2016

People whose last names are highlighted in bold are Skoltech students, researchers, and faculty.

Dynamics of Escherichia coli type I-E CRISPR spacers over 42,000 years. Savitskaya E, Lopatina A, Medvedeva S, Kapustin M, Shmakov S, Tikhonov A, Artamonova I, Logacheva M, Severinov K. Mol Ecol. 2016 Dec 20. doi: 10.1111/mec.13961. [Epub ahead of print]

Come Together: CRISPR-Cas Immunity Senses the Quorum. Ekaterina Semenova and Konstantin SeverinovMolecular Cell 64, December 15, 2016, Pages 1013–1015.

Analysis of Transcriptional Variability in a Large Human iPSC Library Reveals Genetic and Non-genetic Determinants of Heterogeneity. Carcamo-Orive I, Hoffman GE, Cundiff P, Beckmann ND, D’Souza SL, Knowles JW, Patel A, Papatsenko D, Abbasi F, Reaven GM, Whalen S, Lee P, Shahbazi M, Henrion MY, Zhu K, Wang S, Roussos P, Schadt EE, Pandey G, Chang R, Quertermous T, Lemischka I. Cell Stem Cell. 2016 Dec 2. pii: S1934-5909(16)30401-5. doi: 10.1016/j.stem.2016.11.005.

Multiplex gene editing by CRISPR-Cpf1 through autonomous processing of a single crRNA array. Bernd Zetsche, Matthias Heidenreich, Prarthana Mohanraju, Iana Fedorova, Jeroen Kneppers, Ellen M DeGennaro, Nerges Winblad, Sourav R Choudhury, Omar O Abudayyeh, Jonathan S Gootenberg, Wen Y Wu, David A Scott, Konstantin Severinov, John van der Oost, Feng Zhang. Nature Biotechnology (2016) doi:10.1038/nbt.3737. Published online 05 December 2016.

A Trojan-horse peptide-carboxymethyl-cytidine antibiotic from Bacillus amyloliquefaciens. Serebryakova, M., Tsibulskaya, D., Mokina, O., Kulikovsky, A., Nautiyal, M., Van Aerschot, A., Severinov, K., and Dubiley, S. (2016)  J. Am. Chem. Soc., DOI: 10.1021/jacs.6b09853, Publication Date (Web): November 10, 2016

Altered stoichiometry Escherichia coli Cascade complexes with shortened CRISPR RNA spacers are capable of interference and primed adaptation Konstantin Kuznedelov, Vladimir Mekler, Sofia Lemak, Monika Tokmina-Lukaszewska, Kirill A. Datsenko, Ishita Jain, Ekaterina Savitskaya, John Mallon, Sergey Shmakov, Brian Bothner, Scott Bailey, Alexander F. Yakunin, Konstantin Severinov and Ekaterina Semenova, Nucleic Acids Research,   13 October 2016, doi: 10.1093/nar/gkw914

The Influence of Copy-Number of Targeted Extrachromosomal Genetic Elements on the Outcome of CRISPR-Cas Defense. Konstantin Severinov, Iaroslav Ispolatov and Ekaterina Semenova. Front. Mol. Biosci., 31 August 2016 | http://dx.doi.org/10.3389/fmolb.2016.00045

Diversity of CRISPR-Cas-Mediated Mechanisms of Adaptive Immunity in Prokaryotes and Their Application in Biotechnology. Savitskaya EE, Musharova OS, Severinov KV. Biochemistry (Mosc). 2016 Jul;81(7):653-61. doi: 10.1134/S0006297916070026.

Mice carrying a human GLUD2 gene recapitulate aspects of human transcriptome and metabolome development. Li Q, Guo S, Jiang X, Bryk J, Naumann R, Enard W, Tomita M, Sugimoto M, Khaitovich P, Pääbo S. Proc Natl Acad Sci U S A. 2016 May 10;113(19):5358-63. doi: 10.1073/pnas.1519261113. Epub 2016 Apr 26.

