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AaronDarlings library [258 articles]

Senaste artiklarna i AaronDarlings bibliotek.
  • MSOAR: A High-Throughput Ortholog Assignment System Based on Genome Rearrangement
    Journal of Computational Biology, Vol. 14, No. 9. (2007), pp. 1160-1175.
    by Zheng Fu, Xin Chen, Vladimir Vacic, Peng Nan, Yang Zhong, Tao Jiang
    posted to genomerearrangement by AaronDarling on 2008-06-13 08:37:50 as **
  • VISTA : visualizing global DNA sequence alignments of arbitrary length.
    Bioinformatics (Oxford, England), Vol. 16, No. 11. (November 2000), pp. 1046-1047.
    by C Mayor, M Brudno, JR Schwartz, A Poliakov, EM Rubin, KA Frazer, LS Pachter, I Dubchak
    posted to no-tag by AaronDarling on 2008-06-13 05:41:44 as ** along with 1 person natstreet
  • Uncertainty in homology inferences: Assessing and improving genomic sequence alignment
    Genome Res., Vol. 18, No. 2. (1 February 2008), pp. 298-309.
    by Gerton Lunter, Andrea Rocco, Naila Mimouni, Andreas Heger, Alexandre Caldeira, Jotun Hein
    posted to alignment by AaronDarling on 2008-06-12 12:21:56 as ** along with 8 people aprasad brant treangen djkt grahamc dandaman mailund gjuggler
  • 28-Way vertebrate alignment and conservation track in the UCSC Genome Browser
    Genome Res. (5 November 2007), gr.6761107.
    by Webb Miller, Kate Rosenbloom, Ross C Hardison, Minmei Hou, James Taylor, Brian Raney, Richard Burhans, David C King, Robert Baertsch, Daniel Blankenberg, Kosakovsky, Anton Nekrutenko, Belinda Giardine, Robert S Harris, Svitlana Tyekucheva, Mark Diekhans, Thomas H Pringle, William J Murphy, Arthur Lesk, George M Weinstock, Kerstin Lindblad-Toh, Richard A Gibbs, Eric S Lander, Adam Siepel, David Haussler, James W Kent
    posted to alignment by AaronDarling on 2008-06-12 12:20:58 as ** along with 10 people aprasad dchughes nklee maximilianh idonaldson fpattyn gjuggler clearbluespring joavah jyuh
  • Transforming men into mice (polynomial algorithm for genomic distance problem)
    (1995)
    by S Hannenhalli, PA Pevzner
    posted to genomerearrangement by AaronDarling on 2008-06-11 02:56:45 as **
  • Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals
    (1997)
    by Kaplan, Shamir, Tarjan
    posted to genomerearrangement by AaronDarling on 2008-06-11 02:53:00 as **
  • Sorting by Reversals in Subquadratic Time
    Combinatorial Pattern Matching (2004), pp. 1-13.
    by Eric Tannier, Marie-France Sagot
    posted to genomerearrangement by AaronDarling on 2008-06-11 02:51:15 as **
  • A linear-time algorithm for computing inversion distance between signed permutations with an experimental study.
    Journal of computational biology : a journal of computational molecular cell biology, Vol. 8, No. 5. (2001), pp. 483-491.
    by DA Bader, BM Moret, M Yan
    posted to genomerearrangement by AaronDarling on 2008-06-11 02:48:29 as **
  • An algorithm to enumerate sorting reversals for signed permutations.
    Journal of computational biology : a journal of computational molecular cell biology, Vol. 10, No. 3-4. (2003), pp. 575-597.
    by AC Siepel
    posted to genomerearrangement by AaronDarling on 2008-06-11 02:46:18 as **
  • An algorithm to enumerate all sorting reversals
    (2002), pp. 281-290.
    by Adam C Siepel
    posted to genomerearrangement by AaronDarling on 2008-06-11 02:44:51 as **
  • Protein evolution viewed through Escherichia coli protein sequences: introducing the notion of a structural segment of homology, the module.
