Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: bwa
https://packages.ecosyste.ms/registries/pypi.org/packages/bwa
Bwa: Simple Notification Sender(Discord, Slack, Gmail and Telegram)
1 version
Latest release: about 4 years ago
170 downloads last month
Papers Mentioning bwa 989
10.1371/journal.pone.0136407
Exome Sequencing of Cell-Free DNA from Metastatic Cancer Patients Identifies Clinically Actionable Mutations Distinct from Primary DiseaseCited by: 92
Author(s): Timothy Butler, Katherine Johnson-Camacho, Myron Peto, Nicholas J. Wang, Tara A. Macey, James E. Korkola, Theresa M. Koppie, Christopher L. Corless, Joe W. Gray, Paul T. Spellman
Software Mentions: 1
Published: about 9 years ago
10.1371/journal.pone.0098521
HCV Infection Enhances Th17 Commitment, Which Could Affect the Pathogenesis of Autoimmune DiseasesCited by: 18
Author(s): Yasuteru Kondo, Masashi Ninomiya, Osamu Kimura, Keigo Machida, Ryo Funayama, Takeshi Nagashima, Koju Kobayashi, Eiji Kakazu, Takanobu Kato, Keiko Nakayama, Michael M. C. Lai, Tooru Shimosegawa
Software Mentions: 1
Published: over 10 years ago
10.1371/journal.pone.0032891
Characterization of Within-Host Plasmodium falciparum Diversity Using Next-Generation Sequence DataCited by: 100
Author(s): Sarah Auburn, Susana Campino, Olivo Miotto, Abdoulaye Djimdé, Issaka Zongo, Magnus Manske, G. Maslen, Valentina Mangano, Daniel Alcock, Bronwyn MacInnis, Kirk A. Rockett, Taane G. Clark, Ogobara K. Doumbo, Jean Bosco Ouédraogo, Dominic P. Kwiatkowski
Software Mentions: 1
Published: over 12 years ago
10.1371/journal.pone.0026161
Decontamination of MDA Reagents for Single Cell Whole Genome AmplificationCited by: 147
Author(s): Tanja Woyke, Alexander Sczyrba, Janey Lee, Christian Rinke, Damon Tighe, Scott Clingenpeel, Rex R. Malmstrom, Ramunas Stepanauskas, Jan‐Fang Cheng
Software Mentions: 1
Published: about 13 years ago
10.1371/journal.pone.0102645
The South Asian GenomeCited by: 41
Author(s): John C. Chambers, James Abbott, Weihua Zhang, Ernest Turro, William R. Scott, Sian-Tsung Tan, Uzma Afzal, Saima Afaq, Marie Loh, Benjamin Lehne, Paul F. O’Reilly, Kyle J. Gaulton, Richard D. Pearson, Xinzhong Li, Anita Lavery, Jana Vandrovcová, Mark N. Wass, Kathryn Miller, Joban Sehmi, Laticia Oozageer, Ishminder K. Kooner, Abtehale Al-Hussaini, Rebecca Mills, Jagvir Grewal, Vasileios F. Panoulas, Arie Y. Lewin, Korrinne Northwood, Gurpreet Singh Wander, Frank Geoghegan, Yingrui Li, Jun Wang, Timothy J. Aitman, Mark I. McCarthy, James A. Scott, Sarah Butcher, Paul Elliott, Jaspal S. Kooner
Software Mentions: 1
Published: over 10 years ago
10.1371/journal.pone.0019838
The Sensitivity of Massively Parallel Sequencing for Detecting Candidate Infectious Agents Associated with Human TissueCited by: 55
Author(s): Richard A. Moore, René L. Warren, Jamie Freeman, Julia Gustavsen, Caroline Chénard, Jan M. Friedman, Curtis A. Suttle, Yongjun Zhao, Robert A. Holt
Software Mentions: 1
Published: over 13 years ago
10.1371/journal.pone.0076059
QTL Mapping of Leafy Heads by Genome Resequencing in the RIL Population of Brassica rapaCited by: 57
Author(s): Xiang Yu, Han Wang, Weizhuo Zhong, Jinjuan Bai, Pinglin Liu, Yuqing He
