Home »

Денис Ларкин

After graduating from the Novosibirsk State University, Dr. Larkin obtained Ph.D. degree in Genetics from the Institute of Cytology and Genetics, Novosibirsk. Then he spent nine years at the University of Illinois at Urbana-Champaign where his research was focused on studying chromosomal evolution and selection in mammals and other species using state-of-the-art methods of molecular genomics and bioinformatics. Earlier in his career he constructed high-resolution cattle radiation hybrid and physical maps which were used as backbones for the assembly of the cattle and pig genome sequences.

Dr. Larkin developed Evolution Highway an interactive tool to visualise comparative chromosome maps as well as SyntenyTracker, an algorithm to build homologous synteny blocks from the whole-genome maps or sequence alignments. He performed the analysis of milk production traits in the North American Holstein-Friesian population, and the genetic structure of Welsh sheep breeds.

After his move to the UK in 2010 Dr. Larkin spent three years as a lecturer in animal genetics at Aberystwyth University. Dr. Larkin joined the Royal Veterinary College in 2013. In 2012 Denis Larkin was awarded a BBSRC New Investigator award to support his research on comparative assembly of vertebrate genomes and later he received a BBSRC responsive mode grant to improve genome assemblies and study chromosome evolution in birds.

Тарас Олексик

Taras K Oleksyk holds PhD from the University of Georgia (Athens, GA, USA) and M.S. from Bowling Green State University (Bowling Green, OH, USA) His main scientific interests are in the genetic epidemiology, evolutionary genetics and comparative genomics: genome evolution and its implication to the adaptation and human disease. He is involved in several studies focusing on admixture populations, and participated in the analysis of the data that successfully identified candidate disease genes from admixture scans, while his comparative genomic efforts today are directed towards sequencing and assembling genomes of Caribbean parrots, specifically the Puerto Rican parrot (Amazona vittata). The genome alignments of the Amazona parrots are further interrogated for similarities and differences in the evolutionary context examining past migration, colonization and adaptation events, and stepwise migrations from island to island.

Ал-др Графодатский

Institute of molecular and cellular biology of SВ. RAS, Novosibirsk, Russia.
Senior Fellow
Homepage:

https://mcb.nsc.ru/mcb/directorate/science_vice

Агостиньо Антунес

Curriculum vitae (December 2014)

1. Biography
Name: Agostinho Antunes
Local and Place of Birth: Porto, 16 November 1972
Citizenship: Portuguese
Civil Status: Married (3 daughters)

2. Education and Academic Degrees

  • • 1997-2002. Ph.D. in Biology (Population Genetics and Molecular Evolution), University of Porto, Porto, Portugal, INRA, Paris, France, and Washington University, St. Louis, United States of America. Approved by unanimity with distinction.
  • • M.Sc. in Applied Ecology (Population Genetics), University of Porto, Porto, Portugal.
  • • 1990-1994. Graduation in Biology, University of Porto, Porto, Portugal.

3. Brief Chronology of Employment

  • • 2013-presente. Group leader (Evolutionary Genomics and Bioinformatics Group), CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Portugal.
  • • 2011 – present. Adjunct Professor, Faculty of Science, University of Porto, Portugal.
  • • 2007-present. Researcher (Genomics, Evolution and Bioinformatics), CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, Laboratory of Ecotoxicology, Genomics and Evolution, University of Porto, Portugal.
  • • 2004-2011. Affiliated as Researcher of the Laboratory of Genomic Diversity (LGD), National Cancer Institute (NCI) – National Institute of Health (NIH), Maryland, United States of America.
  • • 2004-2007. Researcher (Bioinformatics and Computational Genomics), REQUIMTE, Chemistry Department, FCUP, Portugal.
  • • 2002-2003. Post-doctoral fellow, Laboratory of Genomic Diversity, NCI-NIH, Maryland, USA.
  • • February-June 1994. Teaching Monitor in Zoology-Anthropology Department, FCUP.

