nat Commun 2014 Dec 4;5:5692. Epub 2014 Dec 4.

1] Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, 310 Wartik Lab, University Park, Pennsylvania 16802, USA [2] Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, Singapore 637551, Singapore.

View Article

Download full-text PDF

Source
http://www.nature.com/articles/ncomms6692
Publisher Site
http://dx.doi.org/10.1038/ncomms6692DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4268704PMC
December 2014

Galaxy tools to study genome diversity.

Gigascience 2013 Dec 30;2(1):17. Epub 2013 Dec 30.

Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/2047-217X-2-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3877877PMC
December 2013

Some phenotype association tools in Galaxy: looking for disease SNPs in a full genome.

Curr Protoc Bioinformatics 2012 Sep;Chapter 15:Unit15.2

Pennsylvania State University, University Park, PA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/0471250953.bi1502s39DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3548453PMC
September 2012

Comparative and demographic analysis of orang-utan genomes.

Authors:
Devin P Locke LaDeana W Hillier Wesley C Warren Kim C Worley Lynne V Nazareth Donna M Muzny Shiaw-Pyng Yang Zhengyuan Wang Asif T Chinwalla Pat Minx Makedonka Mitreva Lisa Cook Kim D Delehaunty Catrina Fronick Heather Schmidt Lucinda A Fulton Robert S Fulton Joanne O Nelson Vincent Magrini Craig Pohl Tina A Graves Chris Markovic Andy Cree Huyen H Dinh Jennifer Hume Christie L Kovar Gerald R Fowler Gerton Lunter Stephen Meader Andreas Heger Chris P Ponting Tomas Marques-Bonet Can Alkan Lin Chen Ze Cheng Jeffrey M Kidd Evan E Eichler Simon White Stephen Searle Albert J Vilella Yuan Chen Paul Flicek Jian Ma Brian Raney Bernard Suh Richard Burhans Javier Herrero David Haussler Rui Faria Olga Fernando Fleur Darré Domènec Farré Elodie Gazave Meritxell Oliva Arcadi Navarro Roberta Roberto Oronzo Capozzi Nicoletta Archidiacono Giuliano Della Valle Stefania Purgato Mariano Rocchi Miriam K Konkel Jerilyn A Walker Brygg Ullmer Mark A Batzer Arian F A Smit Robert Hubley Claudio Casola Daniel R Schrider Matthew W Hahn Victor Quesada Xose S Puente Gonzalo R Ordoñez Carlos López-Otín Tomas Vinar Brona Brejova Aakrosh Ratan Robert S Harris Webb Miller Carolin Kosiol Heather A Lawson Vikas Taliwal André L Martins Adam Siepel Arindam Roychoudhury Xin Ma Jeremiah Degenhardt Carlos D Bustamante Ryan N Gutenkunst Thomas Mailund Julien Y Dutheil Asger Hobolth Mikkel H Schierup Oliver A Ryder Yuko Yoshinaga Pieter J de Jong George M Weinstock Jeffrey Rogers Elaine R Mardis Richard A Gibbs Richard K Wilson

Nature 2011 Jan;469(7331):529-33

The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature09687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060778PMC
January 2011

Calling SNPs without a reference sequence.

BMC Bioinformatics 2010 Mar 15;11:130. Epub 2010 Mar 15.

Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-11-130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2851604PMC
March 2010

DUPCAR: reconstructing contiguous ancestral regions with duplications.

J Comput Biol 2008 Oct;15(8):1007-27

Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1089/cmb.2008.0069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3205822PMC
October 2008

The infinite sites model of genome evolution.

Proc Natl Acad Sci U S A 2008 Sep 11;105(38):14254-61. Epub 2008 Sep 11.

Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.0805217105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2533685PMC
September 2008