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David J. Lipman

National Institutes of Health

DOI: 10.1038/nbt.4267
Nature Biotechnology ·
2018
Cited 31 times
How user intelligence is improving PubMed.
Nicolas Fiorini, Robert Leaman, David J. Lipman, Zhiyong Lu
World Wide Web
Information retrieval
DOI: 10.7554/elife.28801
eLife ·
2017
Cited 39 times
Towards PubMed 2.0.
Nicolas Fiorini, David J. Lipman, Zhiyong Lu
Computer science
MEDLINE
DOI: 10.1186/1745-6150-8-11
Biology Direct ·
2013
Cited 6 times
Biology Direct: celebrating 7 years of open, published peer review
Eugene V. Koonin, Laura F. Landweber, David J. Lipman
Biology
Computational biology
Library science
DOI: 10.1093/gbe/evt024
Genome Biology and Evolution ·
2013
Cited 5 times
Why Does a Protein’s Evolutionary Rate Vary over Time?
Xiangjun Du, David J. Lipman, Joshua L. Cherry
Biology
Evolutionary biology
Molecular evolution
DOI: 10.1128/jvi.02257-12
Journal of Virology ·
2013
Cited 57 times
Sequential Seasonal H1N1 Influenza Virus Infections Protect Ferrets against Novel 2009 H1N1 Influenza Virus
Donald M. Carter, Chalise E. Bloom, Eduardo J. M. Nascimento, Ernesto T. A. Marques, Jodi K. Craigo, Joshua L. Cherry, David J. Lipman, Ted M. Ross
Influenza A virus
Influenza A virus subtype H5N1
Orthomyxoviridae
DOI: 10.1038/493026a
Nature ·
2013
NIH funding: Agency rebuts critique
George M. Santangelo, David J. Lipman
Agency (philosophy)
Political science
Public administration
DOI: 10.1371/journal.pone.0039435
PLOS ONE ·
2012
Cited 11 times
Complex Patterns of Human Antisera Reactivity to Novel 2009 H1N1 and Historical H1N1 Influenza Strains
Donald M. Carter, Hai-Rong Lu, Chalise E. Bloom, Corey J. Crevar, Joshua L. Cherry, David J. Lipman, Ted M. Ross
Virology
Virus
Influenza A virus
DOI: 10.1186/1745-6150-7-12
Biology Direct ·
2012
Cited 565 times
Domain enhanced lookup time accelerated BLAST.
Grzegorz M. Boratyn, Alejandro A. Schäffer, Richa Agarwala, Stephen F. Altschul, David J. Lipman, Thomas L. Madden
Computer science
Sequence database
Context (archaeology)
DOI: 10.1109/bibmw.2011.6112529
bioinformatics and biomedicine ·
2011
An approach to phylogenomic analysis of bacterial pathogens
Leonid Zaslavsky, Vyacheslav Chetvernin, Dmitry Dernovoy, Boris Fedorov, William Klimke, Alexandre Souvorov, Igor Tolstoy, Tatiana Tatusova, David J. Lipman
Biology
Phylogenomics
Computational biology
DOI: 10.1186/gb-2011-12-3-402
Genome Biology ·
2011
Cited 26 times
Closure of the NCBI SRA and implications for the long-term future of genomics data storage.
David J. Lipman, Paul Flicek, Steven L. Salzberg, Mark Gerstein, Rob Knight
Biology
Genomics
Computational biology
DOI: 10.1371/currents.rrn1200
PLOS Currents ·
2010
Cited 11 times
Projection of seasonal influenza severity from sequence and serological data.
Yuri I. Wolf, Anastasia N. Nikolskaya, Joshua L. Cherry, Cécile Viboud, Eugene V. Koonin, David J. Lipman
Novelty
Antigenic drift
Hemagglutinin (influenza)
DOI: 10.1093/gbe/evq010
Genome Biology and Evolution ·
2010
Cited 24 times
Relative Contributions of Intrinsic Structural–Functional Constraints and Translation Rate to the Evolution of Protein-Coding Genes
Yuri I. Wolf, Irina V. Gopich, David J. Lipman, Eugene V. Koonin
Biology
Gene
Genetics
DOI: 10.1093/nar/gkp712
Nucleic Acids Research ·
2009
Cited 33 times
Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage
Yang Huang, Eugene V. Koonin, David J. Lipman, Teresa M. Przytycka
Biology
Translational frameshift
Codon usage bias
DOI: 10.1371/currents.rrn1001
PLOS Currents ·
2009
Cited 42 times
Evolutionary dynamics of N-glycosylation sites of influenza virus hemagglutinin.
