Gelfand Laboratory

Start date – June 2016

The main research areas of the lab are systems biology, functional and comparative genomics.

The lab combines data on three-dimensional structure of chromatin, epigenetic state, and gene expression to obtain an integrated view of genome functioning in diverse eukaryotes, from human to amoebae. One more research direction is evolution of transcript splicing and editing. Comparative analysis of bacterial genomes yields numerous functional annotations of novel enzymes, transporters, and transcription factors; understanding of general principles of evolution of bacterial genomes and regulatory networks. Metagenomic studies are mainly performed in the areas of general or practical interest (coral disease, aphids, oil wells).

Supervisor – Mikhail Gelfand

• Predictive models of protease specificity based on quantitative protease-activity profiling data. Fedonin G, Eroshkin A, Cieplak P, Matveev E, Ponomarev G, Gelfand M, Ratnikov B, Kazanov M. Biochim Biophys Acta Proteins Proteom. 01.11.2019; 1867(11):140253. doi: 10.1016/j.bbapap.2019.07.006.

• Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Sigalova O, Chaplin A, Bochkareva O, Shelyakin P, Filaretov V, Akkuratov E, Burskaia V, Gelfand M; BMC Genomics. 01.09.2019; 20(1):710. doi: 10.1186/s12864-019-6059-5.

• Comparative Genomic Analysis of the Regulation of Aromatic Metabolism in Betaproteobacteria. Front Microbiol.03.2019;10:642. doi: 10.3389/fmicb.2019.00642. eCollection Suvorova I, Gelfand M.

• Micro-evolution of three Streptococcus species: selection, antigenic variation, and horizontal gene inflow.Shelyakin P, Bochkareva O, Karan A, Gelfand M. BMC Evol Biol. 27.03.2019;19(1):83. doi: 10.1186/s12862-019-1403-6.

• Nuclear lamina integrity is required for proper spatial organization of chromatin in Drosophila.Ulianov S, Doronin S, Khrameeva E, Kos P, Luzhin A, Starikov S, Galitsyna A, Nenasheva V, Ilyin A, Flyamer I, Mikhaleva E, Logacheva M, Gelfand M, Chertovich A, Gavrilov A, Razin S, Shevelyov Y Nat Commun.03.2019;10(1):1176. doi: 10.1038/s41467-019-09185-y.

• Genome rearrangements and phylogeny reconstruction in Yersinia pestis. Bochkareva O, Dranenko N, Ocheredko E, Kanevsky G, Lozinsky Y, Khalaycheva V, Artamonova I, Gelfand M. PeerJ. 2018 Mar 27;6:e4545. doi: 10.7717/peerj.4545. eCollection 2018.

• Microbiomes of gall-inducing copepod crustaceans from the corals Stylophora pistillata (Scleractinia) and Gorgonia ventalina (Alcyonacea). Shelyakin P, Garushyants S, Nikitin M, Mudrova S, Berumen M, Speksnijder A, Hoeksema B, Fontaneto D, Gelfand M, Ivanenko V  Sci Rep. 2018 Aug 1;8(1):11563. doi: 10.1038/s41598-018-29953-y.

• Neanderthal and Denisovan ancestry in Papuans: A functional study Akkuratov E, Gelfand M, Khrameeva E. J Bioinform Comput Biol. 2018 Apr;16(2):1840011. doi: 10.1142/S0219720018400115

• Conservation, evolution, and regulation of splicing during prefrontal cortex development in humans, chimpanzees and macaques. Mazin P, Jiang X, Fu N, Han D, Guo M, Gelfand M, Khaitovich P. RNA. 2018 Jan 23. pii: rna.064931.117. doi:10.1261/rna.064931.117. PMID:29363555

• The genes of the sulphoquinovose catabolism in Escherichia coli are also associated with a previously unknown pathway of lactose degradation. Kaznadzey A, Shelyakin P, Belousova E, Eremina A, Shvyreva U, Bykova D, Emelianenko V, Korosteleva A, Tutukina M, Gelfand M. Sci Rep. 2018 Feb 16;8(1):3177. doi: 10.1038/s41598-018-21534-3. PMID:29453395

• Cooption of heat shock regulatory system for anhydrobiosis in the sleeping chironomid Polypedilum vanderplanki. Mazin P, Shagimardanova E, Kozlova O, Cherkasov A, Sutormin R, Stepanova V, Stupnikov A, Logacheva M, Penin A, Sogame Y, Cornette R, Tokumoto S, Miyata Y, Kikawada T, Gelfand M, Gusev O. Proc Natl Acad Sci U S A. 2018 Feb 20. pii: 201719493. doi: 10.1073/pnas.1719493115. PMID:29463761

