VU Gyvybės mokslų centro autoriaus 'Tomas Šinkūnas' publikacijų sąrašas

2024
1 Bigelytė, Greta; Duchovska, Brigita; Žedaveinytė, Rimantė; Sasnauskas, Giedrius; Šinkūnas, Tomas; Dalgėdienė, Indrė; Tamulaitienė, Giedrė; Šilanskas, Arūnas; Kazlauskas, Darius; Valančauskas, Lukas; Madariaga-Marcos, Julene; Seidel, Ralf; Šikšnys, Virginijus; Karvelis, Tautvydas. Innate programmable DNA binding by CRISPR-Cas12m effectors enable efficient base editing // Nucleic acids research. Oxford : Oxford University Press. ISSN 0305-1048. eISSN 1362-4962. 2024, vol. 52, iss. 6, p. 3234-3248. DOI: 10.1093/nar/gkae016. [DB: Science Citation Index Expanded (Web of Science), Scopus] [IF: 13.100; AIF: 5.300; Q1 (2024 InCities JCR SCIE)]
2 Zaremba, Mindaugas (autorius, išradimo); Toliušis, Paulius (autorius, išradimo); Karvelis, Tautvydas (autorius, išradimo); Sasnauskas, Giedrius (autorius, išradimo); Šinkūnas, Tomas (autorius, išradimo); Grybauskas, Algirdas (autorius, išradimo); Šilanskas, Arūnas (autorius, išradimo); Zagorskaitė, Evelina (autorius, išradimo). CRISPR nuclease off-target detection by sequencing (CROFT-Seq). US20240401126A1. 2024-12-05. 23 p. Prieiga per internetą: <https://worldwide.espacenet.com/patent/search/family/093653985/publication/US2024401126A1?q=US20240401126A1>. [DB: Espacenet]
3 Zaremba, Mindaugas (autorius, išradimo); Toliušis, Paulius (autorius, išradimo); Karvelis, Tautvydas (autorius, išradimo); Sasnauskas, Giedrius (autorius, išradimo); Šinkūnas, Tomas (autorius, išradimo); Grybauskas, Algirdas (autorius, išradimo); Šilanskas, Arūnas (autorius, išradimo); Zagorskaitė, Evelina (autorius, išradimo). CRISPR nuclease off-target detection by sequencing (CROFT-Seq). EP4471159A1. 2024-12-04. 29 p. Prieiga per internetą: <https://worldwide.espacenet.com/patent/search/family/086646501/publication/EP4471159A1?q=EP4471159A1>. [DB: Espacenet]
4 Zaremba, Mindaugas (autorius, išradimo); Toliušis, Paulius (autorius, išradimo); Karvelis, Tautvydas (autorius, išradimo); Sasnauskas, Giedrius (autorius, išradimo); Šinkūnas, Tomas (autorius, išradimo); Grybauskas, Algirdas (autorius, išradimo); Šilanskas, Arūnas (autorius, išradimo); Zagorskaitė, Evelina (autorius, išradimo). CRISPR nuclease off-target detection by sequencing (CROFT-Seq). JP2024172618A. 2024-12-12. 33 p. Prieiga per internetą: <https://worldwide.espacenet.com/patent/search/family/093798213/publication/JP2024172618A?q=JP2024172618A>. [DB: Espacenet]
5 Petrauskaitė, Aistė; Šinkūnas, Tomas. Functional analysis of antiviral BREX proteins // Open Readings 2024. The 67th international conference for students of physics and natural sciences, April 23-26, 2024 : book of abstracts. Vilnius : Vilniaus universiteto leidykla, 2024. ISBN 9786090710517. p. 334. (Vilnius University proceedings, eISSN 2669-0233 ; vol. 46). DOI: 10.15388/Proceedings.2024.46. [DB: Dimensions]
6 Graužinytė, Melita; Šinkūnas, Tomas. Inhibition of CRISPR-Cas defence by Anti-CRISPR proteins // Open Readings 2024. The 67th international conference for students of physics and natural sciences, April 23-26, 2024 : book of abstracts. Vilnius : Vilniaus universiteto leidykla, 2024. ISBN 9786090710517. p. 358. (Vilnius University proceedings, eISSN 2669-0233 ; vol. 46). DOI: 10.15388/Proceedings.2024.46. [DB: Dimensions]
7 Adomaitytė, Justė; Šinkūnas, Tomas. Inhibition of a bacterial antiviral BREX defense system // Open Readings 2024. The 67th international conference for students of physics and natural sciences, April 23-26, 2024 : book of abstracts. Vilnius : Vilniaus universiteto leidykla, 2024. ISBN 9786090710517. p. 377. (Vilnius University proceedings, eISSN 2669-0233 ; vol. 46). DOI: 10.15388/Proceedings.2024.46. [DB: Dimensions]
8 Naujokaitė, Gabija; Juozapaitis, Jonas; Šilanskas, Arūnas; Šinkūnas, Tomas; Šikšnys, Virginijus; Songailienė, Inga. Functional analysis of CRISPR-Cas type I-D system and WYL domain-containing protein // Open Readings 2024. The 67th international conference for students of physics and natural sciences, April 23-26, 2024 : book of abstracts. Vilnius : Vilniaus universiteto leidykla, 2024. ISBN 9786090710517. p. 390. (Vilnius University proceedings, eISSN 2669-0233 ; vol. 46). DOI: 10.15388/Proceedings.2024.46. [DB: Dimensions]

