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Group: gatech-compgenomics - library [33 articles]

Recent papers posted by members of the gatech-compgenomics group
  • Mauve: multiple alignment of conserved genomic sequence with rearrangements.
    Genome Res, Vol. 14, No. 7. (July 2004), pp. 1394-1403.
    by AC Darling, B Mau, FR Blattner, NT Perna
    posted to qual by azazello to the group gatech-compgenomics on 2008-03-25 13:59:11 as ** along with 6 people Neeperando mariakmejia operon catmat AaronDarling leelarcombe
  • Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis.
    Proc Natl Acad Sci U S A, Vol. 105, No. 9. (4 March 2008), pp. 3473-3478.
    by C Schoen, J Blom, H Claus, A Schramm-Glück, P Brandt, T Müller, A Goesmann, B Joseph, S Konietzny, O Kurzai, C Schmitt, T Friedrich, B Linke, U Vogel, M Frosch
    posted to qual by azazello to the group gatech-compgenomics on 2008-03-24 13:38:46 as ** along with 1 person martainn
  • Whole-genome sequencing and assembly with high-throughput, short-read technologies.
    PLoS ONE, Vol. 2 (2007)
    by A Sundquist, M Ronaghi, H Tang, P Pevzner, S Batzoglou
    posted to qual by azazello to the group gatech-compgenomics on 2008-03-21 15:41:38 as ** along with 3 people iris42 jyuh nedwards
  • De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer.
    Genome Res (10 March 2008)
    by David Hernandez, Patrice Francois, Laurent Farinelli, Magne Osteras, Jacques Schrenzel
    posted to qual by azazello to the group gatech-compgenomics on 2008-03-21 15:40:48 as ** along with 6 people and 2 groups balicea Neeperando jmeppley stajich Katje iris42 microbiology_nijmegen Berkeley Mycology
  • Pyrobayes: an improved base caller for SNP discovery in pyrosequences
    Nature Methods, Vol. 5, No. 2. (13 January 2008), pp. 179-181.
    by Aaron R Quinlan, Donald A Stewart, Michael P Strömberg, Gábor T Marth
    posted to no-tag by azazello to the group gatech-compgenomics on 2008-03-21 15:38:46 as ** along with 3 people jyuh mariakmejia jmeppley
  • A general approach to single-nucleotide polymorphism discovery.
    Nat Genet, Vol. 23, No. 4. (December 1999), pp. 452-456.
    by GT Marth, I Korf, MD Yandell, RT Yeh, Z Gu, H Zakeri, NO Stitziel, L Hillier, PY Kwok, WR Gish
    posted to qual by azazello to the group gatech-compgenomics on 2008-03-21 15:37:44 as ** along with 3 people farhat gpappas Ayest
  • Hawkeye: a visual analytics tool for genome assemblies
    Genome Biology, Vol. 8 (09 March 2007), R34.
    by Michael C Schatz, Adam M Phillippy, Ben Shneiderman, Steven L Salzberg
    posted to no-tag by azazello to the group gatech-compgenomics on 2008-02-12 23:36:36 as ** along with 2 people and 1 group Neeperando stajich Berkeley Mycology
  • Characterization of ST-4821 complex, a unique Neisseria meningitidis clone.
    Genomics, Vol. 91, No. 1. (January 2008), pp. 78-87.
    by J Peng, L Yang, F Yang, J Yang, Y Yan, H Nie, X Zhang, Z Xiong, Y Jiang, F Cheng, X Xu, S Chen, L Sun, W Li, Y Shen, Z Shao, X Liang, J Xu, Q Jin
    posted to meningitidis by tpreeprem to the group gatech-compgenomics on 2008-01-28 21:10:13 as *****
  • A sequencing method based on real-time pyrophosphate.
    Science, Vol. 281, No. 5375. (17 July 1998)
    by M Ronaghi, M Uhlén, P Nyrén
    posted to pyrosequencing by tpreeprem to the group gatech-compgenomics on 2008-01-28 06:43:22 as ** along with 1 person kieran101
  • Improved performance of pyrosequencing using single-stranded DNA-binding protein.
    Anal Biochem, Vol. 286, No. 2. (15 November 2000), pp. 282-288.
    by M Ronaghi
    posted to pyrosequencing by tpreeprem to the group gatech-compgenomics on 2008-01-28 06:36:15 as ***
  • Pyrosequencing sheds light on DNA sequencing.