• Comparative genomic analysis of fungal TPP-riboswitches. Moldovan M, Petrova S, Gelfand M. Fungal Genet Biol. 2018 Mar 13;114:34-41. doi: 10.1016/j.fgb.2018.03.004.  PMID: 29548845

• Application of sorting and next generation sequencing to study 5΄-UTR influence on translation efficiency in Escherichia coli. Evfratov S, Osterman I, Komarova E, Pogorelskaya A, Rubtsova M, Zatsepin T, Semashko T, Kostryukova E, Mironov A, Burnaev E, Krymova E, Gelfand M, Govorun V, Bogdanov A, Sergiev P, Dontsova O. Nucleic Acids Res. 2017 Apr 7;45(6):3487-3502. doi: 10.1093/nar/gkw1141. PubMed PMID: 27899632; PubMed Central PMCID: PMC5389652.

• Sugar Lego: gene composition of bacterial carbohydrate metabolism genomic loci. Kaznadzey A, Shelyakin P, Gelfand MS. Biol Direct. 2017 Nov 25;12(1):28. doi: 10.1186/s13062-017-0200-7.PMID:29178959

• Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota. Kublanov I, Sigalova O, Gavrilov S, Lebedinsky A, Rinke C, Kovaleva O, Chernyh N, Ivanova N, Daum C, Reddy T, Klenk H, Spring S, Göker M, Reva O, Miroshnichenko M, Kyrpides N, Woyke T, Gelfand M, Bonch-Osmolovskaya E. Front Microbiol. 2017 Feb 20;8:195. doi: 10.3389/fmicb.2017.00195. eCollection 2017.

• Activation of the alpha-globin gene expression correlates with dramatic upregulation of nearby non-globin genes and changes in local and large-scale chromatin spatial structure. Ulianov S, Galitsyna A, Flyamer I, Golov A, Khrameeva E, Imakaev M, Abdennur N, Gelfand M, Gavrilov A, Razin S. Epigenetics Chromatin. 2017 Jul 11;10(1):35. doi: 10.1186/s13072-017-0142-4.PMID:28693562

• Genome analysis of E. coli isolated from Crohn’s disease patients. Rakitina D, Manolov A, Kanygina A, Garushyants S, Baikova J, Alexeev D, Ladygina V, Kostryukova E, Larin A, Semashko T, Karpova I, Babenko VV, Ismagilova R, Malanin S, Gelfand M, Ilina EN, Gorodnichev R, Lisitsyna E, Aleshkin G, Scherbakov P, Khalif I, Shapina M, Maev I, Andreev D, Govorun V. BMC Genomics. 2017 Jul 19;18(1):544. doi: 10.1186/s12864-017-3917-x. PMID:28724357

• Small Open Reading Frames, Non-Coding RNAs and Repetitive Elements in Bradyrhizobium japonicum USDA 110. Hahn J, Tsoy O, Thalmann S, Čuklina J, Gelfand M, Evguenieva-Hackenberg E. PLoS One. 2016 Oct 27;11(10):e0165429. doi: 10.1371/journal.pone.0165429. eCollection 2016.

• Nitrogen Fixation and Molecular Oxygen: Comparative Genomic Reconstruction of Transcription Regulation in Alphaproteobacteria.Tsoy O, Ravcheev D, Čuklina J, Gelfand M. Front Microbiol. 2016 Aug 26;7:1343. doi: 10.3389/fmicb.2016.01343. eCollection 2016.

• Evolution of the Exon-Intron Structure in Ciliate Genomes. Bondarenko V, Gelfand M. PLoS One. 2016 Sep 7;11(9):e0161476. doi: 10.1371/journal.pone.0161476. eCollection 2016.

• Changes in segmentation and setation along the anterior/posterior axis of the homonomous trunk limbs of a remipede (Crustacea, Arthropoda). Ivanenko V, Antonenko E, Gelfand M, Yager J, Ferrari F. PeerJ. 2016 Aug 10;4:e2305. doi: 10.7717/peerj.2305. eCollection 2016.

• History of chromosome rearrangements reflects the spatial organization of yeast chromosomes. Khrameeva E, Fudenberg G, Gelfand M, Mirny L. J Bioinform Comput Biol. 2016 Apr;14(2):1641002. doi: 10.1142/S021972001641002X. Epub 2016 Jan 28.

Research grants/Industry funded research

Skoltech Biomedical Initiative

Skoltech Translational and Research Innovation Program – STRIP

Systems biology fellowship