2023
1 Aldag, Pierre; Rutkauskas, Marius; Madariaga-Marcos, Julene; Songailienė, Inga; Šinkūnas, Tomas; Kemmerich, Felix; Kauert, Dominik; Šikšnys, Virginijus; Seidel, Ralf. Dynamic interplay between target search and recognition for a Type I CRISPR-Cas system // Nature communications. Berlin : Nature Portfolio. eISSN 2041-1723. 2023, vol. 14, iss. 1, art. no. 3654, p. [1-14]. DOI: 10.1038/s41467-023-38790-1. [DB: Science Citation Index Expanded (Web of Science), Scopus]
2 Kauert, Dominik J; Madariaga-Marcos, Julene; Rutkauskas, Marius; Wulfken, Alexander; Songailienė, Inga; Šinkūnas, Tomas; Šikšnys, Virginijus; Seidel, Ralf. The energy landscape for R-loop formation by the CRISPR-Cas Cascade complex // Nature structural & molecular biology. Berlin : Springer Nature Limited. ISSN 1545-9993. eISSN 1545-9985. 2023, vol. 30, iss. 7, p. 1040-1047. DOI: 10.1038/s41594-023-01019-2. [DB: Science Citation Index Expanded (Web of Science), Scopus] [IF: 12.500; AIF: 5.166; Q1 (2023 InCities JCR SCIE)]

2022
1 Kupčinskaitė, Eglė; Tutkus, Marijonas; Kopūstas, Aurimas; Ašmontas, Simonas Vytautas; Jankunec, Marija; Zaremba, Mindaugas; Tamulaitienė, Giedrė; Šinkūnas, Tomas. Disarming of type I-F CRISPR-Cas surveillance complex by anti-CRISPR proteins AcrIF6 and AcrIF9 // Scientific reports : Springer Science and Business Media LLC. ISSN 2045-2322. eISSN 2045-2322. 2022, vol. 12, art. no. 15548, p. 1-14. DOI: 10.1038/s41598-022-19797-y. [DB: Scopus, Science Citation Index Expanded (Web of Science)] [IF: 4.600; AIF: 7.200; Q2 (2022 InCities JCR SCIE)]
2 Rutkauskas, Marius; Songailienė, Inga; Irmisch, Patrick; Kemmerich, Felix E; Šinkūnas, Tomas; Šikšnys, Virginijus; Seidel, Ralf. A quantitative model for the dynamics of target recognition and off-target rejection by the CRISPR-Cas Cascade complex // Nature communications. Berlin : Nature Portfolio. eISSN 2041-1723. 2022, vol. 13, no. 1, art. no. 7460, p. [1-13]. DOI: 10.1038/s41467-022-35116-5. [DB: Science Citation Index Expanded (Web of Science), Scopus]
3 Marcos, Julene Madariaga; Kauert, Dominik J.; Rutkauskas, Marius; Wulfken, Alexander; Songailienė, Inga; Šinkūnas, Tomas; Šikšnys, Virginijus; Seidel, Ralf. Energy landscapes of CRISPR/Cas R-loop formation from ultrafast twist measurements // Biophysical journal. Cambridge : Cell Press. ISSN 0006-3495. eISSN 1542-0086. 2022, vol. 121, iss. 3, suppl. 1, art. no. 1369-Pos, p. 283a. DOI: 10.1016/j.bpj.2021.11.1334. [DB: Science Citation Index Expanded (Web of Science)] [IF: 3.400; AIF: 4.200; Q2 (2022 InCities JCR SCIE)]