    Journal of molecular biology, Vol. 268, No. 5. (23 May 1997), pp. 857-868.
    by M Riley, B Labedan
    posted to no-tag by AaronDarling on 2008-06-04 07:05:55 as **
  • Selfish Operons: Horizontal Transfer May Drive the Evolution of Gene Clusters
    Genetics, Vol. 143, No. 4. (1 August 1996), pp. 1843-1860.
    by JG Lawrence, JR Roth
    posted to genomeevolution by AaronDarling on 2008-06-04 07:03:13 as ** along with 1 person mjoach
  • Genome size reduction through multiple events of gene disintegration in Buchnera APS
    Trends in Genetics, Vol. 17, No. 11. (1 November 2001), pp. 615-618.
    by Francisco J Silva, Amparo Latorre, Andrés Moya
    posted to no-tag by AaronDarling on 2008-04-30 07:14:15 as **
  • Monte Carlo sampling methods using Markov chains and their applications
    Biometrika, Vol. 57, No. 1. (1 April 1970), pp. 97-109.
    by WK Hastings
    posted to mcmc by AaronDarling on 2008-03-01 09:25:16 as ** along with 6 people and 1 group tobin iris_2001 Xavier petermilner przem naegele LIGO
  • A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: Convergence or divergence by homologous recombination.
    Genome Res (7 November 2006)
    by Xavier Didelot, Mark Achtman, Julian Parkhill, Nicholas R R Thomson, Daniel Falush
    posted to geneconversion microbialevolution phylogenetics populationgenetics by AaronDarling on 2008-02-28 09:00:06 as ** along with 4 people aswin aiolozil pnicolas Xavier
  • The Nature and Dynamics of Bacterial Genomes
    Science, Vol. 311, No. 5768. (24 March 2006), pp. 1730-1733.
    by Howard Ochman, Liliana M Davalos
    posted to genomeevolution by AaronDarling on 2008-02-28 07:17:22 as ** along with 6 people and 1 group operon dayjm cmm treangen perpetuale pkm FAB-lab
  • FtsK and SpoIIIE: the tale of the conserved tails.
    Mol Microbiol, Vol. 66, No. 5. (December 2007), pp. 1051-1055.
    by FX Barre
    posted to dna-replication by AaronDarling on 2008-02-28 06:59:37 as **
  • Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
    Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 760-774.
    by Elliott H Margulies, Gregory M Cooper, George Asimenos, Daryl J Thomas, Colin N Dewey, Adam Siepel, Ewan Birney, Damian Keefe, Ariel S Schwartz, Minmei Hou, James Taylor, Sergey Nikolaev, Juan I Montoya-Burgos, Ari Loytynoja, Simon Whelan, Fabio Pardi, Tim Massingham, James B Brown, Peter Bickel, Ian Holmes, James C Mullikin, Abel Ureta-Vidal, Benedict Paten, Eric A Stone, Kate R Rosenbloom, James W Kent, Gerard G Bouffard, Xiaobin Guan, Nancy F Hansen, Jacquelyn R Idol, Valerie V Maduro, Baishali Maskeri, Jennifer C Mcdowell, Morgan Park, Pamela J Thomas, Alice C Young, Robert W Blakesley, Donna M Muzny, Erica Sodergren, David A Wheeler, Kim C Worley, Huaiyang Jiang, George M Weinstock, Richard A Gibbs, Tina Graves, Robert Fulton, Elaine R Mardis, Richard K Wilson, Michele Clamp, James Cuff, Sante Gnerre, David B Jaffe, Jean L Chang, Kerstin Lindblad-Toh, Eric S Lander, Angie Hinrichs, Heather Trumbower, Hiram Clawson, Ann Zweig, Robert M Kuhn, Galt Barber, Rachel Harte, Donna Karolchik, Matthew A Field, Richard A Moore, Carrie A Matthewson, Jacqueline E Schein, Marco A Marra, Stylianos E Antonarakis, Serafim Batzoglou, Nick Goldman, Ross Hardison, David Haussler, Webb Miller, Lior Pachter, Eric D Green, Arend Sidow
    posted to alignment by AaronDarling on 2008-01-23 11:20:02 as ** along with 7 people and 4 groups dpollard dchughes djkt ghattem Garamonfok gjuggler elfar Bioinformatics EisenLab G4ID Genetics-of-Gambling
  • Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes.
