pypi: Arachne | Projects | Ecosyste.ms: Papers

10.1038/s42003-021-02009-0

Pests, diseases, and aridity have shaped the genome of Corymbia citriodora
Cited by: 15
Author(s): Adam Healey, Mervyn Shepherd, Graham J. King, Jakob B. Butler, Jules S. Freeman, David J Lee, Brad M. Potts, Orzenil B. Silva‐Junior, Abdul Baten, Jerry Jenkins, Shengqiang Shu, John T. Lovell, Avinash Sreedasyam, Jane Grimwood, Agnelo Furtado, Dário Grattapaglia, Kerrie Barry, Hope Hundley, Blake A. Simmons, Jeremy Schmutz, René E. Vaillancourt, Robert J. Henry
Software Mentions: 10
Published: over 3 years ago

10.7554/eLife.62362

Accelerating with FlyBrainLab the discovery of the functional logic of the Drosophila brain in the connectomic and synaptomic era
Cited by: 17
Author(s): Aurel A. Lazar, Tingkai Liu, Mehmet Kerem Türkcan, Yiyin Zhou
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0207531

The conservation landscape of the human ribosomal RNA gene repeats
Cited by: 50
Author(s): Saumya Agrawal, Austen R. D. Ganley
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.ppat.1002567

Comparative Genomics of the Apicomplexan Parasites Toxoplasma gondii and Neospora caninum: Coccidia Differing in Host Range and Transmission Strategy
Cited by: 197
Author(s): Adam J. Reid, Sarah J. Vermont, James A. Cotton, David J. Harris, Grant A. Hill-Cawthorne, Stephanie Könen‐Waisman, Sophia M. Latham, Tobias Mourier, Rebecca Norton, Michael A. Quail, Mandy Sanders, Dhanasekaran Shanmugam, Amandeep Sohal, James D. Wasmuth, Brian P. Brunk, Michael E. Grigg, Jonathan C. Howard, John Parkinson, David S. Roos, A. J. Trees, Matthew Berriman, Arnab Pain, Jonathan M. Wastling
Software Mentions: 5
Published: over 12 years ago

10.1371/journal.pone.0067511

Evolutionary Dynamics of the Accessory Genome of Listeria monocytogenes
Cited by: 55
Author(s): Henk C. den Bakker, Christopher A. Desjardins, Allison Griggs, Joseph E. Peters, Qiandong Zeng, Sarah Young, Chinnappa D. Kodira, Chandri Yandava, Theresa A. Hepburn, Brian J. Haas, Bruce W. Birren, Martin Wiedmann
Software Mentions: 4
Published: over 11 years ago

10.1093/bioinformatics/bts458

MolBioLib: a C++11 framework for rapid development and deployment of bioinformatics tasks
Cited by: 9
Author(s): Toshiro K. Ohsumi, Mark Borowsky
Software Mentions: 4
Published: over 12 years ago

10.1186/1755-8794-8-S2-S13

SeedsGraph: an efficient assembler for next-generation sequencing data
Cited by: 2
Author(s): Chuyu Wang, Maozu Guo, Xiaoyan Liu, Yang Liu, Quan Zou
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pgen.1004261

Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation
Cited by: 329
Author(s): Guilhem Janbon, Kate L. Ormerod, Damien Paulet, Edmond J. Byrnes, Vikas Yadav, Gautam Chatterjee, Nandita Mullapudi, Chung-Chau Hon, R. Blake Billmyre, François Brunel, Yong-Sun Bahn, Weidong Chen, Yuan Chen, Eve W. L. Chow, Jean Yves Coppée, Anna Floyd-Averette, Claude Gaillardin, Kimberly J. Gerik, Jonathan M. Goldberg, Sara Gonzalez-Hilarion, Sharvari Gujja, Joyce L. Hamlin, Yu-Ting Hsueh, Giuseppe Ianiri, Steven J.M. Jones, Chinnappa D. Kodira, Lukasz Kozubowski, Woei C. Lam, Marco A. Marra, Larry D. Mesner, Piotr A. Mieczkowski, Frédérique Moyrand, Kirsten Nielsen, Caroline Proux, Tristan Rossignol, Jacqueline E. Schein, Sheng Sun, Carolin Wollschlaeger, Ian Wood, Qiandong Zeng, Cécile Neuvéglise, Carol S. Newlon, John R. Perfect, Jennifer K. Lodge, Alexander Idnurm, Jason E. Stajich, James W. Kronstad, Kaustuv Sanyal, Joseph Heitman, James A. Fraser, Christina A. Cuomo, Fred S. Dietrich
Software Mentions: 4
Published: over 10 years ago