    Genome Res, Vol. 11, No. 1. (January 2001), pp. 3-11.
    by M Ronaghi
    posted to pyrosequencing by tpreeprem to the group gatech-compgenomics on 2008-01-28 06:32:44 as *** along with 4 people balicea darioacha kieran101 mariakmejia
  • Genome sequencing in microfabricated high-density picolitre reactors
    Nature (31 July 2005)
    by Marcel Margulies, Michael Egholm, William E Altman, Said Attiya, Joel S Bader, Lisa A Bemben, Jan Berka, Michael S Braverman, Yi-Ju Chen, Zhoutao Chen, Scott B Dewell, Lei Du, Joseph M Fierro, Xavier V Gomes, Brian C Godwin, Wen He, Scott Helgesen, Chun H Ho, Gerard P Irzyk, Szilveszter C Jando, Maria LI Alenquer, Thomas P Jarvie, Kshama B Jirage, Jong-Bum Kim, James R Knight, Janna R Lanza, John H Leamon, Steven M Lefkowitz, Ming Lei, Jing Li, Kenton L Lohman, Hong Lu, Vinod B Makhijani, Keith E Mcdade, Michael P Mckenna, Eugene W Myers, Elizabeth Nickerson, John R Nobile, Ramona Plant, Bernard P Puc, Michael T Ronan, George T Roth, Gary J Sarkis, Jan F Simons, John W Simpson, Maithreyan Srinivasan, Karrie R Tartaro, Alexander Tomasz, Kari A Vogt, Greg A Volkmer, Shally H Wang, Yong Wang, Michael P Weiner, Pengguang Yu, Richard F Begley, Jonathan M Rothberg
    posted to 454 by tpreeprem to the group gatech-compgenomics on 2008-01-26 21:17:47 as *** along with 22 people and 2 groups kieran101 GustavoLacerda farhat mcox bpb carpi bjorns dayjm jmeppley arve RMGraze JAShapiro balajis cdawson AaronDarling treangen usagi-kirin azazello beatrizfernandez wenhan xingxu erbon Microbial-Ecology GIG
  • The Genome Assembly Archive: A New Public Resource
    PLoS Biology, Vol. 2, No. 9. (1 September 2004), e285.
    by Steven L Salzberg, Deanna Church, Michael Dicuccio, Eugene Yaschenko, James Ostell
    posted to assembly software by tpreeprem to the group gatech-compgenomics on 2008-01-25 20:45:51 as ** along with 1 person GustavoLacerda
  • Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005)
    by SA van Hijum, AL Zomer, OP Kuipers, J Kok
    posted to scaffolding by azazello to the group gatech-compgenomics on 2008-01-25 17:14:23 as **
  • Projector: automatic contig mapping for gap closure purposes.
    Nucleic Acids Res, Vol. 31, No. 22. (15 November 2003)
    by SA van Hijum, AL Zomer, OP Kuipers, J Kok
    posted to scaffolding by azazello to the group gatech-compgenomics on 2008-01-25 17:13:26 as **
  • Comparative genome assembly.
    Brief Bioinform, Vol. 5, No. 3. (September 2004), pp. 237-248.
    by M Pop, A Phillippy, AL Delcher, SL Salzberg
    posted to assembly comparasion by tpreeprem to the group gatech-compgenomics on 2008-01-22 06:54:31 as *** along with 7 people and 1 group Ema Neeperando mariakmejia treangen azazello wenhan urgi MBLAB
  • A whole-genome assembly of Drosophila.
