PUB - Publikationen an der Universität Bielefeld

Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712

FastML: a web server for probabilistic reconstruction of ancestral sequences
Ashkenazy H., 2012

Controlling the false discovery rate: a practical and powerful approach to multiple testing
Benjamini Y, Hochberg Y.., 1995

Comparative studies of high performance swimming in sharks II. Metabolic biochemistry of locomotor and myocardial muscle in endothermic and ectothermic sharks.
Bernal D, Smith D, Lopez G, Weitz D, Grimminger T, Dickson K, Graham JB., J. Exp. Biol. 206(Pt 16), 2003
PMID: 12847128

AUTHOR UNKNOWN, 2012

Analysis of the evolutionary convergence for high performance swimming in lamnid sharks and tunas [Review]
Bernal D, Dickson KA, Shadwick RE, Graham JB.., 2001

Comparative studies of high performance swimming in sharks I. Red muscle morphometrics, vascularization and ultrastructure.
Bernal D, Sepulveda C, Mathieu-Costello O, Graham JB., J. Exp. Biol. 206(Pt 16), 2003
PMID: 12847127

Evidence for temperature elevation in the aerobic swimming musculature of the common thresher shark
Bernal D, Sepulveda CA.., 2005

Influence of swimming speed on metabolic rates of juvenile pacific bluefin tuna and yellowfin tuna.
Blank JM, Farwell CJ, Morrissette JM, Schallert RJ, Block BA., Physiol. Biochem. Zool. 80(2), 2007
PMID: 17252513

Endothermy in fishes: a phylogenetic analysis of constraints, predispositions, and selection pressures
Block BA, Finnerty JR.., 1994

Functional genomics tool: gene silencing in Ixodes scapularis eggs and nymphs by electroporated dsRNA.
Karim S, Troiano E, Mather TN., BMC Biotechnol. 10(), 2010
PMID: 20074328

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.
Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, Ravi V, Lee AP, Nakamura T, Chalopin D, Fan S, Wcisel D, Canestro C, Sydes J, Beaudry FE, Sun Y, Hertel J, Beam MJ, Fasold M, Ishiyama M, Johnson J, Kehr S, Lara M, Letaw JH, Litman GW, Litman RT, Mikami M, Ota T, Saha NR, Williams L, Stadler PF, Wang H, Taylor JS, Fontenot Q, Ferrara A, Searle SM, Aken B, Yandell M, Schneider I, Yoder JA, Volff JN, Meyer A, Amemiya CT, Venkatesh B, Holland PW, Guiguen Y, Bobe J, Shubin NH, Di Palma F, Alfoldi J, Lindblad-Toh K, Postlethwait JH., Nat. Genet. 48(4), 2016
PMID: 26950095

Competition of electrons to enter the respiratory chain: a new regulatory mechanism of oxidative metabolism in Saccharomyces cerevisiae.
Bunoust O, Devin A, Averet N, Camougrand N, Rigoulet M., J. Biol. Chem. 280(5), 2004
PMID: 15557339

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T., Bioinformatics 25(15), 2009
PMID: 19505945

Warm-bodied Fish
Carey FG, Teal JM, Kanwish JW, Lawson KD, Beckett JS.., 1971

Adaptive evolution and functional redesign of core metabolic proteins in snakes.
Castoe TA, Jiang ZJ, Gu W, Wang ZO, Pollock DD., PLoS ONE 3(5), 2008
PMID: 18493604

Conformational plasticity of glycogenin and its maltosaccharide substrate during glycogen biogenesis.
Chaikuad A, Froese DS, Berridge G, von Delft F, Oppermann U, Yue WW., Proc. Natl. Acad. Sci. U.S.A. 108(52), 2011
PMID: 22160680

TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction.
Chang JM, Di Tommaso P, Notredame C., Mol. Biol. Evol. 31(6), 2014
PMID: 24694831

Isolation, nucleotide sequence, and physiological relevance of the gene encoding triose phosphate isomerase from Kluyveromyces lactis.
Compagno C, Boschi F, Daleffe A, Porro D, Ranzi BM., Appl. Environ. Microbiol. 65(9), 1999
PMID: 10473437

Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research.
Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M., Bioinformatics 21(18), 2005
PMID: 16081474

Differences between glycogen biogenesis in fast- and slow-twitch rabbit muscle.
Cusso R, Lerner LR, Cadefau J, Gil M, Prats C, Gasparotto M, Krisman CR., Biochim. Biophys. Acta 1620(1-3), 2003
PMID: 12595075

