2017

• Slightly deleterious genomic variants and transcriptome perturbations in Down syndrome embryonic selection. Popadin K, Peischl S, Garieri M, Sailani M, Letourneau A, Santoni F, Lukowski S, Bazykin G, Nikolaev S, Meyer D, Excoffier L, Reymond A, Antonarakis S. Genome Res. Epub 2017 Dec 13. Jan;28(1):1-10. doi: 10.1101/gr.228411.117.

• Mining for Small Translated ORFs. Chugunova A, Navalayeu T, Dontsova O, Sergiev P J Proteome Res. Epub 2017 Dec 11;17(1):1-11. doi: 10.1021/acs.jproteome.7b00707.

• Comparative analysis of murine T-cell receptor repertoires. Izraelson M, Nakonechnaya T, Moltedo B, Egorov E, Kasatskaya S, Putintseva E, Mamedov I, Staroverov D, Shemiakina I, Zakharova M, Davydov A, Bolotin D, Shugay M, Chudakov D, Rudensky A, Britanova O Immunology. Epub 2017 Nov 27;153(2):133-144. doi: 10.1111/imm.12857.

• A Thermus phage protein inhibits host RNA polymerase by preventing template DNA strand loading during open promoter complex formation. Ooi W, Murayama Y, Mekler V, Minakhin L, Severinov K, Yokoyama S, Sekine S. Nucleic Acids Res. Epub Nov 20;46(1):431-441. doi: 10.1093/nar/gkx1162.

• Hypoxic renal injury in newborns with abdominal compartment syndrome (clinical and experimental study). Morozov D, Morozova O, Pervouchine D, Severgina L, Tsyplakov A, Zakharova N, Sushentsev N, Maltseva L, Budnik I Pediatr Res.  Epub 2017 Nov 15;83(2):520-526. doi: 10.1038/pr.2017.263.

• VDJdb: a curated database of T-cell receptor sequences with known antigen specificity. Shugay M, Bagaev D, Zvyagin I, Vroomans R, Crawford J, Dolton G, Komech E, Sycheva A, Koneva A, Egorov ES, Eliseev A, Van Dyk E, Dash P, Attaf M, Rius C, Ladell K, McLaren J, Matthews K, Clemens E, Douek D, Luciani F, van Baarle D, Kedzierska K, Kesmir C, Thomas P, Price D, Sewell A, Chudakov D  Nucleic Acids Res. Epub 2017 Sep 1 4;46(D1):D419-D427. doi: 10.1093/nar/gkx760.

• Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data. Guinney J, Wang T, Laajala T, Winner K, Bare J, Neto E, Khan S, Peddinti G, Airola A, Pahikkala T, Mirtti T, Yu T, Bot BM, Shen L, Abdallah K, Norman T, Friend S, Stolovitzky G, Soule H, Sweeney C, Ryan C, Scher H, Sartor O, Xie Y, Aittokallio T, Zhou F, Costello J; Prostate Cancer Challenge DREAM Community (Kazanov M). Lancet Oncol. 2017 Jan;18(1):132-142. doi: 10.1016/S1470-2045(16)30560-5. Epub 2016 Nov 16. PMID: 27864015

• High-resolution mass spectra processing for the identification of different pathological tissue types of brain tumors. Zhvansky E, Sorokin A, Popov I, Shurkhay V, Potapov A, Nikolaev E. Eur J Mass Spectrom (Chichester). 2017 Aug;23(4):213-216. doi: 10.1177/1469066717721484.

• Feature selection algorithm for spray-from-tissue mass spectrometry. Sorokin A, Zhvansky E, Shurkhay V, Bocharov K, Popov I, Levin N, Zubtsov D, Bormotov D, Kostyukevich Y, Potapov A, Nikolaev E  Eur J Mass Spectrom (Chichester). 2017 Aug;23(4):237-241. doi: 10.1177/1469066717721843.

•  Evaluation of plasma peptides extraction methods by high-resolution mass spectrometry. Zakharova N, Shornikova A, Bugrova A, Baybakova V, Indeykina M, Kononikhin A, Popov I, Kechko O, Makarov A, Nikolaev E. Eur J Mass Spectrom (Chichester). 2017 Aug;23(4):209-212. doi: 10.1177/1469066717720907.

• 2-Guanidino-quinazolines as a novel class of translation inhibitors. Komarova Andreyanova E, Osterman I, Pletnev P, Ivanenkov Y, Majouga A, Bogdanov A, Sergiev P.Biochimie. 2017 Feb;133:45-55. doi: 10.1016/j.biochi.2016.11.008. Epub 2016 Dec 21.

