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Items: 31

1.

High-Throughput Next-Generation Sequencing of Polioviruses.

Montmayeur AM, Ng TF, Schmidt A, Zhao K, Magaña L, Iber J, Castro CJ, Chen Q, Henderson E, Ramos E, Shaw J, Tatusov RL, Dybdahl-Sissoko N, Endegue-Zanga MC, Adeniji JA, Oberste MS, Burns CC.

J Clin Microbiol. 2017 Feb;55(2):606-615. doi: 10.1128/JCM.02121-16. Epub 2016 Dec 7.

2.

Finished Annotated Genome Sequence of Burkholderia pseudomallei Strain Bp1651, a Multidrug-Resistant Clinical Isolate.

Bugrysheva JV, Sue D, Hakovirta J, Loparev VN, Knipe K, Sammons SA, Ranganathan-Ganakammal S, Changayil S, Srinivasamoorthy G, Weil MR, Tatusov RL, Gee JE, Elrod MG, Hoffmaster AR, Weigel LM.

Genome Announc. 2015 Dec 3;3(6). pii: e01427-15. doi: 10.1128/genomeA.01427-15.

3.

Database resources of the National Center for Biotechnology Information.

Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Ostell J, Pruitt KD, Schuler GD, Shumway M, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E.

Nucleic Acids Res. 2008 Jan;36(Database issue):D13-21. Epub 2007 Nov 27.

4.

Database resources of the National Center for Biotechnology Information.

Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Geer LY, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Ostell J, Miller V, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E.

Nucleic Acids Res. 2007 Jan;35(Database issue):D5-12. Epub 2006 Dec 14.

5.

The COG database: an updated version includes eukaryotes.

Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA.

BMC Bioinformatics. 2003 Sep 11;4:41. Epub 2003 Sep 11.

6.

Congruent evolution of different classes of non-coding DNA in prokaryotic genomes.

Rogozin IB, Makarova KS, Natale DA, Spiridonov AN, Tatusov RL, Wolf YI, Yin J, Koonin EV.

Nucleic Acids Res. 2002 Oct 1;30(19):4264-71.

7.

Purifying and directional selection in overlapping prokaryotic genes.

Rogozin IB, Spiridonov AN, Sorokin AV, Wolf YI, Jordan IK, Tatusov RL, Koonin EV.

Trends Genet. 2002 May;18(5):228-32.

PMID:
12047938
8.

Connected gene neighborhoods in prokaryotic genomes.

Rogozin IB, Makarova KS, Murvai J, Czabarka E, Wolf YI, Tatusov RL, Szekely LA, Koonin EV.

Nucleic Acids Res. 2002 May 15;30(10):2212-23.

9.

The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens.

Slesarev AI, Mezhevaya KV, Makarova KS, Polushin NN, Shcherbinina OV, Shakhova VV, Belova GI, Aravind L, Natale DA, Rogozin IB, Tatusov RL, Wolf YI, Stetter KO, Malykh AG, Koonin EV, Kozyavkin SA.

Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4644-9.

10.

Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins.

Jordan IK, Kondrashov FA, Rogozin IB, Tatusov RL, Wolf YI, Koonin EV.

Genome Biol. 2001;2(12):RESEARCH0053. Epub 2001 Nov 20.

11.

Genome trees constructed using five different approaches suggest new major bacterial clades.

Wolf YI, Rogozin IB, Grishin NV, Tatusov RL, Koonin EV.

BMC Evol Biol. 2001 Oct 20;1:8.

12.

Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum.

Nölling J, Breton G, Omelchenko MV, Makarova KS, Zeng Q, Gibson R, Lee HM, Dubois J, Qiu D, Hitti J, Wolf YI, Tatusov RL, Sabathe F, Doucette-Stamm L, Soucaille P, Daly MJ, Bennett GN, Koonin EV, Smith DR.

J Bacteriol. 2001 Aug;183(16):4823-38.

13.

Organelle genome resource at NCBI.

Wolfsberg TG, Schafer S, Tatusov RL, Tatusov TA.

Trends Biochem Sci. 2001 Mar;26(3):199-203. No abstract available.

PMID:
11339208
14.

Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics.

Makarova KS, Aravind L, Wolf YI, Tatusov RL, Minton KW, Koonin EV, Daly MJ.

Microbiol Mol Biol Rev. 2001 Mar;65(1):44-79. Review.

15.

Using the COG database to improve gene recognition in complete genomes.

Natale DA, Galperin MY, Tatusov RL, Koonin EV.

Genetica. 2000;108(1):9-17.

PMID:
11145426
16.

The COG database: new developments in phylogenetic classification of proteins from complete genomes.

Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV.

Nucleic Acids Res. 2001 Jan 1;29(1):22-8.

17.

The COG database: a tool for genome-scale analysis of protein functions and evolution.

Tatusov RL, Galperin MY, Natale DA, Koonin EV.

Nucleic Acids Res. 2000 Jan 1;28(1):33-6.

18.

Reply

Aravind L, Tatusov RL, Wolf YI, Walker DR, Koonin EV.

Trends Genet. 1999 Aug;15(8):299-300. No abstract available.

PMID:
10431190
19.

Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell.

Makarova KS, Aravind L, Galperin MY, Grishin NV, Tatusov RL, Wolf YI, Koonin EV.

Genome Res. 1999 Jul;9(7):608-28.

20.

Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles.

Aravind L, Tatusov RL, Wolf YI, Walker DR, Koonin EV.

Trends Genet. 1998 Nov;14(11):442-4. No abstract available. Erratum in: Trends Genet 1999 Jan;15(1):41.

PMID:
9825671
21.

Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis.

Stephens RS, Kalman S, Lammel C, Fan J, Marathe R, Aravind L, Mitchell W, Olinger L, Tatusov RL, Zhao Q, Koonin EV, Davis RW.

Science. 1998 Oct 23;282(5389):754-9.

22.

Beyond complete genomes: from sequence to structure and function.

Koonin EV, Tatusov RL, Galperin MY.

Curr Opin Struct Biol. 1998 Jun;8(3):355-63. Review.

PMID:
9666332
23.

A genomic perspective on protein families.

Tatusov RL, Koonin EV, Lipman DJ.

Science. 1997 Oct 24;278(5338):631-7. Review.

PMID:
9381173
24.

Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli.

Tatusov RL, Mushegian AR, Bork P, Brown NP, Hayes WS, Borodovsky M, Rudd KE, Koonin EV.

Curr Biol. 1996 Mar 1;6(3):279-91.

25.

Protein sequence comparison at genome scale.

Koonin EV, Tatusov RL, Rudd KE.

Methods Enzymol. 1996;266:295-322.

PMID:
8743691
26.

Applications of network BLAST server.

Madden TL, Tatusov RL, Zhang J.

Methods Enzymol. 1996;266:131-41.

PMID:
8743682
27.

Sequence similarity analysis of Escherichia coli proteins: functional and evolutionary implications.

Koonin EV, Tatusov RL, Rudd KE.

Proc Natl Acad Sci U S A. 1995 Dec 5;92(25):11921-5.

28.

Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks.

Tatusov RL, Altschul SF, Koonin EV.

Proc Natl Acad Sci U S A. 1994 Dec 6;91(25):12091-5.

30.
31.

A simple tool to search for sequence motifs that are conserved in BLAST outputs.

Tatusov RL, Koonin EV.

Comput Appl Biosci. 1994 Jul;10(4):457-9. No abstract available.

PMID:
7804881

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