RAD-seq derived genome-wide nuclear markers resolve the phylogeny of tunas.
Diaz-Arce N, Arrizabalaga H, Murua H, Irigoien X, Rodriguez-Ezpeleta N., Mol. Phylogenet. Evol. 102(), 2016
PMID: 27286653

Locomotor muscle of high performance fishes: What do comparisons of tunas with ectothermic sister taxa reveal?
Dickson KA.., 1996

Evolution and consequences of endothermy in fishes.
Dickson KA, Graham JB., Physiol. Biochem. Zool. 77(6), 2004
PMID: 15674772

Convergent evolution in mechanical design of lamnid sharks and tunas
Donley JM, Supelveda CA, Konstanidis P, Gemballa S, Shadwick RE.., 2004

Positive selection in glycolysis among Australasian stick insects.
Dunning LT, Dennis AB, Thomson G, Sinclair BJ, Newcomb RD, Buckley TR., BMC Evol. Biol. 13(), 2013
PMID: 24079656

Molecular population genetics and selection in the glycolytic pathway.
Eanes WF., J. Exp. Biol. 214(Pt 2), 2011
PMID: 21177937

OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy.
Emms DM, Kelly S., Genome Biol. 16(), 2015
PMID: 26243257

Respiratory metabolism: glycolysis, the TCA cycle and mitochondrial electron transport.
Fernie AR, Carrari F, Sweetlove LJ., Curr. Opin. Plant Biol. 7(3), 2004
PMID: 15134745

Protein function at thermal extremes: balancing stability and flexibility [Review]
Fields PA.., 2001

Hot spots in cold adaptation: localized increases in conformational flexibility in lactate dehydrogenase A4 orthologs of Antarctic notothenioid fishes.
Fields PA, Somero GN., Proc. Natl. Acad. Sci. U.S.A. 95(19), 1998
PMID: 9736762

Pfam: the protein families database.
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M., Nucleic Acids Res. 42(Database issue), 2013
PMID: 24288371

The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection.
Fletcher W, Yang Z., Mol. Biol. Evol. 27(10), 2010
PMID: 20447933

The sarcoplasmic reticulum and the control of muscle contraction.
Franzini-Armstrong C., FASEB J. 13 Suppl 2(), 1999
PMID: 10619141

CD-HIT: accelerated for clustering the next-generation sequencing data.
Fu L, Niu B, Zhu Z, Wu S, Li W., Bioinformatics 28(23), 2012
PMID: 23060610

Evolution of high-performance swimming in sharks: transformations of the musculotendinous system from subcarangiform to thunniform swimmers.
Gemballa S, Konstantinidis P, Donley JM, Sepulveda C, Shadwick RE., J. Morphol. 267(4), 2006
PMID: 16429422

The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC.
Gharib WH, Robinson-Rechavi M., Mol. Biol. Evol. 30(7), 2013
PMID: 23558341

MaxAlign: maximizing usable data in an alignment.
Gouveia-Oliveira R, Sackett PW, Pedersen AG., BMC Bioinformatics 8(), 2007
PMID: 17725821

Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A., Nat. Biotechnol. 29(7), 2011
PMID: 21572440

Role of glycerol 3-phosphate dehydrogenase in glyceride metabolism. Effect of diet on enzyme activities in chicken liver.
Harding JW Jr, Pyeritz EA, Copeland ES, White HB 3rd., Biochem. J. 146(1), 1975
PMID: 167714

Role of fructose 2,6-bisphosphate in the control of glycolysis in mammalian tissues.
Hue L, Rider MH., Biochem. J. 245(2), 1987
PMID: 2822019

Peroxisome proliferator-induced long chain acyl-CoA thioesterases comprise a highly conserved novel multi-gene family involved in lipid metabolism.
Hunt MC, Nousiainen SE, Huttunen MK, Orii KE, Svensson LT, Alexson SE., J. Biol. Chem. 274(48), 1999
PMID: 10567408

The mitochondrial carnitine/acylcarnitine carrier: function, structure and physiopathology.
Indiveri C, Iacobazzi V, Tonazzi A, Giangregorio N, Infantino V, Convertini P, Console L, Palmieri F., Mol. Aspects Med. 32(4-6), 2011
PMID: 22020112

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell.
Junier T, Zdobnov EM., Bioinformatics 26(13), 2010
PMID: 20472542

MAFFT multiple sequence alignment software version 7: improvements in performance and usability.
Katoh K, Standley DM., Mol. Biol. Evol. 30(4), 2013
PMID: 23329690

