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David Lipman

Research Profile

Organizations

National Library of Medicine (U.S.)

Concepts & Ideas

Activities & Behaviors

Geographic Areas

United States

Chemicals & Drugs

Occupations

Genes & Molecular Sequences

Phenomena

Evolution, Molecular

Procedures

Sequence Alignment

Co-author Network

Publications

TOP 3
Eugene V Koonin; Laura F Landweber; David Lipman
Biology direct: celebrating 7 years of open, published peer review.
Xiangjun Du; David Lipman; Joshua L Cherry
Why does a protein's evolutionary rate vary over time?
Dennis A Benson; Mark Cavanaugh; Karen Clark; Ilene Karsch-Mizrachi; David Lipman; James Ostell; Eric W Sayers
GenBank.

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All Publications

2013: Eugene V Koonin; Laura F Landweber; David Lipman
Biology direct: celebrating 7 years of open, published peer review.
Biology direct 2013;8(1):11.
2013: Xiangjun Du; David Lipman; Joshua L Cherry
Why does a protein's evolutionary rate vary over time?
Genome biology and evolution 2013;5(3):494-503.
2013: Dennis A Benson; Mark Cavanaugh; Karen Clark; Ilene Karsch-Mizrachi; David Lipman; James Ostell; Eric W Sayers
GenBank.
Nucleic acids research 2013;41(Database issue):D36-42.
2012: Grzegorz M Boratyn; David Lipman; Richa Agarwala; Stephen F Altschul; Alejandro A Schäffer; Thomas L Madden
Domain enhanced lookup time accelerated BLAST.
Biology direct 2012;7():12.
2011: Dennis A Benson; Ilene Karsch-Mizrachi; David Lipman; James Ostell; Eric W Sayers
GenBank.
Nucleic acids research 2011;39(Database issue):D32-7.
2010: Yuri I Wolf; Anastasia Nikolskaya; Joshua L Cherry; Cécile Viboud; Eugene Koonin; David Lipman
Projection of seasonal influenza severity from sequence and serological data.
PLoS currents 2010;2():RRN1200.
2010: Yuri I Wolf; Irina V Gopich; David Lipman; Eugene V Koonin
Relative contributions of intrinsic structural-functional constraints and translation rate to the evolution of protein-coding genes.
Genome biology and evolution 2010;2():190-9.
2010: Dennis A Benson; Ilene Karsch-Mizrachi; David Lipman; James Ostell; Eric W Sayers
GenBank.
Nucleic acids research 2010;38(Database issue):D46-51.
2009: Yang Huang; Eugene V Koonin; David Lipman; Teresa M Przytycka
Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage.
Nucleic acids research 2009;37(20):6799-810.
2009: Kim D Pruitt; Jennifer Harrow; Rachel A Harte; Craig Wallin; Mark Diekhans; Donna R Maglott; Steve Searle; Catherine M Farrell; Jane E Loveland; Barbara J Ruef; Elizabeth 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 Lee; Michael F Lin; Michael Schuster; Andrew Shkeda; Clara Amid; Garth Brown; Oksana Dukhanina; Adam Frankish; Jennifer Hart; Bonnie L Maidak; Jonathan Mudge; Michael R Murphy; Terence Murphy; Jeena Rajan; Bhanu Rajput; Lillian D Riddick; Catherine Snow; Charles Steward; David Webb; Janet A Weber; Laurens Wilming; Wenyu Wu; Ewan Birney; David Haussler; Tim Hubbard; James Ostell; Richard Durbin; David Lipman
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.
Genome research 2009;19(7):1316-23.
2009: Yuri I Wolf; Pavel Novichkov; Georgy P Karev; Eugene V Koonin; David Lipman
The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(18):7273-80.
2009: Joshua L Cherry; David Lipman; Anastasia Nikolskaya; Yuri I Wolf
Evolutionary dynamics of N-glycosylation sites of influenza virus hemagglutinin.
