AaronDarling's library 329 articles Export

	Genome sequence of enterohaemorrhagic Escherichia coli O157:H7 [My Copy] Nature, Vol. 409, No. 6819. (25 January 2001), pp. 529-533. by Nicole T. Perna, Guy Plunkett, Valerie Burland, et al.Bob Mau, Jeremy D. Glasner, Debra J. Rose, George F. Mayhew, Peter S. Evans, Jason Gregor, Heather A. Kirkpatrick, Gyorgy Posfai, Jeremiah Hackett, Sara Klink, Adam Boutin, Ying Shao, Leslie Miller, Erik J. Grotbeck, N. Wayne Davis, Alex Lim, Eileen T. Dimalanta, Konstantinos D. Potamousis, Jennifer Apodaca, Thomas S. Anantharaman, Jieyi Lin, Galex Yen, David C. Schwartz, Rodney A. Welch, Frederick R. Blattner posted to aaaa by AaronDarling on 2009-03-23 06:15:29 as along with 4 people katholt kaarsinogen treangen Xavier
	Population genomics and the bacterial species concept. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 532 (2009), pp. 367-377. by M. A. Riley, M. Lizotte-Waniewski posted to aaaa by AaronDarling on 2009-03-23 06:09:57 as along with 4 people and 1 group jasontsai Zephyrus jmeppley Thaverkamp Microbial-Ecology
	The bacterial species definition in the genomic era. [My Copy] Philos Trans R Soc Lond B Biol Sci, Vol. 361, No. 1475. (29 November 2006), pp. 1929-1940. by K. T. Konstantinidis, A. Ramette, J. M. Tiedje posted to aaaa by AaronDarling on 2009-03-23 06:09:00 as along with 6 people and 3 groups druvus skembel treangen jmeppley kinestetika Thaverkamp iSEEM Microbial-Ecology microbiology_nijmegen
	The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families. [My Copy] PLoS Biol, Vol. 5, No. 3. (13 March 2007) by Shibu Yooseph, Granger Sutton, Douglas B B. Rusch, et al.Aaron L L. Halpern, Shannon J J. Williamson, Karin Remington, Jonathan A A. Eisen, Karla B B. Heidelberg, Gerard Manning, Weizhong Li, Lukasz Jaroszewski, Piotr Cieplak, Christopher S S. Miller, Huiying Li, Susan T T. Mashiyama, Marcin P P. Joachimiak, Christopher van Belle, John-Marc M. Chandonia, David A A. Soergel, Yufeng Zhai, Kannan Natarajan, Shaun Lee, Benjamin J J. Raphael, Vineet Bafna, Robert Friedman, Steven E E. Brenner, Adam Godzik, David Eisenberg, Jack E E. Dixon, Susan S S. Taylor, Robert L L. Strausberg, Marvin Frazier, J Craig C. Venter posted to aaarchaeansf by AaronDarling on 2009-03-23 05:03:34 as along with 9 people and 4 groups Thaverkamp skembel azazello jmeppley kaspermunch michC mjetten vrich jlgreen Bioinformatics microbiology_nijmegen Green Lab iSEEM
	The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific [My Copy] PLoS Biol, Vol. 5, No. 3. (13 March 2007), e77. by Douglas B. Rusch, Aaron L. Halpern, Granger Sutton, et al.Karla B. Heidelberg, Shannon Williamson, Shibu Yooseph, Dongying Wu, Jonathan A. Eisen, Jeff M. Hoffman, Karin Remington, Karen Beeson, Bao Tran, Hamilton Smith, Holly Baden-Tillson, Clare Stewart, Joyce Thorpe, Jason Freeman, Cynthia Andrews-Pfannkoch, Joseph E. Venter, Kelvin Li, Saul Kravitz, John F. Heidelberg, Terry Utterback, Yu-Hui Rogers, Luisa I. Falcón, Valeria Souza, Germán Bonilla-Rosso, Luis E. Eguiarte, David M. Karl, Shubha Sathyendranath, Trevor Platt, Eldredge Bermingham, Victor Gallardo, Giselle Tamayo-Castillo, Michael R. Ferrari, Robert L. Strausberg, Kenneth Nealson, Robert Friedman, Marvin Frazier, J. Craig Venter posted to aaanew by AaronDarling on 2009-03-23 05:02:35 as along with 17 people and 5 groups antonkratz dakelley maria_hauser mlangill azazello skembel aramata jmeppley kaspermunch michC jdelcampo stajich skoch3 beatrizfernandez kinestetika Thaverkamp djkt Bioinformatics Microbial-Ecology Koch_Lab microbiology_nijmegen iSEEM
	Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes [My Copy] PLoS Biol, Vol. 5, No. 3. (13 March 2007), e82. by Jonathan A. Eisen posted to aaanew by AaronDarling on 2009-03-23 05:02:12 as along with 16 people and 3 groups druvus skembel hwright Thaverkamp anphony precale adgrativol silberbauer jmeppley jdelcampo azazello beatrizfernandez xingxu jlgreen olympos djkt Microbial-Ecology Green Lab iSEEM
	Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). [My Copy] Omics : a journal of integrative biology, Vol. 10, No. 2. (2006), pp. 231-237. by J. Leebens-Mack, T. Vision, E. Brenner, et al.J. E. Bowers, S. Cannon, M. J. Clement, C. W. Cunningham, C. dePamphilis, R. deSalle, J. J. Doyle, J. A. Eisen, X. Gu, J. Harshman, R. K. Jansen, E. A. Kellogg, E. V. Koonin, B. D. Mishler, H. Philippe, J. C. Pires, Y. L. Qiu, S. Y. Rhee, K. Sjölander, D. E. Soltis, P. S. Soltis, D. W. Stevenson, K. Wall, T. Warnow, C. Zmasek posted to aaanew by AaronDarling on 2009-03-23 05:01:04 as along with 3 people and 1 group cmzmasek jandot rvosa FAB-lab
	Characterization of bacterial communities associated with deep-sea corals on Gulf of Alaska seamounts. [My Copy] Applied and environmental microbiology, Vol. 72, No. 2. (February 2006), pp. 1680-1683. by K. Penn, D. Wu, J. A. Eisen, N. Ward posted to aaanew by AaronDarling on 2009-03-23 04:59:46 as
	New directions and interactions in metagenomics research. [My Copy] FEMS Microbiol Ecol, Vol. 55, No. 3. (March 2006), pp. 331-338. by N. Ward posted to aaanew by AaronDarling on 2009-03-23 04:57:38 as along with 2 people knaseanka jmeppley
	How genomics has affected the concept of microbiology [My Copy] Current Opinion in Microbiology, Vol. 8, No. 5. (October 2005), pp. 564-571. by N. Ward, C. Fraser posted to aaanew by AaronDarling on 2009-03-23 04:56:25 as along with 2 people druvus Thaverkamp
	Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA gene-based phylogenetic analysis: implications for the taxonomy of the orders 'Rhodobacterales' and Caulobacterales. [My Copy] International journal of systematic and evolutionary microbiology, Vol. 55, No. Pt 3. (May 2005), pp. 1021-1026. by J. H. Badger, J. A. Eisen, N. L. Ward posted to aaanew by AaronDarling on 2009-03-23 04:55:15 as
	An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP) [My Copy] PLoS ONE, Vol. 3, No. 7. (2 July 2008), e2566. by Dongying Wu, Amber Hartman, Naomi Ward, Jonathan A. Eisen posted to aaanew by AaronDarling on 2009-03-23 04:53:26 as along with 7 people and 4 groups Katje skembel sriesenfeld druvus vaulot skato_toyaku djkt microbiology_nijmegen Papers recommended by the Roscoff Plankton Group Microbial-Ecology iSEEM
	Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. [My Copy] Genome research, Vol. 8, No. 3. (1 March 1998), pp. 163-167. by J. A. Eisen posted to aaanew by AaronDarling on 2009-03-23 04:52:52 as along with 4 people pansapiens druvus gjuggler sgoetz
	From genomics to chemical genomics: new developments in KEGG [My Copy] Nucl. Acids Res., Vol. 34, No. suppl_1. (1 January 2006), pp. D354-357. by Minoru Kanehisa, Susumu Goto, Masahiro Hattori, et al.Kiyoko F. Aoki-Kinoshita, Masumi Itoh, Shuichi Kawashima, Toshiaki Katayama, Michihiro Araki, Mika Hirakawa posted to aaanew by AaronDarling on 2009-03-23 04:50:41 as along with 17 people VGreiff srp33 namunet guhjy aalibes kuhn balajis alexg eweaver tny dullhunk michC frohike incovoma sgoetz yggdrasil natstreet
	Phylogenomics: Intersection of Evolution and Genomics [My Copy] Science, Vol. 300, No. 5626. (13 June 2003), pp. 1706-1707. by Jonathan A. Eisen, Claire M. Fraser posted to aaanew by AaronDarling on 2009-03-23 04:48:00 as along with 2 people operon taka