• Is myelin basic protein a potential biomarker of brain cancer? Zavialova M, Shevchenko V, Nikolaev E, Zgoda V. Eur J Mass Spectrom (Chichester). 2017 Aug;23(4):192-196. doi: 10.1177/1469066717719810.

• Modification of human serum albumin under induced oxidation. Gorobets M, Wasserman L, Vasilyeva A, Bychkova A, Pronkin P, Bugrova A, Indeykina M, Shilkina N, Konstantinova M, Kononikhin A, Nikolaev E, Rosenfeld M. Dokl Biochem Biophys. 2017 May ;474(1):231-235. doi: 10.1134/S1607672917030218. Epub 2017 Jul 20.

• Lutein and its oxidized forms in eye structures throughout prenatal human development. Panova I, Yakovleva M, Tatikolov A, Kononikhin A, Feldman T, Poltavtseva R, Nikolaev E, Sukhikh G, Ostrovsky M. Exp Eye Res. 2017 Jul;160:31-37. doi: 10.1016/j.exer.2017.04.008. Epub 2017 Apr 25.

• Lipidome determinants of maximal lifespan in mammals. Bozek K, Khrameeva E, Reznick J, Omerbašić D, Bennett N, Lewin G, Azpurua J, Gorbunova V, Seluanov A, Regnard P, Wanert F, Marchal J, Pifferi F, Aujard F, Liu Z, Shi P, Pääbo S, Schroeder F, Willmitzer L, Giavalisco P, Khaitovich P. Sci Rep. 2017 Dec;7(1):5. doi: 10.1038/s41598-017-00037-7. Epub 2017 Jan 31. PubMed PMID: 28127055; PubMed Central PMCID: PMC5428381.

• Negative selection in humans and fruit flies involves synergistic epistasis. Sohail M, Vakhrusheva O, Sul J, Pulit S, Francioli L, Genome of the Netherlands Consortium, Alzheimer’s Disease Neuroimaging Initiative, van den Berg L, Veldink J, de Bakker P, Bazykin G, Kondrashov AS, Sunyaev SR. Science. 2017 May 5;356(6337):539-542. doi: 10.1126/science.aah5238.

• Substitutions into amino acids that are pathogenic in human mitochondrial proteins are more frequent in lineages closely related to human than in distant lineages. Klink G, Golovin A, Bazykin G. PeerJ. 2017 Dec 12;5:e4143. doi: 10.7717/peerj.4143. eCollection 2017.

• A high-throughput assay for quantitative measurement of PCR errors. Shagin D, Shagina I, Zaretsky A, Barsova E, Kelmanson I, Lukyanov S, Chudakov D, Shugay M. Sci Rep. 2017 Jun 2;7(1):2718. doi: 10.1038/s41598-017-02727-8. PubMed PMID: 28578414.

• A non-canonical multisubunit RNA polymerase encoded by the AR9 phage recognizes the template strand of its uracil-containing promoters. Sokolova M, Borukhov S, Lavysh D, Artamonova T, Khodorkovskii M, Severinov K. Nucleic Acids Res. 2017 Jun 2;45(10):5958-5967. doi: 10.1093/nar/gkx264. PubMed PMID: 28402520.

• Comprehensive transcriptome analysis of neocortical layers in humans, chimpanzees and macaques. He Z, Han D, Efimova O, Guijarro P, Yu Q, Oleksiak A, Jiang S, Anokhin K, Velichkovsky B, Grünewald S, Khaitovich P. Nat Neurosci. 2017 Jun;20(6):886-895. doi: 10.1038/nn.4548. Epub 2017 Apr 17. PubMed PMID: 28414332.

• Mechanism of duplex DNA destabilization by RNA-guided Cas9 nuclease during target interrogation. Mekler V, Minakhin L, Severinov K. Proc Natl Acad Sci U S A. 2017 May 23;114(21):5443-5448. doi: 10.1073/pnas.1619926114. Epub 2017 May 8. PubMed PMID: 28484024.

• MAGERI: Computational pipeline for molecular-barcoded targeted resequencing. Shugay M, Zaretsky A, Shagin D, Shagina I, Volchenkov I, Shelenkov A, Lebedin M, Bagaev D, Lukyanov S, Chudakov D. PLoS Comput Biol. 2017 May 5;13(5):e1005480. doi: 10.1371/journal.pcbi.1005480. eCollection 2017 May. PubMed PMID: 28475621; PubMed Central PMCID: PMC5419444.