Software Mentions: 1
Published: about 11 years ago
10.1371/journal.pone.0122636
Target-Dependent Enrichment of Virions Determines the Reduction of High-Throughput Sequencing in Virus DiscoveryCited by: 26
Author(s): Randi Holm Jensen, Sarah Mollerup, Tobias Mourier, Thomas Arn Hansen, Helena Fridholm, Lars Peter Nielsen, Eske Willerslev, Anders J. Hansen, Lasse Vinner
Software Mentions: 1
Published: over 9 years ago
10.1371/journal.pone.0075042
Variation in the Form of Pavlovian Conditioned Approach Behavior among Outbred Male Sprague-Dawley Rats from Different Vendors and Colonies: Sign-Tracking vs. Goal-TrackingCited by: 120
Author(s): Christopher Fitzpatrick, Shyam Gopalakrishnan, Elizabeth S. Cogan, Lindsay M. Yager, Paul J. Meyer, Vedran Lovic, Benjamin T. Saunders, Clarissa C. Parker, Natalia M. Gonzales, Emmanuel Aryee, Shelly B. Flagel, Abraham A. Palmer, Terry E. Robinson, Jonathan D. Morrow
Software Mentions: 1
Published: about 11 years ago
10.1371/journal.pone.0241997
High genetic diversity of ancient horses from the Ukok PlateauCited by: 5
Author(s): Nadezhda V. Vorobieva, Alexey I Makunin, Anna S. Druzhkova, Mariya A. Kusliy, Владимир Трифонов, Kseniya O. Popova, N.V. Polosmak, В.И. Молодин, S. Vasiliev, M.V. Shunkov, Alexander S. Graphodatsky
Software Mentions: 1
Published: about 4 years ago
10.1371/journal.pone.0081899
Proteomic and Genomic Analyses of Antimony Resistant Leishmania infantum MutantCited by: 59
Author(s): Marie‐Christine Brotherton, Sylvie Bourassa, Philippe Leprohon, Danielle Légaré, Guy G. Poirier, Arnaud Droit, Marc Ouellette
Software Mentions: 1
Published: almost 11 years ago
10.1371/journal.pone.0109125
Carrot yellow leaf virus Is Associated with Carrot Internal NecrosisCited by: 66
Author(s): Ian Adams, A. Skelton, Roy Macarthur, Tobias Hodges, Howard Hinds, L.J. Flint, Palash Deb Nath, Neil Boonham, Adrian Fox
Software Mentions: 1
Published: about 10 years ago
10.1371/journal.pone.0164212
Paternal Age Explains a Major Portion of De Novo Germline Mutation Rate Variability in Healthy IndividualsCited by: 40
Author(s): Simon L. Girard, Cynthia V. Bourassa, Louis‐Philippe Lemieux Perreault, Marc‐André Legault, Amina Barhdadi, Amirthagowri Ambalavanan, Mara Brendgen, Frank Vitaro, Anne Noreau, Ginette Dionne, Richard E. Tremblay, Patrick A. Dion, Michel Boivin, Marie‐Pierre Dubé, Guy A. Rouleau
Software Mentions: 1
Published: about 8 years ago
10.1371/journal.pone.0130149
KIT Mutation and Loss of 14q May Be Sufficient for the Development of Clinically Symptomatic Very Low-Risk GISTCited by: 5
Author(s): Olaf Klinke, Tuba Mizani, Gouri Baldwin, Brigitte Bancel, Mojgan Devouassoux‐Shisheboran, Jean Yves Scoazec, Pierre Paul Bringuier, Regina Feederle, Anna Jauch, Katrin Hinderhofer, Philippe Tanière, Henri Jacques Delecluse
Software Mentions: 1
Published: over 9 years ago
10.3390/cancers7040878
Aberrant MUC1-TRIM46-KRTCAP2 Chimeric RNAs in High-Grade Serous Ovarian CarcinomaCited by: 9
Author(s): K. P. Kannan, Gona Karimi Kordestani, Anika Galagoda, Cristian Coarfa, Laising Yen
Software Mentions: 1
Published: about 9 years ago
10.3390/cancers13102446
