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Nick Grishin
Department of Biochemistry, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, United States of America

Faculty Member: GENOMICS & GENETICS > Bioinformatics [ since 5 July 2001 ]
[ Evaluations ]
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Evaluations

Structure of a site-2 protease family intramembrane metalloprotease.
Feng L, Yan H, …, Jeffrey PD, Shi Y
Science 2007 Dec 7 318(5856):1608-12 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Nick Grishin
Evaluated 25 Feb 2008

Detection of DNA structural motifs in functional genomic elements.
Greenbaum JA, Parker SC, Tullius TD
Genome Res 2007 Jun 17(6):940-6 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Nick Grishin
Evaluated 18 Feb 2008

A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution of cradle-loop barrels.
Ammelburg M, Hartmann MD, …, Lupas AN, Coles M
Structure 2007 Dec 15(12):1577-90 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Nick Grishin
Evaluated 18 Feb 2008

The design and characterization of two proteins with 88% sequence identity but different structure and function.
Alexander PA, He Y, …, Orban J, Bryan PN
Proc Natl Acad Sci U S A 2007 Jul 17 104(29):11963-8 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Barry Stoddard / Nick Grishin / Tobin Sosnick
Evaluated 26 Jul 2007

Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution.
Dantas G, Watters AL, …, Varani G, Baker D
J Mol Biol 2006 Oct 6 362(5):1004-24 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Nick Grishin
Evaluated 5 Jan 2007

Introns and the origin of nucleus-cytosol compartmentalization.
Martin W, Koonin EV
Nature 2006 Mar 2 440(7080):41-5 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Nick Grishin / Marilyn Parsons
Evaluated 13 Mar 2006

Placing confidence limits on the molecular age of the human-chimpanzee divergence.
Kumar S, Filipski A, …, Walker A, Hedges SB
Proc Natl Acad Sci U S A 2005 Dec 27 102(52):18842-7 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Nick Grishin
Evaluated 13 Feb 2006

A simple physical model for scaling in protein-protein interaction networks.
Deeds EJ, Ashenberg O, Shakhnovich EI
Proc Natl Acad Sci U S A 2006 Jan 10 103(2):311-6 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Nick Grishin / Deyou Zheng
Evaluated 11 Jan 2006

Quasi-consensus-based comparison of profile hidden Markov models for protein sequences.
Kahsay RY, Wang G, …, Liao L, Dunbrack R
Bioinformatics 2005 May 15 21(10):2287-93 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Nick Grishin
Evaluated 16 Aug 2005

ProbCons: Probabilistic consistency-based multiple sequence alignment.
Do CB, Mahabhashyam MS, Brudno M, Batzoglou S
Genome Res 2005 Feb 15(2):330-40 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Nick Grishin
Evaluated 15 Feb 2005

Recapitulation of protein family divergence using flexible backbone protein design.
Saunders CT, Baker D
J Mol Biol 2005 Feb 18 346(2):631-44 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Nick Grishin
Evaluated 8 Feb 2005

A universal trend of amino acid gain and loss in protein evolution.
Jordan IK, Kondrashov FA, …, Kondrashov AS, Sunyaev S
Nature 2005 Feb 10 433(7026):633-8 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Nick Grishin / Jeffrey Thorne / Ulf Pettersson / Andrew Wilkie
Dissenters | Steven Henikoff
Author Response | Eugene Koonin
Evaluated 1 Feb 2005


Protein homology detection by HMM-HMM comparison.
Söding J
Bioinformatics 2005 Apr 1 21(7):951-60 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Nick Grishin
Evaluated 21 Jan 2005

The SHS2 module is a common structural theme in functionally diverse protein groups, like Rpb7p, FtsA, GyrI, and MTH1598/TM1083 superfamilies.
Anantharaman V, Aravind L
Proteins 2004 Sep 1 56(4):795-807 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Nick Grishin
Evaluated 21 Jan 2005

A novel ADP- and zinc-binding fold from function-directed in vitro evolution.
Lo Surdo P, Walsh MA, Sollazzo M
Nat Struct Mol Biol 2004 Apr 11(4):382-3 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Burckhard Seelig / Nick Grishin
Evaluated 8 Apr 2004

Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis.
Wolf YI, Rogozin IB, Koonin EV
Genome Res 2004 Jan 14(1):29-36 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Nick Grishin / Arcady Mushegian / Alejandro Sanchez-Alvarado
Evaluated 23 Feb 2004

Design of a novel globular protein fold with atomic-level accuracy.
Kuhlman B, Dantas G, …, Stoddard BL, Baker D
Science 2003 Nov 21 302(5649):1364-8 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Kristina Downing / Gideon Schreiber / Rob Russell / Wolfgang Guba / Nick Grishin / Padmanabhan Balaram / Robert Kelley / Kevin Plaxco / Sachdev Sidhu
Evaluated 18 Dec 2003

Evolution and classification of P-loop kinases and related proteins.
Leipe DD, Koonin EV, Aravind L
J Mol Biol 2003 Oct 31 333(4):781-815 [abstract on PubMed] [related articles] [order article]
Selected by | Nick Grishin
Evaluated 17 Dec 2003

Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors.
Mirny LA, Gelfand MS
J Mol Biol 2002 Aug 2 321(1):7-20 [abstract on PubMed] [related articles] [order article]
Selected by | Rob Russell / Nick Grishin
Evaluated 24 Jan 2003

Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction.
Xiang Z, Soto CS, Honig B
Proc Natl Acad Sci U S A 2002 May 28 99(11):7432-7 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Nick Grishin
Evaluated 11 Jun 2002

Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins.
Makarova KS, Ponomarev VA, Koonin EV
Genome Biol 2001 2(9):RESEARCH 0033 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Nick Grishin
Evaluated 29 Oct 2001

A simple algorithm to infer gene duplication and speciation events on a gene tree.
Zmasek CM, Eddy SR
Bioinformatics 2001 Sep 17(9):821-8 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Nick Grishin / Jonathan A. Eisen
Evaluated 26 Oct 2001

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