4. Principal Investigator in Scientific Research Projects

  • • Proj. POCTI/BSE/47559/2002, “A global study of the molecular genetics of pangolins, the scaly anteaters.” (2003-2007; 84,300 euros).
  • • National Geographic Society Grant 7483-03, “A global study of the molecular genetics of pangolins, the scaly anteaters.” (2003-2007; 17,500 dólares).
  • • Proj. PTDC/BIA-BDE/70982/2006, “Phenogenetic drift in evolution: insights into the genetic basis of vertebrate developmental genes.” (2008-2010; 148,000 euros).
  • • PTDC/AAC-AMB/104983/2008 “Evolutionary genomic analyses of toxic cyanobacteria and study of the molecular mechanisms for detoxification of cyanotoxins across metazoan species.” (2010-2013; 199,997 euros).
  • • PTDC/AAC-CLI/116122/2009 “CyanoPrimer — Developing new tools for the early warning of cyanobacteria and cyanotoxins.” (2011-2014; 180,000 euros).
  • • PTDC/AAC-AMB/121301/2010 “Biological warfare: unraveling the genomics of natural venoms and the mechanisms of natural venom-resistance.” (2012-2015; 170,000 euros).
  • • PP-IJUP2011-315 IJUP Projectos 2013-2014 “Simulation laboratory of gene/protein evolution.” (2013-2014; 3,500 euros).
  • 4.1. Participation in Scientific Research Projects with dedicated funding
    • INTERREG IV B Atlantic Area. “ShareBiotech — Sharing life science infrastructures and skills to benefit the Atlantic area biotechnology sector.” (2010-2014; 2,600,000 euros) Coordinated by Celine Queron (Biogenouest, Rennes, França) and Claire Bontemps (Bretagne innovation, França) (Partners: France, Irlend, Spain and Portugal). Agostinho Antunes (dedicated budget: 209,969 euros).
    • Research grant from Iceland, Liechtenstein and Norway through the EEA Financial Mechanism and the Norwegian Financial Mechanism. “Managing effects of global climate on estuarine biodiversidty and productivity” (PT0010). (2009-2011; 809,390 euros) (Partners: Portugal, Holland and Norway). Agostinho Antunes (dedicated budget: 20,000 euros).
    •PTDC/MAR/115199/2009 “The modulation of retinoid and thyroid signalling pathways by endocrine disrupting chemicals: invertebrate insights” (2011-2014; 173,116 euros). Coordinated by Miguel Santos (CIIMAR, UP); Agostinho Antunes (dedicated budget: 43,000 euros).
    • PTDC/AAC-CLI/112936/2009 “Sex at the edge: How temperature influences sexual selection” (2011-2014; 175.800,00 euros). Coordinated by Nuno Monteiro (CIBIO, UP); Agostinho Antunes (dedicated budget: 53,652 euros).
    • PTDC/AAC-AMB/102121/2008 “NISTRACKS – Processes influencing the invasive behaviour of the non indigenous species Corbicula fluminea (Mollusca: Bivalvia) in estuaries – identification of genetic and environmental key factors”. (2010-2013; 198,767 euros). Coordinated by Lúcia Guilhermino (CIIMAR, UP); Agostinho Antunes (dedicated budget: 30,000 euros).
    • PTDC/MAR/68106/2006 “The modulation of retinoic acid signalling pathways by environmental pollutants in teleosts” (2008-2011; 188.980,00 euros). Coordinated by Miguel Santos (CIIMAR, UP); Agostinho Antunes (dedicated budget: 46.651,00 euros).

    5. Supervision of students

    • • Supervision of 4 postdocs.
    • • Supervision of 7 PhD students completed.
    • • Supervision of 10 Master students completed.
    • • Supervision of 21 undergraduated students completed.

    6. Selected Peer Review Publications (from a total of 84 ISI publications)

      ANTUNES A, TEMPLETON AR, GUYOMARD R, ALEXANDRINO P. (2002) The role of nuclear genes in intraspecific evolutionary inference: genealogy of the transferrin gene in the brown trout. Molecular Biology and Evolution 19:1272-1287. (Impact factor: 6.233).

      ANTUNES A, FARIA R, JOHNSON WE, GUYOMARD R, ALEXANDRINO P. 2006. Life on the edge: the long-term persistence and contrasting spatial genetic structure of distinct brown trout life histories at their ecological limits. Journal of Heredity 97(3):193-205. (Impact factor: 2.110).

      JOHNSON WE, EIZIRK E, MURPHY, WJ, PECON-SLATERRY J, ANTUNES A, TEELING E, AND O’BRIEN SJ. 2006. The late Miocene radiation of the Felidae: a genetic assessment. Science 311:73-77. (Impact factor: 30.927).