    Bioinformatics, Vol. 23, No. 13. (1 July 2007)
    by G Lunter
    posted to alignment by AaronDarling on 2008-01-23 11:19:28 as ** along with 3 people and 1 group aprasad mailund elfar Bioinformatics
  • Statistics of local multiple alignments.
    Bioinformatics, Vol. 21 Suppl 1 (June 2005)
    by A Prakash, M Tompa
    posted to motifdetection by AaronDarling on 2007-12-19 08:34:11 as ** along with 2 people treangen timflutre
  • HMMoC a compiler for hidden Markov models
    Bioinformatics, Vol. 23, No. 18. (15 September 2007), pp. 2485-2487.
    by Gerton Lunter
    posted to hmm by AaronDarling on 2007-12-19 08:32:19 as read along with 6 people jyuh operon rdiaz niallhaslam carlescorbi Alfie
  • Inference of Bacterial Microevolution Using Multilocus Sequence Data
    Genetics, Vol. 175, No. 3. (1 March 2007), pp. 1251-1266.
    by Xavier Didelot, Daniel Falush
    posted to genomeevolution microbialevolution recombination speciestree by AaronDarling on 2007-11-01 05:52:36 as ** along with 5 people operon echinotrix Xavier CharlesM pcarbo
  • Genetic flux over time in the Salmonella lineage
    Genome Biology, Vol. 8 (04 June 2007), R100.
    by Georgios S Vernikos, Nicholas R Thomson, Julian Parkhill
    posted to genomeevolution horizontaltransfer by AaronDarling on 2007-11-01 05:40:15 as **
  • How to find small non-coding RNAs in bacteria.
    Biol Chem, Vol. 386, No. 12. (December 2005), pp. 1219-1238.
    by J Vogel, CM Sharma
    posted to noncoding-rna by AaronDarling on 2007-11-01 03:11:47 as **
  • Reduced selection leads to accelerated gene loss in Shigella
    Genome Biology, Vol. 8 (08 August 2007), R164.
    by Ruth Hershberg, Hua Tang, Dmitri A Petrov
    posted to genomeevolution by AaronDarling on 2007-10-31 03:40:07 as ** along with 2 people operon PetrovLab
  • OWEN: aligning long collinear regions of genomes.
    Bioinformatics, Vol. 18, No. 12. (December 2002), pp. 1703-1704.
    by AY Ogurtsov, MA Roytberg, SA Shabalina, AS Kondrashov
    posted to alignment by AaronDarling on 2007-10-30 04:13:04 as ** along with 1 person operon
  • A bayesian analysis of metazoan mitochondrial genome arrangements.
    Mol Biol Evol, Vol. 22, No. 3. (March 2005), pp. 486-495.
    by B Larget, DL Simon, JB Kadane, D Sweet
    posted to genomeevolution genomerearrangement inversions phylogenetics by AaronDarling on 2007-10-15 06:41:04 as **
  • Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome.