2021
1 Madariaga-Marcos, Julene; Kauert, Dominik J.; Rutkauskas, Marius; Wulfken, Alexander; Songailienė, Inga; Šinkūnas, Tomas; Šikšnys, Virginijus; Seidel, Ralf. Dissecting the target recognition by CRISPR/Cas effector complexes with ultrafast twist measurements // European biophysics journal with biophysics letters: 13th EBSA congress, July 24–28, 2021, Vienna, Austria – Abstracts. New York : Springer. ISSN 0175-7571. eISSN 1432-1017. 2021, vol. 50, suppl. 1, art. no. P-111, p. 124. DOI: 10.1007/s00249-021-01558-w. [DB: Science Citation Index Expanded (Web of Science)] [IF: 2.095; AIF: 4.632; Q3 (2021 InCities JCR SCIE)]

2020
1 Tuminauskaitė, Donata; Norkūnaitė, Danguolė; Fiodorovaitė, Marija; Tumas, Šarūnas; Songailienė, Inga; Tamulaitienė, Giedrė; Šinkūnas, Tomas. DNA interference is controlled by R-loop length in a type I-F1 CRISPR-Cas system // BMC Biology. London : BMC. eISSN 1741-7007. 2020, vol.18, art. no. 65, p. [1-16]. DOI: 10.1186/s12915-020-00799-z. [DB: Scopus, Science Citation Index Expanded (Web of Science)]

2019
1 Gordeeva, Julia; Morozova, Natalya; Sierro, Nicolas; Isaev, Artem; Šinkūnas, Tomas; Tsvetkova, Ksenia; Matlashov, Mikhail; Truncaitė, Lidija; Morgan, Richard D; Ivanov, V; Šikšnys, Virginijus; Zeng, Lanying; Severinov, Konstantin. BREX system of Escherichia coli distinguishes self from non-self by methylation of a specific DNA site // Nucleic acids research. Oxford : Oxford University Press. ISSN 0305-1048. eISSN 1362-4962. 2019, vol. 47, iss. 1, p. 253-265. DOI: 10.1093/nar/gky1125. [DB: MEDLINE, Embase, Veterinary Science Database, BIOSIS Previews, Scopus, Science Citation Index Expanded (Web of Science)] [IF: 11.502; AIF: 4.696; Q1 (2019 InCities JCR SCIE)]
2 Songailienė, Inga; Rutkauskas, Marius; Šinkūnas, Tomas; Manakova, Elena; Wittig, Sabine; Schmidt, Carla; Šikšnys, Virginijus; Seidel, Ralf. Decision-making in cascade complexes harboring crRNAs of altered length // Cell reports. Cambridge, MA : Cell Press. eISSN 2211-1247. 2019, vol. 28, iss. 12, p. 3157-3166. DOI: 10.1016/j.celrep.2019.08.033. [DB: Biological Abstracts, MEDLINE, Scopus, Science Citation Index Expanded (Web of Science)]