Korsmeyer KE, Dewar H.., 2001

The aerobic capacity of tunas: adaptation for multiple metabolic demands
Korsmeyer KE, Dewar H, Lai NC, Graham JB.., 1996

Effects of exercise on GLUT-4 and glycogenin gene expression in human skeletal muscle.
Kraniou Y, Cameron-Smith D, Misso M, Collier G, Hargreaves M., J. Appl. Physiol. 88(2), 2000
PMID: 10658052

An algorithm for progressive multiple alignment of sequences with insertions.
Loytynoja A, Goldman N., Proc. Natl. Acad. Sci. U.S.A. 102(30), 2005
PMID: 16000407

Assessing niche width of endothermic fish from genes to ecosystem.
Madigan DJ, Carlisle AB, Gardner LD, Jayasundara N, Micheli F, Schaefer KM, Fuller DW, Block BA., Proc. Natl. Acad. Sci. U.S.A. 112(27), 2015
PMID: 26100889

High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes.
Markova-Raina P, Petrov D., Genome Res. 21(6), 2011
PMID: 21393387

Evolutionary origin of the Scombridae (tunas and mackerels): members of a paleogene adaptive radiation with 14 other pelagic fish families
Miya M., 2013

Patterns of positive selection and neutral evolution in the protein-coding genes of Tetraodon and Takifugu.
Montoya-Burgos JI., PLoS ONE 6(9), 2011
PMID: 21935469

Using new tools to solve an old problem: the evolution of endothermy in vertebrates.
Nespolo RF, Bacigalupe LD, Figueroa CC, Koteja P, Opazo JC., Trends Ecol. Evol. (Amst.) 26(8), 2011
PMID: 21571391

Molecular pathogenesis of a new glycogenosis caused by a glycogenin-1 mutation.
Nilsson J, Halim A, Moslemi AR, Pedersen A, Nilsson J, Larson G, Oldfors A., Biochim. Biophys. Acta 1822(4), 2011
PMID: 22198226

T-Coffee: A novel method for fast and accurate multiple sequence alignment.
Notredame C, Higgins DG, Heringa J., J. Mol. Biol. 302(1), 2000
PMID: 10964570

Genome-wide signatures of convergent evolution in echolocating mammals.
Parker J, Tsagkogeorga G, Cotton JA, Liu Y, Provero P, Stupka E, Rossiter SJ., Nature 502(7470), 2013
PMID: 24005325

GUIDANCE: a web server for assessing alignment confidence scores.
Penn O, Privman E, Ashkenazy H, Landan G, Graur D, Pupko T., Nucleic Acids Res. 38(Web Server issue), 2010
PMID: 20497997

jModelTest: phylogenetic model averaging.
Posada D., Mol. Biol. Evol. 25(7), 2008
PMID: 18397919

Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests.
Posada D, Buckley TR., Syst. Biol. 53(5), 2004
PMID: 15545256

Scombroid fishes provide novel insights into the trait/rate associations of molecular evolution.
Qiu F, Kitchen A, Burleigh JG, Miyamoto MM., J. Mol. Evol. 78(6), 2014
PMID: 24810994

Rambaut A, Suchard M, Drummond AJ.., 2013

Erasing errors due to alignment ambiguity when estimating positive selection.
Redelings B., Mol. Biol. Evol. 31(8), 2014
PMID: 24866534

Characterization of the heart transcriptome of the white shark (Carcharodon carcharias).
Richards VP, Suzuki H, Stanhope MJ, Shivji MS., BMC Genomics 14(), 2013
PMID: 24112713

Patterns of positive selection in seven ant genomes.
Roux J, Privman E, Moretti S, Daub JT, Robinson-Rechavi M, Keller L., Mol. Biol. Evol. 31(7), 2014
PMID: 24782441

First molecular scombrid timetree (Percomorpha: Scombridae) shows recent radiation of tunas following invasion of pelagic habitat
Santini FG, Carnevale G, Sorenson L.., 2013

The Atlantic Bonito (Sarda sarda, Bloch 1793) transcriptome and detection of differential expression during larvae development.
Sarropoulou E, Moghadam HK, Papandroulakis N, De la Gandara F, Ortega Garcia A, Makridis P., PLoS ONE 9(2), 2014
PMID: 24503907

Elevated red myotomal muscle temperatures in the most basal tuna species, Allothunnus fallai
Sepulveda CA, Dickson KA, Bernal D, Graham JB.., 2008

The effect of habitat on modern shark diversification.
Sorenson L, Santini F, Alfaro ME., J. Evol. Biol. 27(8), 2014
PMID: 24890604

