Dr Igor Makunin
eResearch Analyst - Bioinformatics
Research Computing Centre
+61 7 334 62276
Journal Articles
Abueg, Linelle Ann L., Afgan, Enis, Allart, Olivier, Awan, Ahmed H., Bacon, Wendi A., Baker, Dannon, Bassetti, Madeline, Batut, Bérénice, Bernt, Matthias, Blankenberg, Daniel, Bombarely, Aureliano, Bretaudeau, Anthony, Bromhead, Catherine J., Burke, Melissa L., Capon, Patrick K., Čech, Martin, Chavero-Díez, María, Chilton, John M., Collins, Tyler J., Coppens, Frederik, Coraor, Nate, Cuccuru, Gianmauro, Cumbo, Fabio, Davis, John, De Geest, Paul F., de Koning, Willem, Demko, Martin, DeSanto, Assunta, Begines, José Manuel Domínguez ... Zoabi, Rand (2024). The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update. Nucleic Acids Research, 52 (W1), W83-W94. doi: 10.1093/nar/gkae410
Kolesnikova, T. D., Antonenko, O. and Makunin, I. (2019). Replication timing in Drosophila and its peculiarities in polytene chromosomes. Vavilovskii Zhurnal Genetiki I Selektsii, 23 (2), 140-147. doi: 10.18699/VJ19.473
Li, Jun, Li, Hongyan, Makunin, Igor, Thompson, Bryony A., Tao, Kayoko, Young, Erin L., Lopez, Jacqueline, Camp, Nicola J., Tavtigian, Sean V., John, Esther M., Andrulis, Irene L., Khanna, Kum Kum, Goldgar, David and Chenevix-Trench, Georgia (2017). Panel sequencing of 264 candidate susceptibility genes and segregation analysis in a cohort of non-BRCA1, non-BRCA2 breast cancer families. Breast Cancer Research and Treatment, 166 (3), 937-949. doi: 10.1007/s10549-017-4469-0
Afgan, Enis, Sloggett, Clare, Goonasekera, Nuwan, Makunin, Igor, Benson, Derek, Crowe, Mark, Gladman, Simon, Kowsar, Yousef, Pheasant, Michael, Horst, Ron and Lonie, Andrew (2015). Genomics virtual laboratory: a practical bioinformatics workbench for the cloud. PLoS One, 10 (10) e0140829, e0140829. doi: 10.1371/journal.pone.0140829
Makunin, Igor V., Kolesnikova, Tatyana D. and Andreyenkova, Natalya G. (2014). Underreplicated regions in Drosophila melanogaster are enriched with fast-evolving genes and highly conserved noncoding sequences. Genome Biology and Evolution, 6 (8), 2050-2060. doi: 10.1093/gbe/evu156
Andreyenkova, Natalya G., Kolesnikova, Tatyana D., Makunin, Igor V., Pokholkova, Galina V., Boldyreva, Lidiya V., Zykova, Tatyana Yu., Zhimulev, Igor F. and Belyaeva, Elena S. (2013). Late replication domains are evolutionary conserved in the Drosophila genome. PloS One, 8 (12) e83319, e83319. doi: 10.1371/journal.pone.0083319
Makunin, Igor V., Shloma, Viktor V., Stephen, Stuart J., Pheasant, Michael and Belyakin, Stepan N. (2013). Comparison of ultra-conserved elements in drosophilids and vertebrates. PLoS One, 8 (12) e82362, e82362.1-e82362.12. doi: 10.1371/journal.pone.0082362
Jung, Chol-Hee, Makunin, Igor V. and Mattick, John S. (2010). Identification of conserved Drosophila-specific euchromatin-restricted non-coding sequence motifs. Genomics, 96 (3), 154-166. doi: 10.1016/j.ygeno.2010.05.006
Jung, Chol-Hee, Hansen, Martin A., Makunin, Igor V., Korbie, Darren J. and Mattick, John S. (2010). Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data. BMC Genomics, 11 (1 Article # 77) 77, 1-12. doi: 10.1186/1471-2164-11-77
Solda, Guilia, Makunin, Igor V., Sezerman, Osman U., Corradin, Alberto, Corti, Giorgio and Guffanti, Alessandro (2009). An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes. Briefings in Bioinformatics, 10 (5), 475-489. doi: 10.1093/bib/bbp022
Stephen, S., Pheasant, M., Makunin, I. V. and Mattick, J. S. (2008). Large-scale appearance of ultraconserved elements in tetrapod genomes and slowdown of the molecular clock. Molecular Biology and evolution, 25 (2), 402-408. doi: 10.1093/molbev/msm268
Makunin, Igor, Pheasant, Michael, Simons, Cas and Mattick, John S. (2007). Orthologous MicroRNA genes are located in cancer-associated genomic regions in human and mouse. PLoS One, 2 (11) e1133, e1133. doi: 10.1371/journal.pone.0001133
Simons, Cas, Makunin, Igor V., Pheasant, Michael and Mattick, John S. (2007). Maintenance of transposon-free regions throughout vertebrate evolution. BMC Genomics, 8 (1) 470, 470-479. doi: 10.1186/1471-2164-8-470
