Experience

Other Professional Activities

·         Co-organizer of the international conference BioGrid 2006, 2007

·         Organizer of the “Mathematics for Systems Biology” seminar series at the University of Chicago/ Argonne National Laboratory Joint Theory Institute

·         Invited participant, “Science-Foo 2006 Camp”, organized by Nature Publishing Group and Google Corporation.

·         Member of Oracle Corporation Consumer Advisory Board

·         Member of the BioPAX committee

·         Member of the International e-Genomic Standards Working Group

·         Member of the Editorial Board, Archaea Journal

Review panels

·         Member of DOE OBER review panels on Structural Biology and SBIR

·         Member of NSF Biological Databases Review Panel

·         Reviewer for a number of journals, including: Nature, Bioinformatics, BMC Bioinformatics, BMC Evolutionary Biology, PloS Bioinformatics and others.

Membership in Professional Societies:

·         American Society of Microbiology

·         International Society of Computational Biology

·         Member of the New York Academy of Sciences

References:

Upon request 

Selected peer-reviewed publications (in reverse chronological order):

1. D. Sulakhe, M. D'Souza, M. Syed, A. Rodriguez, Y. Zhang, E. Glass, M. Romine,  N. Maltsev. GNARE ­ A Grid-based Server for the Analysis of User Submitted Genomes. Accepted for publication in Nucleic Acids Res. 2007 (special issue). NAR-00335-Web-B-2007.R1

Contribution: Project leader, design and architecture of the system, writing of a paper

2. A. Rodriguez, T. Bompada, M. Syed, N. Maltsev. Evolutionary Analysis of Enzymatic Sequences. Accepted for publication in Bioinformatics journal.

Contribution: Project leader, design and architecture of the system, writing of a paper

3. Maier TM, Casey MS, Becker RH, Dorsey CW, Glass EM, Maltsev N, Zahrt TC, FrankDW. Identification of Francisella tularensis Himar1-based Transposon Mutants Defective for Replication in Macrophages. Infect Immun. 2007 Aug 6; [Epub ahead of print]

Contribution: Performed analysis of genomic data, participated in writing a paper

4. D. Field, G. Garrity,.., N. Maltsev, et al. Towards a richer description of our complete collection of genomes and metagenomes: the “Minimum Information about a Genome Sequence”. Accepted for publication in Nature Biotechnology.

Contribution: design of controlled vocabulary for phenotypic data

5.      Y. Zhang, B. Liu, N. Maltsev. Dragonfly: An Web-based, Partial-Order Multiple Sequence Alignment Viewer. Submitted to Bioinformatics journal.

Contribution: Project leader, design and architecture of the system, writing a paper

6.      E. Glass and N. Maltsev. Patho-Gene and Pathos Databases – New Tools for Infectious Disease Research. Submitted to the Journal of Environmental Bacteriology

Contribution: Project leader, design and architecture of the system, writing of a paper

7.      M. D’Souza, E. Glass, M. Syed, Yi Zhang, M. Galperin, N. Maltsev. Sentra – a database of Prokaryotic Signal Transduction. Nucleic Acids Res. 2007 Jan;35 (Database issue):D271-3. Epub 2006 Nov 29).

Contribution: Project leader, design and architecture of the system, writing a paper

Citations: 3 (Google Scholar)

8.      Maltsev N, Glass E, Sulakhe D, Rodriguez A, Syed MH, Bompada T, Zhang Y, D’Souza M. PUMA2 – grid-based high-throughput analysis of genomes and metabolic pathways. Nucleic Acids Res. 2006 Jan 1;34(Database issue) :D369-372.

Contribution: Project leader, design and architecture of the system, writing a paper

Citations: 9 (Google Scholar)

9.      G. Neglur, R. L. Grossman, N. Maltsev, and C. Yu, Using Term Lists and Inverted Files to Improve Search Speed for Metabolic Pathway Databases, Lectures in Bioinformatics, Volume 4075, Springer-Verlag, Berlin, 2006, pages 168-184.

Contribution: Participated in design of an algorithmic approach

Citations:  (Google Scholar)

10.  Yu GX, Glass EM, Karonis NT, Maltsev N. Knowledge-based voting algorithm for automated protein functional annotation. Proteins. 2005 Dec 1;61(4):907-17.

Contribution: Participated in design of an algorithmic approach

Citations:  (Google Scholar)

11.  Sulakhe D., Rodrigues A., D’Souza M., Wilde M., Nefedova V., Foster I., Maltsev N. GNARE: An Environment for Grid-based High-throughput Genome Analysis. J Clin Monit Comput. 2005 Oct;19(4-5):361-9.

Contribution: Project leader, design and architecture of the system, writing a paper

Citations: 6 (Google Scholar)

12.  Maltsev N, Glass EM, Ovchinnikova G, Gu Z.(2005) Molecular mechanisms involved in robustness of yeast central metabolism against null mutations. J. Biochem. 2005 Feb;137(2):177-87.

