Hawkeye: an interactive visual analytics tool for genome assemblies

Michael C Schatz, Adam M Phillippy, Ben Shneiderman, Steven L Salzberg

Genome Biol. 2007; 8(3): R34. Published online 2007 March 9. doi: 10.1186/gb-2007-8-3-r34

PMCID:: PMC1868940

Is Cited by the Following 24 Articles in this Archive:

The Cotton Centromere Contains a Ty3-gypsy-like LTR Retroelement

Song Luo, Jennifer Mach, Bradley Abramson, Rolando Ramirez, Robert Schurr, Pierluigi Barone, Gregory Copenhaver, Otto Folkerts

PLoS One. 2012; 7(4): e35261. Published online 2012 April 19. doi: 10.1371/journal.pone.0035261

PMCID:: PMC3334964

Abstract Full Text PDF–605K Supplementary Material

Bacteriophages ϕMR299-2 and ϕNH-4 Can Eliminate Pseudomonas aeruginosa in the Murine Lung and on Cystic Fibrosis Lung Airway Cells

Debebe Alemayehu, Pat G. Casey, Olivia McAuliffe, Caitriona M. Guinane, James G. Martin, Fergus Shanahan, Aidan Coffey, R. Paul Ross, Colin Hill

mBio. 2012 Mar-Apr; 3(2): e00029-12. Published online 2012 March 6. doi: 10.1128/mBio.00029-12

PMCID:: PMC3302570

Abstract Full Text PDF–1.4M Supplementary Material

Complete Genome Sequence of the Beer Spoilage Organism Pediococcus claussenii ATCC BAA-344^T

Vanessa Pittet, Teju Abegunde, Travis Marfleet, Monique Haakensen, Kendra Morrow, Teenus Jayaprakash, Kristen Schroeder, Brett Trost, Sydney Byrns, Jordyn Bergsveinson, Anthony Kusalik, Barry Ziola

J Bacteriol. 2012 March; 194(5): 1271–1272. doi: 10.1128/JB.06759-11

PMCID:: PMC3294761

Free in PMC on 2012/09/01

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

Tim Carver, Simon R. Harris, Matthew Berriman, Julian Parkhill, Jacqueline A. McQuillan

Bioinformatics. 2012 February 15; 28(4): 464–469. Published online 2011 December 22. doi: 10.1093/bioinformatics/btr703

PMCID:: PMC3278759

Abstract Full Text PDF–811K

Major Families of Multiresistant Plasmids from Geographically and Epidemiologically Diverse Staphylococci

Julia E. S. Shearer, Joy Wireman, Jessica Hostetler, Heather Forberger, Jon Borman, John Gill, Susan Sanchez, Alexander Mankin, Jacqueline LaMarre, Jodi A. Lindsay, Kenneth Bayles, Ainsley Nicholson, Frances O’Brien, Slade O. Jensen, Neville Firth, Ronald A. Skurray, Anne O. Summers

G3 (Bethesda) 2011 December; 1(7): 581–591. Published online 2011 December 1. doi: 10.1534/g3.111.000760

PMCID:: PMC3276174

Abstract Full Text PDF–1.0M

Two New Complete Genome Sequences Offer Insight into Host and Tissue Specificity of Plant Pathogenic Xanthomonas spp.

Adam J. Bogdanove, Ralf Koebnik, Hong Lu, Ayako Furutani, Samuel V. Angiuoli, Prabhu B. Patil, Marie-Anne Van Sluys, Robert P. Ryan, Damien F. Meyer, Sang-Wook Han, Gudlur Aparna, Misha Rajaram, Arthur L. Delcher, Adam M. Phillippy, Daniela Puiu, Michael C. Schatz, Martin Shumway, Daniel D. Sommer, Cole Trapnell, Faiza Benahmed, George Dimitrov, Ramana Madupu, Diana Radune, Steven Sullivan, Gopaljee Jha, Hiromichi Ishihara, Sang-Won Lee, Alok Pandey, Vikas Sharma, Malinee Sriariyanun, Boris Szurek, Casiana M. Vera-Cruz, Karin S. Dorman, Pamela C. Ronald, Valérie Verdier, J. Maxwell Dow, Ramesh V. Sonti, Seiji Tsuge, Volker P. Brendel, Pablo D. Rabinowicz, Jan E. Leach, Frank F. White, Steven L. Salzberg

J Bacteriol. 2011 October; 193(19): 5450–5464. doi: 10.1128/JB.05262-11

PMCID:: PMC3187462

Abstract Full Text PDF–3.5M Supplementary Material

Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths

Jacob Enk, Alison Devault, Regis Debruyne, Christine E King, Todd Treangen, Dennis O'Rourke, Steven L Salzberg, Daniel Fisher, Ross MacPhee, Hendrik Poinar

Genome Biol. 2011; 12(5): R51. Published online 2011 May 31. doi: 10.1186/gb-2011-12-5-r51

PMCID:: PMC3219973

Abstract Full Text PDF–809K Supplementary Material

Host Specific Diversity in Lactobacillus johnsonii as Evidenced by a Major Chromosomal Inversion and Phage Resistance Mechanisms

Caitriona M. Guinane, Robert M. Kent, Sarah Norberg, Colin Hill, Gerald F. Fitzgerald, Catherine Stanton, R. Paul Ross

PLoS One. 2011; 6(4): e18740. Published online 2011 April 20. doi: 10.1371/journal.pone.0018740

PMCID:: PMC3080392

Abstract Full Text PDF–552K Supplementary Material

Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies

Joshua Wetzel, Carl Kingsford, Mihai Pop

BMC Bioinformatics. 2011; 12: 95. Published online 2011 April 13. doi: 10.1186/1471-2105-12-95

PMCID:: PMC3103447

Abstract Full Text PDF–360K Supplementary Material

Next Generation Sequence Assembly with AMOS

Todd J Treangen, Dan D Sommer, Florent E Angly, Sergey Koren, Mihai Pop

Curr Protoc Bioinformatics. Author manuscript; available in PMC 2012 March 1.