	Complete Genome Sequence of the Aerobic CO-Oxidizing Thermophile Thermomicrobium roseum [My Copy] PLoS ONE, Vol. 4, No. 1. (16 January 2009), e4207. by Dongying Wu, Jason Raymond, Martin Wu, et al.Sourav Chatterji, Qinghu Ren, Joel E. Graham, Donald A. Bryant, Frank Robb, Albert Colman, Luke J. Tallon, Jonathan H. Badger, Ramana Madupu, Naomi L. Ward, Jonathan A. Eisen posted to aaanew by AaronDarling on 2009-03-23 04:45:41 as along with 2 people kiekyon neils
	Genome rearrangement by replication-directed translocation. [My Copy] Nat Genet, Vol. 26, No. 2. (October 2000), pp. 195-197. by E. R. Tillier, R. A. Collins posted to aaanew by AaronDarling on 2009-03-23 03:05:26 as along with 2 people operon rabu
	Evidence for symmetric chromosomal inversions around the replication origin in bacteria. [My Copy] Genome Biol, Vol. 1, No. 6. (2000) by J. A. Eisen, J. F. Heidelberg, O. White, S. L. Salzberg posted to aaanew by AaronDarling on 2009-03-23 03:04:48 as along with 3 people druvus braneyboo treangen
	The Design, Implementation, and Evaluation of mpiBLAST [My Copy] In In Proceedings of ClusterWorld 2003 (2003) by Aaron E. Darling, Lucas Carey, Wu-Chun Feng posted to aaanew by AaronDarling on 2009-03-23 03:02:05 as along with 1 person bozdagd
	Genome Rearrangement in Mitochondria and Its Computational Biology [My Copy] Comparative Genomics (2005), pp. 85-96. by István Miklós, Jotun Hein posted to aaanew by AaronDarling on 2009-03-23 03:00:17 as
	MCMC genome rearrangement. [My Copy] Bioinformatics, Vol. 19 Suppl 2 (October 2003) by I. Miklós posted to aaanew by AaronDarling on 2009-03-23 02:58:55 as along with 1 person Ayest
	Bayesian phylogenetic inference from animal mitochondrial genome arrangements [My Copy] Journal Of The Royal Statistical Society Series B, Vol. 64, No. 4. (2002), pp. 681-693. by Bret Larget, Donald L. Simon, Joseph B. Kadane posted to aaanew by AaronDarling on 2009-03-23 02:58:23 as
	Three-Dimensional Phylogeny Explorer: Distinguishing paralogs, lateral transfer, and violation of "molecular clock" assumption with 3D visualization [My Copy] BMC Bioinformatics, Vol. 8 (20 June 2007), 213. by Namshin Kim, Christopher Lee posted to aatol by AaronDarling on 2009-03-23 02:05:37 as along with 1 person and 1 group Einat structural_bioinformatics
	Paloverde: an OpenGL 3-D phylogeny browser. [My Copy] Bioinformatics (24 February 2006) by Michael J J. Sanderson posted to aatol by AaronDarling on 2009-03-23 02:04:42 as along with 4 people dparks aprasad eckart_bindewald akifumi
	Optimal, efficient reconstruction of phylogenetic networks with constrained recombination. [My Copy] Journal of bioinformatics and computational biology, Vol. 2, No. 1. (March 2004), pp. 173-213. by D. Gusfield, S. Eddhu, C. Langley posted to aatol by AaronDarling on 2009-03-23 02:03:09 as
	Multiple replication origins of the archaeon Halobacterium species NRC-1 [My Copy] Biochemical and Biophysical Research Communications, Vol. 302, No. 4. (21 March 2003), pp. 728-734. by R. Zhang posted to aatol by AaronDarling on 2009-03-23 02:01:46 as
	Expected Gene Order Distances and Model Selection in Bacteria. [My Copy] Bioinformatics (Oxford, England) (1 April 2008) by Daniel Dalevi, Niklas Eriksen posted to aatol by AaronDarling on 2009-03-23 01:59:22 as along with 4 people and 1 group maximilianh Ema cisevol sharpton BergmanLab
	The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. [My Copy] Nucleic acids research, Vol. 36, No. Database issue. (January 2008) by K. Liolios, K. Mavromatis, N. Tavernarakis, N. C. Kyrpides posted to aatol by AaronDarling on 2009-03-23 01:55:31 as along with 7 people Thaverkamp coela semin diamantis guhjy jmeppley stsaft
	Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 3. (16 January 2007), pp. 870-875. by Tal Dagan, William Martin posted to aatol by AaronDarling on 2009-03-23 01:54:16 as along with 2 people treangen operon
	Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 29. (22 July 2008), pp. 10039-10044. by Tal Dagan, Yael Artzy-Randrup, William Martin posted to aatol by AaronDarling on 2009-03-23 01:53:41 as along with 3 people treangen tomhebbron druvus
	GeneTRACE-reconstruction of gene content of ancestral species. [My Copy] Bioinformatics (Oxford, England), Vol. 19, No. 11. (22 July 2003), pp. 1412-1416. by V. Kunin, C. A. Ouzounis posted to aatol by AaronDarling on 2009-03-23 01:52:50 as
	The net of life: Reconstructing the microbial phylogenetic network [My Copy] Genome Research, Vol. 15, No. 7. (July 2005), pp. 954-959. by Victor Kunin, Leon Goldovsky, Nikos Darzentas, Christos A. Ouzounis posted to aatol by AaronDarling on 2009-03-23 01:51:51 as along with 2 people and 1 group druvus operon LabDros
	ESTIMATING SPECIES TREES USING MULTIPLE-ALLELE DNA SEQUENCE DATA [My Copy] Evolution, Vol. 62, No. 8. (August 2008), pp. 2080-2091. by Liang Liu, Dennis K. Pearl, Robb T. Brumfield, Scott V. Edwards posted to aatol by AaronDarling on 2009-03-23 01:50:29 as along with 2 people lizbiogen druvus
	BEST: Bayesian estimation of species trees under the coalescent model [My Copy] Bioinformatics, Vol. 24, No. 21. (1 November 2008), pp. 2542-2543. by Liang Liu posted to aatol by AaronDarling on 2009-03-23 01:49:02 as along with 6 people lizbiogen robfsouza gjuggler druvus alexeid nuin
	A simple, fast, and accurate method of phylogenomic inference [My Copy] Genome Biology, Vol. 9, No. 10. (13 October 2008), R151. by Martin Wu, Jonathan Eisen posted to aatol by AaronDarling on 2009-03-23 01:47:10 as along with 12 people and 2 groups dakelley jeargle zwang cgaugain treangen Katje operon ellakat scryrps djkt aramata druvus microbiology_nijmegen iSEEM
	FastBLAST: Homology Relationships for Millions of Proteins [My Copy] PLoS ONE, Vol. 3, No. 10. (31 October 2008), e3589. by Morgan N. Price, Paramvir S. Dehal, Adam P. Arkin posted to aatol by AaronDarling on 2009-03-23 01:46:02 as along with 4 people treangen natstreet druvus reyez
	MACHOS: Markov clusters of homologous subsequences. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 13. (1 July 2008) by S. Wong, M. A. Ragan posted to aatol by AaronDarling on 2009-03-23 01:45:02 as along with 4 people operon treangen nuin gulkur
	Algorithm of OMA for large-scale orthology inference [My Copy] BMC Bioinformatics, Vol. 9 (04 December 2008), 518. by Alexander, Christophe Dessimoz posted to aatol by AaronDarling on 2009-03-23 01:43:33 as along with 5 people alpae cgaugain grahamc barriot druvus
	Phylogenetic and functional assessment of orthologs inference projects and methods. [My Copy] PLoS computational biology, Vol. 5, No. 1. (16 January 2009), e1000262. by Adrian M. Altenhoff, Christophe Dessimoz posted to aatol by AaronDarling on 2009-03-23 01:43:08 as along with 10 people and 1 group avilella skembel isimpson hpaces natstreet alpae kshameer djkt bpcusack druvus Ensembl Compara citations
	Estimating true evolutionary distances under the DCJ model. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 13. (1 July 2008) by Y. Lin, B. M. Moret posted to aatol by AaronDarling on 2009-03-23 01:41:07 as along with 1 person nuin
	Sorting Genomes with Insertions, Deletions and Duplications by DCJ [My Copy] Comparative Genomics (2008), pp. 170-183. by Sophia Yancopoulos, Richard Friedberg posted to aatol by AaronDarling on 2009-03-23 01:38:52 as
	Descendants of Whole Genome Duplication within Gene Order Phylogeny. [My Copy] Journal of computational biology : a journal of computational molecular cell biology (12 September 2008) by Chunfang Zheng, Qian Zhu, David Sankoff posted to aatol by AaronDarling on 2009-03-23 01:37:28 as along with 2 people druvus nuin