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.
Stamatakis A., Bioinformatics 22(21), 2006
PMID: 16928733

A rapid bootstrap algorithm for the RAxML Web servers.
Stamatakis A, Hoover P, Rougemont J., Syst. Biol. 57(5), 2008
PMID: 18853362

Transcriptome of the Deep-Sea Black Scabbardfish, Aphanopus carbo (Perciformes: Trachiuridae): Tissue-Specific Expression Patterns and characterization of depth-related functional genes
Stefanni S., 2014

The genetic causes of convergent evolution.
Stern DL., Nat. Rev. Genet. 14(11), 2013
PMID: 24105273

Causes of molecular convergence and parallelism in protein evolution.
Storz JF., Nat. Rev. Genet. 17(4), 2016
PMID: 26972590

Red muscle function in stiff-bodied swimmers: there and almost back again.
Syme DA, Shadwick RE., Philos. Trans. R. Soc. Lond., B, Biol. Sci. 366(1570), 2011
PMID: 21502122

UniProt: a hub for protein information.
UniProt Consortium, Bateman A, Martin MJ, O'Donovan C, Magrane M, Apweiler R, Alpi E, Antunes R, Arganiska J, Bely B, Bingley M, Bonilla C, Britto R, Bursteinas B, Chavali G, Cibrian-Uhalte E, Silva AD, De Giorgi M, Dogan T, Fazzini F, Gane P, Castro LG, Garmiri P, Hatton-Ellis E, Hieta R, Huntley R, Legge D, Liu W, Luo J, MacDougall A, Mutowo P, Nightingale A, Orchard S, Pichler K, Poggioli D, Pundir S, Pureza L, Qi G, Rosanoff S, Saidi R, Sawford T, Shypitsyna A, Turner E, Volynkin V, Wardell T, Watkins X, Zellner H, Cowley A, Figueira L, Li W, McWilliam H, Lopez R, Xenarios I, Bougueleret L, Bridge A, Poux S, Redaschi N, Aimo L, Argoud-Puy G, Auchincloss A, Axelsen K, Bansal P, Baratin D, Blatter MC, Boeckmann B, Bolleman J, Boutet E, Breuza L, Casal-Casas C, de Castro E, Coudert E, Cuche B, Doche M, Dornevil D, Duvaud S, Estreicher A, Famiglietti L, Feuermann M, Gasteiger E, Gehant S, Gerritsen V, Gos A, Gruaz-Gumowski N, Hinz U, Hulo C, Jungo F, Keller G, Lara V, Lemercier P, Lieberherr D, Lombardot T, Martin X, Masson P, Morgat A, Neto T, Nouspikel N, Paesano S, Pedruzzi I, Pilbout S, Pozzato M, Pruess M, Rivoire C, Roechert B, Schneider M, Sigrist C, Sonesson K, Staehli S, Stutz A, Sundaram S, Tognolli M, Verbregue L, Veuthey AL, Wu CH, Arighi CN, Arminski L, Chen C, Chen Y, Garavelli JS, Huang H, Laiho K, McGarvey P, Natale DA, Suzek BE, Vinayaka C, Wang Q, Wang Y, Yeh LS, Yerramalla MS, Zhang J., Nucleic Acids Res. 43(Database issue), 2014
PMID: 25348405

Determining the Null Model for Detecting Adaptive Convergence from Genomic Data: A Case Study using Echolocating Mammals.
Thomas GW, Hahn MW., Mol. Biol. Evol. 32(5), 2015
PMID: 25631926

PDBe: Protein Data Bank in Europe.
Velankar S, Best C, Beuth B, Boutselakis CH, Cobley N, Sousa Da Silva AW, Dimitropoulos D, Golovin A, Hirshberg M, John M, Krissinel EB, Newman R, Oldfield T, Pajon A, Penkett CJ, Pineda-Castillo J, Sahni G, Sen S, Slowley R, Suarez-Uruena A, Swaminathan J, van Ginkel G, Vranken WF, Henrick K, Kleywegt GJ., Nucleic Acids Res. 38(Database issue), 2009
PMID: 19858099

Shark tales: a molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes).
Velez-Zuazo X, Agnarsson I., Mol. Phylogenet. Evol. 58(2), 2010
PMID: 21129490

Assembly of titin, myomesin and M-protein into the sarcomeric M band in differentiating human skeletal muscle cells in vitro.
van der Ven PF, Furst DO., Cell Struct. Funct. 22(1), 1997
PMID: 9113403