PLoS currents 2009;1():RRN1001.
2009: Dennis A Benson; Ilene Karsch-Mizrachi; David Lipman; James Ostell; Eric W Sayers
GenBank.
Nucleic acids research 2009;37(Database issue):D26-31.
2009: Eric W Sayers; Tanya Barrett; Dennis A Benson; Stephen H Bryant; Kathi Canese; Vyacheslav Chetvernin; Deanna M Church; Michael DiCuccio; Ron Edgar; Scott Federhen; Michael Feolo; Lewis Y Geer; Wolfgang Helmberg; Yuri Kapustin; David Landsman; David Lipman; Thomas L Madden; Donna R Maglott; Vadim Miller; Ilene Mizrachi; James Ostell; Kim D Pruitt; Gregory D Schuler; Edwin Sequeira; Stephen T Sherry; Martin Shumway; Karl Sirotkin; Alexandre Souvorov; Grigory Starchenko; Tatiana A Tatusova; Lukas Wagner; Eugene Yaschenko; Jian Ye
Database resources of the National Center for Biotechnology Information.
Nucleic acids research 2009;37(Database issue):D5-15.
2008: Teresa M Przytycka; Raja Jothi; L Aravind; David Lipman
Differences in evolutionary pressure acting within highly conserved ortholog groups.
BMC evolutionary biology 2008;8():208.
2008: Yuri Kapustin; Alexander Souvorov; Tatiana Tatusova; David Lipman
Splign: algorithms for computing spliced alignments with identification of paralogs.
Biology direct 2008;3():20.
2008: Dennis A Benson; Ilene Karsch-Mizrachi; David Lipman; James Ostell; david wheeler
GenBank.
Nucleic acids research 2008;36(Database issue):D25-30.
2008: David L Wheeler; Tanya Barrett; Dennis A Benson; Stephen H Bryant; Kathi Canese; Vyacheslav Chetvernin; Deanna M Church; Michael Dicuccio; Ron Edgar; Scott Federhen; Michael Feolo; Lewis Y Geer; Wolfgang Helmberg; Yuri Kapustin; Oleg Khovayko; David Landsman; David Lipman; Thomas L Madden; Donna R Maglott; Vadim Miller; James Ostell; Kim D Pruitt; Gregory D Schuler; Martin Shumway; Edwin Sequeira; Steven T Sherry; Karl Sirotkin; Alexandre Souvorov; Grigory Starchenko; Roman L Tatusov; Tatiana A Tatusova; Lukas Wagner; Eugene Yaschenko
Database resources of the National Center for Biotechnology Information.
Nucleic acids research 2008;36(Database issue):D13-21.
2008: Yiming Bao; Pavel Bolotov; Dmitry Dernovoy; Boris Kiryutin; Leonid Zaslavsky; Tatiana Tatusova; James Ostell; David Lipman
The influenza virus resource at the National Center for Biotechnology Information.
Journal of virology 2008;82(2):596-601.
2007: Dennis A Benson; Ilene Karsch-Mizrachi; David Lipman; James Ostell; david wheeler
GenBank.
Nucleic acids research 2007;35(Database issue):D21-5.
2007: david wheeler; Tanya Barrett; Dennis A Benson; Stephen H Bryant; Kathi Canese; Vyacheslav Chetvernin; Deanna M Church; Michael DiCuccio; Ron Edgar; Scott Federhen; Lewis Y Geer; Yuri Kapustin; Oleg Khovayko; David Landsman; David Lipman; Thomas L Madden; Donna R Maglott; James Ostell; Vadim Miller; Kim D Pruitt; Gerold Schuler; Edwin Sequeira; Stephen T Sherry; Karl Sirotkin; Alexander Souvorov; Grigory Starchenko; Roman L Tatusov; Tatiana Tatusova; Lukas Wagner; Eugene Yaschenko
Database resources of the National Center for Biotechnology Information.
Nucleic acids research 2007;35(Database issue):D5-12.
2006: Martha I Nelson; Lone Simonsen; Cécile Viboud; mark miller; Jill Taylor; Kirsten St George; Sara B Griesemer; Elodie Ghedin; Elodie Ghedi; Naomi A Sengamalay; David Spiro; Igor Volkov; Bryan T Grenfell; David Lipman; Jeffery Taubenberger; Edward C Holmes
Stochastic processes are key determinants of short-term evolution in influenza a virus.