• Evolution of Local Mutation Rate and Its Determinants.Terekhanova N, Seplyarskiy V, Soldatov R, Bazykin G. Mol Biol Evol. 2017 May 1;34(5):1100-1109. doi: 10.1093/molbev/msx060. PubMed PMID: 28138076.

• Changes in Lipidome Composition during Brain Development in Humans, Chimpanzees, and Macaque Monkeys. Li Q, Bozek K, Xu C, Guo Y, Sun J, Pääbo S, Sherwood C, Hof P, Ely J, Li Y, Willmitzer L, Giavalisco P, Khaitovich P. Mol Biol Evol. 2017 May 1;34(5):1155-1166. doi: 10.1093/molbev/msx065. PubMed PMID: 28158622; PubMed Central PMCID: PMC5400384.

• Peptide-nucleotide antibiotic Microcin C is a potent inducer of stringent response and persistence in both sensitive and producing cells. Piskunova J, Maisonneuve E, Germain E, Gerdes K, Severinov K. Mol Microbiol. 2017 May;104(3):463-471. doi: 10.1111/mmi.13640. Epub 2017 Feb 24. PubMed PMID: 28164379.

• Viral genome packaging terminase cleaves DNA using the canonical RuvC-like two-metal catalysis mechanism. Xu RG, Jenkins HT, Chechik M, Blagova E, Lopatina A, Klimuk E, Minakhin L, Severinov K, Greive S, Antson A. Nucleic Acids Res. 2017 Apr 7;45(6):3580-3590. doi: 10.1093/nar/gkw1354. PubMed PMID: 28100693; PubMed Central PMCID: PMC5389553.

• Spacer-length DNA intermediates are associated with Cas1 in cells undergoing primed CRISPR adaptation. Musharova O, Klimuk E, Datsenko A, Metlitskaya A, Logacheva M, Semenova E, Severinov K, Savitskaya E. Nucleic Acids Res. 2017 Apr 7;45(6):3297-3307. doi: 10.1093/nar/gkx097. PubMed PMID: 28204574; PubMed Central PMCID: PMC5389516.

• 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. 2017 Apr;26(7):2019-2026. doi: 10.1111/mec.13961. Epub 2017 Jan 17. PubMed PMID: 27997045.

• Acinetodin and Klebsidin, RNA Polymerase Targeting Lasso Peptides Produced by Human Isolates of Acinetobacter gyllenbergii and Klebsiella pneumoniae. Metelev M, Arseniev A, Bushin LB, Kuznedelov K, Artamonova T, Kondratenko R, Khodorkovskii M, Seyedsayamdost M, Severinov K. ACS Chem Biol. 2017 Mar 17;12(3):814-824. doi: 10.1021/acschembio.6b01154. Epub 2017 Feb 3. PubMed PMID: 28106375.

• Diversity and evolution of class 2 CRISPR-Cas systems. Shmakov S, Smargon A, Scott D, Cox D, Pyzocha N, Yan W, Abudayyeh O, Gootenberg JS, Makarova KS, Wolf Y, Severinov K, Zhang F, Koonin E. Nat Rev Microbiol. 2017 Mar;15(3):169-182. doi: 10.1038/nrmicro.2016.184. Epub 2017 Jan 23. PubMed PMID: 28111461.

• Automated Solid-Phase Click Synthesis of Oligonucleotide Conjugates: From Small Molecules to Diverse N-Acetylgalactosamine Clusters. Farzan V, Ulashchik E, Martynenko-Makaev Y, Kvach M, Aparin I, Brylev V, Prikazchikova T, Maklakova S, Majouga A, Ustinov A, Shipulin G, Shmanai V, Korshun V, Zatsepin T. Bioconjug Chem. 2017 Oct 18;28(10):2599-2607. doi: 10.1021/acs.bioconjchem.7b00462. Epub 2017 Oct 4.

• The action of Escherichia coli CRISPR-Cas system on lytic bacteriophages with different lifestyles and development strategies. Strotskaya A, Savitskaya E, Metlitskaya A, Morozova N, Datsenko K, Semenova E, Severinov K. Nucleic Acids Res. 2017 Feb 28;45(4):1946-1957. doi: 10.1093/nar/gkx042. PubMed PMID: 28130424; PubMed Central PMCID: PMC5389539.