2018
1 Drabavičius, Gediminas; Šilanskas, Arūnas; Šinkūnas, Tomas; Gasiūnas, Giedrius. Proofreading domain facilitates spacer integration in CRISPR-Cas - an adaptive prokaryotic immunity // Vita Scientia : international conference, 3rd January 2018, Vilnius : conference book. Vilnius : Vita Scientia. ISSN 2538-791X. 2018, p. 56-57. Prieiga per internetą: <http://www.vitascientia.lt/book> [žiūrėta 2018-04-27].
2 Drabavičius, Gediminas; Šinkūnas, Tomas; Šilanskas, Arūnas; Gasiūnas, Giedrius; Venclovas, Česlovas; Šikšnys, Virginijus. DnaQ exonuclease-like domain of Cas2 promotes spacer integration in a type I-E CRISPR-Cas system // EMBO reports. Hoboken : Wiley-VCH Verlag. ISSN 1469-221X. eISSN 1469-3178. 2018, vol. 19, no 7, art. no. e45543, p. 1709-1712. DOI: 10.15252/embr.201745543. [DB: Scopus, Science Citation Index Expanded (Web of Science)] [IF: 8.383; AIF: 5.202; Q1 (2018 InCities JCR SCIE)]
3 Songailienė, Inga; Juozapaitytė, Ieva; Šinkūnas, Tomas; Juozapaitis, Jonas; Šulčius, S.; Šilanskas, Arūnas; Venclovas, Česlovas; Šikšnys, Virginijus. Melsvabakterių Aphanizomenon flos-aquae CRISPR-Cas sistemos tyrimai // Bioateitis: gamtos ir gyvybės mokslų perspektyvos : 11-oji jaunųjų mokslininkų konferencija, 2018 m. gruodžio 14 d.: pranešimų santraukos. Vilnius : Lietuvos mokslų akademijos leidykla. 2018, p. 12. Prieiga per internetą: <http://www.lma.lt/uploads/2017-12-07_BIOATEITIS_pranesimu_santraukos.pdf> [žiūrėta 2019-09-25].
4 Rutkauskas, Marius; Šinkūnas, Tomas; Songailienė, Inga; Šikšnys, Virginijus; Seidel, Ralf. Investigating and Modelling the Target Recognition Dynamics of the CRISPR-Cas Surveillance Complex Cascade // Biophysical journal. Cambridge, MA : Cell Press. ISSN 0006-3495. eISSN 1542-0086. 2018, vol. 114, iss. 3, suppl. 1, art. no. 978-Plat, p. 194a. DOI: 10.1016/j.bpj.2017.11.1083. [DB: MEDLINE, Scopus, Science Citation Index Expanded (Web of Science)] [IF: 3.665; AIF: 3.561; Q2 (2018 InCities JCR SCIE)]

2017
1 Drabavičius, Gediminas; Šilanskas, Arūnas; Šinkūnas, Tomas; Gasiūnas, Giedrius. Proofreading domain facilitates spacer integration in CRISPR-Cas - an adaptive prokaryotic immunity // Open Readings 2017 : 60th International conference for students of physics and natural sciences, March 14-17, 2017, Vilnius, Lithuania : programme and abstracts. Vilnius : Vilniaus universitetas. ISSN 2029-4425. 2017, p. 338. Prieiga per internetą: <http://www.openreadings.eu/wp-content/uploads/2017/03/OR2017_abstracts_book.pdf> [žiūrėta 2017-08-31].

2016
1 Songailienė, Inga; Šinkūnas, Tomas; Rutkauskas, Marius; Seidel, Ralf; Šikšnys, Virginijus. Cascade complex reconstitution in vitro and R-loop formation by single molecule experiments // Open readings 2016 : 59th scientific conference for students of physics and natural sciences : programme and abstracts. Vilnius : Vilniaus universiteto leidykla. ISSN 2029-4425. 2016, p. 108. Prieiga per internetą: <http://www.openreadings.eu/wp-content/uploads/2016/03/OR2016_abstract_book.pdf> [žiūrėta 2016-10-12].
2 Songailienė, Inga; Šinkūnas, Tomas; Rutkauskas, M.; Seidel, R.; Šikšnys, Virginijus. Reconstitution of Cascade complex in vitro and R-loop formation // XIVth International Conference of the Lithuanian Biochemical Society : the program and abstract book. Vilnius : Lithuanian Biochemical Society. 2016, p. 17. Prieiga per internetą: <https://cloudup.com/itEl9IF2n8q> [žiūrėta 2018-03-14].

2015
1 Rutkauskas, Marius; Šinkūnas, Tomas; Songailienė, Inga; Tikhomirova, Maria S.; Šikšnys, Virginijus; Seidel, Ralf. Directional R-loop formation by the CRISPR-Cas surveillance complex cascade provides efficient off-target site rejection // Cell reports. New York : Elsevier Inc. eISSN 2211-1247. 2015, vol. 10, no. 9, p. 1534-1543. DOI: 10.1016/j.celrep.2015.01.067. [DB: Scopus, MEDLINE, Science Citation Index Expanded (Web of Science), Biological Abstracts]
2 Rutkauskas, Marius; Šinkūnas, Tomas; Tikhomirova, Maria S.; Šikšnys, Virginijus; Seidel, Ralf. Dynamic DNA target proofreading in a CRISPR-Cas system // Biophysical journal. Cambridge : Cell Press. ISSN 0006-3495. 2015, vol. 108, no. 2, suppl 1, p. 206. DOI: 10.1016/j.bpj.2014.11.1137. [DB: CAB Abstracts, MEDLINE, Scopus, Science Citation Index Expanded (Web of Science)] [IF: 3.632; AIF: 3.254; Q1 (2015 InCities JCR SCIE)]
3 Šinkūnas, Tomas; Gasiūnas, Giedrius; Šikšnys, Virginijus. Cas3 nuclease-helicase activity assays // CRISPR: Methods and Protocols / Editors: Lundgren, Magnus, Charpentier, Emmanuelle, Fineran, Peter C. New York : Springer Science+Business Media New York, 2015. ISBN 9781493926862. eISBN 9781493926879. p. 277-291. (Methods in Molecular Biology, ISSN 1064-3745 ; vol. 1311). DOI: 10.1007/978-1-4939-2687-9_18. [DB: SpringerLink]

