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Biography:

Lajos Kalmar graduated as a Zoologist / Microbiologist at the University of Veterinary Medicine (Budapest, Hungary). During his PhD at the Semmelweis University (Budapest, Hungary), he worked as an experimental scientist in the field of human genetics and discovered several novel disease causing mutations in hereditary angioneurotic oedema (HAE). He started his transition from in vitro to in silico field at the end of his PhD by establishing a locus specific mutational database for the SERPING1 gene. Lajos spent his first long postdoc period (2007-2015) at the Institute of Enzymology of the Hungarian Academy of sciences where he investigated the structural and functional evolution of proteins (particularly intrinsically disordered proteins) using bioinformatics tools. He joined the University of Cambridge in 2015 and worked as a research associate in Dr David Sargan group at the Department of Veterinary Medicine investigating the genetic background of brachycephalic obstructive airway syndrome (BOAS) in dogs, using state-of-the-art genomics techniques. In 2018, as a senior research associate, he joined Professor Mark Holmes’s group in the same department and worked on microbial genomics and metagenomics for 2.5 years. He established a complete bioinformatics pipeline for the Hi-C assisted metagenomics, a technique that can be used to assign mobile genetic element (e.g. plasmids) to their host genome in complex microbial communities. Lajos joined the MRC Toxicology Unit in the beginning of 2021 as the manager of the core Bioinformatics Facility.

Research Interests:

By managing and maintaining the bioinformatics facility, my task is to provide continuous bioinformatics support for every member of the Unit. I am doing personal support and supervision, small group trainings and perform complete bioinformatics projects, depending on the needs of group leaders senior and junior researchers.

Key Publications:

1. Kalmar L, Gupta S, Kean IRL, Ba X, Hadjirin N, Lay E, Vries S, Bateman M, Bartlett H, Hernandez-Garcia J, Tucker AW, Restiff O, Stevens MP, Wood J, Maskell DJ, Grant AJ, Holmes M. HAM-ART: An optimised culture-free Hi- C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities. (Manuscript under submission).

2. Kovacs E, Tompa P, Liliom K, Kalmar L*. Dual coding in alternative reading frames correlates with intrinsic protein disorder. Proc Natl Acad Sci U S A. 2010 Mar 23;107(12):5429-34. (*corresponding author)

3. Bergman P, Adori C, Vas S, Kai-Larsen Y, Sarkanen T, Cederlund A, Agerberth B, Julkunen I, Horvath B, Kostyalik D, Kalmár L, Bagdy G, Huutoniemi A, Partinen M, Hökfelt T. Narcolepsy patients have antibodies that stain distinct cell populations in rat brain and influence sleep patterns. Proc Natl Acad Sci U S A. 2014 Sep 2;111(35):E3735-44.

4. Tompa P, Schad E, Tantos A, Kalmar L. Intrinsically disordered proteins: emerging interaction specialists. Curr Opin Struct Biol. 2015 Sep 21;35:49-59.

5. Schad E, Kalmar L, Tompa P. Exon-phase symmetry and intrinsic structural disorder promote modular evolution in the human genome. Nucleic Acids Res. 2013 Apr;41(8):4409-22.

6. Hegyi H, Kalmar L, Horvath T, Tompa P. Verification of alternative splicing variants based on domain integrity, truncation length and intrinsic protein disorder. Nucleic Acids Res. 2011 Mar;39(4):1208-19.

7. Tusnády GE, Kalmár L, Simon I. TOPDB: topology data bank of transmembrane proteins. Nucleic Acids Res. 2008 Jan;36(Database issue):D234-9.

8. Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE5, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, Leonardi E, Lazar T, Macedo-Ribeiro S, Macossay-Castillo M, Meszaros A, Minervini G, Murvai N, Pujols J, Roche DB, Salladini E, Schad E, Schramm A, Szabo B, Tantos A, Tonello F, Tsirigos KD, Veljković N, Ventura S, Vranken W, Warholm P, Uversky VN, Dunker AK, Longhi S, Tompa P, Tosatto SC. DisProt 7.0: a major update of the database of disordered proteins. Nucleic Acids Res. 2016 Dec 13. pii: gkw1279.

9. Kalmar L, Acs V, Silhavy D, Tompa P. Long-range interactions in nonsense-mediated mRNA decay are mediated by intrinsically disordered protein regions. J Mol Biol. 2012 Dec 7;424(3-4):125-31.

10. Kalmar L, Homola D, Varga G, Tompa P. Structural disorder in proteins brings order to crystal growth in biomineralization. Bone. 2012 Sep;51(3):528-34.

11. Kalmár L, Hegedüs T, Farkas H, Nagy M, Tordai A. HAEdb: a novel interactive, locus-specific mutation database for the C1 inhibitor gene. Hum Mutat. 2005 Jan;25(1):1-5. Times cited: 51

12. Kalmár L, Bors A, Farkas H, Vas S, Fandl B, Varga L, Füst G, Tordai A. Mutation screening of the C1 inhibitor gene among Hungarian patients with hereditary angioedema. Hum Mutat. 2003 Dec;22(6):498.

Bioinformatics Facility Manager

Contact Details

MRC Toxicology Unit
Gleeson Building
Tennis Court Road
Cambridge

CB2 1QR

Telephone and Email

Office 01-0138
+44 (0)1223 3 35457

Affiliations

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