Highly efficient primed spacer acquisition from targets destroyed by the Escherichia coli type I-E CRISPR-Cas interfering complex. Ekaterina Semenova, Ekaterina Savitskaya, Olga Musharova, Alexandra Strotskaya, Daria Vorontsova, Kirill A. Datsenko, Maria D. Logacheva, and Konstantin Severinov.Proc Natl Acad Sci U S A., 7626–7631, doi: 10.1073/pnas.1602639113.

C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Abudayyeh OO, Gootenberg JS, Konermann S, Joung J, Slaymaker IM, Cox DB, Shmakov S, Makarova KS, Semenova E, Minakhin L, Severinov K, Regev A, Lander ES, Koonin EV, Zhang F.  Science. 2016 Jun 2. pii: aaf5573.

The genome of AR9, a giant transducing Bacillus phage encoding two multisubunit RNA polymerases. Lavysh D, Sokolova M, Minakhin L, Yakunina M, Artamonova T, Kozyavkin S, Makarova KS, Koonin EV, Severinov K. Virology. 2016 May 26;495:185-196. doi: 10.1016/j.virol.2016.04.030.

Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA. Yamano T, Nishimasu H, Zetsche B, Hirano H, Slaymaker IM, Li Y, Fedorova I, Nakane T, Makarova KS, Koonin EV, Ishitani R, Zhang F, Nureki O. Cell. 2016 Apr 21. pii: S0092-8674(16)30394-4. doi: 10.1016/j.cell.2016.04.003.

Recent mobility of casposons, self-synthesizing transposons at the origin of the CRISPR-Cas immunity. Krupovic M, Shmakov S, Makarova KS, Forterre P, Koonin EV. Genome Biol Evol. 2016 Jan 13. pii: evw006.

Metagenomic Analysis of Bacterial Communities of Antarctic Surface Snow. Anna Lopatina, Sofia Medvedeva, Sergey Shmakov, Maria D. Logacheva, Vjacheslav Krylenkov and Konstantin Severinov. Front. Microbiol. | doi: 10.3389/fmicb.2016.00398

Complex Selection on Human Polyadenylation Signals Revealed by Polymorphism and Divergence Data. Kainov YA, Aushev VN, Naumenko SA, Tchevkina EM, Bazykin GA. Genome Biol Evol. 2016 Jul 2;8(6):1971-9. doi: 10.1093/gbe/evw137.

Transcriptome-based phylogeny of endemic Lake Baikal amphipod species flock: fast speciation accompanied by frequent episodes of positive selection. Naumenko SA, Logacheva MD, Popova NV, Klepikova AV, Penin AA, Bazykin GA, Etingova AE, Mugue NS, Kondrashov AS, Yampolsky LY. Mol Ecol. 2016 Nov 17. doi: 10.1111/mec.13927.

APOBEC3A/B-induced mutagenesis is responsible for 20% of heritable mutations in the TpCpW context. Seplyarskiy VB, Andrianova MA, Bazykin GA. Genome Res. 2016 Dec 9. pii: gr.210336.116.

Application of sorting and next generation sequencing to study 5′-UTR influence on translation efficiency in Escherichia coli. Evfratov SA, Osterman IA, Komarova ES, Pogorelskaya AM, Rubtsova MP, Zatsepin TS, Semashko TA, Kostryukova ES, Mironov AA, Burnaev E, Krymova E, Gelfand MS, Govorun VM, Bogdanov AA, Sergiev PV, Dontsova OA. Nucleic Acids Res. 2016 Nov 29. pii: gkw1141.

Small Open Reading Frames, Non-Coding RNAs and Repetitive Elements in Bradyrhizobium japonicum USDA 110. Hahn J, Tsoy OV, Thalmann S, Čuklina J, Gelfand MS, Evguenieva-Hackenberg E1. 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 OV, Ravcheev DA, Čuklina J, Gelfand MS. 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 VS, Gelfand MS. 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 VN, Antonenko EA, Gelfand MS, Yager J, Ferrari FD. 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 EE, Fudenberg G, Gelfand MS, Mirny LA. J Bioinform Comput Biol. 2016 Apr;14(2):1641002. doi: 10.1142/S021972001641002X. Epub 2016 Jan 28.

