Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

[1]  Evan Bolton,et al.  Database resources of the National Center for Biotechnology Information , 2017, Nucleic Acids Res..

[2]  M. Schatz,et al.  Phased diploid genome assembly with single-molecule real-time sequencing , 2016, Nature Methods.

[3]  C. Oosterhout,et al.  hybridcheck: software for the rapid detection, visualization and dating of recombinant regions in genome sequence data , 2016, Molecular ecology resources.

[4]  Russell E. Durrett,et al.  Assembly and diploid architecture of an individual human genome via single-molecule technologies , 2015, Nature Methods.

[5]  Jodi N. Young,et al.  Gross and net production during the spring bloom along the Western Antarctic Peninsula. , 2015, The New phytologist.

[6]  Marika M. Holland,et al.  Impact of sea ice on the marine iron cycle and phytoplankton productivity , 2014 .

[7]  Paul Theodor Pyl,et al.  HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[8]  P. Boyd,et al.  Surface-water iron supplies in the Southern Ocean sustained by deep winter mixing , 2014 .

[9]  María Martín,et al.  Activities at the Universal Protein Resource (UniProt) , 2013, Nucleic Acids Res..

[10]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[11]  J. Tison,et al.  Role of sea ice in global biogeochemical cycles: emerging views and challenges , 2013 .

[12]  Timothy M. Lenton,et al.  The impact of temperature on marine phytoplankton resource allocation and metabolism , 2013 .

[13]  F. Morel,et al.  Preparation and chemistry of the artificial algal culture medium aquil , 2013 .

[14]  D. Cavalieri,et al.  Antarctic sea ice variability and trends, 1979-2010 , 2012 .

[15]  Rüdiger Röttgers,et al.  Deep carbon export from a Southern Ocean iron-fertilized diatom bloom , 2012, Nature.

[16]  P. Boyd,et al.  Iron‐light interactions differ in Southern Ocean phytoplankton , 2012 .

[17]  J. Raymond,et al.  Possible Role of Horizontal Gene Transfer in the Colonization of Sea Ice by Algae , 2012, PloS one.

[18]  Davis J. McCarthy,et al.  Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation , 2012, Nucleic acids research.

[19]  David M Schruth,et al.  Comparative metatranscriptomics identifies molecular bases for the physiological responses of phytoplankton to varying iron availability , 2012, Proceedings of the National Academy of Sciences.

[20]  P. Croot,et al.  The distribution of dissolved zinc in the Atlantic sector of the Southern Ocean , 2011 .

[21]  M. Nei,et al.  MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.

[22]  P. Sedwick,et al.  Iron Limitation of a Springtime Bacterial and Phytoplankton Community in the Ross Sea: Implications for Vitamin B12 Nutrition , 2011, Front. Microbio..

[23]  Matko Bosnjak,et al.  REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms , 2011, PloS one.

[24]  David S. Goodsell,et al.  The RCSB Protein Data Bank: redesigned web site and web services , 2010, Nucleic Acids Res..

[25]  Andrew J. Alverson,et al.  The model marine diatom Thalassiosira pseudonana likely descended from a freshwater ancestor in the genus Cyclotella , 2011, BMC Evolutionary Biology.

[26]  N. Perna,et al.  progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement , 2010, PloS one.

[27]  Philip E. Bourne,et al.  History of biological metal utilization inferred through phylogenomic analysis of protein structures , 2010, Proceedings of the National Academy of Sciences.

[28]  Serban Nacu,et al.  Fast and SNP-tolerant detection of complex variants and splicing in short reads , 2010, Bioinform..

[29]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[30]  François Massonnet,et al.  Importance of physics, resolution and forcing in hindcast simulations of Arctic and Antarctic sea ice variability and trends , 2010 .

[31]  Matthew D. Young,et al.  Gene ontology analysis for RNA-seq: accounting for selection bias , 2010, Genome Biology.

[32]  S. Salzberg,et al.  Phymm and PhymmBL: Metagenomic Phylogenetic Classification with Interpolated Markov Models , 2009, Nature Methods.

[33]  Pablo Librado,et al.  DnaSP v5: a software for comprehensive analysis of DNA polymorphism data , 2009, Bioinform..

[34]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[35]  Leszek Rychlewski,et al.  The Phaeodactylum genome reveals the evolutionary history of diatom genomes , 2008, Nature.

[36]  Yoshihiro Yamanishi,et al.  KEGG for linking genomes to life and the environment , 2007, Nucleic Acids Res..

[37]  Janet M. Thornton,et al.  PROCOGNATE: a cognate ligand domain mapping for enzymes , 2007, Nucleic Acids Res..

[38]  A. Rogers.  Evolution and biodiversity of Antarctic organisms: a molecular perspective , 2007, Philosophical Transactions of the Royal Society B: Biological Sciences.

