Sameer Paithankar
Baylor College of Medicine
8 Papers
54 Citations
Sameer Paithankar is an academic researcher from Baylor College of Medicine. The author has contributed to research in topics: Epigenomics & Genomics. The author has an hindex of 7, co-authored 8 publications.
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Papers
The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences.
Kevin Riehle,Cristian Coarfa,Andrew R. Jackson,Jun Ma,Arpit Tandon,Sameer Paithankar,Sriram Raghuraman,Toni-Ann Mistretta,Delphine M. Saulnier,Sabeen Raza,Maria Alejandra Diaz,Robert J. Shulman,Kjersti Aagaard,James Versalovic,Aleksandar Milosavljevic +14 more
TL;DR: The Genboree Microbiome Toolset provides an interactive environment for users at all bioinformatic experience levels in which to conduct microbiome analysis and empowers investigators to translate high-volume sequencing data into valuable biomedical discoveries.
ClinGen Allele Registry links information about genetic variants
Piotr Pawliczek,Ronak Y. Patel,Lillian Ashmore,Andrew R. Jackson,Chris Bizon,Tristan Nelson,Bradford C. Powell,Robert R. Freimuth,Natasha T. Strande,Neethu Shah,Sameer Paithankar,Matthew Wright,Selina S. Dwight,Jimmy Zhen,Melissa J. Landrum,Peter B. McGarvey,Larry Babb,Sharon E. Plon,Aleksandar Milosavljevic,Clinical Genome (ClinGen) Resource +19 more
TL;DR: A core element of the Registry is a canonicalization service, implemented using in‐memory sequence alignment‐based index, which groups variant identifiers denoting the same nucleotide variant and assigns unique and dereferenceable CAids.
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Atlas2 Cloud: a framework for personal genome analysis in the cloud
Uday S. Evani,Danny Challis,Jin Yu,Andrew R. Jackson,Sameer Paithankar,Matthew N. Bainbridge,Adinarayana Jakkamsetti,Peter Pham,Cristian Coarfa,Aleksandar Milosavljevic,Fuli Yu +10 more
TL;DR: It is found that providing a web interface and an optimized pipeline clearly facilitates usage of cloud computing for personal genome analysis, but for it to be routinely used for large scale projects there needs to be a paradigm shift in the way tools are developed, in standard operating procedures, and in funding mechanisms.
Enabling Atlas2 personal genome analysis on the cloud
Uday S. Evani,Danny Challis,Jin Yu,Andrew R. Jackson,Sameer Paithankar,Matthew N. Bainbridge,Cristian Coarfa,Aleksandar Milosavljevic,Fuli Yu +8 more
- 01 Dec 2011
TL;DR: The Atlas2 Cloud Pipeline is deployed for personal genome analysis via the Genboree Workbench using software-as-a-service model and a successful case study of personal genomeAnalysis using this pipeline is reported on.
Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs
Viren Amin,R. Alan Harris,Vitor Onuchic,Andrew R. Jackson,Tim Charnecki,Sameer Paithankar,Sai Lakshmi Subramanian,Kevin Riehle,Cristian Coarfa,Aleksandar Milosavljevic +9 more
TL;DR: The exquisitely tissue-specific epigenetic regulation of lincRNAs and the assignment of a majority of them to specific tissue types will inform future studies of this newly discovered class of genes.