Generation of Non-Small Cell Lung Cancer Patient-Derived Xenografts to Study Intratumor HeterogeneityCited by: 4
Author(s): Zoi Kanaki, Alexandra Voutsina, Athina Markou, Ioannis S. Pateras, Konstantinos Potaris, Margaritis Avgeris, Periklis Makrythanasis, Emmanouil Athanasiadis, Ioannis Vamvakaris, Eleni Patsea, Konstantinos Vachlas, Evi Lianidou, Vassilis Georgoulias, Athanasios Κotsakis, Apostolos Klinakis
Software Mentions: 1
Published: over 3 years ago
10.1038/s41419-020-2505-1
Dual targeting of BCL2 and MCL1 rescues myeloma cells resistant to BCL2 and MCL1 inhibitors associated with the formation of BAX/BAK hetero-complexesCited by: 29
Author(s): Carolane Seiller, Sophie Maïga, Cyrille Touzeau, Céline Bellanger, Charlotte Kervoëlen, Géraldine Descamps, Laurent Maillet, Philippe Moreau, Catherine Pellat‐Deceunynck, Patricia Gomez‐Bougie, Martine Amiot
Software Mentions: 1
Published: over 4 years ago
10.1016/j.chom.2019.12.004
Exploitation of the Cooperative Behaviors of Anti-CRISPR PhagesCited by: 38
Author(s): Anne Chevallereau, Sean Meaden, Olivier Fradet, Mariann Landsberger, Alice Maestri, Ambarish Biswas, Sylvain Gandon, Stineke van Houte, Edze R. Westra
Software Mentions: 1
Published: almost 5 years ago
10.3390/cells8010053
Dystrophin Deficiency Leads to Genomic Instability in Human Pluripotent Stem Cells via NO Synthase-Induced Oxidative StressCited by: 25
Author(s): Šárka Jelínková, Petr Fojtík, Aneta Kohutová, Aleksandra Vilotić, Lenka Marková, Martin Pešl, Tereza Juráková, Miriama Krutá, Jan Vrbský, Renata Gaillyová, Iveta Valášková, Ivan Frák, Alain Lacampagne, Giancarlo Forte, Petr Dvořák, Albano C. Méli, Vladimír Rotrekl
Software Mentions: 1
Published: almost 6 years ago
10.1093/cid/ciz600
A Rare Mutation in <i>SPLUNC1</i> Affects Bacterial Adherence and Invasion in Meningococcal DiseaseCited by: 3
Author(s): Bayarchimeg Mashbat, Evangelos Bellos, Stephanie Hodeib, Fadil A. Bidmos, Ryan S. Thwaites, Yaxuan Lu, Victoria J. Wright, Jethro Herberg, Daniela S. Klobassa, Werner Zenz, Trevor T. Hansel, Simon Nadel, Paul Langford, Luregn J Schlapbach, Mingshi Li, Matthew R. Redinbo, Y. Peter Di, Michael Levin, Vanessa Sancho‐Shimizu
Software Mentions: 1
Published: over 5 years ago
10.1038/s42003-018-0034-6
Light-activated cell identification and sorting (LACIS) for selection of edited clones on a nanofluidic deviceCited by: 34
Author(s): Annamaria Mocciaro, Theodore L. Roth, Hayley M. Bennett, Magali Soumillon, Abhik Shah, Joseph Hiatt, Kevin Chapman, Alexander Marson, Grégory Lavieu
Software Mentions: 1
Published: over 6 years ago
10.1038/s42003-020-01199-3
Multiple ancestral haplotypes harboring regulatory mutations cumulatively contribute to a QTL affecting chicken growth traitsCited by: 15
Author(s): Yuzhe Wang, Xianglin Cao, Chenglong Luo, Zheya Sheng, Chunyuan Zhang, Cheng Bian, Chungang Feng, Jinxiu Li, Fei Gao, Yaofeng Zhao, Zhengqiang Jiang, Hao Qu, Dingming Shu, Örjan Carlborg, Xiaoxiang Hu, Ning Li
Software Mentions: 1
Published: about 4 years ago
10.1093/dnares/dsab008
Chromosome-scale genome assembly of the transformation-amenable common wheat cultivar ‘Fielder’Cited by: 58
Author(s): Kazuhiro Sato, Fumitaka Abe, Martin Mascher, Georg Haberer, Heidrun Gundlach, Manuel Spannagl, Kenta Shirasawa, Sachiko Isobe
