Selected Publications & Patents

Recent research from the AI in Genomics and Engineering Biology Lab.

Anna B Trofimova, Alina O Demkina, Sergey A Shmakov, Alexei D Livenskyi, Marina V Serebryakova, Aleksandr A Dmitriev, Ilya D Rubinshteyn, Konstantin V Severinov, Matvey V Kolesnik (2026). A Unique Type V CRISPR-Cas System Encoded by a Group of Thermus Viruses. bioRxiv.
Kira S Makarova, Sergey A Shmakov, Yuri I Wolf, Pascal Mutz, Han Altae-Tran, Chase L Beisel, Stan JJ Brouns, Emmanuelle Charpentier, David Cheng, Jennifer Doudna, others (2025). An updated evolutionary classification of CRISPR--Cas systems including rare variants. Nature microbiology.
Shai Zilberzwige-Tal, Han Altae-Tran, Soumya Kannan, Max E Wilkinson, Samuel Chau-Duy-Tam Vo, Daniel Strebinger, KeHuan K Edmonds, Chun-Chen Jerry Yao, Kepler S Mears, Sergey A Shmakov, others (2025). Reprogrammable RNA-targeting CRISPR systems evolved from RNA toxin-antitoxins. Cell.
Han Altae-Tran, Sergey A Shmakov, Kira S Makarova, Yuri I Wolf, Soumya Kannan, Feng Zhang, Eugene V Koonin (2023). Diversity, evolution, and classification of the RNA-guided nucleases TnpB and Cas12. Proceedings of the National Academy of Sciences.
Sergey A Shmakov, Zachary K Barth, Kira S Makarova, Yuri I Wolf, Vyacheslav Brover, Joseph E Peters, Eugene V Koonin (2023). Widespread CRISPR-derived RNA regulatory elements in CRISPR-Cas systems. Nucleic acids research.
Sean Benler, Guilhem Faure, Han-Altae Tran, Sergey Shmakov, Feng Zhang, Eugene Koonin (2022). 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”. Mbio.
Natalya Yutin, Sean Benler, Sergei A Shmakov, Yuri I Wolf, Igor Tolstoy, Mike Rayko, Dmitry Antipov, Pavel A Pevzner, Eugene V Koonin (2021). Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features. Nature communications.
Sean Benler, Guilhem Faure, Han Altae-Tran, Sergey Shmakov, Feng Zhang, Eugene Koonin (2021). Cargo genes of Tn 7-like transposons comprise an enormous diversity of defense systems, mobile genetic elements, and antibiotic resistance genes. MBio.
Alexander Mitrofanov, Omer S Alkhnbashi, Sergey A Shmakov, Kira S Makarova, Eugene V Koonin, Rolf Backofen (2021). CRISPRidentify: identification of CRISPR arrays using machine learning approach. Nucleic acids research.
Ana Moya-Beltrán, Kira S Makarova, Lillian G Acuña, Yuri I Wolf, Paulo C Covarrubias, Sergey A Shmakov, Cristian Silva, Igor Tolstoy, D Barrie Johnson, Eugene V Koonin, others (2021). Evolution of type IV CRISPR-Cas systems: insights from CRISPR loci in integrative conjugative elements of Acidithiobacillia. The CRISPR journal.
Sean Benler, Natalya Yutin, Dmitry Antipov, Mikhail Rayko, Sergey Shmakov, Ayal B Gussow, Pavel Pevzner, Eugene V Koonin (2021). Thousands of previously unknown phages discovered in whole-community human gut metagenomes. Microbiome.
Ming Li, Luyao Gong, Feiyue Cheng, Haiying Yu, Dahe Zhao, Rui Wang, Tian Wang, Shengjie Zhang, Jian Zhou, Sergey A Shmakov, others (2021). Toxin-antitoxin RNA pairs safeguard CRISPR-Cas systems. Science.
Sergey A Shmakov, Irina Utkina, Yuri I Wolf, Kira S Makarova, Konstantin V Severinov, Eugene V Koonin (2020). CRISPR arrays away from cas genes. The CRISPR journal.
