Natalia Maltsev, M.D., Ph.D.

Research Associate (Professor)

Research Description

My major scientific interest is the development of the approaches for representation and analysis of complex biological systems and how these approaches can be applied to the discovery of the molecular mechanisms contributing to complex heritable disorders. Together with Prof. Gilliam I am leading a number of projects in Bioinformatics group (Prof. Gilliam’s lab):

  1.  We have developed Lynx (http://lynx.ci.uchicago.edu) -- a web-based database and a knowledge extraction engine, supporting annotation and analysis of experimental data and generation of weighted hypotheses on molecular mechanisms contributing to human phenotypes and disorders of interest. Its underlying knowledge base (LynxKB) integrates various classes of information from over thirty-five public databases and private collections, as well as manually curated data from our group and collaborators. Lynx provides advanced search capabilities and a variety of algorithms for enrichment analysis and network-based gene prioritization to assist the user in extracting meaningful knowledge from LynxKB and experimental data, while its Service Oriented Architecture provides public access to LynxKB and its analytical tools via user-friendly web services and interfaces.
  2. Clinical collaborations. The main emphasis of our clinical and experimental collaborations is on understanding of molecular mechanisms underlying neurodevelopmental and mental disorders (e.g. autism, schizophrenia, brain malformations), however the analytical approaches being developed by our group may be successfully applied to other classes of disorders. Some examples of such collaborations include: reconstructions of molecular networks and predictions of genetic factors contributing to: mid- and hind- brain malformations (with Prof. Dobyns, University of Washington), cerebellum disorders (with Prof. K. Millen, Seattle Children’s Hospital), pathogenesis of spina bifida (with Prof. M Ross, Cornell University), Aicardi syndrome (Prof. Elliott Sherr, UCSF), autism and mental retardations (Prof. D. Geschwind, UCLA), epilepsy (with Dr. A. Paciorkowski, University of Rochester) and others.
  3. Algorithms development. In collaboration with Prof. Jinbo Xu, TTIC, the University of Chicago, we are developing a workbench for reconstruction and comparative analysis of biological networks.
  4. Study of molecular mimicry (in collaboration with Prof. Barteneva, Harvard Children’s Hospital, Prof. Fasano, Mass General Hospital, Harvard and Drs. Jinbo Xu and Dr. Sheng Wang, TTIC). This project aims to explore the pathophysiological and evolutionary relationships between the host and parasite.

Selected Publications

Disease gene prioritization using network and feature.
Xie B, Agam G, Balasubramanian S, Xu J, Gilliam TC, Maltsev N, Bornigen D
(2015 Apr) J Comput Biol. 2015 Apr;22(4):313-23. doi: 10.1089/cmb.2015.0001. 25844670 (Full Text)

High-throughput translational medicine: challenges and solutions.
Sulakhe D, Balasubramanian S, Xie B, Berrocal E, Feng B, Taylor A, Chitturi B, Dave U, Agam G, Xu J, Bornigen D, Dubchak I, Gilliam TC, Maltsev N
(2014) Adv Exp Med Biol. 2014;799:39-67. doi: 10.1007/978-1-4614-8778-4_3. 24292961

Systems Analysis of Human Multigene Disorders Series: Advances in Experimental Medicine and Biology, Vol. 799
Maltsev, PhD, Natalia, Rzhetsky, Andrey, Gilliam, PhD, T. Conrad (Eds.) 2014, XIII, 122 p. 12 illus. in color. With online files/update. ISBN 978-1-4614-8778-4

Lynx: a database and knowledge extraction engine for integrative medicine.
Sulakhe D, Balasubramanian S, Xie B, Feng B, Taylor A, Wang S, Berrocal E, Dave U, Xu J, Bornigen D, Gilliam TC, Maltsev N
(2014 Jan) Nucleic Acids Res. 2014 Jan;42(Database issue):D1007-12. doi: 10.1093/nar/gkt1166. Epub 2013 Nov 21. 24270788 (Full Text)

Microvesicles and intercellular communication in the context of parasitism.
Barteneva NS, Maltsev N, Vorobjev IA
(2013) Front Cell Infect Microbiol. 2013 Sep 6;3:49. doi: 10.3389/fcimb.2013.00049. eCollection 2013. 24032108 (Full Text)

Copy number variants and infantile spasms: evidence for abnormalities in ventral forebrain development and pathways of synaptic function.
Paciorkowski AR, Thio LL, Rosenfeld JA, Gajecka M, Gurnett CA, Kulkarni S, Chung WK, Marsh ED, Gentile M, Reggin JD, Wheless JW, Balasubramanian S, Kumar R, Christian SL, Marini C, Guerrini R, Maltsev N, Shaffer LG, Dobyns WB
(2011 Dec) Eur J Hum Genet. 2011 Dec;19(12):1238-45. doi: 10.1038/ejhg.2011.121. Epub 2011 Jun 22. 21694734 (Full Text)

The BioPAX community standard for pathway data sharing.
Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Ruebenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Le Novere N, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD
(2010 Sep) Nat Biotechnol. 2010 Sep;28(9):935-42. doi: 10.1038/nbt.1666. Epub 2010 Sep 9. 20829833 (Full Text)

The minimum information about a genome sequence (MIGS) specification.
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glockner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A
(2008 May) Nat Biotechnol. 2008 May;26(5):541-7. doi: 10.1038/nbt1360. 18464787 (Full Text)

Evolutionary analysis of enzymes using Chisel.
Rodriguez AA, Bompada T, Syed M, Shah PK, Maltsev N
(2007 Nov) Bioinformatics. 2007 Nov 15;23(22):2961-8. Epub 2007 Sep 13. 17855417

PUMA2--grid-based high-throughput analysis of genomes and metabolic pathways.
Maltsev N, Glass E, Sulakhe D, Rodriguez A, Syed MH, Bompada T, Zhang Y, D'Souza M
(2006 Jan) Nucleic Acids Res. 2006 Jan 1;34(Database issue):D369-72. 16381888 (Full Text)

GNARE: automated system for high-throughput genome analysis with grid computational backend.
Sulakhe D, Rodriguez A, D'Souza M, Wilde M, Nefedova V, Foster I, Maltsev N
(2005 Oct) J Clin Monit Comput. 2005 Oct;19(4-5):361-9. 16328950

WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction.
Overbeek R, Larsen N, Pusch GD, D'Souza M, Selkov E Jr, Kyrpides N, Fonstein M, Maltsev N, Selkov E
(2000 Jan) Nucleic Acids Res. 2000 Jan 1;28(1):123-5. 10592199 (Full Text)

The use of gene clusters to infer functional coupling.
Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N
(1999 Mar) Proc Natl Acad Sci U S A. 1999 Mar 16;96(6):2896-901. 10077608 (Full Text)