Software Mentions: 1
Published: over 3 years ago
10.1093/dnares/dsv010
High-fidelity target sequencing of individual molecules identified using barcode sequences:<i>de novo</i>detection and absolute quantitation of mutations in plasma cell-free DNA from cancer patientsCited by: 68
Author(s): Yoji Kukita, Ryo Matoba, Junji Uchida, Takuya Hamakawa, Yuichiro Doki, Fumio Imamura, Kikuya Kato
Software Mentions: 1
Published: over 9 years ago
10.1242/dmm.028035
Blood RNA biomarkers in prodromal PARK4 and REM sleep behavior disorder show role of complexin-1 loss for risk of Parkinson's diseaseCited by: 18
Author(s): Suna Lahut, Suzana Gispert, Özgür Ömür, Candan Depboylu, Kay Seidel, Jorge Antolio Domínguez-Bautista, Nadine Brehm, Hülya Tireli, Karl Hackmann, Caroline Pirkevi, Barbara Leube, Vincent Ries, Kerstin Reim, Nils Brose, Wilfred F. A. den Dunnen, Madrid Johnson, Zsuzsanna Wolf, Marc Schindewolf, Wiebke Schrempf, Kathrin Reetz, Peter Young, Dávid Vadász, Achilleas S. Frangakis, Evelin Schröck, Helmuth Steinmetz, Marina Jendrach, Udo Rüb, A. Nazlı Başak, Wolfgang H. Oertel, Georg Auburger
Software Mentions: 1
Published: almost 8 years ago
10.1002/ece3.5496
Evolution and diversity of two cisco forms in an outlet of glacial Lake AlgonquinCited by: 13
Author(s): Gabriel Piette‐Lauzière, Allan H. Bell, Mark S. Ridgway, Jean Turgeon
Software Mentions: 1
Published: over 5 years ago
10.1002/ece3.5131
Evaluation of introgressive hybridization among Cervidae in Japan's Kinki District via two novel genetic markers developed from public NGS dataCited by: 6
Author(s): Yuki Matsumoto, Toshihito Takagi, Ryosuke Koda, Akira Tanave, Asuka Yamashiro, Hideo Tamate
Software Mentions: 1
Published: over 5 years ago
10.1002/ece3.2574
Transcriptomic comparison of invasive bigheaded carps ( Hypophthalmichthys nobilis and Hypophthalmichthys molitrix ) and their hybridsCited by: 5
Author(s): Jun Wang, James T. Lamer, Sarah Gaughan, Michael Wachholtz, Chenghui Wang, Guoquing Lu
Software Mentions: 1
Published: about 8 years ago
10.1002/ece3.3449
Genome comparisons indicate recent transfer of<i>w</i>Ri-like<i>Wolbachia</i>between sister species<i>Drosophila suzukii</i>and<i>D. subpulchrella</i>Cited by: 46
Author(s): William R. Conner, Mark Blaxter, G. Anfora, Lino Ometto, Omar Rota‐Stabelli, Michael Turelli
Software Mentions: 1
Published: about 7 years ago
10.1002/ece3.6266
Host plant genetic control of associated fungal and insect species in a <i>Populus</i> hybrid crossCited by: 2
Author(s): Sandra Simon, Timothy J. Tschaplinski, Jared M. LeBoldus, Ken Keefover‐Ring, Muhammad Azeem, Jay Chen, David Macaya‐Sanz, William L. MacDonald, Wellington Muchero, Stephen P. DiFazio
Software Mentions: 1
Published: over 4 years ago
10.1530/EC-20-0460
Genetic predisposition to neural crest-derived tumors: revisiting the role of KIF1BCited by: 4
Author(s): C. Bauters, Emmanuelle Leteurtre, B. Carnaille, Christine Do Cao, Stéphanie Espiard, Malo Penven, Evelyne Destailleur, Isabelle Szuster, Tonio Lovecchio, Julie Leclerc, Frédéric Frénois, Emmanuel Esquivel, Patricia L.M. Dahia, Emilie Ait‐Yahya, Michel Crépin, Pascal Pigny