    Science (27 September 2007)
    by Jan O O Korbel, Alexander Eckehart E Urban, Jason P P Affourtit, Brian Godwin, Fabian Grubert, Jan Fredrik F Simons, Philip M M Kim, Dean Palejev, Nicholas J J Carriero, Lei Du, Bruce E E Taillon, Zhoutao Chen, Andrea Tanzer, A C Eugenia C Saunders, Jianxiang Chi, Fengtang Yang, Nigel P P Carter, Matthew E E Hurles, Sherman M M Weissman, Timothy T T Harkins, Mark B B Gerstein, Michael Egholm, Michael Snyder
    posted to genomeevolution populationgenetics by AaronDarling on 2007-10-15 02:31:44 as ** along with 10 people and 1 group matthewsuderman dpollard dchughes rdiaz giovanni jlangdon annacarina07 Neeperando jfr caseybrown EisenLab
  • Structural variation in the human genome
    Nature Reviews Genetics, Vol. 7, No. 2., pp. 85-97.
    by Lars Feuk, Andrew R Carson, Stephen W Scherer
    posted to genomeevolution genomerearrangement genomesequencing by AaronDarling on 2007-10-15 02:25:05 as ** along with 15 people and 10 groups jandot cgreal balajis bala balicea dchughes tabu darcyduke adepace rdiaz massivemayhem cat_worth jmrivort ccr Lip CGREL structural_bioinformatics Bioinformatics EisenLab SFX-Verde-team-MITLibraries G4ID G-quadruplex Supramolecular DictyosteliumGroup Genetics-of-Gambling
  • Comparative organization of chloroplast genomes.
    Annu Rev Genet, Vol. 19 (1985), pp. 325-354.
    by JD Palmer
    posted to genomerearrangement by AaronDarling on 2007-10-11 06:46:24 as **
  • Intramolecular recombination of chloroplast genome mediated by short direct-repeat sequences in wheat species.
    Proc Natl Acad Sci U S A, Vol. 85, No. 22. (November 1988), pp. 8573-8577.
    by Y Ogihara, T Terachi, T Sasakuma
    posted to genomerearrangement by AaronDarling on 2007-10-11 06:44:21 as **
  • Structural rearrangements, including parallel inversions, within the chloroplast genome of Anemone and related genera.
    J Mol Evol, Vol. 38, No. 3. (March 1994), pp. 274-281.
    by SB Hoot, JD Palmer
    posted to genomerearrangement by AaronDarling on 2007-10-11 06:43:25 as **
  • Genomic rearrangements at rrn operons in Salmonella.
    Genetics, Vol. 165, No. 3. (November 2003), pp. 951-959.
    by RA Helm, AG Lee, HD Christman, S Maloy
    posted to genomerearrangement by AaronDarling on 2007-10-09 07:24:55 as **
  • Bi-directional chromosomal replication in Salmonella typhimurium.
    J Bacteriol, Vol. 115, No. 1. (July 1973), pp. 168-176.
    by T Fujisawa, A Eisenstark
    posted to dna-replication by AaronDarling on 2007-10-09 06:45:52 as **
  • A new implementation and detailed study of breakpoint analysis
    (2001)
    by B Moret, S Wyman, D Bader, T Warnow, M Yan
    posted to genomerearrangement by AaronDarling on 2007-10-09 06:40:14 as **
  • Dependence of paracentric inversion rate on tract length
    BMC Bioinformatics, Vol. 8 (03 April 2007), 115.
    by Thomas L York, Rick Durrett, Rasmus Nielsen
    posted to genomerearrangement by AaronDarling on 2007-09-15 10:54:55 as **
  • Rare genomic changes as a tool for phylogenetics.
    Trends Ecol Evol, Vol. 15, No. 11. (1 November 2000), pp. 454-459.
    by A Rokas, PW Holland
    posted to genomerearrangement by AaronDarling on 2007-09-15 10:50:25 as **
  • M-GCAT: Interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species
    BMC Bioinformatics, Vol. 7 (05 October 2006), 433.
    by Todd J Treangen, Xavier Messeguer
    posted to alignment genomecomparison genomerearrangement by AaronDarling on 2007-09-09 08:59:45 as ** along with 1 person treangen
  • An Integrative Method for Accurate Comparative Genome Mapping.
    PLoS Comput Biol, Vol. 2, No. 8. (4 August 2006)
    by Firas Swidan, Eduardo P C P Rocha, Michael Shmoish, Ron Y Y Pinter
    posted to alignment genomerearrangement by AaronDarling on 2007-09-09 08:53:38 as ** along with 1 person bjorns
  • Pairwise alignment with rearrangements.