2014
1 Szczelkun, Mark. D.; Tikhomirova, Maria S.; Šinkūnas, Tomas; Gasiūnas, Giedrius; Karvelis, Tautvydas; Pschera, Patrizia; Šikšnys, Virginijus; Seidel, Ralf. Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes // PNAS : Proceedings of the National Academy of Sciences. Washington : National Academy of Sciences. ISSN 0027-8424. 2014, vol.111, no 27, p. 9798-9803. DOI: 10.1073/pnas.1402597111. [DB: Biological Abstracts, Scopus, MEDLINE, Elsevier Biobase, Science Citation Index Expanded (Web of Science)] [IF: 9.674; AIF: 5.269; Q1 (2014 InCities JCR SCIE)]
2 Songailienė, Inga; Šinkūnas, Tomas; Šikšnys, Virginijus. Cascade complex – identifying the clue to PAM recognition // 50th anniversary of FEBS : Abstracts book of The XIIIth International Conference of Lithuanian Biochemical Society, June 18-20, 2014. Vilnius. 2014, p. 15. Prieiga per internetą: <http://www.elib.grsu.by/katalog/481236pdf.pdf?d=true> [žiūrėta 2016-05-16].
3 Gasiūnas, Giedrius; Šinkūnas, Tomas; Šikšnys, Virginijus. Molecular mechanisms of CRISPR-mediated microbial immunity // Cellular and molecular life sciences. Basel : Birkhaeuser Science. ISSN 1420-682X. 2014, vol. 71, iss. 3, p. 449-465. DOI: 10.1007/s00018-013-1438-6. [DB: MEDLINE, Scopus, Biobase, CABI Abstracts Databases, Science Citation Index Expanded (Web of Science)] [IF: 5.808; AIF: 4.964; Q1 (2014 InCities JCR SCIE)]

2013
1 Šinkūnas, Tomas; Gasiūnas, Giedrius; Waghmare, Sakharam; Barrangou, Rodolphe; Horvath, Philippe; Šikšnys, Virginijus. In vitro reconstitution of Cascade-mediated CRISPR immunity in Streptococcus thermophilus // The EMBO journal. London : Nature Publishing Group. ISSN 0261-4189. 2013, vol. 32, no. 3, p. 385-394. DOI: 10.1038/emboj.2012.352. [DB: CABI Abstracts Databases, BIOSIS Previews, Science Citation Index Expanded (Web of Science)] [IF: 10.748; AIF: 5.064; Q1 (2013 InCities JCR SCIE)]

2011
1 Šinkūnas, Tomas; Gasiūnas, Giedrius; Fremaux, Christophe; Barrangou, Rodolphe; Horvath, Philippe; Šikšnys, Virginijus. Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system // The EMBO journal. London : Nature Publishing Group. ISSN 0261-4189. 2011, vol. 30, no. 7, p. 1335-1342. DOI: 10.1038/emboj.2011.41. [DB: CABI Abstracts Databases, BIOSIS Previews, Science Citation Index Expanded (Web of Science)] [IF: 9.205; AIF: 5.017; Q1 (2011 InCities JCR SCIE)]
2 Šinkūnas, Tomas. Bakterijų imuninės sistemos CRISPR/CAS baltymas CAS3: du viename // Bioateitis: gamtos ir gyvybės mokslų perspektyvos : 2011 m. jaunųjų mokslininkų konferencijos pranešimų santraukos. Vilnius. 2011, p. 13-14.