10.3390/genes3030545

Next Generation Sequence Analysis and Computational Genomics Using Graphical Pipeline Workflows
Cited by: 47
Author(s): Federica Torri, Ivo D. Dinov, Alen Zamanyan, Sam Hobel, Alex Genco, Petros Petrosyan, Andrew P. Clark, Zhizhong Liu, Paul Eggert, Jonathan Pierce, James A. Knowles, Joseph Ames, Carl Kesselman, Arthur W. Toga, Steven G. Potkin, Marquis P. Vawter, Fabìo Macciardi
Software Mentions: 3
Published: about 12 years ago

10.1534/g3.111.001834

Integration of the Draft Sequence and Physical Map as a Framework for Genomic Research in Soybean (Glycine max (L.) Merr.) and Wild Soybean (Glycine soja Sieb. and Zucc.)
Cited by: 8
Author(s): Jung Min Ha, Brian Abernathy, William M. Nelson, David Grant, Xiaolei Wu, Henry T. Nguyen, Gary Stacey, Yeisoo Yu, Rod A. Wing, Randy C. Shoemaker, Scott A. Jackson
Software Mentions: 3
Published: over 12 years ago

10.1186/gb-2012-13-8-r74

Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage
Cited by: 139
Author(s): Hervé Moreau, Bram Verhelst, Arnaud Couloux, Évelyne Derelle, Stéphane Rombauts, Nigel Grimsley, Michiel Van Bel, Julie Poulain, Michaël Katinka, Martin F. Hohmann‐Marriott, Gwenaël Piganeau, Pierre Rouzé, Corinne Da Silva, Patrick Wincker, Yves Van de Peer, Klaas Vandepoele
Software Mentions: 3
Published: almost 13 years ago

10.3390/pharmaceutics8020015

Challenges, Solutions, and Quality Metrics of Personal Genome Assembly in Advancing Precision Medicine
Cited by: 12
Author(s): Wenming Xiao, Leihong Wu, Gökhan Yavaş, Vahan Simonyan, Baitang Ning, Huixiao Hong
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2105-9-215

Binning sequences using very sparse labels within a metagenome
Cited by: 77
Author(s): Chon‐Kit Kenneth Chan, Arthur Hsu, Saman K. Halgamuge, Sen‐Lin Tang
Software Mentions: 2
Published: over 16 years ago

10.1186/1471-2105-12-95

Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies
Cited by: 53
Author(s): Joshua L. Wetzel, Carl Kingsford, Mihai Pop
Software Mentions: 2
Published: over 13 years ago

10.1186/1756-0381-6-13

Unraveling genomic variation from next generation sequencing data
Cited by: 45
Author(s): Georgios A. Pavlopoulos, Anastasis Oulas, Ernesto Iacucci, Alejandro Sifrim, Yves Moreau, Reinhard Schneider, Jan Aerts, Ioannis Iliopoulos
Software Mentions: 2
Published: over 11 years ago

10.3390/life10120356

An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota
Cited by: 10
Author(s): Lucía Muggia, Claudio Gennaro Ametrano, Katja Sterflinger, Donatella Tesei
Software Mentions: 2
Published: almost 4 years ago

10.3390/molecules23020193

Genome-Wide Identification and Comparative Analysis of the 3-Hydroxy-3-methylglutaryl Coenzyme A Reductase (HMGR) Gene Family in Gossypium
Cited by: 13
Author(s): Wei Liu, Zhiqiang Zhang, Wei Li, Wei Zhu, Zhongying Ren, Zhenyu Wang, Lingli Li, Lin Jia, Shuijin Zhu, Zongbin Ma
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pcbi.1000186

Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads
Cited by: 51
Author(s): Steven L. Salzberg, Daniel Sommer, Daniela Puiu, Vincent T. Lee
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pone.0091172