Published in final edited form as: Curr Protoc Bioinformatics. 2011 March; CHAPTER: Unit11.8. doi: 10.1002/0471250953.bi1108s33

PMCID:: PMC3072823

Abstract Full Text PDF–1020K

An Sp185/333 gene cluster from the purple sea urchin and putative microsatellite-mediated gene diversification

Chase A Miller, Katherine M Buckley, Rebecca L Easley, L Courtney Smith

BMC Genomics. 2010; 11: 575. Published online 2010 October 18. doi: 10.1186/1471-2164-11-575

PMCID:: PMC3091723

Abstract Full Text PDF–2.2M

Gap5—editing the billion fragment sequence assembly

James K. Bonfield, Andrew Whitwham

Bioinformatics. 2010 July 15; 26(14): 1699–1703. Published online 2010 May 30. doi: 10.1093/bioinformatics/btq268

PMCID:: PMC2894512

Abstract Full Text PDF–305K Supplementary Material

Genome assembly quality: Assessment and improvement using the neutral indel model

Stephen Meader, LaDeana W. Hillier, Devin Locke, Chris P. Ponting, Gerton Lunter

Genome Res. 2010 May; 20(5): 675–684. doi: 10.1101/gr.096966.109

PMCID:: PMC2860169

Abstract Full Text PDF–632K

Tablet—next generation sequence assembly visualization

Iain Milne, Micha Bayer, Linda Cardle, Paul Shaw, Gordon Stephen, Frank Wright, David Marshall

Bioinformatics. 2010 February 1; 26(3): 401–402. Published online 2009 December 4. doi: 10.1093/bioinformatics/btp666

PMCID:: PMC2815658

Abstract Full Text PDF–217K

LookSeq: A browser-based viewer for deep sequencing data

Heinrich Magnus Manske, Dominic P. Kwiatkowski

Genome Res. 2009 November; 19(11): 2125–2132. doi: 10.1101/gr.093443.109

PMCID:: PMC2775587

Abstract Full Text PDF–1.7M

Genome assembly reborn: recent computational challenges

Mihai Pop

Brief Bioinform. 2009 July; 10(4): 354–366. Published online 2009 May 29. doi: 10.1093/bib/bbp026

PMCID:: PMC2691937

Abstract Full Text PDF–184K

A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads

Tobias Rausch, Sergey Koren, Gennady Denisov, David Weese, Anne-Katrin Emde, Andreas Döring, Knut Reinert

Bioinformatics. 2009 May 1; 25(9): 1118–1124. Published online 2009 March 5. doi: 10.1093/bioinformatics/btp131

PMCID:: PMC2732307

Abstract Full Text PDF–342K

The HuRef Browser: a web resource for individual human genomics

Nelson Axelrod, Yuan Lin, Pauline C. Ng, Timothy B. Stockwell, Jonathan Crabtree, Jiaqi Huang, Ewen Kirkness, Robert L. Strausberg, Marvin E. Frazier, J. Craig Venter, Saul Kravitz, Samuel Levy

Nucleic Acids Res. 2009 January; 37(Database issue): D1018–D1024. Published online 2009 January. doi: 10.1093/nar/gkn939

PMCID:: PMC2686481

Abstract Full Text PDF–7.4M

Re-Assembly of the Genome of Francisella tularensis Subsp. holarctica OSU18

Daniela Puiu, Steven L. Salzberg

PLoS ONE. 2008; 3(10): e3427. Published online 2008 October 17. doi: 10.1371/journal.pone.0003427

PMCID:: PMC2561293

Abstract Full Text PDF–259K Supplementary Material

EagleView: A genome assembly viewer for next-generation sequencing technologies

Weichun Huang, Gabor Marth

Genome Res. 2008 September; 18(9): 1538–1543. doi: 10.1101/gr.076067.108

PMCID:: PMC2527701

Abstract Full Text PDF–717K

A visual analytics approach for understanding biclustering results from microarray data

Rodrigo Santamaría, Roberto Therón, Luis Quintales

BMC Bioinformatics. 2008; 9: 247. Published online 2008 May 27. doi: 10.1186/1471-2105-9-247

PMCID:: PMC2416653

Abstract Full Text PDF–2.4M Supplementary Material

Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99^A

Steven L Salzberg, Daniel D Sommer, Michael C Schatz, Adam M Phillippy, Pablo D Rabinowicz, Seiji Tsuge, Ayako Furutani, Hirokazu Ochiai, Arthur L Delcher, David Kelley, Ramana Madupu, Daniela Puiu, Diana Radune, Martin Shumway, Cole Trapnell, Gudlur Aparna, Gopaljee Jha, Alok Pandey, Prabhu B Patil, Hiromichi Ishihara, Damien F Meyer, Boris Szurek, Valerie Verdier, Ralf Koebnik, J Maxwell Dow, Robert P Ryan, Hisae Hirata, Shinji Tsuyumu, Sang Won Lee, Pamela C Ronald, Ramesh V Sonti, Marie-Anne Van Sluys, Jan E Leach, Frank F White, Adam J Bogdanove

BMC Genomics. 2008; 9: 204. Published online 2008 May 1. doi: 10.1186/1471-2164-9-204