[39]  A. Rambaut,et al.  BEAST: Bayesian evolutionary analysis by sampling trees , 2007, BMC Evolutionary Biology.

[40]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[41]  C. Bowler,et al.  Genetic and phenotypic characterization of Phaeodactylum tricornutum (Bacillariophyceae) accessions 1 , 2007 .

[42]  Ziheng Yang.  PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.

[43]  Keith Bradnam,et al.  CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes , 2007, Bioinform..

[44]  Merlin Crossley,et al.  Sticky fingers: zinc-fingers as protein-recognition motifs. , 2007, Trends in biochemical sciences.

[45]  Philip E. Bourne,et al.  Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry , 2006, Proceedings of the National Academy of Sciences.

[46]  P. Chomczyński,et al.  The single-step method of RNA isolation by acid guanidinium thiocyanate–phenol–chloroform extraction: twenty-something years on , 2006, Nature Protocols.

[47]  Julian Gough,et al.  Genomic scale sub-family assignment of protein domains , 2006, Nucleic acids research.

[48]  N. M. Price,et al.  Copper-containing plastocyanin used for electron transport by an oceanic diatom , 2006, Nature.

[49]  D. Bryant,et al.  A Simple and Robust Statistical Test for Detecting the Presence of Recombination , 2006, Genetics.

[50]  Mary K. Kuhner,et al.  LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters , 2006, Bioinform..

[51]  S. Ho,et al.  Relaxed Phylogenetics and Dating with Confidence , 2006, PLoS biology.

[52]  D. Huson,et al.  Application of phylogenetic networks in evolutionary studies. , 2006, Molecular biology and evolution.

[53]  Marek Kimmel,et al.  simuPOP: a forward-time population genetics simulation environment , 2005, Bioinform..

[54]  J. Jurka,et al.  Repbase Update, a database of eukaryotic repetitive elements , 2005, Cytogenetic and Genome Research.

[55]  Rolf Apweiler,et al.  InterProScan: protein domains identifier , 2005, Nucleic Acids Res..

[56]  H. Kishino,et al.  Dating of the human-ape splitting by a molecular clock of mitochondrial DNA , 2005, Journal of Molecular Evolution.

[57]  Pavel A. Pevzner,et al.  De novo identification of repeat families in large genomes , 2005, ISMB.

[58]  Nicholas H. Putnam,et al.  The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution, and Metabolism , 2004, Science.

[59]  B. Bowen,et al.  Allelic Variation of Gene Expression in Maize Hybrids , 2004, The Plant Cell Online.

[60]  J. Knight,et al.  Allele-specific gene expression uncovered. , 2004, Trends in genetics : TIG.

[61]  G. Fryxell,et al.  Fragilariopsis cylindrus (Grunow) Krieger: The most abundant diatom in water column assemblages of Antarctic marginal ice-edge zones , 1992, Polar Biology.

[62]  M. Fiala,et al.  Light-temperature interactions on the growth of Antarctic diatoms , 1990, Polar Biology.

[63]  C. Quillfeldt.  The diatom Fragilariopsis cylindrus and its potential as an indicator species for cold water rather than for sea ice , 2004 .

[64]  Jodie J. Yin,et al.  A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes , 2004, Genome Biology.

[65]  A. Pingoud,et al.  Real-time PCR-based method for the estimation of genome sizes. , 2003, Nucleic acids research.

[66]  A. Krogh,et al.  Reliability measures for membrane protein topology prediction algorithms. , 2003, Journal of molecular biology.

[67]  E. Mauceli,et al.  Whole-genome sequence assembly for mammalian genomes: Arachne 2. , 2003, Genome research.

[68]  Matthew R. Pocock,et al.  The Bioperl toolkit: Perl modules for the life sciences. , 2002, Genome research.

[69]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[70]  G. Dieckmann,et al.  Antarctic Sea Ice--a Habitat for Extremophiles , 2002, Science.

[71]  C. Chothia,et al.  Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. , 2001, Journal of molecular biology.

[72]  E. Brook,et al.  Timing of millennial-scale climate change in Antarctica and Greenland during the last glacial period. , 2001, Science.

[73]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[74]  R. Durbin,et al.  Using GeneWise in the Drosophila annotation experiment. , 2000, Genome research.

[75]  V. Solovyev,et al.  Ab initio gene finding in Drosophila genomic DNA. , 2000, Genome research.

[76]  S. Eddy,et al.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.

[77]  S. Brunak,et al.  SHORT COMMUNICATION Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites , 1997 .

[78]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.

[79]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[80]  J. Doyle,et al.  Isolation of plant DNA from fresh tissue , 1990 .

[81]  G. Yule,et al.  A Mathematical Theory of Evolution Based on the Conclusions of Dr. J. C. Willis, F.R.S. , 1925 .

[82]  G. Yule,et al.  A Mathematical Theory of Evolution, Based on the Conclusions of Dr. J. C. Willis, F.R.S. , 1925 .