Mattick, John S. and Makunin, Igor V. (2006). Non-coding RNA. Human Molecular Genetics, 15 (suppl 1), R17-R29. doi: 10.1093/hmg/ddl046
Simons, Cas, Pheasant, Michael, Makunin, Igor V. and Mattick, John S. (2006). Transposon-free regions in mammalian genomes. Genome Research, 16 (2), 164-172. doi: 10.1101/gr4624306
Kolesnikova, T. D., Andreeva, E. N., Pindyurin, A. V., Ananko, N. G., Belyakin, S. N., Shloma, V. V., Yurlova, A. A., Makunin, I. V., Pokholkova, G. V., Volkova, E. I., Zarutskaya, E. A., Kokoza, E. B., Semeshin, V. F., Belyaeva, E. S. and Zhimulev, I. F. (2006). Contribution of the SuUR gene to the organization of epigenetically repressed regions of Drosophila melanogaster chromosomes. Russian Journal of Genetics, 42 (8), 831-844. doi: 10.1134/S1022795406080011
Mattick, J. S. and Makunin, I. V. (2005). Small regulatory RNAs in mammals. Human Molecular Genetics, 14 (Sp. Iss. 1), R121-R132. doi: 10.1093/hmg/ddi101
Kolesnikova, T. D., Makunin, I. V., Volkova, E. I., Pirrotta, V., Belyaeva, E. S. and Zhimulev, I. F. (2005). Functional dissection of the Suppressor of UnderReplication protein of Drosophila melanogaster: identification of domains influencing chromosome binding and DNA replication. Genetica, 124 (2-3), 187-200. doi: 10.1007/s10709-005-1167-3
Belyakin, S. N., Christophides, G. K., Alekseyenko, A. A., Kriventseva, E. V., Belyaeva, E. S., Nanayev, R. A., Makunin, I. V., Kafatos, F. C. and Zhimulev, I. F. (2005). Genomic analysis of Drosophila chromosome underreplication reveals a link between replication control and transcriptional territories. Proceedings of The National Academy of Sciences of The United States of America, 102 (23), 8269-8274. doi: 10.1073/pnas.0502702102
Bejerano, G., Pheasant, M., Makunin, I. V., Stephen, S., Kent, W. J., Mattick, J. S. and Haussler, D. (2004). Ultraconserved elements in the human genome. Science, 304 (5675), 1321-1325. doi: 10.1126/science.1098119
Volkova, E. I., Yurlova, A. A., Kolesnikova, T. D., Makunin, I. V. and Zhimulev, I. F. (2004). Ectopic expression of the Suppressor of Underreplication gene inhibits endocycles but not the mitotic cell cycle in Drosophila melanogaster. Molecular Genetics And Genomics, 270 (5), 387-393. doi: 10.1007/s00438-003-0924-1
Zhimulev, I. F., Belyaeva, E. S., Makunin, I. V., Pirrotta, V., Semeshin, V. F., Alekseyenko, A. A., Belyakin, S. N., Volkova, E. I., Koryakov, D. E., Andreyeva, E. N., Demakova, O. V., Kotlikova, I. V., Kolesnikova, T. D., Boldyreva, L. V. and Nanayev, R. A. (2003). Intercalary heterochromatin in Drosophila melanogaster polytene chromosomes and the problem of genetic silencing. Genetica, 117 (2-3), 259-270. doi: 10.1023/A:1022912716376
Zhimulev, Igor F., Belyaeva, Elena S., Semeshin, Valerii F., Shloma, Victor V., Makunin, Igor V. and Volkova, Elena I. (2003). Overexpression of the SuUR gene induces reversible modifications at pericentric, telomeric and intercalary heterochromatin of Drosophila melanogaster polytene chromosomes. Journal of Cell Science, 116 (1), 169-176. doi: 10.1242/jcs.00196
Zhimulev, I. F., Belyaeva, E. S., Makunin, I. V., Pirrotta, V., Volkova, E. I., Alekseyenko, A. A., Andreyeva, E. N., Makarevich, G. F., Boldyreva, L. V., Nanayev, R. A. and Demakova, O. V. (2003). Influence of the SuUR gene on intercalary heterochromatin in Drosophila melanogaster polytene chromosomes. Chromosoma, 111 (6), 377-398. doi: 10.1007/s00412-002-0218-0
Moshkin, Y. M., Belyakin, S. N., Rubtsov, N. B., Kokoza, E. B., Alekseyenko, A. A., Volkova, E. I., Belyaeva, E. S., Makunin, I. V., Spierer, P. and Zhimulev, I. F. (2002). Microdissection and sequence analysis of pericentric heterochromatin from the Drosophila melanogaster mutant Suppressor of Underreplication. Chromosoma, 111 (2), 114-125. doi: 10.1007/s00412-002-0190-8
Makunin, I. V., Volkova, E. I., Belyaeva, E. S., Nabirochkina, E. N., Pirrotta, V. and Zhimulev, I. F. (2002). The drosophila suppressor of underreplication protein binds to late-replicating regions of polytene chromosomes. Genetics, 160 (3), 1023-1034.