      PONTIUS JU, MULLIKIN JC, SMITH D, AGENCOURT SEQUENCING TEAM, LINDBLAD-TOH K, GNERRE S, CLAMP M, CHANG J, STEPHENS R, NEELAM B, VOLFOVSKY N, SCHÄFFER AA, AGARWALA R, NARFSTRÖM K, MURPHY WJ, GIGER U, ROCA AL, ANTUNES A, MENOTTI-RAYMOND M, YUHKI N, PECON-SLATTERY J, JOHNSON WE, BOURQUE G, TESLER G, NISC SEQUENCING PROGRAM, O’BRIEN SJ. 2007. Initial sequence and comparative analysis of the cat genome. Genome Research 17:1675–1689. (Impact factor: 10.139).

      DA FONSECA R, JOHNSON WE, O’BRIEN SJ, RAMOS MJ, ANTUNES A (2008). The adaptive evolution of the mammalian mitochondrial genome. BMC Genomics 9:119. (Impact factor: 4.092).

      LUO SJ, JOHNSON WE, MARTENSON J, ANTUNES A, MARTELLI P, UPHYRKINA O, TRAYLOR-HOLZER K, SMITH JLD, O’BRIEN SJ. 2008. Subspecies genetic assignments of worldwide captive tigers increase conservation value of captive populations. Current Biology 18: 592–596. (Impact factor: 10.988).

      ANTUNES A, TROYER JL, ROELKE ME, PECON-SLATERRY J, PACKER C, WINTERBACH C, WINTERBACH H, HEMSON G, FRANK L, STANDER P, SIEFERT L, DRICIRU M, FUNSTON PJ, ALEXANDER K, PRAGER KC, MILLS G, WILDT D, BUSH M, O’BRIEN SJ, JOHNSON WE. 2008. The Evolutionary Dynamics of Lion Panthera leo Revealed by Host and Viral Population Genomics. PLoS Genetics 4(11): e1000251. (Impact factor: 8.721).

      AGÜERO-CHAPÍN G, PÉREZ-MACHADO G, MOLINA-RUIZ R, PÉREZ-CASTILLO Y, MORALES- HELGUERA A, VASCONCELOS V, ANTUNES A (2011) TI2BioP: A free-alignment tool to identify proteinaceous Bacteriocins. Its practical application to the discovery of new Bacteriocin-like domains. Amino Acids 40(2):431-442, DOI: 10.1007/s00726-010-0653-9 (Impact factor: 4.132).

      PEREIRA S, VASCONCELOS V, ANTUNES A. (2011) Inhibition of Serine/Threonine Protein Phosphatases by Naturally-Occurring Toxins. Critical Reviews in Toxicology. 41(2):83-110 (Impact factor: 7.204).

      LEÃO PN, ENGENE N, ANTUNES A, GERWICK HW, VASCONCELOS V (2012) The chemical ecology of cyanobacteria. Natural Product Reports 29, 372–391. (Impact factor: 10.178).

      SUNAGAR K, JOHNSON WE, O’BRIEN SJ, VASCONCELOS V, ANTUNES A. 2012. Evolution of CRISPs associated with toxicoferan-reptilian venom and mammalian reproduction. Molecular Biology and Evolution 29(7): 1807-1822. (Impact factor: 14.353).

      PHILIP S, MACHADO JP, MALDONADO E, VASCONCELOS V, O’BRIEN SJ, JOHNSON WE, ANTUNES A. 2012. Fish lateral line innovation: insights into the evolutionary genomic dynamics of a unique mechanosensory organ. Molecular Biology and Evolution 29(12):3887-3898. (Impact factor: 14.353).

      ALEX, A., VASCONCELOS, V., TAMAGNINI, P., SANTOS, A., ANTUNES, A., 2012. Unusual symbiotic cyanobacteria association in the genetically diverse intertidal marine sponge Hymeniacidon perlevis (Demospongiae, Halichondrida). PLoS One 7(12): e51834. (Impact factor: 4.092).

      BORGES R, JOHNSON WE, O’BRIEN SJ, VASCONCELOS V, ANTUNES A. 2012. The emergence and the duplication events in the melanopsin gene family (OPN4m and OPN4x) during vertebrate evolution. PLoS One 7(12): e52413. (Impact factor: 4.092).

      BRUST A, SUNAGAR K, UNDHEIM EA, VETTER I, YANG D, CASEWELL NR, RUDER T, JACKSON TN, KOLUDAROV I, ALEWOOD PF, HODGSON WC, LEWIS RJ, KING GF, ANTUNES A, HENDRIKX I, FRY BG (2013) Differential Evolution and Neofunctionalization of Snake Venom Metalloprotease Domains. Molecular & Cellular Proteomics 12(3):651-663. (Impact factor: 7.398).