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains. Ulianov SV, Khrameeva EE, Gavrilov AA, Flyamer IM, Kos P, Mikhaleva EA, Penin AA, Logacheva MD, Imakaev MV, Chertovich A, Gelfand MS, Shevelyov YY, Razin SV. Genome Res. 2016 Jan;26(1):70-84. doi: 10.1101/gr.196006.115. Epub 2015 Oct 30.

Changes in snoRNA and snRNA abundance in the human, chimpanzee, macaque and mouse brain. Zhang B, Han D, Korostelev Y, Yan Z, Shao N, Khrameeva E, Velichkovsky BM, Chen YP, Gelfand MS, Khaitovich P. Genome Biol Evol. 2016 Feb 28. pii: evw038.

Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry. Flegontov P, Changmai P, Zidkova A, Logacheva MD, Altınışık NE, Flegontova O, Gelfand MS, Gerasimov ES, Khrameeva EE, Konovalova OP, Neretina T, Nikolsky YV, Starostin G, Stepanova VV, Travinsky IV, Tříska M, Tříska P, Tatarinova TV. Sci Rep. 2016 Feb 11;6:20768. doi: 10.1038/srep20768.

Understanding autism and other neurodevelopmental disorders through experimental translational neurobehavioral models. Homberg JR, Kyzar EJ, Nguyen M, Norton WH, Pittman J, Poudel MK, Gaikwad S, Nakamura S, Koshiba M, Yamanouchi H, Scattoni ML, Ullman JF, Diamond DM, Kaluyeva AA, Parker MO, Klimenko VM, Apryatin SA, Brown RE, Song C, Gainetdinov RR, Gottesman II, Kalueff AV. Neurosci Biobehav Rev. 2016 Jun;65:292-312. doi: 10.1016/j.neubiorev.2016.03.013. Epub 2016 Apr 2. Review.
Dopamine transporter mutant animals: a translational perspective. Efimova EV, Gainetdinov RR, Budygin EA, Sotnikova TD.  J Neurogenet. 2016 Mar;30(1):5-15. doi: 10.3109/01677063.2016.1144751.
G protein-coupled receptor kinases as regulators of dopamine receptor functions. Gurevich EV, Gainetdinov RR, Gurevich VV. Pharmacol Res. 2016 Sep;111:1-16. doi: 10.1016/j.phrs.2016.05.010. Epub 2016 May 10. Review.

SOX2 Is the Determining Oncogenic Switch in Promoting Lung Squamous Cell Carcinoma from Different Cells of Origin. Ferone G, Song JY, Sutherland KD, Bhaskaran R, Monkhorst K, Lambooij JP, Proost N, Gargiulo G, Berns A. Cancer Cell. 2016 Oct 10;30(4):519-532. doi: 10.1016/j.ccell.2016.09.001.

Transcription Factor NFIB Is a Driver of Small Cell Lung Cancer Progression in Mice and Marks Metastatic Disease in Patients. Semenova EA, Kwon MC, Monkhorst K, Song JY, Bhaskaran R, Krijgsman O, Kuilman T, Peters D, Buikhuisen WA, Smit EF, Pritchard C, Cozijnsen M, van der Vliet J, Zevenhoven J, Lambooij JP, Proost N, van Montfort E, Velds A, Huijbers IJ, Berns A. Cell Rep. 2016 Jul 19;16(3):631-43. doi: 10.1016/j.celrep.2016.06.020.

The steady progress of targeted therapies, promising advances for lung cancer. Bombardelli L, Berns AEcancermedicalscience. 2016 Apr 28;10:638. doi: 10.3332/ecancer.2016.638. Review.