• Transcription Profiling of Bacillus subtilis Cells Infected with AR9, a Giant Phage Encoding Two Multisubunit RNA Polymerases. Lavysh D, Sokolova M, Slashcheva M, Förstner KU, Severinov K. MBio. 2017 Feb 14;8(1). pii: e02041-16. doi: 10.1128/mBio.02041-16. PubMed PMID: 28196958; PubMed Central PMCID: PMC5312081.

• APOBEC3A/B-induced mutagenesis is responsible for 20% of heritable mutations in the TpCpW context. Seplyarskiy V, Andrianova M, Bazykin G. Genome Res. 2017 Feb;27(2):175-184. doi: 10.1101/gr.210336.116. Epub 2016 Dec 9. PubMed PMID: 27940951; PubMed Central PMCID: PMC5287224.

• Single-Molecule Insight Into Target Recognition by CRISPR-Cas Complexes. Rutkauskas M, Krivoy A, Szczelkun MD, Rouillon C, Seidel R. Methods Enzymol. 2017;582:239-273. doi: 10.1016/bs.mie.2

• Recruitment of CRISPR-Cas systems by Tn7-like transposons. Peters J, Makarova K, Shmakov S, Koonin E. Proc Natl Acad Sci U S A. 2017 Aug 15. pii: 201709035. doi: 10.1073/pnas.1709035114. PMID:28811374

• Klebsazolicin inhibits 70S ribosome by obstructing the peptide exit tunnel. Metelev M, Osterman I, Ghilarov D, Khabibullina N, Yakimov A, Shabalin K, Utkina I, Travin D, Komarova E, Serebryakova M, Artamonova T, Khodorkovskii M, Konevega A, Sergiev P, Severinov K, Polikanov Y. Nat Chem Biol. 2017 Aug 28. doi: 10.1038/nchembio.2462. PMID: 28846667

• Cross-species comparison of the gut: Differential gene expression sheds light on biological differences in closely related tenebrionids. Oppert B, Perkin L, Martynov A, Elpidina E. J Insect Physiol. 2017 Mar 28. pii: S0022-1910(16)30325-0. doi: 10.1016/j.jinsphys.2017.03.010. PMID:28359776

• Achieving global perfect homeostasis through transporter regulation. Savir Y, Martynov A, Springer M. PLoS Comput Biol. 2017 Apr 17;13(4):e1005458. doi: 10.1371/journal.pcbi.1005458. eCollection 2017 Apr. PMID:28414718

• Multiplex gene editing by CRISPR-Cpf1 through autonomous processing of a single crRNA array. Zetsche B, Heidenreich M, Mohanraju P, Fedorova I, Kneppers J, DeGennaro E, Winblad N, Choudhury S, Abudayyeh O, Gootenberg J, Wu W, Scott D, Severinov K, Oost J, Zhang F. Nature Biotechnology, 2017 35, 31-34 (2017) doi:10.1038/nbt.3737.

• Transcriptome-based phylogeny of endemic Lake Baikal amphipod species flock: fast speciation accompanied by frequent episodes of positive selection. Naumenko S, Logacheva M, Popova N, Klepikova A, Penin A, Bazykin G, Etingova A, Mugue N, Kondrashov A, Yampolsky L. Mol Ecol. 2017 Jan;26(2):536-553.Nov 17. doi: 10.1111/mec.13927

• Novel Fri1-like Viruses Infecting Acinetobacter baumannii-vB_AbaP_AS11 and vB_AbaP_AS12-Characterization, Comparative Genomic Analysis, and Host-Recognition Strategy. Popova A, Lavysh D, Klimuk E, Edelstein M, Bogun A, Shneider M, Goncharov A, Leonov S, Severinov K. Viruses. 2017 Jul 17;9(7). pii: E188. doi: 10.3390/v9070188. PMID:28714913

• Parallel Evolution of Metazoan Mitochondrial Proteins. Klink G, Bazykin G. Genome Biol Evol. 2017 May 1;9(5):1341-1350. doi: 10.1093/gbe/evx025. PMID: 28595327

• Human mismatch repair system balances mutation rates between strands by removing more mismatches from the lagging strand. Andrianova M, Bazykin G, Nikolaev S, Seplyarskiy V. Genome Res. 2017 May 16. doi: 10.1101/gr.219915.116.  PMID:28512192

• A coarse-grained model for DNA origami. Reshetnikov R, Stolyarova A, Zalevsky A, Panteleev D, Pavlova G, Klinov D, Golovin A, Protopopova A. Nucleic Acids Res. 2017 Dec 18. doi: 10.1093/nar/gkx1262. PMID: 29267876

• 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.