Joshua L. Cherry, David J. Lipman, Anastasia N. Nikolskaya, Yuri I. Wolf
Virus
Glycan
Virology
DOI: 10.1101/gr.080531.108
Genome Research ·
2009
Cited 496 times
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes
Kim D. Pruitt, Jennifer Harrow, Rachel A. Harte, Craig Wallin, Mark Diekhans, Donna Maglott, Steve Searle, Catherine M. Farrell, Jane E. Loveland, Barbara J. Ruef, Elizabeth M. Hart, Marie-Marthe Suner, Melissa J. Landrum, Bronwen Aken, Sarah Ayling, Robert Baertsch, Julio Fernandez-Banet, Joshua L. Cherry, Val Curwen, Michael DiCuccio, Manolis Kellis, Jennifer M. Lee, Michael F. Lin, Michael Schuster, Andrew Shkeda, Clara Amid, Garth Brown, Oksana Dukhanina, Adam Frankish, Jennifer Hart, Bonnie L. Maidak, Jonathan M. Mudge, Michael R. Murphy, Terence Murphy, Jeena Rajan, Bhanu Rajput, Lillian D. Riddick, Catherine E. Snow, Charles A. Steward, David Webb, Janet Weber, Laurens G. Wilming, Wenyu Wu, Ewan Birney, David Haussler, Tim Hubbard, James Ostell, Richard Durbin, David J. Lipman
ENCODE
Coding (social sciences)
Gene
DOI: 10.1073/pnas.0901808106
Proceedings of the National Academy of Sciences of the United States of America ·
2009
Cited 199 times
The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages.
Yuri I. Wolf, Pavel S. Novichkov, Georgy P. Karev, Eugene V. Koonin, David J. Lipman
Evolutionary biology
Molecular evolution
Phylogenetics
DOI: 10.1093/nar/gkn723
Nucleic Acids Research ·
2009
Cited 17 times
GenBank
D. A. Benson, I. Karsch-Mizrachi, David J. Lipman, J. Ostell, E. W. Sayers
Biology
GenBank
Computational biology
DOI: 10.1186/1471-2148-8-208
BMC Evolutionary Biology ·
2008
Cited 4 times
Differences in evolutionary pressure acting within highly conserved ortholog groups
Teresa M. Przytycka, Raja Jothi, L. Aravind, David J. Lipman
Biology
Genetics
Evolutionary biology
DOI: 10.1186/1745-6150-3-20
Biology Direct ·
2008
Cited 239 times
Splign: algorithms for computing spliced alignments with identification of paralogs
Yuri Kapustin, Alexander Souvorov, Tatiana Tatusova, David J. Lipman
Computational biology
Computer science
Identification (biology)
DOI: 10.1128/jvi.02005-07
Journal of Virology ·
2008
Cited 863 times
The influenza virus resource at the National Center for Biotechnology Information.
Yiming Bao, Pavel Bolotov, Dmitry Dernovoy, Boris Kiryutin, Leonid Zaslavsky, Tatiana Tatusova, Jim Ostell, David J. Lipman
Influenza A virus
Coronavirus disease 2019 (COVID-19)
Center (category theory)
MAG: 2184127838
·
2008
GUEST COMMENTARY The Influenza Virus Resource at the National Center for Biotechnology Information
Yiming Bao, Pavel Bolotov, Dmitry Dernovoy, Boris Kiryutin, Leonid Zaslavsky, Tatiana Tatusova, Jim Ostell, David J. Lipman
Center (category theory)
Pandemic
Coronavirus disease 2019 (COVID-19)
DOI: 10.1371/journal.ppat.0020125
PLOS Pathogens ·
2006
Cited 162 times
Stochastic processes are key determinants of short-term evolution in influenza a virus.
Martha I. Nelson, Lone Simonsen, Cécile Viboud, Mark A. Miller, Jill Taylor, Kirsten St. George, Sara B. Griesemer, Elodie Ghedin, Naomi Sengamalay, David J. Spiro, Igor Volkov, Bryan T. Grenfell, David J. Lipman, Jeffery K. Taubenberger, Edward C. Holmes
Virus
Influenza A virus subtype H5N1
Virology
DOI: 10.1371/journal.ppat.0020138
PLOS Pathogens ·
2006
Correction: Stochastic Processes Are Key Determinants of Short-Term Evolution in Influenza A Virus.
Martha I. Nelson, Lone Simonsen, Cécile Viboud, Mark A. Miller, Jill Taylor, Kirsten St. George, Sara B. Griesemer, Elodie Ghedin, Naomi Sengamalay, David J. Spiro, Igor Volkov, Brian T. Grenfell, David J. Lipman, Jeffrey K. Taubenberger, Edward C. Holmes
Biology
Virus
Influenza A virus
DOI: 10.1371/journal/ppat.0020138
PLOS Pathogens ·
2006
Cited 19 times
Erratum: Stochastic processes are key determinants of short-term evolution in influenza A virus (PLoS pathogens 2, 12 DOI: 10.1371/journal.ppat.0020125)
Martha I. Nelson, Lone Simonsen, Cécile Viboud, Mark A. Miller, Jill Taylor, Kirsten St. George, Sara B. Griesemer, Elodie Ghedin, Naomi Sengamalay, David J. Spiro, Igor Volkov, Brian T. Grenfell, David J. Lipman, Jeffrey K. Taubenberger, Edward C. Holmes
Virology
Biology
DOI: 10.1186/1745-6150-1-34
Biology Direct ·
2006
Cited 168 times
Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus
Yuri I. Wolf, Cécile Viboud, Edward C. Holmes, Eugene V. Koonin, David J. Lipman
Evolutionary biology
Population
Virology