      FRY BG, UNDHEIM EAB, ALI SA, DEBONO J, SCHEIB H, RUDER T, JACKSON TNW, MORGENSTERN D, CADWALLADER L, WHITEHEAD D, NABUURS R, VAN DER WEERD L, VIDAL N, ROELANTS K, HENDRIKX I, GONZALEZ SP, JONES A, KING GF, ANTUNES A, SUNAGAR K (2013) Squeezers and leaf-cutters: differential diversification and degeneration of the venom system in toxicoferan reptiles. Molecular & Cellular Proteomics 12(7):1881-1899. (Impact factor: 7.398).

      AGÜERO-CHAPIN G, MOLINA-RUIZ R, MALDONADO E, DE LA RIVA G, SÁNCHEZ-RODRÍGUEZ A, VASCONCELOS V, ANTUNES A (2013) Exploring the Adenylation Domain Repertoire of Nonribosomal Peptide Synthetases Using an Ensemble of Sequence-Search Methods. PLoS One 8(7): e65926. (Impact factor: 4.092).

      NEVES J, CAMPOS A, OSÓRIO H, ANTUNES A, VASCONCELOS V. (2013) Conopeptides from Cape Verde Conus crotchii. Marine Drugs 11(6):2203-2215. (Impact factor: 3.978).

      LOW DHW, SUNAGAR K, UNDHEIM EAB, ALI SA, ALAGON AC, RUDER T, JACKSON TNW, KURNIAWAN N, GONZALEZ SP, KING GF, JONES A, ANTUNES A, FRY BG (2013) Dracula’s children: Molecular evolution of vampire bat venom. Journal of Proteomics 89: 95–111. (Impact factor: 4.878).

      ALEX, A., SILVA V, VASCONCELOS, V., ANTUNES, A. (2013). Evidence of unique and generalist microbes in distantly related sympatric intertidal marine sponges (Porifera: Demospongiae). PLoS One 8(11):e80653. (Impact factor: 4.092).

      SUNAGAR K, FRY B, JACKSON TNW, CASEWELL NR, UNDHEIM EAB, VIDAL N, ALI SA, KING GF, VASUDEVAN K, VASCONCELOS V, ANTUNES A. 2013. Molecular evolution of vertebrate neurotrophins: Co-option of the highly conserved nerve growth factor gene into the advanced snake venom arsenal. PLoS One 8(11):e81827. (Impact factor: 4.092).

      LUO SJ, ZHANG Y, JOHNSON WE, MIAO L, MARTELLI P, ANTUNES A, SMITH JLD, O’BRIEN SJ (2014) Sympatric Asian Felid Phylogeography Reveals a Major Indochinese-Sundaic Divergence. Molecular Ecology 23(8):2072-92. (Impact factor: 6.275).

      DUTERTRE S, JIN A, VETTER I, HAMILTON B, SUNAGAR K, LAVERGNE V, DUTERTRE V, FRY BG, ANTUNES A, VENTER D, ALEWOOD P, LEWIS R. 2014. Evolution of separate predation- and defence-evoked venoms in carnivorous snails. Nature communications 5:3521. (Impact factor: 10.015).

      MALDONADO E, SUNAGAR K, ALMEIDA D, VASCONCELOS V, ANTUNES A. 2014. IMPACT_S: Integrated Multiprogram Platform to Analyze and Combine Tests of Selection. PLoS One 9(10): e96243. doi:10.1371/journal.pone.0096243. (Impact factor: 3.790)
      80) KHAN I, MALDONADO E, VASCONCELOS V, O’BRIEN SJ, JOHNSON WE, ANTUNES A. 2014. Mammalian keratin associated proteins (KRTAPs) subgenomes: disentangling hair diversity and adaptation to terrestrial and aquatic environments. BMC Genomics BMC Genomics 15:779 (doi:10.1186/1471-2164-15-779). (Impact factor: 4.04).

      TAMAZIAN G, SIMONOV S, DOBRYNIN P, MAKUNIN A, LOGACHEV A, KOMISSAROV A, SHEVCHENKO A, BRUKHIN V, CHERKASOV N, SVITIN A, KOEPFLI KP, PONTIUS J, DRISCOLL CA, BLACKISTONE K, BARR C, GOLDMAN D, ANTUNES A, QUILEZ J, LORENTE-GALDOS B, ALKAN C, MARQUES-BONET T, MENOTTI-RAYMOND M, DAVID VA, NARFSTRÖM K, O’BRIEN SJ. (2014) Gigascience.