An Improved Canine Genome and a Comprehensive Catalogue of Coding Genes and Non-Coding Transcripts
Cited by: 190
Author(s): Marc P. Hoeppner, Andrew L. Lundquist, Mono Pirun, Jennifer R. S. Meadows, Neda Zamani, Jeremy Johnson, Görel Sundström, April Cook, Michael G. FitzGerald, Ross Swofford, Evan Mauceli, Behrooz Torabi Moghadam, Anna Greka, Jessica Alföldi, Amr Abouelleil, Lynne Aftuck, Daniel Bessette, Aaron M. Berlin, Adam D. Brown, Gary Gearin, Annie Lui, J. Pendexter Macdonald, Margaret Priest, Terrance Shea, Jason Turner-Maier, Andrew Zimmer, Eric S. Lander, Federica Di Palma, Kerstin Lindblad‐Toh, Manfred Grabherr
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0022728

The Genome Sequence of the North-European Cucumber (Cucumis sativus L.) Unravels Evolutionary Adaptation Mechanisms in Plants
Cited by: 110
Author(s): Rafał Wóycicki, Justyna Witkowicz, Piotr Gawroński, Joanna Dąbrowska, Alexandre Lomsadze, Magdalena Pawełkowicz, Ewa Siedlecka, Kohei Yagi, Wojciech Pląder, Anna Seroczyńska, M. Śmiech, Wojciech Gutman, K. Niemirowicz-Szczytt, Grzegorz Bartoszewski, Norikazu Tagashira, Yoshikazu Hoshi, Mark Borodovsky, Stanisław Karpiński, S. Malepszy, Zbigniew Przybecki
Software Mentions: 2
Published: over 13 years ago

10.1534/g3.112.004044

Comparative Genomics of a Plant-Pathogenic Fungus,Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence
Cited by: 142
Author(s): Viola A. Manning, Iovanna Pandelova, Braham Dhillon, Larry J. Wilhelm, Stephen B. Goodwin, Aaron M. Berlin, Melania Figueroa, Michael Freitag, James K. Hane, Bernard Henrissat, Wade H. Holman, Chinnappa D. Kodira, Joel Martin, Richard P. Oliver, Barbara Robbertse, Wendy Schackwitz, David C. Schwartz, Joseph W. Spatafora, B. Gillian Turgeon, Chandri Yandava, Sarah Young, Shiguo Zhou, Qiandong Zeng, Igor V. Grigoriev, Lijun Ma, Lynda M. Ciuffetti
Software Mentions: 2
Published: almost 12 years ago

10.1186/gb-2008-9-5-r77

The genome sequence of the model ascomycete fungus Podospora anserina
Cited by: 278
Author(s): Eric Espagne, Olivier Lespinet, Fabienne Malagnac, Corinne Da Silva, Olivier Jaillon, Betina M. Porcel, Arnaud Couloux, Jean‐Marc Aury, Béatrice Ségurens, Julie Poulain, Véronique Anthouard, Sandrine Grossetête, Hamid Khalili, Evelyne Coppin, Michelle Déquard-Chablat, Marguerite Picard, Véronique Contamine, Sylvie Arnaise, A Bourdais, Véronique Berteaux‐Lecellier, Daniel Gautheret, Ronald P. de Vries, Evy Battaglia, Pedro M. Coutinho, Étienne Danchin, Bernard Henrissat, Riyad El Khoury, Annie Sainsard-Chanet, Antoine Boivin, Bérangère Pinan‐Lucarré, Carole H. Sellem, Robert Debuchy, Patrick Wincker, Jean Weissenbach, Philippe Silar
Software Mentions: 2
Published: almost 17 years ago

10.1186/gb-2010-11-3-r28

Detection and correction of false segmental duplications caused by genome mis-assembly
Cited by: 81
Author(s): David R. Kelley, Steven L. Salzberg
Software Mentions: 2
Published: almost 15 years ago

10.1186/gb-2013-14-1-r2

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline
Cited by: 176
Author(s): Todd J. Treangen, Sergey Koren, Daniel Sommer, Bo Liu, Irina Astrovskaya, Brian D. Ondov, Aaron E. Darling, Adam M. Phillippy, Mihai Pop
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0001836

Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps
Cited by: 4
Author(s): Michael R. Roberts, Aleksey V. Zimin, Wayne B. Hayes, Brian R. Hunt, Cevat Ustun, James R. White, Paul Havlak, James A. Yorke
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0031386

Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data
Cited by: 218
Author(s): Daniel R. Mende, Alison S. Waller, Shinichi Sunagawa, Aino I Järvelin, M.K. Chan, Manimozhiyan Arumugam, Jeroen Raes, Peer Bork
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0000220

A North American Yersinia pestis Draft Genome Sequence: SNPs and Phylogenetic Analysis
Cited by: 33
Author(s): Jeffrey W. Touchman, David M. Wagner, Jicheng Hao, Stephen D. Mastrian, Maulik K. Shah, Amy J. Vogler, Christopher John Allender, Erin A.S. Clark, Debbie S. Benitez, David Youngkin, Jessica Girard, Raymond K. Auerbach, Stephen M. Beckstrom-Sternberg, Paul Keim
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2164-9-603

High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies
Cited by: 85
Author(s): Jean‐Marc Aury, Corinne Cruaud, Valérie Barbe, Odile Rogier, Sophie Mangenot, Gaëlle Samson, Julie Poulain, Véronique Anthouard, Claude Scarpelli, François Artiguenave, Patrick Wincker
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2164-11-325

Metabolic flexibility revealed in the genome of the cyst-forming α-1 proteobacterium Rhodospirillum centenum
Cited by: 32
Author(s): Yih‐Kuang Lu, Jeremiah N. Marden, Mira V. Han, Wesley D. Swingley, Stephen D. Mastrian, Sugata Roy Chowdhury, Jicheng Hao, Tamer Helmy, Sun Kim, Ahmet Kurdoglu, H Matthies, David Rollo, Paul Stothard, Robert E. Blankenship, Carl E. Bauer, Jeffrey W. Touchman
Software Mentions: 1
Published: over 14 years ago

10.4056/sigs.571102

Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07T)
Cited by: 8
Author(s): Brian Foster, Rüdiger Pukall, Birte Abt, Matt Nolan, Tijana Glavina del Rio, Feng Chen, Susan Lucas, Hope Tice, Sam Pitluck, Jan‐Fang Cheng, Olga Chertkov, Thomas Brettin, Cliff Han, John C. Detter, David Bruce, Lynne Goodwin, Natalia Ivanova, Konstantinos Mavromatis, Amrita Pati, Natalia Mikhailova, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun Juan Chang, Cynthia D. Jeffries, Patrick Chain, Manfred Rohde, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans Peter Klenk, Alla Lapidus
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2164-10-S3-S10

The oligonucleotide frequency derived error gradient and its application to the binning of metagenome fragments
Cited by: 19
Author(s): Isaam Saeed, Saman K. Halgamuge
Software Mentions: 1
Published: almost 16 years ago

10.1128/genomeA.00021-15

Draft Genome Sequence of the Cellulolytic Fungus Chaetomium globosum
Cited by: 24
Author(s): Christina A. Cuomo, Wendy A. Untereiner, Lijun Ma, Manfred Grabherr, Bruce W. Birren
Software Mentions: 1
Published: over 9 years ago

10.1186/gb-2008-9-3-r55

Genome assembly forensics: finding the elusive mis-assembly
Cited by: 258
Author(s): Adam M. Phillippy, Michael C. Schatz, Mihai Pop
Software Mentions: 1
Published: almost 17 years ago

10.4056/sigs.1092865

Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207T)
Cited by: 10
Author(s): Kurt LaButti, Shanmugam Mayilraj, Alicia Clum, Susan Lucas, Tijana Glavina del Rio, Matt Nolan, Hope Tice, Jan‐Fang Cheng, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, Lynne Goodwin, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun Juan Chang, Cynthia D. Jeffries, Manfred Rohde, Stefan Spring, Markus Göker, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans Peter Klenk, Alla Lapidus
Software Mentions: 1
Published: over 14 years ago