Software Mentions: 1
Published: about 4 years ago
10.1530/EC-18-0326
Novel SLCO2A1 mutations cause gender-differentiated pachydermoperiostosisCited by: 6
Author(s): Lijuan Yuan, Xihui Chen, Ziyu Liu, Dan Wu, Jianguo Lü, Guoqiang Bao, Sijia Zhang, lIfeng Wang, Yuanming Wu
Software Mentions: 1
Published: about 6 years ago
10.1038/s41431-019-0551-x
A bird’s-eye view of Italian genomic variation through whole-genome sequencingCited by: 26
Author(s): Massimiliano Cocca, Caterina Barbieri, Maria Pina Concas, Antonietta Robino, Marco Brumat, Ilaria Gandin, Matteo Trudu, Cinzia Sala, Dragana Vuckovic, Giorgia Girotto, Giuseppe Matullo, Ozren Polašek, Ivana Kolčić, Paolo Gasparini, Nicole Soranzo, Daniela Toniolo, Massimo Mezzavilla
Software Mentions: 1
Published: almost 5 years ago
10.1038/ejhg.2016.146
Clinical exome sequencing: results from 2819 samples reflecting 1000 familiesCited by: 270
Author(s): Daniel Trujillano, Aida M. Bertoli‐Avella, Krishna Kumar Kandaswamy, Maximilian E. R. Weiss, Julia Köster, Anett Marais, Omid Paknia, Rolf Schröder, José María García-Aznar, Martin Werber, Oliver Brandau, María Teresa Muñoz Calvo, Caterina Baldi, Karen Wessel, Shivendra Kishore, Nahid Nahavandi, Wafaa Eyaid, Muhammad Talal Al Rifai, Ahmed Al‐Rumayyan, Waleed Altwaijri, Ali Alothaim, Amal Alhashem, Nouriya Al‐Sannaa, Mohammed Al Balwi, Majid Alfadhel, Arndt Rolfs, Rami Abou Jamra
Software Mentions: 1
Published: about 8 years ago
10.1038/s41431-019-0388-3
Linkage analysis revealed risk loci on 6p21 and 18p11.2-q11.2 in familial colon and rectal cancer, respectivelyCited by: 4
Author(s): Susanna von Holst, Xiang Jiao, Wen Li, Vinaykumar Kontham, Jessada Thutkawkorapin, Jenny Ringdahl, Patrick Bryant, Annika Lindblom
Software Mentions: 1
Published: over 5 years ago
10.1111/eva.12770
Deciphering the patterns of genetic admixture and diversity in southern European cattle using genome‐wide SNPsCited by: 21
Author(s): Maulik Upadhyay, Chiara Bortoluzzi, Mario Barbato, Paolo Ajmone‐Marsan, Licia Colli, Catarina Ginja, Tad S. Sonstegard, Mirte Bosse, Johannes A. Lenstra, M.A.M. Groenen, R.P.M.A. Crooijmans
Software Mentions: 1
Published: almost 6 years ago
10.1002/evl3.29
Inconsistent reproductive isolation revealed by interactions between<i>Catostomus</i>fish speciesCited by: 46
Author(s): Elizabeth G. Mandeville, Thomas L. Parchman, Kevin G. Thompson, Robert I. Compton, Kevin R. Gelwicks, Se Jin Song, C. Alex Buerkle
Software Mentions: 1
Published: about 7 years ago
10.12688/f1000research.1-3.v1
Low budget analysis of Direct-To-Consumer genomic testing familial dataCited by: 11
Author(s): Gustavo Glusman, Mike Cariaso, Rafael C. Jiménez, Daniel Swan, Bastian Greshake, Jong Bhak, Darren W. Logan, Manuel Corpas
Software Mentions: 1
Published: over 12 years ago
10.1002/2211-5463.13225
Establishment and characterization of a primary cell culture derived from external auditory canal squamous cell carcinomaCited by: 3
Author(s): Yuki Sekino, Akira Imaizumi, Noritaka Komune, Masahiro Ono, Kuniaki Sato, S. Masuda, Akiko Fujimura, Kensuke Koike, Takahiro Hongo, Ryutaro Uchi, Hideya Onishi, Takashi Nakagawa
Software Mentions: 1