PLoS pathogens 2006;2(12):e125.
2006: Edward C Holmes; David Lipman; Dmitriy Zamarin; jon yewdell
Comment on "Large-scale sequence analysis of avian influenza isolates".
Science (New York, N.Y.) 2006;313(5793):1573; author reply 1573.
2006: Yuri I Wolf; Cécile Viboud; Edward C Holmes; Eugene V Koonin; David Lipman
Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus.
Biology direct 2006;1():34.
2006: Eugene V Koonin; Laura F Landweber; David Lipman
A community experiment with fully open and published peer review.
Biology direct 2006;1():1.
2006: David L Wheeler; Tanya Barrett; Dennis A Benson; Stephen H Bryant; Kathi Canese; Vyacheslav Chetvernin; Deanna M Church; Michael DiCuccio; Ron Edgar; Scott Federhen; Lewis Y Geer; Wolfgang Helmberg; Yuri Kapustin; David L Kenton; Oleg Khovayko; David Lipman; Thomas L Madden; Donna R Maglott; James Ostell; Kim D Pruitt; Gregory D Schuler; Lynn M Schriml; Edwin Sequeira; Stephen T Sherry; Karl Sirotkin; Alexandre Souvorov; Grigory Starchenko; Tugba O Suzek; Roman Tatusov; Tatiana A Tatusova; Lukas Wagner; Eugene Yaschenko
Database resources of the National Center for Biotechnology Information.
Nucleic acids research 2006;34(Database issue):D173-80.
2006: Dennis A Benson; Ilene Karsch-Mizrachi; David Lipman; James Ostell; david wheeler
GenBank.
Nucleic acids research 2006;34(Database issue):D16-20.
2005: Elodie Ghedin; Naomi A Sengamalay; Martin Shumway; Jennifer Zaborsky; Tamara Feldblyum; Vik Subbu; David Spiro; Jeff Sitz; Hean Koo; Pavel Bolotov; Dmitry Dernovoy; Tatiana Tatusova; Yiming Bao; Kirsten St George; Jill Taylor; David Lipman; Claire M Fraser-Liggett; Jeffery Taubenberger; Steven L Salzberg
Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution.
Nature 2005;437(7062):1162-6.
2005: Edward C Holmes; Elodie Ghedin; Naomi Miller; Jill Taylor; Yiming Bao; Kirsten St George; Bryan T Grenfell; Steven L Salzberg; Claire M Fraser-Liggett; David Lipman; Jeffery Taubenberger
Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses.
PLoS biology 2005;3(9):e300.
2005: david wheeler; Tanya Barrett; Dennis A Benson; Stephen H Bryant; Kathi Canese; Deanna M Church; Michael DiCuccio; Ron Edgar; Scott Federhen; Wolfgang Helmberg; David L Kenton; Oleg Khovayko; David Lipman; Thomas L Madden; Donna R Maglott; James Ostell; Joan U Pontius; Kim D Pruitt; Gerold Schuler; Lynn M Schriml; Edwin Sequeira; Stephen T Sherry; Karl Sirotkin; Grigory Starchenko; Tugba O Suzek; Roman L Tatusov; Tatiana Tatusova; Lukas Wagner; Eugene Yaschenko
Database resources of the National Center for Biotechnology Information.
Nucleic acids research 2005;33(Database issue):D39-45.
2005: Dennis A Benson; Ilene Karsch-Mizrachi; David Lipman; James Ostell; david wheeler
GenBank.
Nucleic acids research 2005;33(Database issue):D34-8.
2004: Daniela S Gerhard; Lukas Wagner; Elise A Feingold; Carolyn M Shenmen; Lynette H Grouse; Greg Schuler; Steven L Klein; Susan Old; Rebekah Rasooly; Peter Good; Mark Guyer; Allison M Peck; Jeffery G Derge; David Lipman; Francis S Collins; Wonhee Jang; Steven Sherry; Michael Feolo; Leonie Misquitta; Eduardo Lee; Kirill Rotmistrovsky; Susan F Greenhut; Carl F Schaefer; Kenneth Buetow; Tom I Bonner; David Haussler; Jim Kent; Mark Kiekhaus; Terry Furey; Michael Brent; Christa Prange; Kirsten Schreiber; Nicole Shapiro; Narayan K Bhat; Ralph F Hopkins; Florence Hsie; Tom Driscoll; M Bento