Balasov, ML, Belyaeva, ES, Shestopal, SA, Makunin, IV and Zhimulev, IF (2000). The transposon A(R)4-24P[white, rosy] in Drosophila melanogaster is subject to position-effect variegation at a non-centromeric insertion site. Molecular and General Genetics, 264 (1-2), 105-111. doi: 10.1007/s004380000288
Zhimulev, IF, Makunin, IV, Volkova, EI, Pirrotta, V and Belyaeva, ES (2000). Effect of four doses of gene Su(UR)ES on intercalary heterochromatin in Drosophila melanogaster. Russian Journal of Genetics, 36 (8), 877-885.
Balasov, ML, Belyaeva, ES, Shestopal, SA, Makunin, IV and Zhimulev, IF (2000). Position effect variegation caused by transposition of A(R)4-24P[white, rosy] in the Drosophila melanogaster genome. Russian Journal of Genetics, 36 (6), 641-649.
Makunin, IV, Shestopal, SA, Belyaeva, ES, Ashburner, M and Zhimulev, IF (1999). Molecular and genetic map comparison of the 2B6-2B7-8 region of the Drosophila melanogaster X chromosome. Russian Journal of Genetics, 35 (8), 918-923.
Makunin, IV, Pokholkova, GV, Kholodilov, NG, Zakharkin, SO, Bonaccorsi, S, Dimitri, P and Zhimulev, IF (1999). A novel simple satellite DNA is colocalized with the Stalker retrotransposon in Drosophila melanogaster heterochromatin. Molecular and General Genetics, 261 (2), 381-387.
Rubtsov, NB, Alekseenko, AA, Belyaeva, ES, Volkova, EI, Kokoza, EB, Makunin, IV, Moshkin, YM, Shestopal, SA and Zhimulev, IF (1999). Microcloning and characterization of DNA from pericentromeric heterochromatin of Drosophila melanogaster polytene chromosomes. Russian Journal of Genetics, 35 (1), 46-51.
Shestopal, SA, Makunin, IV, Belyaeva, ES, Ashburner, M and Zhimulev, IF (1997). Molecular characterisation of the deep orange (dor) gene of Drosophila melanogaster. Molecular & General Genetics, 253 (5), 642-648.
Balasov, ML and Makunin, IV (1996). Model of continuous and discontinuous chromatin compaction, resulting from position effect variegation. Biologisches Zentralblatt, 115 (1), 16-23.
Makunin, IV and Shestopal, SA (1995). Determination of the sequence from Drosophila melanogaster cDNA clone homologous to transcript protein disulphide isomerase gene. Doklady Akademii Nauk, 345 (4), 561-563.
Makunin, IV, Pokholkova, GV, Zakharkin, SO, Kholodilov, NG and Zhimulev, IF (1995). Isolation and Characterization of the Repeated Dna-Sequences From the Centromeric Heterochromatin of the 2nd Chromosome of Drosophila-Melanogaster. Doklady Akademii Nauk, 344 (2), 266-269.
Zhimulev, IF, Belyaeva, ES, Semeshin, VF, Pokholkova, GV, Kokoza, EB, Kozlova, TY, Demakov, SA, Malceva, NI, Demakova, OV, Balasov, ML, Koryakov, DE, Makunin, IV and Belousova, NV (1995). Molecular cytogenetic organization of polytene chromosomes. Russian Chemical Bulletin, 44 (9), 1553-1570. doi: 10.1007/BF01151271
Balasov, ML and Makunin, IV (1994). Position Effect Variegation Model of Chromatin Compaction. Genetika, 30 (7), 869-873.
Pokholkova, GV, Makunin, IV, Belyaeva, ES and Zhimulev, IF (1993). Observations On the Induction of Position Effect Variegation of Euchromatic Genes in Drosophila-Melanogaster. Genetics, 134 (1), 231-242.
Pokholkova, GV, Makunin, IV, Belyaeva, ES and Zhimulev, IF (1993). Molecular and Cytogenetic Analysis of Heterochromatic Fragments, Inducing Position Effect Variation in Drosophila-Melanogaster. Doklady Akademii Nauk, 329 (3), 369-371.
Conference Paper
Mattick, JS, Croft, LJ, Dinger, ME, Pheasant, M, Makunin, IV, Amiri, MA, Mercer, TR, Pang, KC, Simons, C and Taft, RJ (2007). The human genome as an RNA machine. 32nd Congress of the Federation-of-European-Biochemical-Societies (FEBS), Vienna AUSTRIA, JUL 07-12, 2007. OXFORD: BLACKWELL PUBLISHING.