Published: over 3 years ago
10.3389/fcell.2019.00201
NUMT Confounding Biases Mitochondrial Heteroplasmy Calls in Favor of the Reference AlleleCited by: 35
Author(s): Hannah Maude, Mira S. Davidson, Natalie Charitakis, Léo P. M. Diaz, William H. T. Bowers, Eva Gradovich, Toby Andrew, Derek Huntley
Software Mentions: 1
Published: about 5 years ago
10.3389/fgene.2020.555843
Pronounced Plastic and Evolutionary Responses to Unpredictable Thermal Fluctuations in Drosophila simulansCited by: 7
Author(s): Jesper Givskov Sørensen, Tommaso Manenti, Jesper Bechsgaard, Mads Fristrup Schou, Torsten Nygård Kristensen, Volker Loeschcke
Software Mentions: 1
Published: about 4 years ago
10.3389/fgene.2020.00440
The Whole-Genome Sequencing and Hybrid Assembly of Mytilus coruscusCited by: 38
Author(s): Ronghua Li, Weijia Zhang, Junkai Lu, Zhouyi Zhang, Changkao Mu, Weiwei Song, Hervé Migaud, Michaël Bekaert
Software Mentions: 1
Published: over 4 years ago
10.3389/fgene.2020.00951
High-Throughput Sequencing to Investigate Associations Between HLA Genes and Metamizole-Induced AgranulocytosisCited by: 4
Author(s): Anca Liliana Cismaru, Livia Grimm, Deborah Rudin, Luisa Ibáñez, Evangelia Liakoni, Nicolas Bonadies, Reinhold Kreutz, Pär Hallberg, Mia Wadelius, Manuel Haschke, Carlo R. Largiadèr, Ursula Amstutz
Software Mentions: 1
Published: over 4 years ago
10.3389/fgene.2019.00423
A First Y-Chromosomal Haplotype Network to Investigate Male-Driven Population Dynamics in Domestic and Wild Bactrian CamelsCited by: 14
Author(s): Sabine Felkel, Barbara Wallner, Chuluunbat Battsetseg, Adiya Yadamsuren, Bernard Faye, Gottfried Brem, Chris Walzer, Pamela A. Burger
Software Mentions: 1
Published: over 5 years ago
10.3389/fmicb.2015.01259
RNA-seq de novo Assembly Reveals Differential Gene Expression in Glossina palpalis gambiensis Infected with Trypanosoma brucei gambiense vs. Non-Infected and Self-Cured FliesCited by: 14
Author(s): Illiassou Hamidou Soumana, Christophe Klopp, Sophie Ravel, Ibouniyamine Nabihoudine, Bernadette Tchicaya, Hugues Parrinello, Luc Abate, Stéphanie Rialle, Anne Geiger
Software Mentions: 1
Published: about 9 years ago
10.3389/fmicb.2017.01627
Regulatory Mechanisms of a Highly Pectinolytic Mutant of Penicillium occitanis and Functional Analysis of a Candidate Gene in the Plant Pathogen Fusarium oxysporumCited by: 3
Author(s): Gustavo Bravo Ruiz, A. Hadj Sassi, Marina Marcet‐Houben, Antonio Di Pietro, Ali Gargouri, Toni Gabaldón, M. Isabel G. Roncero
Software Mentions: 1
Published: about 7 years ago
10.3389/fmicb.2021.694492
Determinants of Persistent Patterns of Pepino Mosaic Virus Mixed InfectionsCited by: 6
Author(s): Cristina Alcaide, Miguel A. Aranda
Software Mentions: 1
Published: over 3 years ago
10.3389/fonc.2019.00875
Development of Patient-Derived Preclinical Platform for Metastatic Pancreatic Cancer: PDOX and a Subsequent Organoid Model System Using Percutaneous Biopsy SamplesCited by: 29
Author(s): Sun Choi, A-Ra Jeon, Min Kyeong Kim, Yu-Sun Lee, Ji Eun Im, Jung-Wook Koh, Sung‐Sik Han, Sun‐Young Kong, Kyong–Ah Yoon, Young-Hwan Koh, Ju Hee Lee, Woojin Lee, Sang-Jae Park, Eun Kyoung Hong, Sang Myung Woo, Yun-Hee Kim
Software Mentions: 1