Soares; Tom L Casavant; Todd E Scheetz; Michael J Brown-stein; Ted B Usdin; Shiraki Toshiyuki; piero carninci; Yulan Piao; Dawood B Dudekula; Minoru S H Ko; Koichi Kawakami; Yutaka Suzuki; Sumio Sugano; C E Gruber; M R Smith; Blake Simmons; Troy Moore; Richard Waterman; Stephen L Johnson; Yijun Ruan; Chia Lin Wei; S Mathavan; Preethi H Gunaratne; Jiaqian Wu; Angela M Garcia; Stephen W Hulyk; Edwin Fuh; Ye Yuan; Anna Sneed; Carla Kowis; Anne Hodgson; Donna M Muzny; John McPherson; Richard A Gibbs; Jessica Fahey; Erin Helton; Mark Ketteman; Anuradha Madan; Stephanie Rodrigues; Amy Sanchez; Michelle Whiting; Anup Madari; Alice C Young; Keith D Wetherby; Steven J Granite; Peggy N Kwong; Charles P Brinkley; Russell L Pearson; Gerard G Bouffard; Robert W Blakesly; Eric Green; Mark C Dickson; Alex C Rodriguez; Jane Grimwood; Jeremy Schmutz; Richard Myers; Yaron S N Butterfield; Malachi Griffith; Obi L Griffith; Martin I Krzywinski; Nancy Liao; Ryan Morin; Ryan Morrin; Diana Palmquist; Anca S Petrescu; Ursula Skalska; Duane E Smailus; Jeff M Stott; Angelique Schnerch; Jacqueline E Schein; Steven J M Jones; Robert A Holt; Agnes Baross; Marco A Marra; Sandra Clifton; Kathryn A Makowski; Stephanie Bosak; Joel Malek
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).
Genome research 2004;14(10B):2121-7.
2004: Svetlana A Shabalina; Aleksey Y Ogurtsov; Igor Rogozin; Eugene V Koonin; David Lipman
Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals.
Nucleic acids research 2004;32(5):1774-82.
2004: Dennis A Benson; Ilene Karsch-Mizrachi; David Lipman; James Ostell; david wheeler
GenBank: update.
Nucleic acids research 2004;32(Database issue):D23-6.
2003: Svetlana A Shabalina; Aleksey Y Ogurtsov; David Lipman; Alexey S Kondrashov
Patterns in interspecies similarity correlate with nucleotide composition in mammalian 3'UTRs.
Nucleic acids research 2003;31(18):5433-9.
2003: Dennis A Benson; Ilene Karsch-Mizrachi; David Lipman; James Ostell; david wheeler
GenBank.
Nucleic acids research 2003;31(1):23-7.
2002: David Lipman; Alexander Souvorov; Eugene V Koonin; Anna R Panchenko; Tatiana Tatusova
The relationship of protein conservation and sequence length.
BMC evolutionary biology 2002;2():20.
2002: Lewis Y Geer; Michael Domrachev; David Lipman; Stephen H Bryant
CDART: protein homology by domain architecture.
Genome research 2002;12(10):1619-23.
2002: Dennis A Benson; Ilene Karsch-Mizrachi; David Lipman; James Ostell; Barbara Rapp; david wheeler
GenBank.
Nucleic acids research 2002;30(1):17-20.
2001: Johanna R McEntyre; David Lipman
PubMed: bridging the information gap.
CMAJ : Canadian Medical Association journal = journal de l'Association medicale canadienne 2001;164(9):1317-9.
2001: E Sequeira; Johanna R McEntyre; David Lipman
PubMed Central decentralized.
Nature 2001;410(6830):740.
2000: L Aravind; H Watanabe; David Lipman; Eugene V Koonin
Lineage-specific loss and divergence of functionally linked genes in eukaryotes.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(21):11319-24.
2000: Dennis A Benson; Ilene Karsch-Mizrachi; David Lipman; James Ostell; Barbara Rapp; david wheeler
GenBank.
Nucleic acids research 2000;28(1):15-8.
1999: Dennis A Benson; Mark S Boguski; David Lipman; James Ostell; BF Ouellette; Barbara Rapp; david wheeler
GenBank.
Nucleic acids research 1999;27(1):12-7.
1998: Zhaolei Zhang; Alejandro A Schäffer; Webb Miller; Thomas L Madden; David Lipman; Eugene V Koonin; Stephen F Altschul