10.4056/sigs.1393494

Complete genome sequence of Arthrobacter phenanthrenivorans type strain (Sphe3)
Cited by: 31
Author(s): A. Kallimanis, Kurt LaButti, Alla Lapidus, Alicia Clum, Athanasios Lykidis, Konstantinos Mavromatis, Ioanna Pagani, Konstantinos Liolios, Natalia Ivanova, Lynne Goodwin, Sam Pitluck, Amy Chen, Krishna Palaniappan, Victor Markowitz, James Bristow, Athanassios D. Velentzas, Angelos Perisynakis, Christos A. Ouzounis, Nikos C. Kyrpides, Anna‐Irini Koukkou, Constantin Drainas
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2105-11-33

Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction
Cited by: 18
Author(s): Lance E. Palmer, Mathäus Dejori, Randall Bolanos, Daniel Fasulo
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2105-8-64

Minimus: a fast, lightweight genome assembler
Cited by: 359
Author(s): Daniel Sommer, Arthur L. Delcher, Steven L. Salzberg, Mihai Pop
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pone.0105227

Metagenomic Survey for Viruses in Western Arctic Caribou, Alaska, through Iterative Assembly of Taxonomic Units
Cited by: 19
Author(s): Anita C. Schürch, Debby Schipper, M Bijl, Jim Dau, Kimberlee B. Beckmen, Claudia M. E. Schapendonk, V. Stalin Raj, Albert D. M. E. Osterhaus, Bart L. Haagmans, Morten Tryland, Saskia L. Smits
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2105-16-S17-S2

EC: an efficient error correction algorithm for short reads
Cited by: 6
Author(s): Subrata Saha, Sanguthevar Rajasekaran
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0075505

Comparing Memory-Efficient Genome Assemblers on Stand-Alone and Cloud Infrastructures
Cited by: 23
Author(s): Dimitrios Kleftogiannis, Panos Kalnis, Vladimir B. Bajic
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0044229

Bifidobacterium asteroides PRL2011 Genome Analysis Reveals Clues for Colonization of the Insect Gut
Cited by: 118
Author(s): Francesca Bottacini, Christian Milani, Francesca Turroni, Borja Sánchez, Elena Foroni, Sabrina Duranti, Fausta Serafini, Alice Viappiani, Francesco Strati, Alberto Ferrarini, Massimo Delledonne, Bernard Henrissat, Pedro M. Coutinho, Gerald F. Fitzgerald, Abelardo Margollés, Douwe van Sinderen, Marco Ventura
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pgen.1002230

Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea
Cited by: 826
Author(s): Joëlle Amselem, Christina A. Cuomo, Jan A.L. van Kan, Muriel Viaud, Ernesto P. Benito, Arnaud Couloux, Pedro M. Coutinho, Ronald P. de Vries, Paul S. Dyer, Sabine Fillinger, Elisabeth Fournier, Lilian Gout, Matthias Hahn, Linda M. Kohn, Nicolas Lapalu, Kim M. Plummer, Jean‐Marc Pradier, Emmanuel Quévillon, Amir Sharon, Adeline Simon, Arjen ten Have, Bettina Tudzynski, Paul Tudzynski, Patrick Wincker, Marion Andrew, Véronique Anthouard, Ross E. Beever, Rolland Beffa, Isabelle Benoit, Ourdia Bouzid, Baptiste Brault, Zehua Chen, Mathias Choquer, Jérôme Collemare, Pascale Cotton, Etienne G. J. Danchin, Corinne Da Silva, Angélique Gautier, C. Giraud, Tatiana Giraud, Celedonio González, Sandrine Grossetête, Ulrich Güldener, Bernard Henrissat, Barbara J. Howlett, Chinnappa D. Kodira, Matthias Kretschmer, Anne Lappartient, Michaela Leroch, Caroline Levis, Evan Mauceli, Cécile Neuvéglise, Birgitt Oeser, Matthew D. Pearson, Julie Poulain, Nathalie Poussereau, Hadi Quesneville, Christine Rascle, Julia Schumacher, Béatrice Ségurens, Adrienne Sexton, Evelyn Silva, Catherine Sirven, Darren M. Soanes, Nicholas J. Talbot, Templeton Matt, Chandri Yandava, Oded Yarden, Qiandong Zeng, Jeffrey A. Rollins, Marc‐Henri Lebrun, Marty Dickman
Software Mentions: 1
Published: over 13 years ago

Projects: pypi: Arachne

Papers Mentioning Arachne 42