• Optimal number of spacers in CRISPR arrays. Martynov A, Severinov K, Ispolatov I. PLoS Comput Biol. 2017 Dec 18;13(12):e1005891. doi: 10.1371/journal.pcbi.1005891. eCollection 2017 Dec.

• The Origins of Specificity in the Microcin-Processing Protease TldD/E. Ghilarov D, Serebryakova M, Stevenson C, Hearnshaw S, Volkov D, Maxwell A, Lawson D, Severinov K. Structure. 2017 Oct 3;25(10):1549-1561.e5. doi: 10.1016/j.str.2017.08.006. Epub 2017 Sep 21.

• Features of CRISPR-Cas Regulation Key to Highly Efficient and Temporally-Specific crRNA Production. Rodic A, Blagojevic B, Djordjevic M, Severinov K. Front Microbiol. 2017 Nov 3;8:2139. doi: 10.3389/fmicb.2017.02139. eCollection 2017.

• The Product of Yersinia pseudotuberculosis mcc Operon Is a Peptide-Cytidine Antibiotic Activated Inside Producing Cells by the TldD/E Protease. Tsibulskaya D, Mokina O, Kulikovsky A, Piskunova J, Severinov K, Serebryakova M, Dubiley S. Chem Soc. 2017 Nov 15;139(45):16178-16187. doi: 10.1021/jacs.7b07118. Epub 2017 Oct 31.

• Between Lake Baikal and the Baltic Sea: genomic history of the gateway to Europe. Triska P, Chekanov N, Stepanov V, Khusnutdinova E, Kumar G, Akhmetova V, Babalyan K, Boulygina E, Kharkov V, Gubina M, Khidiyatova I, Khitrinskaya I, Khrameeva E, Khusainova R, Konovalova N, Litvinov S, Marusin A, Mazur AM, Puzyrev V, Ivanoshchuk D, Spiridonova M, Teslyuk A, Tsygankova S, Triska M, Trofimova N, Vajda E, Balanovsky O, Baranova A, Skryabin K, Tatarinova TV, Prokhortchouk E. BMC Genet. 2017 Dec 28;18(Suppl 1):110. doi: 10.1186/s12863-017-0578-3. PMID:29297395

• 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

• High-quality genome assembly of Capsella bursa-pastoris reveals asymmetry of regulatory elements at early stages of polyploid genome evolution. Kasianov A, Klepikova A, Kulakovskiy I, Gerasimov E, Fedotova A, Besedina E, Kondrashov A, Logacheva M, Penin A. Plant J. 2017 Jul;91(2):278-291. doi: 10.1111/tpj.13563. Epub 2017 Jun 12. PMID:28387959

• Antigen receptor repertoire profiling from RNA-seq data. Bolotin D, Poslavsky S, Davydov A, Frenkel F, Fanchi L, Zolotareva O, Hemmers S, Putintseva E, Obraztsova A, Shugay M, Ataullakhanov R, Rudensky A, Schumacher T, Chudakov D. Nat Biotechnol. 2017 Oct 11;35(10):908-911. doi: 10.1038/nbt.3979. No abstract available. PMID:29020005

• Application of nonsense-mediated primer exclusion (NOPE) for preparation of unique molecular barcoded libraries. Shagin D, Turchaninova M, Shagina I, Shugay M, Zaretsky A, Zueva O, Bolotin D, Lukyanov S, Chudakov D. BMC Genomics. 2017 Jun 5;18(1):440. doi: 10.1186/s12864-017-3815-2.PMID:28583065

• Phylogenomics of Cas4 family nucleases. Hudaiberdiev S, Shmakov S, Wolf Y, Terns M, Makarova K, Koonin E. BMC Evol Biol. 2017 Nov 28;17(1):232. doi: 10.1186/s12862-017-1081-1.PMID:29179671

• The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes. Shmakov S, Sitnik V, Makarova K, Wolf Y, Severinov K, Koonin E. MBio. 2017 Sep 19;8(5). pii: e01397-17. doi: 10.1128/mBio.01397-17.PMID:28928211

• On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires. Silas S, Makarova K, Shmakov S, Páez-Espino D, Mohr G, Liu Y, Davison M, Roux S, Krishnamurthy S, Fu BXH, Hansen L, Wang D, Sullivan M, Millard A, Clokie M, Bhaya D, Lambowitz A, Kyrpides N, Koonin E, Fire A. MBio. 2017 Jul 11;8(4). pii: e00897-17. doi: 10.1128/mBio.00897-17.PMID:28698278

• Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28. Smargon A, Cox D, Pyzocha N, Zheng K, Slaymaker I, Gootenberg J, Abudayyeh O, Essletzbichler P, Shmakov S, Makarova K, Koonin E, Zhang F. Mol Cell. 2017 Feb 16;65(4):618-630.e7. doi: 10.1016/j.molcel.2016.12.023. Epub 2017 Jan 5. PMID:28065598

• 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

• De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus. Moskalev A, Kudryavtseva A, Graphodatsky A, Beklemisheva V, Serdyukova N, Krutovsky KV, Sharov V, Kulakovskiy I, Lando A, Kasianov A, Kuzmin D, Putintseva Y, Feranchuk S, Shaposhnikov M, Fraifeld V, Toren D, Snezhkina A, Sitnik V. BMC Evol Biol. 2017 Dec 28;17(Suppl 2):258. doi: 10.1186/s12862-017-1103-z. PMID:29297306

• Naked Mole Rat Induced Pluripotent Stem Cells and Their Contribution to Interspecific Chimera. Lee S, Mikhalchenko A, Yim S, Lobanov A, Park J, Choi K, Bronson R, Lee C, Park T, Gladyshev V. Stem Cell Reports. 2017 Nov 14;9(5):1706-1720. doi: 10.1016/j.stemcr.2017.09.013. Epub 2017 Oct 26. PMID: 29107591

• Compensatory Evolution of Intrinsic Transcription Terminators in Bacillus Cereus. Safina K, Mironov A, Bazykin G. Genome Biol Evol. 2017 Feb 1;9(2):340-349. doi: 10.1093/gbe/evw295.PMID:28201729

• Enumeration of carboxyl groups carried on individual components of humic systems using deuteromethylation and Fourier transform mass spectrometry Zherebker A, Kostyukevich Y, Kononikhin A, Kharybin O, Konstantinov AI, Zaitsev KV, Nikolaev E, Perminova IV. Analytical Bioanalytical Chem. 2017, 409, 9, 2477-2488.

• Thermal dissociation of ions limits the degree of the gas-phase H/D exchange at the atmosphericpressure Kostyukevich Y, Kononikhin A, Popov I, Nikolaev E. J Mass Spectrom. 2017, 52, 4, 204-209.

• The investigation of the bio-oil produced by hydrothermal liquefaction of Spirulina platensisusing ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry Kostyukevich Y, Vlaskin M, Vladimirov G, Zherebker A, Kononikhin A, Popov I, Nikolaev E. Eur J Mass Spectrom 2017, 23, 2, 83-88.

• Secondary Structure of A?(1-16) Complexes with Zinc: A Study in the Gas Phase Using Deuterium/Hydrogen Exchange and Ultra-High-Resolution Mass Spectrometry Kostyukevich Y, Kononikhin A, Indeykina M, Popov I, Bocharov K, Spassky A, Kozin S, Makarov A, Nikolaev E. Mol Biol. 2017, 51, 4, 710-716.

• CID fragmentation, H/D exchange and supermetallization of Barnase-Barstar complex Kostyukevich Y, Shulga A, Kononikhin A, Popov I, Nikolaev E, Deyev S. Sci Rep. 2017, 7, 1, 6176.

• Effect of ion clouds micromotion on measured signal in Fourier transform ion cyclotronresonance: Computer simulation. Vladimirov G, Kostyukevich Y, Kharybin O, Nikolaev E. Eur J Mass Spectrom. 2017, 23, 4, 162-166.

• Static harmonization of dynamically harmonized Fourier transform ion cyclotron resonance cell. Zhdanova E, Kostyukevich Y, Nikolaev E.Eur J Mass Spectrom. 2017, 4, 197-201.

• Synthesis of carboxylated styrene polymer for internal calibration of Fourier transform ioncyclotron resonance mass-spectrometry of humic substances Zherebker A, Turkova A, Kostyukevich Y, Kononikhin A, Zaitsev K, Popov I, Nikolaev E, Perminova I. Eur J Mass Spectrom. 2017, 23, 4, 156-161

• Investigation of the ozonation products of natural complex mixtures using Fourier transform ion cyclotron resonance mass spectrometry Kostyukevich Y, Stavitskaya A, Zherebker A, Konstantinova M, Vlaskin M, Borisova L, Kononikhin A, Popov I, Nikolaev E. Eur J Mass Spectrom. 2017, 23. 4, 152-155.