    Science, Vol. 287, No. 5461. (24 March 2000), pp. 2196-2204.
    by EW Myers, GG Sutton, AL Delcher, IM Dew, DP Fasulo, MJ Flanigan, SA Kravitz, CM Mobarry, KH Reinert, KA Remington, EL Anson, RA Bolanos, HH Chou, CM Jordan, AL Halpern, S Lonardi, EM Beasley, RC Brandon, L Chen, PJ Dunn, Z Lai, Y Liang, DR Nusskern, M Zhan, Q Zhang, X Zheng, GM Rubin, MD Adams, JC Venter
    posted to assembly by tpreeprem to the group gatech-compgenomics on 2008-01-17 01:45:30 as ** along with 4 people and 1 group bluto azazello wenhan yoanjacquemin MBLAB
  • The greedy path-merging algorithm for contig scaffolding
    J. ACM, Vol. 49, No. 5. (September 2002), pp. 603-615.
    by Daniel H Huson, Knut Reinert, Eugene W Myers
    posted to algorithm by tpreeprem to the group gatech-compgenomics on 2008-01-17 01:41:30 as ** along with 1 person azazello
  • The greedy path-merging algorithm for sequence assembly
    (2001), pp. 157-163.
    by Daniel H Huson, Knut Reinert, Eugene Myers
    posted to algorithm by tpreeprem to the group gatech-compgenomics on 2008-01-17 01:36:38 as **
  • Genome Sequence Assembly: Algorithms and Issues
    posted to algorithms and assembly genome issues sequence by vineith to the group gatech-compgenomics on 2008-01-16 15:03:15 as ** along with 1 person tpreeprem
  • PCAP: A Whole-Genome Assembly Program
    Genome Res., Vol. 13, No. 9. (1 September 2003), pp. 2164-2170.
    by Xiaoqiu Huang, Jianmin Wang, Srinivas Aluru, Shiaw-Pyng Yang, Ladeana Hillier
    posted to no-tag by vineith to the group gatech-compgenomics on 2008-01-16 14:54:02 as ** along with 2 people Neeperando wenhan
  • Comparative genomics of Neisseria meningitidis: core genome, islands of horizontal transfer and pathogen-specific genes.
    Microbiology, Vol. 152, No. Pt 12. (December 2006), pp. 3733-3749.
    by JC Hotopp, R Grifantini, N Kumar, YL Tzeng, D Fouts, E Frigimelica, M Draghi, MM Giuliani, R Rappuoli, DS Stephens, G Grandi, H Tettelin
    posted to functional meningitidis by tpreeprem to the group gatech-compgenomics on 2008-01-16 05:26:26 as ** along with 1 person treangen
  • Complete Genome Sequence of Neisseria meningitidis Serogroup B Strain MC58
    Science, Vol. 287, No. 5459. (10 March 2000), pp. 1809-1815.
    by Hervé Tettelin, Nigel J Saunders, John Heidelberg, Alex C Jeffries, Karen E Nelson, Jonathan A Eisen, Karen A Ketchum, Derek W Hood, John F Peden, Robert J Dodson, William C Nelson, Michelle L Gwinn, Robert Deboy, Jeremy D Peterson, Erin K Hickey, Daniel H Haft, Steven L Salzberg, Owen White, Robert D Fleischmann, Brian A Dougherty, Tanya Mason, Anne Ciecko, Debbie S Parksey, Eric Blair, Henry Cittone, Emily B Clark, Matthew D Cotton, Terry R Utterback, Hoda Khouri, Haiying Qin, Jessica Vamathevan, John Gill, Vincenzo Scarlato, Vega Masignani, Mariagrazia Pizza, Guido Grandi, Li Sun, Hamilton O Smith, Claire M Fraser, Richard E Moxon, Rino Rappuoli, Craig J Venter
    posted to meningitidis sequence by tpreeprem to the group gatech-compgenomics on 2008-01-16 04:37:08 as ***** along with 2 people treangen karenidwilson
  • Meningococcal genetic variation mechanisms viewed through comparative analysis of serogroup C strain FAM18.
    PLoS Genet, Vol. 3, No. 2. (16 February 2007)
    by SD Bentley, GS Vernikos, LA Snyder, C Churcher, C Arrowsmith, T Chillingworth, A Cronin, PH Davis, NE Holroyd, K Jagels, M Maddison, S Moule, E Rabbinowitsch, S Sharp, L Unwin, S Whitehead, MA Quail, M Achtman, B Barrell, NJ Saunders, J Parkhill
    posted to meningitidis sequence by tpreeprem to the group gatech-compgenomics on 2008-01-16 04:21:14 as *****
  • Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491.