Iana Fedorova, Anatolii Arseniev, Polina Selkova, Georgii Pobegalov, Ignatiy Goryanin, Aleksandra Vasileva, Olga Musharova, Marina Abramova, Maksim Kazalov, Tatyana Zyubko, others (2020). DNA targeting by Clostridium cellulolyticum CRISPR--Cas9 Type II-C system. Nucleic acids research.
Kira S Makarova, Yuri I Wolf, Jaime Iranzo, Sergey A Shmakov, Omer S Alkhnbashi, Stan JJ Brouns, Emmanuelle Charpentier, David Cheng, Daniel H Haft, Philippe Horvath, others (2020). Evolutionary classification of CRISPR--Cas systems: a burst of class 2 and derived variants. Nature Reviews Microbiology.
Ayal B Gussow, Allyson E Park, Adair L Borges, Sergey A Shmakov, Kira S Makarova, Yuri I Wolf, Joseph Bondy-Denomy, Eugene V Koonin (2020). Machine-learning approach expands the repertoire of anti-CRISPR protein families. Nature communications.
Sergey A Shmakov, Yuri I Wolf, Ekaterina Savitskaya, Konstantin V Severinov, Eugene V Koonin (2020). Mapping CRISPR spaceromes reveals vast host-specific viromes of prokaryotes. Communications biology.
Iana Fedorova, Aleksandra Vasileva, Polina Selkova, Marina Abramova, Anatolii Arseniev, Georgii Pobegalov, Maksim Kazalov, Olga Musharova, Ignatiy Goryanin, Daria Artamonova, others (2020). PpCas9 from Pasteurella pneumotropica—a compact Type II-C Cas9 ortholog active in human cells. Nucleic acids research.
Natalya Yutin, Sean Benler, Sergei A Shmakov, Yuri I Wolf, Igor Tolstoy, Mike Rayko, Dmitry Antipov, Pavel A Pevzner, Eugene V Koonin (2020). Unique genomic features of crAss-like phages, the dominant component of the human gut virome. BioRxiv.
Kira S Makarova, Yuri I Wolf, Sergey A Shmakov, Yang Liu, Meng Li, Eugene V Koonin (2020). Unprecedented diversity of unique CRISPR-Cas-related systems and Cas1 homologs in Asgard archaea. The CRISPR Journal.
Ayal B Gussow, Sergey A Shmakov, Kira S Makarova, Yuri I Wolf, Joseph Bondy-Denomy, Eugene V Koonin (2020). Vast diversity of anti-CRISPR proteins predicted with a machine-learning approach. BioRxiv.
Guilhem Faure, Sergey A Shmakov, Kira S Makarova, Yuri I Wolf, Alexandra B Crawley, Rodolphe Barrangou, Eugene V Koonin (2019). Comparative genomics and evolution of trans-activating RNAs in Class 2 CRISPR-Cas systems. RNA biology.
Guilhem Faure, Sergey A Shmakov, Winston X Yan, David R Cheng, David A Scott, Joseph E Peters, Kira S Makarova, Eugene V Koonin (2019). CRISPR--Cas in mobile genetic elements: counter-defence and beyond. Nature Reviews Microbiology.
Sergey A Shmakov, Guilhem Faure, Kira S Makarova, Yuri I Wolf, Konstantin V Severinov, Eugene V Koonin (2019). Systematic prediction of functionally linked genes in bacterial and archaeal genomes. Nature protocols.
Sergey A Shmakov, Kira S Makarova, Yuri I Wolf, Konstantin V Severinov, Eugene V Koonin (2018). Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis. Proceedings of the National Academy of Sciences.
Sergey A Shmakov, Kira S Makarova, Yuri I Wolf, Konstantin V Severinov, Eugene V Koonin (2018). Towards comprehensive characterization of CRISPR-linked genes. BioRxiv.
Aaron A Smargon, David BT Cox, Neena K Pyzocha, Kaijie Zheng, Ian M Slaymaker, Jonathan S Gootenberg, Omar A Abudayyeh, Patrick Essletzbichler, Sergey Shmakov, Kira S Makarova, others (2017). Cas13b is a type VI-B CRISPR-associated RNA-guided RNase differentially regulated by accessory proteins Csx27 and Csx28. Molecular cell.
