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NCBI, NLM, NIH
Computational Biology
Branch
Building 38A 8S814
Bethesda , MD 20894
Tel:
301-435-5891
Email: panch@ncbi.nlm.nih.gov
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Current appointments:
Associate Investigator
National
Center for Biotechnology
Information
National Institutes of Health
Faculty
Whiting
School of Engineering
Johns
Hopkins University
__________________
List of Publications:
1.
Saikat Chakrabarti, Stephen Bryant and Anna R. Panchenko “Functional specificity lies within the properties
and evolutionary changes of amino acids”, J Mol Biol, v. 373(3), p.801 (2007).
2.
Benjamin A. Shoemaker and Anna R. Panchenko "Deciphering
protein- protein interactions. I. Experimental techniques and
databases", PLoS Comput
Biol, v. 3(4) (2007).
3.
Thomas Madej, Anna R. Panchenko, Jie Chen and Stephen Bryant “Protein
homologous cores and loops: important clues to evolutionary relationships
between structurally similar proteins”, BMC Struct Biol, v
7:23 (2007).
4.
Benjamin A. Shoemaker and Anna R. Panchenko "Deciphering
protein-protein interactions. II. Computational methods to predict protein
and domain interaction partners", PLoS Comput Biol, v. 3(3) (2007).
5.
Yuri Wolf, Thomas Madej, Vladimir Babenko, Benjamin A. Shoemaker and Anna
R. Panchenko “Long-term
trends in evolution of indels in protein sequences”, BMC Evol
Biol, v.7:19 (2007).
6.
Jessica H. Fong, Lewis Geer, Anna R. Panchenko and Stephen
Bryant "Modeling the
evolution of protein domain architectures using maximum parsimony", J Mol Biol, v. 366(1), p.307 (2007).
7.
Saikat Chakrabarti, Christopher J. Lanczycki, Anna R. Panchenko,
Teresa M. Przytycka, Paul A.
Thiessen and Stephen H. Bryant "State
of the art: refinement of multiple sequence alignments", BMC
Bioinformatics, v. 7:499 (2006).
8.
Saikat Chakrabarti, Christopher J. Lanczycki, Anna R. Panchenko,
Teresa M. Przytycka, Paul A. Thiessen and Stephen H. Bryant "Refining multiple sequence
alignments with conserved core regions", Nucleic Acids Res., v.34(9),
p.2598 (2006).
9.
Benjamin A. Shoemaker, Anna R. Panchenko and Stephen H. Bryant
"Finding biologically
relevant domain interactions: Conserved Binding Mode analysis",
Protein Science, v. 15, p. 352 (2006).
10.
Anna R. Panchenko, Yuri I. Wolf, Larisa
Panchenko and Thomas Madej "Evolutionary
plasticity of protein families: coupling between sequence and structure
variation", Proteins, v.61, p. 535 (2005).
11.
Anna R.
Panchenko and Thomas Madej"Structural
similarity of loops in protein families: toward the understanding of
protein evolution", BMC Evolutionary Biology, 5(1), p.10
(2005).
12.
Maricel Kann, Paul Thiessen, Anna R. Panchenko, Alejandro Schaffer,
Stephen Altschul and Stephen Bryant "A Structure-based Method for Protein Sequence
Alignment",
Bioinformatics, v. 21(8), p.1451 (2005).
13.
Anna R.
Panchenko and Thomas Madej "Analysis of protein homology by
assessing the (dis)similarity in protein loop regions", Proteins,
v.57(3), p.539(2004).
14.
Anna R.
Panchenko, Fyodor Kondrashov and Stephen
Bryant "Prediction of functional sites by analysis of sequence and
structure conservation",
Protein Science, v.13, p. 884-892 (2004).
15.
Anna R.
Panchenko "Finding
weak protein similarities by sequence profile comparison",
Nucleic Acids Res., v. 31(2), p.683-689 (2003).
16. Jie Chen,
John B. Anderson, Carol DeWeese-Scott, Natalie Fedorova, Lewis Y. Geer,
Siqian He, David I. Hurwitz, Cynthia A. Liebert, Chunlei Liu, Thomas Madej,
Aron Marchler-Bauer, Gabriele H. Marchler, Raja Mazumder, Anastasia N.
Nikolskaya, Bachoti S. Rao, Anna R. Panchenko, Benjamin A.