    Genome Inform, Vol. 17, No. 2. (2006), pp. 141-151.
    by le S Vinh, A Varón, WC Wheeler
    posted to alignment genomerearrangement by AaronDarling on 2007-09-09 08:52:43 as **
  • Measuring the accuracy of genome-size multiple alignments
    Genome Biology, Vol. 8 (26 June 2007), R124.
    by Amol Prakash, Martin Tompa
    posted to alignment by AaronDarling on 2007-09-06 09:21:24 as ** along with 3 people and 2 groups dpollard stajich lilou EisenLab Berkeley Mycology
  • A local alignment tool for very long DNA sequences.
    Comput Appl Biosci, Vol. 11, No. 2. (April 1995), pp. 147-153.
    by KM Chao, J Zhang, J Ostell, W Miller
    posted to alignment by AaronDarling on 2007-09-06 08:57:58 as **
  • Multiseed Lossless Filtration
    IEEE/ACM Trans. Comput. Biol. Bioinformatics, Vol. 2, No. 1. (January 2005), pp. 51-61.
    by Gregory Kucherov, Laurent Noe, Mikhail Roytberg
    posted to alignment by AaronDarling on 2007-09-06 08:46:55 as ** along with 1 person nedwards
  • Characterization and modeling of the Haemophilus influenzae core- and supra-genomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains
    Genome Biology, Vol. 8 (05 June 2007), R103.
    by JS Hogg, Fen Z Hu, Benjamin Janto, Robert Boissy, Jay Hayes, Randy Keefe, Christopher J Post, Garth D Ehrlich
    posted to genomecomparison by AaronDarling on 2007-09-06 08:43:03 as **
  • Mutational bias suggests that replication termination occurs near the dif site, not at Ter sites
    Molecular Microbiology, Vol. 64, No. 1. (April 2007), pp. 42-56.
    by Hendrickson, Heather, Lawrence, G Jeffrey
    posted to dna-replication by AaronDarling on 2007-08-30 11:49:04 as **
  • A molecular mousetrap determines polarity of termination of DNA replication in E. coli.
    Cell, Vol. 125, No. 7. (30 June 2006), pp. 1309-1319.
    by MD Mulcair, PM Schaeffer, AJ Oakley, HF Cross, C Neylon, TM Hill, NE Dixon
    posted to dna-replication by AaronDarling on 2007-08-30 11:43:34 as ** along with 1 person CameronNeylon
  • F-prime factors of Salmonella typhimurium and an inversion between S. typhimurium and Escherichia coli.
    Genetics, Vol. 64, No. 2. (February 1970), pp. 215-228.
    by KE Sanderson, CA Hall
    posted to genomerearrangement by AaronDarling on 2007-08-30 11:40:54 as **
  • Comment on "Phylogenetic MCMC Algorithms Are Misleading on Mixtures of Trees"
    Science, Vol. 312, No. 5772. (21 April 2006), 367a.
    by Fredrik Ronquist, Bret Larget, John P Huelsenbeck, Joseph B Kadane, Donald Simon, Paul van der Mark
    posted to phylogenetics by AaronDarling on 2007-08-21 01:45:44 as read along with 1 person aprasad
  • The Fragile Breakage versus Random Breakage Models of Chromosome Evolution.
    PLoS Comput Biol, Vol. 2, No. 2. (24 February 2006)
    by Qian Peng, Pavel A A Pevzner, Glenn Tesler
    posted to genomerearrangement by AaronDarling on 2007-08-21 01:07:37 as ** along with 1 person maximilianh
  • Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution
    PNAS, Vol. 100, No. 13. (24 June 2003), pp. 7672-7677.
    by Pavel Pevzner, Glenn Tesler
    posted to genomerearrangement by AaronDarling on 2007-08-21 01:03:57 as **
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