A Cluster algorithm for graphs
Van S.., 2000

Elephant shark genome provides unique insights into gnathostome evolution.
Venkatesh B, Lee AP, Ravi V, Maurya AK, Lian MM, Swann JB, Ohta Y, Flajnik MF, Sutoh Y, Kasahara M, Hoon S, Gangu V, Roy SW, Irimia M, Korzh V, Kondrychyn I, Lim ZW, Tay BH, Tohari S, Kong KW, Ho S, Lorente-Galdos B, Quilez J, Marques-Bonet T, Raney BJ, Ingham PW, Tay A, Hillier LW, Minx P, Boehm T, Wilson RK, Brenner S, Warren WC., Nature 505(7482), 2014
PMID: 24402279

Comparative analyses of animal-tracking data reveal ecological significance of endothermy in fishes.
Watanabe YY, Goldman KJ, Caselle JE, Chapman DD, Papastamatiou YP., Proc. Natl. Acad. Sci. U.S.A. 112(19), 2015
PMID: 25902489

Mammalian metabolite flux rates in a teleost: lactate and glucose turnover in tuna.
Weber JM, Brill RW, Hochachka PW., Am. J. Physiol. 250(3 Pt 2), 1986
PMID: 3953854

The horizontal septum: mechanisms of force transfer in locomotion of scombrid fishes (Scombridae, Perciformes)
Westneat MW, Hoese W, Pell CA, Wainwright SA.., 1993

Wikström M.., 2010

Orthology inference in non-model organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics
Yang Y, Smith SA.., 2014

PAML 4: phylogenetic analysis by maximum likelihood.
Yang Z., Mol. Biol. Evol. 24(8), 2007
PMID: 17483113

Statistical methods for detecting molecular adaptation.
Yang Z, Bielawski JP., Trends Ecol. Evol. (Amst.) 15(12), 2000
PMID: 11114436

A functional genomics tool for the Pacific bluefin tuna: Development of a 44K oligonucleotide microarray from whole-genome sequencing data for global transcriptome analysis.
Yasuike M, Fujiwara A, Nakamura Y, Iwasaki Y, Nishiki I, Sugaya T, Shimizu A, Sano M, Kobayashi T, Ototake M., Gene 576(2 Pt 1), 2015
PMID: 26477480

Ensembl 2016.
Yates A, Akanni W, Amode MR, Barrell D, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Fitzgerald S, Gil L, Giron CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Johnson N, Juettemann T, Keenan S, Lavidas I, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Nuhn M, Parker A, Patricio M, Pignatelli M, Rahtz M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Birney E, Harrow J, Muffato M, Perry E, Ruffier M, Spudich G, Trevanion SJ, Cunningham F, Aken BL, Zerbino DR, Flicek P., Nucleic Acids Res. 44(D1), 2015
PMID: 26687719

Leiomodin-3 dysfunction results in thin filament disorganization and nemaline myopathy.
Yuen M, Sandaradura SA, Dowling JJ, Kostyukova AS, Moroz N, Quinlan KG, Lehtokari VL, Ravenscroft G, Todd EJ, Ceyhan-Birsoy O, Gokhin DS, Maluenda J, Lek M, Nolent F, Pappas CT, Novak SM, D'Amico A, Malfatti E, Thomas BP, Gabriel SB, Gupta N, Daly MJ, Ilkovski B, Houweling PJ, Davidson AE, Swanson LC, Brownstein CA, Gupta VA, Medne L, Shannon P, Martin N, Bick DP, Flisberg A, Holmberg E, Van den Bergh P, Lapunzina P, Waddell LB, Sloboda DD, Bertini E, Chitayat D, Telfer WR, Laquerriere A, Gregorio CC, Ottenheijm CA, Bonnemann CG, Pelin K, Beggs AH, Hayashi YK, Romero NB, Laing NG, Nishino I, Wallgren-Pettersson C, Melki J, Fowler VM, MacArthur DG, North KN, Clarke NF., J. Clin. Invest. 124(11), 2014
PMID: 25250574

Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level.
Zhang J, Nielsen R, Yang Z., Mol. Biol. Evol. 22(12), 2005
PMID: 16107592

Effect of muscle-fiber type on glycogenin-1 gene expression and its relationship with the glycolytic potential and pH of pork.
Zhang SH, Zhu L, Wu ZH, Zhang Y, Tang GQ, Jiang YZ, Li MZ, Bai L, Li XW., Genet. Mol. Res. 12(3), 2013
PMID: 24065679

Zou Z, Zhang J.., 2015