Published: about 5 years ago
10.3389/fonc.2019.00450
Utility of Immunophenotypic Measurable Residual Disease in Adult Acute Myeloid Leukemia—Real-World ContextCited by: 12
Author(s): Nikhil Patkar, Chinmayee Kakirde, Prasanna Bhanshe, Shalik Ram Joshi, Shruti Chaudhary, Yajamanam Badrinath, Sitaram Ghoghale, Nilesh Deshpande, Shraddha Kadechkar, Gaurav Chatterjee, Sadhana Kannan, Dhanalaxmi Shetty, Anant Gokarn, Sachin Punatkar, Avinash Bonda, Lingaraj Nayak, Hasmukh Jain, Bhausaheb Bagal, Hari Menon, Manju Sengar, Syed Khizer Hasan, Navin Khattry, Prashant Tembhare, Sumeet Gujral, Papagudi Ganesan Subramanian
Software Mentions: 1
Published: over 5 years ago
10.3389/fpls.2018.00724
Red Clover (Trifolium pratense) and Zigzag Clover (T. medium) – A Picture of Genomic Similarities and DifferencesCited by: 18
Author(s): Jana Dluhošová, Jan Ištvánek, J. Nedêlník, Jana Řepková
Software Mentions: 1
Published: over 6 years ago
10.3389/fpls.2021.715737
No Evidence of Unexpected Transgenic Insertions in T1190 – A Transgenic Apple Used in Rapid Cycle Breeding – Following Whole Genome SequencingCited by: 1
Author(s): Andrea Patocchi, Jens Keilwagen, Thomas Berner, Stefanie Wenzel, Giovanni A. L. Broggini, Lothar Altschmied, Magda‐Viola Hanke, Henryk Flachowsky
Software Mentions: 1
Published: over 3 years ago
10.3389/fpls.2014.00340
Sequencing and de novo assembly of a Dahlia hybrid cultivar transcriptomeCited by: 8
Author(s): Erik Lehnert, Virginia Walbot
Software Mentions: 1
Published: over 10 years ago
10.3389/fpls.2018.00486
Organelle Genome Inheritance in Deparia Ferns (Athyriaceae, Aspleniineae, Polypodiales)Cited by: 19
Author(s): Li‐Yaung Kuo, Te‐Yen Tang, Fay‐Wei Li, Hong‐Ji Su, Wen‐Liang Chiou, Yao‐Moan Huang, Chun‐Neng Wang
Software Mentions: 1
Published: over 6 years ago
10.3389/fpls.2016.01779
Mutations in Rice yellow mottle virus Polyprotein P2a Involved in RYMV2 Gene Resistance BreakdownCited by: 25
Author(s): Agnès Pinel‐Galzi, Christine Tranchant‐Dubreuil, Eugénie Hébrard, Cédric Mariac, Alain Ghesquière, Laurence Albar
Software Mentions: 1
Published: almost 8 years ago
10.3389/fpls.2016.02055
Simultaneous Identification of Multiple Causal Mutations in RiceCited by: 35
Author(s): Yan Wang, Zhufeng Chen, Jian Lü, Chengpei Xu, Gang Xie, Yiqi Li, Xing Wang Deng, Hang He, Xiaoyan Tang
Software Mentions: 1
Published: almost 8 years ago
10.3389/fpsyt.2019.00277
Adenosine-to-Inosine RNA Editing Within Corticolimbic Brain Regions Is Regulated in Response to Chronic Social Defeat Stress in MiceCited by: 14
Author(s): A. Dick, Khen Khermesh, Evan D. Paul, Fabian Stamp, Erez Y. Levanon, Alon Chen
Software Mentions: 1
Published: over 5 years ago
10.3389/fvets.2019.00175
Genetic and Phenotypic Characterization of the Etiological Agent of Canine Orchiepididymitis Smooth Brucella sp. BCCN84.3Cited by: 10
Author(s): Caterina Guzmán-Verri, Marcela Suárez-Esquivel, Nazareth Ruíz-Villalobos, Michel S. Zygmunt, Mathieu Gonnet, Elena Campos, Eunice Víquez-Ruiz, Carlos Chacón-Díaz, Beatriz Aragón-Aranda, Raquel Conde-Álvarez, Ignacio Moriyón, J.M. Blasco, Pilar M. Muñoz, Kate S. Baker, Nicholas R. Thomson, Axel Cloeckaert, Edgardo Moreno
