David M. Kristensen

发表

Geometry-inspired Optimization Methods for Structural Motifs for Protein Function Prediction

Lydia E. Kavraki, Mark Moll, Olivier Lichtarge, 2007 .

ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation

Eugene V. Koonin, Yuri I. Wolf, David M. Kristensen, 2016, Nucleic Acids Res..

Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction

Lydia E. Kavraki, Andreas Martin Lisewski, Olivier Lichtarge, 2006, RECOMB.

Cavity Scaling: Automated Refinement of Cavity-Aware motifs in protein Function Prediction

Lydia E. Kavraki, Olivier Lichtarge, Marek Kimmel, 2007, J. Bioinform. Comput. Biol..

A census of α-helical membrane proteins in double-stranded DNA viruses infecting bacteria and archaea

Dmitrij Frishman, Usman Saeed, Eugene V. Koonin, 2015, BMC Bioinformatics.

The MASH Pipeline for Protein Function Prediction and an Algorithm for the Geometric Refinement of 3D Motifs

Lydia E. Kavraki, Andreas Martin Lisewski, Olivier Lichtarge, 2007, J. Comput. Biol..

A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches

Lavanya Kannan, Arcady R. Mushegian, Eugene V. Koonin, 2010, Bioinform..

Algorithms for Structural Comparison and Statistical Analysis of 3D Protein Motifs

Lydia E. Kavraki, Olivier Lichtarge, Marek Kimmel, 2004, Pacific Symposium on Biocomputing.

Building Genomic Analysis Pipelines in a Hackathon Setting with Bioinformatician Teams: DNA-seq, Epigenomics, Metagenomics and RNA-seq

Paul W. Bible, Lisa Federer, Allissa Dillman, 2015, bioRxiv.

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids

Lydia E. Kavraki, Andreas Martin Lisewski, Olivier Lichtarge, 2008, BMC Bioinformatics.

Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates

Olivier Lichtarge, David M. Kristensen, Stephen Murray, 2009, Bioinform..

Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation

Eugene V. Koonin, David M. Kristensen, Ana Laura Grazziotin, 2016, Nucleic Acids Res..

ET viewer: an application for predicting and visualizing functional sites in protein structures

Olivier Lichtarge, David M. Kristensen, David Mittelman, 2006, Bioinform..

Computational methods for Gene Orthology inference

Arcady R. Mushegian, Eugene V. Koonin, Yuri I. Wolf, 2011, Briefings Bioinform..

Detection of Biochemical Pathways by Probabilistic Matching of Phyletic Vectors

Michael K. Coleman, David M. Kristensen, Arcady Mushegian, 2009, PloS one.

Accurate and scalable identification of functional sites by evolutionary tracing

Olivier Lichtarge, David M. Kristensen, Srinivasan Madabushi, 2004, Journal of Structural and Functional Genomics.

Coupling Between Protein Level Selection and Codon Usage Optimization in the Evolution of Bacteria and Archaea

Eugene V. Koonin, David M. Kristensen, E. Koonin, 2014, mBio.

Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes

Peer Bork, Arcady R. Mushegian, Eugene V. Koonin, 2012, Journal of bacteriology.

De-Orphaning the Structural Proteome through Reciprocal Comparison of Evolutionarily Important Structural Features

Andreas Martin Lisewski, Olivier Lichtarge, David M. Kristensen, 2008, PloS one.

Evolutionary Conservation of Bacterial Essential Metabolic Genes across All Bacterial Culture Media

Eytan Ruppin, David M. Kristensen, E. Ruppin, 2015, PloS one.