AIGEN Lab | Laboratory of AI in Evolutionary Genomics and Engineering Biology https://aigen.bio.msu.ru:1313/ AIGEN Lab HugoBlox Kit (https://hugoblox.com)enTue, 26 May 2026 00:00:00 +0000 https://aigen.bio.msu.ru:1313/media/icon_hu_da05098ef60dc2e7.png AIGEN Lab https://aigen.bio.msu.ru:1313/ Meet the Team https://aigen.bio.msu.ru:1313/team/ Wed, 27 May 2026 00:00:00 +0000 https://aigen.bio.msu.ru:1313/team/ Contact Information https://aigen.bio.msu.ru:1313/contact/ Tue, 26 May 2026 00:00:00 +0000 https://aigen.bio.msu.ru:1313/contact/ <h1 id="get-in-touch">Get in Touch</h1> <p><strong>Evolutionary Genomics and Engineering Biology Lab</strong> Moscow State University<br> Moscow, Russia</p> <p><strong>Email:</strong> </p> <p><em>(Campus map and specific office/lab locations will be soon posted here)</em></p> Publications https://aigen.bio.msu.ru:1313/publications/ Tue, 26 May 2026 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publications/ Research Focus https://aigen.bio.msu.ru:1313/research/ Tue, 26 May 2026 00:00:00 +0000 https://aigen.bio.msu.ru:1313/research/ A Unique Type V CRISPR-Cas System Encoded by a Group of Thermus Viruses https://aigen.bio.msu.ru:1313/publication/trofimova-2026-unique/ Thu, 01 Jan 2026 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/trofimova-2026-unique/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> An updated evolutionary classification of CRISPR--Cas systems including rare variants https://aigen.bio.msu.ru:1313/publication/makarova-2025-updated/ Wed, 01 Jan 2025 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/makarova-2025-updated/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Reprogrammable RNA-targeting CRISPR systems evolved from RNA toxin-antitoxins https://aigen.bio.msu.ru:1313/publication/zilberzwige-2025-reprogrammable/ Wed, 01 Jan 2025 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/zilberzwige-2025-reprogrammable/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Diversity, evolution, and classification of the RNA-guided nucleases TnpB and Cas12 https://aigen.bio.msu.ru:1313/publication/altae-2023-diversity/ Sun, 01 Jan 2023 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/altae-2023-diversity/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Widespread CRISPR-derived RNA regulatory elements in CRISPR-Cas systems https://aigen.bio.msu.ru:1313/publication/shmakov-2023-widespread/ Sun, 01 Jan 2023 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/shmakov-2023-widespread/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Erratum for Benler et al.,“Cargo Genes of Tn 7-Like Transposons Comprise an Enormous Diversity of Defense Systems, Mobile Genetic Elements, and Antibiotic Resistance Genes” https://aigen.bio.msu.ru:1313/publication/benler-2022-erratum/ Sat, 01 Jan 2022 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/benler-2022-erratum/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features https://aigen.bio.msu.ru:1313/publication/yutin-2021-analysis/ Fri, 01 Jan 2021 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/yutin-2021-analysis/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Cargo genes of Tn 7-like transposons comprise an enormous diversity of defense systems, mobile genetic elements, and antibiotic resistance genes https://aigen.bio.msu.ru:1313/publication/benler-2021-cargo/ Fri, 01 Jan 2021 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/benler-2021-cargo/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> CRISPRidentify: identification of CRISPR arrays using machine learning approach https://aigen.bio.msu.ru:1313/publication/mitrofanov-2021-crispridentify/ Fri, 01 Jan 2021 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/mitrofanov-2021-crispridentify/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Evolution of type IV CRISPR-Cas systems: insights from CRISPR loci in integrative conjugative elements of Acidithiobacillia https://aigen.bio.msu.ru:1313/publication/moya-2021-evolution/ Fri, 01 Jan 2021 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/moya-2021-evolution/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Thousands of previously unknown phages discovered in whole-community human gut metagenomes https://aigen.bio.msu.ru:1313/publication/benler-2021-thousands/ Fri, 01 Jan 2021 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/benler-2021-thousands/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Toxin-antitoxin RNA pairs safeguard CRISPR-Cas systems https://aigen.bio.msu.ru:1313/publication/li-2021-toxin/ Fri, 01 Jan 2021 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/li-2021-toxin/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> CRISPR arrays away from cas genes https://aigen.bio.msu.ru:1313/publication/shmakov-2020-crispr/ Wed, 01 Jan 2020 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/shmakov-2020-crispr/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> DNA targeting by Clostridium cellulolyticum CRISPR--Cas9 Type II-C system https://aigen.bio.msu.ru:1313/publication/fedorova-2020-dna/ Wed, 01 Jan 2020 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/fedorova-2020-dna/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Evolutionary classification of CRISPR--Cas systems: a burst of class 2 and derived variants https://aigen.bio.msu.ru:1313/publication/makarova-2020-evolutionary/ Wed, 01 Jan 2020 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/makarova-2020-evolutionary/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Machine-learning approach expands the repertoire of anti-CRISPR protein families https://aigen.bio.msu.ru:1313/publication/gussow-2020-machine/ Wed, 01 Jan 2020 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/gussow-2020-machine/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Mapping CRISPR spaceromes reveals vast host-specific viromes of prokaryotes https://aigen.bio.msu.ru:1313/publication/shmakov-2020-mapping/ Wed, 01 Jan 2020 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/shmakov-2020-mapping/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> PpCas9 from Pasteurella pneumotropica—a compact Type II-C Cas9 ortholog active in human cells https://aigen.bio.msu.ru:1313/publication/fedorova-2020-ppcas-9/ Wed, 01 Jan 2020 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/fedorova-2020-ppcas-9/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Unique genomic features of crAss-like phages, the dominant component of the human gut virome https://aigen.bio.msu.ru:1313/publication/yutin-2020-unique/ Wed, 01 Jan 2020 