• Remote detection of explosives using field asymmetric ion mobility spectrometer installed on multicopter Kostyukevich Y, Efremov D, Ionov V, Kukaev E, Nikolaev E. J Mass Spectrom. 2017, 52, 11, 777-782.

• Thermal dissociation and H/D exchange of streptavidin tetramers at atmospheric pressure  Kostyukevich Y, Ovchinnikov G, Kononikhin A, Popov I, Oseledets I, Nikolaev E. International Journal of Mass Spectrometry 2017, 10, 1016.

• Interstitial telomeric repeats-associated DNA breaks. Shubernetskaya O, Skvortsov D, Evfratov S, Rubtsova M, Belova E, Strelkova O, Cherepaninets V, Zhironkina O, Olovnikov A, Zvereva M, Dontsova O, Kireev I. Nucleus. 2017, 8, 6, 641-653.

• Cytotoxicity Test Based on Human Cells Labeled with Fluorescent Proteins: Fluorimetry, Photography, and Scanning for High-Throughput Assay. Kalinina M, Skvortsov D, Rubtsova M, Komarova E, Dontsova O. Mol Imaging Biol. 2017, 21, 10, 1007.

• Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state Osterman I, Khabibullina N, Komarova E, Kasatsky P, Kartsev V, Bogdanov A, Dontsova O, Konevega A, Sergiev P, Polikanov Y, Nucleic Acids Res. 2017, 45, 12, 7507-7514.

• Chemical shift assignments and the secondary structure of the Est3 telomerase subunit in the yeast Hansenula polymorpha Mariasina S, Efimov S, Petrova O, Rodina E, Malyavko A, Zvereva MI, Klochkov V, Dontsova O, Polshakov V. Biomol NMR Assign. 2017, 12104-017-9780-5.

• No effect of C1473G polymorphism in the tryptophan hydroxylase 2 gene on the response of the brain serotonin system to chronic fluoxetine treatment in mice Bazhenova E, Sinyakova N, Kulikova E, Kazarinova I, Bazovkina D, Gainetdinov R, Kulikov A. Neurosci Lett. 2017, 13, 653, 264-268.

• Pharmacology of human trace amine-associated receptors: Therapeutic opportunities and challenges Berry M, Gainetdinov R, Hoener MC, Shahid M. Pharmacol Ther. 2017, 180:161-180.

• Structure-guided chemical modification of guide RNA enables potent non-viral in vivo genome editing Hao Yin, Chun-Qing Song, Sneha Suresh, Qiongqiong Wu, Walsh S, Hyunsik Rhym L,  Mintzer E, Fatih Bolukbasi,   Zhu J, Kauffman K, Haiwei Mou, Oberholzer A, Junmei Ding, Suet-Yan Kwan, Bogorad R, Zatsepin T, Koteliansky V, Wolfe S, Wen Xue, Langer R, Anderson C. Nature Biotechnology. 2017, 35, 1179–1187.

• Human accelerated regions and other human-specific sequence variations in the context of evolution and their relevance for brain development Levchenko A, Kanapin A, Samsonova A, Gainetdinov R. Genome Biol Evol. 2017.

• Structure and function of the N-terminal domain of the yeast telomerase reverse transcriptase Petrova O, Mantsyzov A, Rodina E, Efimov S, Hackenberg C, Hakanpaa J, Klochkov V, Lebedev A, Chugunova A, Malyavko A, Zatsepin T, Mishin A, Zvereva M, Lamzin V, Dontsova O, Polshakov V. Nucleic Acids Res. 2017.

• Synthesis and biological evaluation of novel mono- and bivalent ASGP-R-targeted drug-conjugates Petrov R, Maklakova S, Ivanenkov Y, Petrov S, Sergeeva O, Yamansarov E, Saltykova I, Kireev I, Alieva I, Deyneka E, Sofronova A, Aladinskaia A, Trofimenko A, Yamidanov R, Kovalev S, Kotelianski V, Zatsepin T, Beloglazkina E, Majouga A. Bioorg Med Chem Lett. 2017, S0960-894X, (17), 31192-7.

• Psychedelic Drugs in Biomedicine Kyzar E, Nichols C, Gainetdinov R, Nichols D, Kalueff A. Trends Pharmacol Sci, 2017, 38, (11), 992-1005.