Sergey Shmakov, Aaron Smargon, David Scott, David Cox, Neena Pyzocha, Winston Yan, Omar O Abudayyeh, Jonathan S Gootenberg, Kira S Makarova, Yuri I Wolf, others (2017). Diversity and evolution of class 2 CRISPR--Cas systems. Nature reviews microbiology.
Ekaterina Savitskaya, Anna Lopatina, Sofia Medvedeva, Mikhail Kapustin, Sergey Shmakov, Alexey Tikhonov, Irena I Artamonova, Maria Logacheva, Konstantin Severinov (2017). Dynamics of Escherichia coli type I-E CRISPR spacers over 42 000 years. Molecular ecology.
Sukrit Silas, Kira S Makarova, Sergey Shmakov, David Páez-Espino, Georg Mohr, Yi Liu, Michelle Davison, Simon Roux, Siddharth R Krishnamurthy, Becky Xu Hua Fu, others (2017). On the origin of reverse transcriptase-using CRISPR-Cas systems and their hyperdiverse, enigmatic spacer repertoires. MBio.
Sanjarbek Hudaiberdiev, Sergey Shmakov, Yuri I Wolf, Michael P Terns, Kira S Makarova, Eugene V Koonin (2017). Phylogenomics of Cas4 family nucleases. BMC evolutionary biology.
Joseph E Peters, Kira S Makarova, Sergey Shmakov, Eugene V Koonin (2017). Recruitment of CRISPR-Cas systems by Tn7-like transposons. Proceedings of the National Academy of Sciences.
Sergey A Shmakov, Vassilii Sitnik, Kira S Makarova, Yuri I Wolf, Konstantin V Severinov, Eugene V Koonin (2017). The CRISPR spacer space is dominated by sequences from species-specific mobilomes. MBio.
Konstantin Severinov, Sergei Shmakov, Omar Abudayyeh, Kira Makarova, Yuri Wolf, Ekaterina Semenova, Leonid Minakhin, Jonathan Gootenberg, Feng Zhang, Eugene Koonin (2016). A pipeline approach for discovery of novel CRISRP-Cas systems. TRANSGENIC RESEARCH.
Konstantin Kuznedelov, Vladimir Mekler, Sofia Lemak, Monika Tokmina-Lukaszewska, Kirill A Datsenko, Ishita Jain, Ekaterina Savitskaya, John Mallon, Sergey Shmakov, Brian Bothner, others (2016). Altered stoichiometry Escherichia coli Cascade complexes with shortened CRISPR RNA spacers are capable of interference and primed adaptation. Nucleic acids research.
Omar O Abudayyeh, Jonathan S Gootenberg, Silvana Konermann, Julia Joung, Ian M Slaymaker, David BT Cox, Sergey Shmakov, Kira S Makarova, Ekaterina Semenova, Leonid Minakhin, others (2016). C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science.
Anna Lopatina, Sofia Medvedeva, Sergey Shmakov, Maria D Logacheva, Vjacheslav Krylenkov, Konstantin Severinov (2016). Metagenomic analysis of bacterial communities of Antarctic surface snow. Frontiers in microbiology.
Mart Krupovic, Sergey Shmakov, Kira S Makarova, Patrick Forterre, Eugene V Koonin (2016). Recent mobility of casposons, self-synthesizing transposons at the origin of the CRISPR-Cas immunity. Genome biology and evolution.
Sergey Shmakov, Omar O Abudayyeh, Kira S Makarova, Yuri I Wolf, Jonathan S Gootenberg, Ekaterina Semenova, Leonid Minakhin, Julia Joung, Silvana Konermann, Konstantin Severinov, others (2015). Discovery and functional characterization of diverse class 2 CRISPR-Cas systems. Molecular cell.
Sergey Shmakov, Omar O Abudayyeh, Kira S Makarova, Yuri I Wolf, Jonathan S Gootenberg, Ekaterina Semenova, Leonid Minakhin, Julia Joung, Silvana Konermann, Konstantin Severinov, others (2015). 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. Mol Cell.
Sergey Shmakov, Ekaterina Savitskaya, Ekaterina Semenova, Maria D Logacheva, Kirill A Datsenko, Konstantin Severinov (2014). Pervasive generation of oppositely oriented spacers during CRISPR adaptation. Nucleic acids research.