CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data - BMC Bioinformatics
Single-cell RNA sequencing, one of the most significant advances in recent genomics [1], is fast becoming the norm in whole-transcriptome expression profiling, providing unique insights into the exact state of individual cells throughout biological processes, such as cell differentiation or tumorigenesis. In opposition to traditional batch sequencing, single-cell expression measurements are not af
BLAST® Command Line Applications User Manual - NCBI Bookshelf
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What is a hidden Markov model? - Nature Biotechnology
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Must-read Papers in Bioinformatics courses
Protein seqeunce-sequence alignment: M. O. Dayhoff, R. M. Schwartz, B. C. Orcutt. A model of evolutionary change in proteins. in Atlas of protein sequence and structure, Volume 5 (M. Dayhoff, ed.). National Biomedical Research Foundation, Washington, D.C. 1978, Pages 345-352 Description: PAM matrix (construct a score matrix for guide protein sequence alignment) (Download PDF file) S. Henikoff, J
Bioinformatics: alive and kicking - Genome Biology
Six years ago I felt like the boy who hit a telephone pole with a wooden stick at the exact instant a power failure darkened all the lights across the US Northeast. In February 2003 I gave a keynote address for the second annual O'Reilly Bioinformatics Technology Conference called 'Bioinformatics: Gone in 2012' in which I predicted that bioinformatics as a discipline separate from mainstream biolo
MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison - PubMed
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backend-exception Exception from Backend: bePfetch (%23PmXmlSrv): Error+111+(Connection+refused)PubMed Result
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A wiki for the life sciences where authorship matters - Nature Genetics
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Genome re-annotation: a wiki solution? - Genome Biology
Opinion Published: 01 February 2007 Genome re-annotation: a wiki solution? Steven L Salzberg1 Genome Biology volume 8, Article number: 102 (2007) Cite this article The annotation of most genomes becomes outdated over time, owing in part to our ever-improving knowledge of genomes and in part to improvements in bioinformatics software. Unfortunately, annotation is rarely if ever updated and resource
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Tissue-based map of the human proteome | Science
Evolutionary-guided de novo structure prediction of self-associated transmembrane helical proteins with near-atomic accuracy - Nature Communications
CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data - Genome Biology
Visualization of protein sequence features using JavaScript and SVG with pViz.js | Bioinformatics
Comparative genome sequencing reveals genomic signature of extreme desiccation tolerance in the anhydrobiotic midge - Nature Communications
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Genetic origins of the Minoans and Mycenaeans
ENCODE-funded Publications
(PDF) Crystal structure of a monomeric retroviral protease solved by protein folding game player
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