• Fine Tuning of Pyrene Excimer Fluorescence in Molecular Beacons by Alteration of the Monomer Structure Aparin I, Proskurin G, Golovin A, Ustinov A, Formanovsky A, Zatsepin T, Korshun V. J Org Chem. 2017, 6, 82, (19), 10015-10024.

• Large-Scale Quantitative Proteomics Identifies the Ubiquitin Ligase Nedd4-1 as an Essential Regulator of Liver Regeneration Bachofner M, Speicher T, Bogorad R, Muzumdar S, Derrer C, Hurlimann F, Bohm F, Nanni P, Kockmann T, Kachaylo E, Meyer M, Padrissa-Altes S, Graf R, Anderson D, Koteliansky V, Auf dem Keller U, Werner S. Dev Cell. 2017, S1534-5807(17)30601-9, 10.1016

• Human Ku70 protein binds hairpin RNA and double stranded DNA through two different sites. Anisenko A, Knyazhanskaya E, Zatsepin T, Gottikh M. Biochimie. 2017 Jan;132:85-93. doi: 10.1016/j.biochi.2016.11.001. Epub 2016 Nov 4.

• Cholangiocytes act as facultative liver stem cells during impaired hepatocyte regeneration Raven A, Lu WY, Man TY, Ferreira-Gonzalez S, O’Duibhir E, Dwyer B, Thomson J, Meehan R, Bogorad R, Koteliansky V, Kotelevtsev Y, French-Constant C, Boulter L, Forbes S Nature, 2017, 20, 547, 7663, 350-354

• Characterization of HIV-1 integrase interaction with human Ku70 protein and initial implications for drug targeting Anisenko A, Knyazhanskaya E, Zalevsky A, Agapkina J, Sizov A, Zatsepin T, Gottikh M. Sci Rep. 2017, 7, 1, 5649

• Design of 2?-phenylethynylpyrene excimer forming DNA/RNA probes for homogeneous SNP detection: The attachment manner matters Astakhova K,  Golovin, Prokhorenkov I, Ustinov A, Stepanova I, Zatsepin T., Korshun V. Tetrahedron, 2017, 73, 3220–3230

• Smooth Muscle Endothelin B Receptors Regulate Blood Pressure but Not Vascular Function or Neointimal Remodeling Miller E, Czopek A, Duthie K, Kirkby N, van de Putte E, Christen S, Kimmitt R, Moorhouse R, Castellan R, Kotelevtsev Y, Kuc R, Davenport A, Dhaun N, Webb D, Hadoke P. Hypertension, 2017, 69, 275-285

• Synthesis of oligonucleotides containing novel G-clamp analog with C8-tethered group in phenoxazine ring: implication to qPCR detection of the low-copy kemerovo virus dsRNA Varizhuk A, Zatsepin T, Golovin A, Belyaev E, Kostyukevich Y, Dedkov V, Shipulin G, Shpakovski G, Aralov A. . Bioorg. Med. Chem., 2017, 25, 3597-3605

• Specificity of SNP detection with molecular beacons is improved by stem and loop separation with spacers  Farzan V, Markelov M,  Skoblov A,  Shipulin G, Zatsepin T. Analyst, 2017 142, 945-950.

• 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, 45, 3487-3502

• HumanKu70 protein binds hairpin RNA and double stranded DNA through two different sites.  Anisenko A, Knyazhanskaya E,  Zatsepin T,  Gottikh M. Biochimie, 2017, 132, 85–93.

• Role of Dopamine D2/D3 Receptors in Development, Plasticity, and Neuroprotection in Human iPSC-Derived Midbrain Dopaminergic Neurons. Bono F, Savoia P, Guglielmi A, Gennarelli M, Piovani G, Sigala S, Leo D, Espinoza S, Gainetdinov R, Devoto P, Spano P, Missale C, Fiorentini C. Mol Neurobiol. 2017

• A Caenorhabditis elegans model to study dopamine transporter deficiency syndrome. Illiano P, Lanzo A, Leo D, Paglione M, Zampi G, Gainetdinov R, Di Schiavi E. Eur J Neurosci. 2017, 45, 207-214

• Recombinant Adeno-Associated Virus-mediated rescue of function in a mouse model of Dopamine Transporter Deficiency Syndrome. Illiano P, Bass CE, Fichera L, Mus L, Budygin E, Sotnikova TD, Leo D, Espinoza S, Gainetdinov R. Sci Rep. 2017, 7, 46280.