Raphael Lab research is focused on Bioinformatics and Computational Biology.
Current research interests include next-generation DNA sequencing, structural variation, genome rearrangements in cancer and evolution, and network analysis of somatic...
satsuma.sourceforge.net - Satsuma is a whole-genome synteny alignment program. It takes two genomes, computes alignments, and then keeps only the parts that are orthologous, i.e. following the conserved order and orientation of features, such as protein coding genes,...
sourceforge.net - DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and...
console.cloud.google.com - List of publically available databases on google server.
More at https://software.broadinstitute.org/gatk/download/bundle
ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/GATK/.
ftp://ftp.broadinstitute.org/bundle/hg38/hg38bundle/
Suhas Rao and Miriam Huntley (of the Aiden Lab) describe a 3D map of the human genome at kilobase resolution, revealing the principles of chromatin looping. Guest Origami Folding: Sarah Nyquist.
Suhas S.P. Rao*, Miriam H. Huntley*, Neva C. Durand,...
github.com - Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules:...
Live Webinar on RNA-Seq Data Analysis
Abstract: Strand NGS supports an extensive workflow for the analysis and visualization of RNA-Seq data. The workflow includes Transcriptome / Genome alignment, Differential expression analysis with Statistical...
Global overview papers
Next generation quantitative genetics in plants. Jiménez-Gómez, Frontiers in Plant Science 2:77, 2011 Full Text [equally relevant to animal and microbial systems]
Sense from sequence reads: methods for...