Shoemaker, Vahan Simonyan, James S. Song, Paul A. Thiessen, Sona Vasudevan,
Yanli Wang, Roxanne A. Yamashita,
Jodie J. Yin and Stephen H. Bryant "MMDB: Entrez's 3D-structure
database", Nucleic Acids Res., v. 31(1), p. 474-477 (2003).
17. Aron
Marchler-Bauer, John B. Anderson, Carol DeWeese-Scott, Natalie Fedorova, Lewis Y. Geer, Siqian He,
David I. Hurwitz, Cynthia A. Liebert, Chunlei Liu, Thomas Madej, Gabriele
H. Marchler, Raja Mazumder, Anastasia N. Nikolskaya, Bachoti S. Rao, Anna
R. Panchenko, Benjamin A. Shoemaker, Vahan Simonyan, James S. Song,
Paul A. Thiessen, Sona Vasudevan, Yanli Wang, Roxanne A. Yamashita, Jodie J. Yin and Stephen H.
Bryant "CDD: a curated Entrez database of conserved domain
alignments", Nucleic Acids Res., v.31(1),
p. 383-387 (2003).
18.
David Lipman, Alexander Souvorov, Eugene
Koonin, Anna R. Panchenko and Tatyana Tatusova "The
relationship of protein conservation and sequence length", BMC
Evol Biol, Nov 1;2(1):20 (2002).
19.
Aron Marcheler-Bauer, Anna R. Panchenko,
Naomi Ariel and Stephen Bryant "Comparison of sequence and
structure alignments for protein domains", Proteins, v.48(3), p.439-446 (2002).
20.
Anna R. Panchenko and Stephen Bryant "A
comparison of Position-Specific Score Matrices based on sequence and structure alignments",
Protein Science, v. 11, p. 361-370 (2002).
21. Yanli
Wang, John B. Anderson, Jie Chen, Lewis Y. Geer, Siqian He, David I.
Hurwitz, Cynthia A. Liebert, Thomas Madej, Gabriele H. Marchler, Aron
Marchler-Bauer, Anna R. Panchenko, Benjamin A. Shoemaker, James S.
Song, Paul A. Thiessen, Roxanne A. Yamashita, Stephen H. Bryant "MMDB:
Entrez's 3D-Structure Database", Nucleic Acids Res., v. 30(1),
p.281-283 (2002).
22.
Aron Marchler-Bauer, Anna R. Panchenko, Benjamin
A. Shoemaker, Paul A. Thiessen,
Lewis Y. Geer and Stephen H. Bryant "CDD: A Database of
Conserved Domain Alignments with links to domain three- dimensional
structure", Nucleic Acids Res., v. 30(1), p. 249-252 (2002).
23.
Anna R.
Panchenko, Aron Marchler-Bauer
and Stephen H. Bryant "Combination of threading potentials and
sequence profiles improves fold- recognition", J. of
Mol. Biol., v.296, p. 1319-1331 (2000).
24.
Anna R.
Panchenko, Aron Marchler-Bauer
and Stephen H. Bryant "Threading with explicit models for
evolutionary conservation of structure and sequence",
Proteins, v. 3, p. 133-141 (1999).
25.
Anna R.
Panchenko, Zaida Luthey-Schulten,
Roland Cole and Peter G. Wolynes "The foldon universe: a survey
of structural similarity and self-recognition of independently folding
units", J. of Mol. Biol., v. 272, p. 95-105 (1997).
26.
Anna R.
Panchenko, Zaida Luthey-Schulten
and Peter G. Wolynes "Foldons as independently folding units of
proteins", Physica D, v. 107, p. 312-315 (1997).
27.
Anna R.
Panchenko, Zaida Luthey-Schulten
and Peter G. Wolynes "Foldons, protein structural modules and
exons", Proc. Natl. Acad. Sci., v. 93, p. 2008-2013 (1996).
28.
Anna R. Panchenko, Jing Wang, G.
Ulrich Nienhaus and Peter G. Wolynes "Analysis of ligand binding
to heme proteins using a fluctuating path description", J. of
Phys. Chem., v. 99, p. 9278-9282 (1995).
29.
Anna R. Panchenko and K. V. Shaitan "Effect
of pressure on intramolecular dynamics of proteins", Molecular
Biology, v. 26, p. 745-748 (1992).
30.