      ZHANG G, CAI LI, QIYE LI, BO LI, DENIS M. LARKIN, CHUL LEE, JAY F. STORZ, AGOSTINHO ANTUNES, MATTHEW J. GREENWOLD, ROBERT W. MEREDITH, ANDERS ÖDEEN, JIE CUI, QI ZHOU, LUOHAO XU, HAILIN PAN, ZONGJI WANG, LIJUN JIN, PEI ZHANG, HAOFU HU, WEI YANG, JIANG HU, JIN XIAO, ZHIKAI YANG, YANG LIU, QIAOLIN XIE, HAO YU, JINMIN LIAN, PING WEN, FANG ZHANG, HUI LI, YONGLI ZENG, ZIJUN XIONG, SHIPING LIU, LONG ZHOU, ZHIYONG HUANG, NA AN, JIE WANG, QIUMEI ZHENG, YINGQI XIONG, GUANGBIAO WANG, BO WANG, JINGJING WANG, YU FAN, RUTE R. DA FONSECA, ALONZO ALFARO-NÚÑEZ, MIKKEL SCHUBERT, LUDOVIC ORLANDO, TOBIAS MOURIER, JASON HOWARD, GANESHKUMAR GANAPATHY, ANDREAS PFENNING, OSCEOLA WHITNEY, MIRIAM V. RIVAS, ERINA HARA, JULIA SMITH, MARTA FARRÉ, JITENDRA NARAYAN, GANCHO SLAVOV, MICHAEL N ROMANOV, RUI BORGES, JOÃO PAULO MACHADO, IMRAN KHAN, MARK S. SPRINGER, JOHN GATESY, FEDERICO G. HOFFMANN, JUAN C. OPAZO, OLLE HÅSTAD, ROGER H. SAWYER, HEEBAL KIM, KYU-WON KIM, HYEON JEONG KIM, SEOAE CHO, NING LI, YINHUA HUANG, MICHAEL W. BRUFORD, XIANGJIANG ZHAN, ANDREW DIXON, MADS F. BERTELSEN, ELIZABETH DERRYBERRY, WESLEY WARREN , RICHARD K WILSON, SHENGBIN LI, DAVID A. RAY, RICHARD E. GREEN, STEPHEN J. O‘BRIEN , DARREN GRIFFIN, WARREN E. JOHNSON, DAVID HAUSSLER, OLIVER A. RYDER, ESKE WILLERSLEV, GARY R. GRAVES, PER ALSTRÖM, JON FJELDSÅ, DAVID P. MINDELL, SCOTT V. EDWARDS, EDWARD L. BRAUN, CARSTEN RAHBEK, DAVID W. BURT, PETER HOUDE, YONG ZHANG, HUANMING YANG, JIAN WANG, ERICH D. JARVIS, M THOMAS P GILBERT, JUN WANG & AVIAN GENOME CONSORTIUM. 2014. Comparative Genomics Reveals Insights into Avian Genome Evolution and Adaptation. Science (in press – 12th December 2014). DOI:10.1126/science. 1251385. (Impact factor: 31.480).

      PEREIRA J, JOHNSON WE, O’BRIEN SJ, JARVIS ED, ZHANG G, GILBERT MTP, VASCONCELOS V, ANTUNES A. (2014) Evolutionary Genomics and Adaptive Evolution of the Hedgehog Gene Family (Shh, Ihh and Dhh) in Vertebrates. PLoS One (DOI: 10.1371/journal.pone.0074132) (In press). (Impact factor: 3.730).

      Марк Диканс

      UCSC software genius

      Павел Певзнер

      University of California, San Diego Academic University, St. Petersburg
      Senior Fellow
      Homepage: http://cseweb.ucsd.edu/~ppevzner/
      See also
      http://bioinf.spbau.ru/en/

      Джоан Понтиус

      Joan Pontius is a bioinformatics expert with an emphasis in comparative genomics and gene expression in vertebrates. She has worked in the United States at the National Center for Bioinformatics (NCBI) on the UniGene project, has played a lead role in the annotation of the cat genome assembly at the Laboratory of Genomic Diversity (LGD), and is currently working for SRA International as a scientist for the project of The Cancer Genome Atlas (TCGA).

      Николай Вяххи

       

      Саймон Истель

      Пр. Саймон Истель