	Multi-Break Rearrangements and Breakpoint Re-Uses: From Circular to Linear Genomes. [My Copy] Journal of computational biology : a journal of computational molecular cell biology (12 September 2008) by Max A A. Alekseyev posted to aatol by AaronDarling on 2009-03-23 01:35:31 as along with 1 person nuin
	A Unifying View of Genome Rearrangements [My Copy] Algorithms in Bioinformatics (2006), pp. 163-173. by Anne Bergeron, Julia Mixtacki, Jens Stoye posted to aatol by AaronDarling on 2009-03-23 01:34:24 as
	The infinite sites model of genome evolution [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 38. (23 September 2008), pp. 14254-14261. by Jian Ma, Aakrosh Ratan, Brian J. Raney, Bernard B. Suh, Webb Miller, David Haussler posted to aatol by AaronDarling on 2009-03-23 01:32:17 as along with 8 people and 1 group sharpton Thaverkamp ilyashl druvus operon inesdesantiago stajich stringertheory Mycology
	A Bayesian approach to the estimation of ancestral genome arrangements. [My Copy] Molecular phylogenetics and evolution, Vol. 36, No. 2. (August 2005), pp. 214-223. by B. Larget, J. B. Kadane, D. L. Simon posted to aatol by AaronDarling on 2009-03-23 01:29:14 as along with 2 people druvus treangen
	In silico identification of genes in bacteriophage DNA. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 502 (2009), pp. 57-89. by A. M. Kropinski, M. Borodovsky, T. J. Carver, et al.A. M. Cerdeño-Tárraga, A. Darling, A. Lomsadze, P. Mahadevan, P. Stothard, D. Seto, G. Van Domselaar, D. S. Wishart posted to aatol by AaronDarling on 2009-03-23 01:27:25 as
	Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria [My Copy] Nucl. Acids Res., Vol. 36, No. suppl_1. (11 January 2008), pp. D519-523. by Jeremy D. Glasner, Guy Plunkett, Bradley D. Anderson, et al.David J. Baumler, Bryan S. Biehl, Valerie Burland, Eric L. Cabot, Aaron E. Darling, Bob Mau, Eric C. Neeno-Eckwall, David Pot, Yu Qiu, Anna I. Rissman, Sara Worzella, Sam Zaremba, Joel Fedorko, Tom Hampton, Paul Liss, Michael Rusch, Matthew Shaker, Lorie Shaull, Panna Shetty, Silpa Thotakura, Jon Whitmore, Frederick R. Blattner, John M. Greene, Nicole T. Perna posted to aatol by AaronDarling on 2009-03-23 01:26:42 as along with 1 person druvus
	Genome rearrangement by the double cut and join operation. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 452 (2008), pp. 385-416. by R. Friedberg, A. E. Darling, S. Yancopoulos posted to aatol by AaronDarling on 2009-03-23 01:25:37 as
	Are Protein Domains Modules of Lateral Genetic Transfer? [My Copy] PLoS ONE, Vol. 4, No. 2. (20 February 2009), e4524. by Cheong X. Chan, Aaron E. Darling, Robert G. Beiko, Mark A. Ragan posted to aatol by AaronDarling on 2009-03-23 01:24:21 as along with 3 people chancx druvus zwang

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recombination	58
evolution	54
genomerearrangement	54
nsfprop	54
genomeevolution	33
populationgenetics	30
aatol	28
phylogenetics	28
alignment	25
horizontaltransfer	21
microbialevolution	19
aaanew	18
genomecomparison	18
dna-replication	16
aarchaeansf	15
speciestree	13
genomesequencing	12
speciation	12
wabi	10
yersinia	10
aaarchaeansf	9
coalescent	9
mcmc	8
inversions	5
statisticalalignment	5
motifdetection	4
randomwalks	4
repeats	4
aaaa	3
geneconversion	3
genomeannotation	3
assembly	2
biodiversity	2
cog	2
hpc	2
metagenomics	2
optical-map	2
visualization	2
alignmentwabi	1
coregenomehypothesis	1
hmm	1
mrbayes	1
noncoding-rna	1
orthology	1
polony	1
positiveselection	1
sequence	1
virus	1

AaronDarling's library 329 articles Export

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