Anna R. Panchenko and K. V. Shaitan "Effect
of dynamic disorder of biological systems on the characteristics of
intramolecular mobility determined by Mossbauer spectroscopy",
J. Biophysics, v. 37, p. 927-931 (1992).
31.
I. V. Kurinov, Yu. F. Krupyanskii, Anna
R. Panchenko, I. P. Suzdalev, I.V. Uporov, K. V. Shaitan, A. B. Rubin,
V. I. Goldanskii "Intramolecular dynamics of hydrated DNA
studied by Rayleigh Scattering of Mossbauer Radiation",
Hyperfine Interactions, v. 58, p. 2355-2358 (1990).
32.
H. Dondog, K. V. Shaitan, I. P. Uporov and
Anna R. Panchenko "Recombination model of protein
conformational dynamics", VINITI Proceedings, v. 1435 (1990).
33.
I. P. Uporov, I. N. Nicolaev, Anna R.
Panchenko and K. V. Shaitan "Effect of the width of relaxation
time distribution on the temperature dependence of Mossbauer spectra
parameters", Biologicheskie Nauki, v. 7, p. 25-29 (1989).
Selected oral presentations.
·
Keynote
speaker at "NBRE bioinformatics research symposium", Jan. 2007, Clemson University, SC.
·
Keynote
speaker at "Inaugural Bioinformatics Australia Conference", Nov.
2006, Sydney, Australia.
·
Invited
speaker at Flinders University, Nov. 2006, Adelaide, Australia.
·
Tutorial at
ISMB2006, "Protein-protein interactions: structure and systems approaches
to analyze diverse genomic data", Aug. 2006, Fortaleza , Brazil.
·
Invited
speaker at the DIMACS workshop "Sequence, Structure and Systems
Approaches to Predict Protein Function", May 2006, Rutgers University, NJ.
·
Invited
speaker at "Structural
Biology Interest Group", March 2006, NIH, Bethesda, MD.
·
Invited
speaker at "The Fifth
virtual conference on Genomics and Bioinformatics", Oct 2005, Arlington, VA.
·
Speaker at
"The 5-th international conference on biological physics ICBP",
Aug 2004, Goteburg , Sweden.
·
Invited
speaker at George Washington University,
Dept of Computer Science, July 2004, Washington
DC .
·
Invited
speaker at "Beyond genome 2002", June 2002, San-Diego, CA.
·
Invited
speaker at the University of California in San Diego , Dept of Chemistry and
Biochemistry, June 2002, CA.
·
Speaker at
"Bioinformatics 2002, North-South Networking", Feb 2002, Bangkok, Thailand.
·
Keynote
speaker at "The first conference on structural genomics", Jan
2001, Tokyo, Japan.
·
Invited
speaker at the National Institute of Genetics, Jan 2001, Mishima , Japan.
·
Invited
speaker at "Protein expression 2000", Oct 2000, Washington, DC.
·
Invited
speaker at Celera Genomics, Dec 1999, Gaithersburg,
MD.
·
Invited
speaker at Harvard University, Dept. of Chemistry and Chemical
Biology, June 1999, Cambridge,
MA.
__________________
Selected awards and Distinctions:
· Chair, NIH Structural Biology Interest
group, 2007-2008 · Ad hoc reviewer, High-end Instrumentation
Grant Program, NIH, 2005 · NIH Intramural Research Training Award,
1997-1999 ·
First place in CASP3 (Critical
Assessment of Structure Prediction), fold recognition category,1999 ·
NSF Research Grant in Physics for
visiting scientists, 1993-1994 · Distinguished Fellowship for graduate
research, Moscow State University, 1990.
__________________
Education:
Ph.D. Biophysics, 1993
Dept. of Biophysics,
Moscow State University,
Russia
B.Sc.
Biophysics (with distinction), 1989
Dept. of Biophysics,
Moscow State University,
Russia
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Appointments and research experience:
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Associate
Investigator
Staff Scientist
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2007 - present
National Center for
Biotechnology Information, NIH
2000 - 2006
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National Center for
Biotechnology Information, NIH
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IRTA Fellow
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1997 - 1999
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National Center for
Biotechnology Information, NIH
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Postdoctoral
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1994 - 1997
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Research Associate
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School of Chemical
Sciences
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University of Illinois
at Urbana-Champaign
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Visiting Scientist
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1993 - 1994
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Dept of Physics,
University of Illinois at Urbana-Champaign
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