Contribution: The development of scientific plan, data analysis, writing a paper

Citations: 3 (Google Scholar)

13.  Sulakhe, D., Rodriguez, A., D'Souza, M., Wilde, M., Nefedova, V., Foster, I., Maltsev, N., "GNARE: an environment for grid-based high-throughput genome analysis." Cluster Computing and the Grid, 2005. CCGrid 2005. IEEE International Symposium on. Vol. 1, pp. 455 - 462, May 9-12, 2005

Contribution: Project leader, design and architecture of the system, writing a paper

Citations: 6 (Google Scholar)

14.  A. Rodriguez, D. Sulakhe, E. Marland, V. Nefedova, G. X. Yu, and N. Maltsev, "GADU - Genome Analysis and Database Update Pipeline." ANL/MCS-P1029-0203, February 2003.

Contribution: Project leader, design and architecture of the system, writing a paper

Citations: 3 (Google Scholar)

15.  Marland, E., Prachumwat, A., Maltsev, N., Gu, Z., Li, W-H. (2004) Higher Gene Duplicabilities or Metabolic Protein than for Non-Metabolic Proteins in Yeast and E.coli. J. Mol. Evol. Dec; 59(6):806-14

Contribution: participated in design of scientific approaches, data analysis, writing a paper

Citations: 6 (Google Scholar)

16.  Moy S, Dieckman L, Schiffer M, Maltsev N, Yu GX, Collart FR. Genome-scale expression of proteins from Bacillus subtilis. J Struct Funct Genomics. 2004;5(1-2):103-9.

Contribution: data analysis, writing a paper

Citations: 8 (Google Scholar)

17.  Rodriguez, A., Sulakhe, D., Marland, E., Nefedova, V., Wilde, M., and Maltsev, N., “Grid Enabled Server for High-Throughput Analysis of Genomes.” Global Grid Forum 10 Proceeddings, March 2004.

Contribution: Project leader, design and architecture of the system, writing a paper

Citations: 5 (Google Scholar)

18.  A. Rodriguez, D. Sulakhe, E. Marland, V. Nefedova, G. X. Yu, and N. Maltsev, "GADU - Genome Analysis and Database Update Pipeline," ANL/MCS-P1029-0203, February 2003.

Contribution: Project leader, design and architecture of the system, writing a paper

Citations: 3 (Google Scholar)

19.  Wu RY, Zhang RG, Zagnitko O, Dementieva I, Maltsev N, Watson JD, Laskowski R, Gornicki P, Joachimiak A.  Crystal structure of Enterococcus faecalis SlyA-like transcriptional factor. J Biol Chem. 2003 May 30;278(22):20240-4. Epub 2003 Mar 20.

Contribution: Data analysis, participated in writing a paper

Citations: 25 (Google Scholar)

20.  Maltsev N, Marland E, Yu GX, Bhatnagar S, Lusk R. Sentra, a database of signal transduction proteins. Nucleic Acids Res 2002 Jan 1;30(1):349-50

Contribution: Project leader, design and architecture of the system, writing a paper

Citations: 11 (Google Scholar)

21.  Zhang RG, Dementieva I, Duke N, Collart F, Quaite-Randall E, Alkire R, Dieckman L, Maltsev N, Korolev O, Joachimiak A. Crystal structure of Bacillus subtilis ioli shows endonuclase IV fold with altered Zn binding. Proteins. 2002 Aug 1;48(2):423-6.

Contribution: data analysis, writing a paper

Citations: 6 (Google Scholar)

22.  Overbeek, R., Larsen, N., Pusch, G., D'Souza, M., Selkov Jr., E., Kyrpides, N., Fonstein, M., Maltsev, N., and Selkov, E. WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction, Nucleic Acids Research, 28, no. 1 (2000) 123-125

Contribution: Participated in design and architecture of the system, writing a paper

Citations: 272 (Google Scholar)

23.  D'Souza, M., Romine, M. F., and Maltsev, N. SENTRA, a database of signal transduction proteins, Nucleic Acids Research, 28, no. 1 (2000) 335-336

Contribution: Project leader, design and architecture of the system, writing a paper

Citations: 6 (Google Scholar)

24.  Overbeek, R. Fonstein, M., D'Souza, M., Pusch, G. D., and Maltsev, N., The Use of Gene Clusters to Infer Functional Coupling, Proc. Natl Acad Sci USA, 96, no. 6 (1999) 2896-901

Contribution: Significant contribution to design of an algorithm, data analysis, writing a paper

Citations: 455 (Google Scholar)

25.  Overbeek, R., Larsen, N., Maltsev, N., Pusch, G., and Selkov, E., WIT/WIT2: Metabolic reconstruction system. Molecular Biology Databases, ed. Stan Letovsky, Kluwer, 1999, pp. 38 – 51.