    Nature, Vol. 404, No. 6777. (30 March 2000), pp. 502-506.
    by J Parkhill, M Achtman, KD James, SD Bentley, C Churcher, SR Klee, G Morelli, D Basham, D Brown, T Chillingworth, RM Davies, P Davis, K Devlin, T Feltwell, N Hamlin, S Holroyd, K Jagels, S Leather, S Moule, K Mungall, MA Quail, MA Rajandream, KM Rutherford, M Simmonds, J Skelton, S Whitehead, BG Spratt, BG Barrell
    posted to meningitidis sequence by tpreeprem to the group gatech-compgenomics on 2008-01-16 03:55:53 as ***** along with 1 person treangen
  • Comparison Of 454 Sequencing Platform With Traditional Sanger Sequencing: A Case Study With De Novo Sequencing Of Prochlorococcus Marinus NATL2A Genome
    by Feng Chen, Joseph Alessi, Edward Kirton, Vasanth Singan, Paul Richardson
    posted to 454 comparasion by tpreeprem to the group gatech-compgenomics on 2008-01-16 03:00:17 as ***
  • Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology
    BMC Genomics, Vol. 7 (24 October 2006), 272.
    by Foo Cheung, Brian J Haas, Susanne MD Goldberg, Gregory D May, Yongli Xiao, Christopher D Town
    posted to 454 sequencing by tpreeprem to the group gatech-compgenomics on 2008-01-16 02:43:48 as ** along with 2 people tonia_schwartz usagi-kirin
  • ARACHNE: A Whole-Genome Shotgun Assembler
    Genome Res., Vol. 12, No. 1. (1 January 2002), pp. 177-189.
    by Serafim Batzoglou, David B Jaffe, Ken Stanley, Jonathan Butler, Sante Gnerre, Evan Mauceli, Bonnie Berger, Jill P Mesirov, Eric S Lander
    posted to arachne assembly software by tpreeprem to the group gatech-compgenomics on 2008-01-16 02:36:32 as ** along with 10 people and 2 groups pradiptaray Neeperando bpb dayjm balajis indigoviolet balicea ccr azazello wenhan EisenLab MBLAB
  • 454 sequencing put to the test using the complex genome of barley
    BMC Genomics, Vol. 7 (26 October 2006), 275.
    by Thomas Wicker, Edith Schlagenhauf, Andreas Graner, Timothy J Close, Beat Keller, Nils Stein
    posted to 454 by tpreeprem to the group gatech-compgenomics on 2008-01-16 02:35:06 as ** along with 5 people and 2 groups jmeppley balicea ghattem azazello cisevol MBLAB BergmanLab
  • High-throughput sequence alignment using Graphics Processing Units
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Michael Schatz, Cole Trapnell, Arthur Delcher, Amitabh Varshney
    posted to gpu sequencing software by tpreeprem to the group gatech-compgenomics on 2008-01-16 02:34:53 as ** along with 10 people Yanno jyuh sephy lusk laughcry nedwards mdimon cndewey heliopais urgi
  • Optical mapping as a routine tool in bacterial genome sequencing
    BMC Genomics, Vol. 8 (14 September 2007), 321.
    by Phil Latreille, Stacie Norton, Barry S Goldman, John Henkhaus, Nancy Miller, Brad Barbazuk, Helge B Bode, Creg Darby, Zijin Du, Steve Forst, Sophie Gaudriault, Brad Goodner, Heidi Goodrich-Blair, Steven Slater
    posted to assembly optical by tpreeprem to the group gatech-compgenomics on 2008-01-16 02:33:33 as **
  • Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey
    BMC Genomics, Vol. 8 (24 May 2007), 132.
    by Kankshita Swaminathan, Kranthi Varala, Matthew E Hudson
    posted to 454 assembly by tpreeprem to the group gatech-compgenomics on 2008-01-16 02:31:38 as ** along with 2 people and 1 group ghattem GustavoLacerda BergmanLab
  • Accuracy and quality of massively-parallel DNA pyrosequencing
    Genome Biology, Vol. 8 (20 July 2007), R143.
    by Susan M Huse, Julie A Huber, Hilary G Morrison, Mitchell L Sogin, David M Welch
    posted to 454 by azazello to the group gatech-compgenomics on 2008-01-14 21:34:38 as ** along with 7 people and 2 groups Olaf_Ilzins gpappas jmeppley mblwhoi grahamc GustavoLacerda blobbybirdman Bioinformatics ParkinsonLab_at_MaRS
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