Protein sequence similarity searches using patterns as seeds.
Nucleic acids research 1998;26(17):3986-90.
1998: Dennis A Benson; Mark S Boguski; David Lipman; James Ostell; BF Ouellette
GenBank.
Nucleic acids research 1998;26(1):1-7.
1997: Roman L Tatusov; Eugene V Koonin; David Lipman
A genomic perspective on protein families.
Science (New York, N.Y.) 1997;278(5338):631-7.
1997: David Lipman
Making (anti)sense of non-coding sequence conservation.
Nucleic acids research 1997;25(18):3580-3.
1997: Stephen F Altschul; Thomas L Madden; Alejandro A Schäffer; J Zhang; Zhaolei Zhang; Webb Miller; David Lipman
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Nucleic acids research 1997;25(17):3389-402.
1997: Andrew F. Neuwald; Jun Liu; David Lipman; C E Lawrence
Extracting protein alignment models from the sequence database.
Nucleic acids research 1997;25(9):1665-77.
1997: Dennis A Benson; Mark S Boguski; David Lipman; James Ostell
GenBank.
Nucleic acids research 1997;25(1):1-6.
1996: Dennis A Benson; Mark S Boguski; David Lipman; James Ostell
GenBank.
Nucleic acids research 1996;24(1):1-5.
1994: Dennis A Benson; Mark S Boguski; David Lipman; James Ostell
GenBank.
Nucleic acids research 1994;22(17):3441-4.
1993: D Benson; David Lipman; James Ostell
GenBank.
Nucleic acids research 1993;21(13):2963-5.
1991: David Lipman; W John Wilbur
Modelling neutral and selective evolution of protein folding.
Proceedings. Biological sciences / The Royal Society 1991;245(1312):7-11.
1991: G D Schuler; Stephen F Altschul; David Lipman
A workbench for multiple alignment construction and analysis.
Proteins 1991;9(3):180-90.
1990: Stephen F Altschul; David Lipman
Equal animals.
Nature 1990;348(6301):493-4.
1990: Stephen F Altschul; W Gish; Webb Miller; E W Myers; David Lipman
Basic local alignment search tool.
Journal of molecular biology 1990;215(3):403-10.
1990: Stephen F Altschul; David Lipman
Protein database searches for multiple alignments.
Proceedings of the National Academy of Sciences of the United States of America 1990;87(14):5509-13.
1990: D Benson; Mark S Boguski; David Lipman; James Ostell
The National Center for Biotechnology Information.
Genomics 1990;6(2):389-91.
1989: Stephen F Altschul; R J Carroll; David Lipman
Weights for data related by a tree.
Journal of molecular biology 1989;207(4):647-53.
1989: David Lipman; Stephen F Altschul; J D Kececioglu
A tool for multiple sequence alignment.
Proceedings of the National Academy of Sciences of the United States of America 1989;86(12):4412-5.
1984: David Lipman; W John Wilbur; T F Smith; M S Waterman
On the statistical significance of nucleic acid similarities.
Nucleic acids research 1984;12(1 Pt 1):215-26.
1984: David Lipman; W John Wilbur
Interaction of silent and replacement changes in eukaryotic coding sequences.
Journal of molecular evolution 1984;21(2):161-7.
1983: W John Wilbur; David Lipman
Rapid similarity searches of nucleic acid and protein data banks.
Proceedings of the National Academy of Sciences of the United States of America 1983;80(3):726-30.
1983: David Lipman; W John Wilbur
Contextual constraints on synonymous codon choice.
Journal of molecular biology 1983;163(3):363-76.
1982: David Lipman; T F Smith; R J Beckman; M S Waterman
Hierarchical analysis of influenza A hemagglutinin gene sequences.
Nucleic acids research 1982;10(17):5375-89.