Contribution: Participated in WIT systems design, writing of a paper

Citations: 28 (Google Scholar)

25. MD'Souza, J Huan, S Sutton, M Romine, N. Maltsev, PUMA2-An environment for comparative analysis of metabolic subsystems and automated reconstruction of metabolism of microbial consortia and individual organisms from sequence data. ANL/MCS-TM-240, 1999 http://en.scientificcommons.org/332099

Contribution: Project leader, design and architecture of the system, writing a paper

Citations: 3 (Google Scholar)

26.  Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G. D., and Maltsev, N., Use of contiguity on the chromosome to predict functional coupling, In Silico Biol., 1, (1998) 0009

Contribution: Significant contribution to design of an algorithm, data analysis, writing a paper

Citations: 68 (Google Scholar)

27.  Haselkorn, R., and Maltsev, N., Synechocystis PCC6803: Functional Reconstruction from the Sequence Data, Cyanonews, 13, no. 1 (1998)

Contribution: Data analysis, writing a paper

Citations: 4 (Google Scholar)

28.  Vlcek, C., Paces, V., Maltsev, N., Paces, J., Haselkorn, R., and Fonstein, M., Sequence of a 189-kb segment of the chromosome of Rhodobacter capsulatus SB1003, Proc. Natl. Acad. Sci. USA, 94, no. 17 (1997) 9384-9388

Contribution:  Data analysis, writing of a paper

Citations: 21 (Google Scholar)

29.  Overbeek, R., Larsen, N., Smith, W., Maltsev, N., and Selkov, E., Representation of function: The next step, Gene, 191, no. 1 (1997) GC1-GC9

Contribution: Data structure design, writing a paper

Citations: 27 (Google Scholar)

30.  Selkov E, Maltsev N, Olsen GJ, Overbeek R, Whitman W. B. A reconstruction of the metabolism of Methanococcus jannaschii from sequence data. Gene. 1997 Sep 15;1997(1-2):GC11-26.

Contribution: Data analysis, writing a paper

Citations: 82 (Google Scholar)

31. Selkov E, Galimova M, Goryanin I, Gretchkin Y, Ivanova N, Komarov Y, Maltsev N, Mikhailova N, Nenashev V, Overbeek R, Panyushkina E, Pronevitch L, Selkov E Jr.  The metabolic pathway collection: an update. Nucleic Acids Res. 1997 Jan 1;25(1):37-8.

Contribution: Participated in database development

Citations: 31 (Google Scholar)

32.  E. Selkov, S. Basmanova, T. Gaasterland, I. Goryanin, Y. Gretchkin, N. Maltsev, V. Nenashev, R. Overbeek, E. Panushkina, L. Pronevitch, E. Selkov jr. and I. Yunus The Methabolic Pathway Collection from EMP: the Enzymes and Metabolic Pathways Database. Nucleic Acids Research, v. 24, No. 1 (Database issue), pages 26-29, 1996.

Contribution: Participated in database development

Citations: 72 (Google Scholar)

33.  H. Kagawa, J. Osipiuk, N. Maltsev, R. Overbeek, E. Quaite-Randall, A. Joachimiak, and J. Trent. The 60-kDa Heat Shock Proteins in Hyperthermophilic Archaeon Sulfolobus shibatae J. Mol. Biol., 253, pages 712-725, 1995

Contribution: Data analysis, writing a paper

Citations: 48 (Google Scholar)

34.  T. Gaasterland, J. Lobo, N. Maltsev, and G. Chen. Assigning Function to CDS Through Qualified Query Answering. In: Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, Stanford University, August, 1994.

Contribution: Participated in algorithm design and data analysis

Citations: 2 (Google Scholar)

35.  V. Korschunov, G. Ginodman, W. Bossart, and N. Maltsev.
Study of Immunomodulating Properties of Indigenous Microflora. : Antibiotics and Chemotherapy, 1, pages 48-52, 1992.

36.  V. Korschunov, M. Schkharupeta, W. Bossart, and N. Maltsev Study of Immunomodulating properties of Lactobacillus. Journal of  Immunobiology,  6, pages 46-54, 1992.

37.  N. Maltsev, V. Korschunov, B. Pinegin. Study of Immunomodulating activity of Indigenous Microorganisms. Immunology, 1989, 2, pp. 26-30.

38.   N. Maltsev, V. Korschunov, and B. Pinegin Indigenous organisms as Immunomodulators. In R. Petrov, editor: Immunostimulators, Medicina, Moscow, pp. 148-156,1988.

39.  N. Maltsev, and V. Korschunov. Immunomodulating Properties of Normal Intestinal Microflora. In B. Pinegin, editor: Factors of Cellular and Humoral Immunity under the Different Physiological Conditions, Medicina, Moscow, pp. 66-72, 1988.

40.   N. Maltsev, E. Chernokhvostova, and G. German. Immune Status of the Patients with the Selective Immunoglobulin A Deficiency. J. Microbiol. Epidemiol. Immunol., 3, pp. 58-64, 1983.

41.  A. Ishmukhametov, V. Ananchenko, and N. Maltsev
In: Correction of Immunocomplex Disease by Haemosorbtion.  V. Ananchenko, editor: Haemostasis, 3d Moscow Medical University Press, pp. 56-58, 1981.

42.  V. Petrov, A. Ishmukhametov, and N. Maltsev
Quantitative Analysis of Circulating Immune complexes in Patients with Bronchial Asthma and Healthy volunteers. Immunology, 3, pp. 57-59, 1982.