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/yutin-2020-unique/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Unprecedented diversity of unique CRISPR-Cas-related systems and Cas1 homologs in Asgard archaea https://aigen.bio.msu.ru:1313/publication/makarova-2020-unprecedented/ Wed, 01 Jan 2020 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/makarova-2020-unprecedented/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Vast diversity of anti-CRISPR proteins predicted with a machine-learning approach https://aigen.bio.msu.ru:1313/publication/gussow-2020-vast/ Wed, 01 Jan 2020 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/gussow-2020-vast/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Comparative genomics and evolution of trans-activating RNAs in Class 2 CRISPR-Cas systems https://aigen.bio.msu.ru:1313/publication/faure-2019-comparative/ Tue, 01 Jan 2019 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/faure-2019-comparative/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> CRISPR--Cas in mobile genetic elements: counter-defence and beyond https://aigen.bio.msu.ru:1313/publication/faure-2019-crispr/ Tue, 01 Jan 2019 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/faure-2019-crispr/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Systematic prediction of functionally linked genes in bacterial and archaeal genomes https://aigen.bio.msu.ru:1313/publication/shmakov-2019-systematic/ Tue, 01 Jan 2019 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/shmakov-2019-systematic/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis https://aigen.bio.msu.ru:1313/publication/shmakov-2018-systematic/ Mon, 01 Jan 2018 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/shmakov-2018-systematic/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Towards comprehensive characterization of CRISPR-linked genes https://aigen.bio.msu.ru:1313/publication/shmakov-2018-towards/ Mon, 01 Jan 2018 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/shmakov-2018-towards/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Cas13b is a type VI-B CRISPR-associated RNA-guided RNase differentially regulated by accessory proteins Csx27 and Csx28 https://aigen.bio.msu.ru:1313/publication/smargon-2017-cas-13-b/ Sun, 01 Jan 2017 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/smargon-2017-cas-13-b/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Diversity and evolution of class 2 CRISPR--Cas systems https://aigen.bio.msu.ru:1313/publication/shmakov-2017-diversity/ Sun, 01 Jan 2017 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/shmakov-2017-diversity/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Dynamics of Escherichia coli type I-E CRISPR spacers over 42 000 years https://aigen.bio.msu.ru:1313/publication/savitskaya-2017-dynamics/ Sun, 01 Jan 2017 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/savitskaya-2017-dynamics/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> On the origin of reverse transcriptase-using CRISPR-Cas systems and their hyperdiverse, enigmatic spacer repertoires https://aigen.bio.msu.ru:1313/publication/silas-2017-origin/ Sun, 01 Jan 2017 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/silas-2017-origin/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Phylogenomics of Cas4 family nucleases https://aigen.bio.msu.ru:1313/publication/hudaiberdiev-2017-phylogenomics/ Sun, 01 Jan 2017 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/hudaiberdiev-2017-phylogenomics/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Recruitment of CRISPR-Cas systems by Tn7-like transposons https://aigen.bio.msu.ru:1313/publication/peters-2017-recruitment/ Sun, 01 Jan 2017 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/peters-2017-recruitment/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> The CRISPR spacer space is dominated by sequences from species-specific mobilomes https://aigen.bio.msu.ru:1313/publication/shmakov-2017-crispr/ Sun, 01 Jan 2017 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/shmakov-2017-crispr/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> A pipeline approach for discovery of novel CRISRP-Cas systems https://aigen.bio.msu.ru:1313/publication/severinov-2016-pipeline/ Fri, 01 Jan 2016 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/severinov-2016-pipeline/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Altered stoichiometry Escherichia coli Cascade complexes with shortened CRISPR RNA spacers are capable of interference and primed adaptation https://aigen.bio.msu.ru:1313/publication/kuznedelov-2016-altered/ Fri, 01 Jan 2016 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/kuznedelov-2016-altered/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector https://aigen.bio.msu.ru:1313/publication/abudayyeh-2016-c-2-c-2/ Fri, 01 Jan 2016 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/abudayyeh-2016-c-2-c-2/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Metagenomic analysis of bacterial communities of Antarctic surface snow https://aigen.bio.msu.ru:1313/publication/lopatina-2016-metagenomic/ Fri, 01 Jan 2016 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/lopatina-2016-metagenomic/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Recent mobility of casposons, self-synthesizing transposons at the origin of the CRISPR-Cas immunity https://aigen.bio.msu.ru:1313/publication/krupovic-2016-recent/ Fri, 01 Jan 2016 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/krupovic-2016-recent/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Discovery and functional characterization of diverse class 2 CRISPR-Cas systems https://aigen.bio.msu.ru:1313/publication/shmakov-2015-discovery/ Thu, 01 Jan 2015 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/shmakov-2015-discovery/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> MD 20894, USA 3 Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA, McGovern Institute for Brain Research, Department of Brain and Cognitive Science, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts https://aigen.bio.msu.ru:1313/publication/shmakov-2015-md/ Thu, 01 Jan 2015 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/shmakov-2015-md/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p> Pervasive generation of oppositely oriented spacers during CRISPR adaptation https://aigen.bio.msu.ru:1313/publication/shmakov-2014-pervasive/ Wed, 01 Jan 2014 00:00:00 +0000 https://aigen.bio.msu.ru:1313/publication/shmakov-2014-pervasive/ <p>Add the <strong>full text</strong> or <strong>supplementary notes</strong> for the publication here using Markdown formatting.</p>