Software Mentions: 1
Published: over 5 years ago
10.1534/g3.115.017046
Genetic Analysis of Substrain Divergence in Non-Obese Diabetic (NOD) MiceCited by: 20
Author(s): Petr Šimeček, Gary A. Churchill, Hyuna Yang, Lucy B. Rowe, L. Herberg, David Serreze, Edward H. Leiter
Software Mentions: 1
Published: over 9 years ago
10.1534/g3.115.018283
Multiple Conserved Heteroplasmic Sites in tRNA Genes in the Mitochondrial Genomes of Terrestrial Isopods (Oniscidea)Cited by: 12
Author(s): Christopher H. Chandler, Myriam Badawi, Bouziane Moumen, Pierre Grève, Richard Cordaux
Software Mentions: 1
Published: over 9 years ago
10.1534/g3.115.020362
Application of Population Sequencing (POPSEQ) for Ordering and Imputing Genotyping-by-Sequencing Markers in Hexaploid WheatCited by: 26
Author(s): Erena A. Edae, Robert L. Bowden, Jesse Poland
Software Mentions: 1
Published: almost 9 years ago
10.1534/g3.115.022087
The Mouse Universal Genotyping Array: From Substrains to SubspeciesCited by: 190
Author(s): Andrew P. Morgan, Chen Fu, Chia Yu Kao, Catherine E. Welsh, John P. Didion, Liran Yadgary, Leeanna Hyacinth, Martin T. Ferris, Timothy A. Bell, Darla R. Miller, Paola Giusti‐Rodríguez, Randal J. Nonneman, Kevin D. Cook, Jason K. Whitmire, Lisa E. Gralinski, Mark P. Keller, Alan D. Attie, Gary A. Churchill, Petko M. Petkov, Patrick F. Sullivan, Jennifer Brennan, Leonard McMillan, Fernando Pardo Manuel de Villena
Software Mentions: 1
Published: almost 9 years ago
10.1534/g3.116.027946
Gene Regulatory Evolution During Speciation in a SongbirdCited by: 32
Author(s): John Davidson, Christopher N. Balakrishnan
Software Mentions: 1
Published: over 8 years ago
10.1534/g3.116.029330
Third Chromosome Balancer Inversions Disrupt Protein-Coding Genes and Influence Distal Recombination Events in<i>Drosophila melanogaster</i>Cited by: 33
Author(s): Danny E. Miller, Kevin R. Cook, Alexandra V. Arvanitakis, R. Scott Hawley
Software Mentions: 1
Published: over 8 years ago
10.1534/g3.117.043349
<i>Drosophila simulans</i>: A Species with Improved Resolution in Evolve and Resequence StudiesCited by: 27
Author(s): Neda Barghi, Raymond Tobler, Viola Nolte, Christian Schlötterer
Software Mentions: 1
Published: over 7 years ago
10.1534/g3.118.200021
The Molecular and Genetic Characterization of Second Chromosome Balancers in <i>Drosophila melanogaster</i>Cited by: 17
Author(s): Danny E. Miller, Kevin R. Cook, Elizabeth A Hemenway, Vivienne Fang, Angela Miller, Karen G. Hales, R. Scott Hawley
Software Mentions: 1
Published: over 6 years ago
10.1534/g3.118.200166
Sex Differences in Recombination in SticklebacksCited by: 60
Author(s): Jason M. Sardell, Changde Cheng, Andrius J. Dagilis, Asano Ishikawa, Jun Kitano, Catherine L. Peichel, Mark Kirkpatrick
Software Mentions: 1
Published: over 6 years ago
10.1534/g3.118.200160
Highly Contiguous Genome Assemblies of 15 <i>Drosophila</i> Species Generated Using Nanopore SequencingCited by: 120
Author(s): Danny E. Miller, Cynthia Staber, Julia Zeitlinger, R. Scott Hawley
Software Mentions: 1
Published: about 6 years ago
10.1534/g3.119.400755
Accurate Allele Frequencies from Ultra-low Coverage Pool-Seq Samples in Evolve-and-Resequence ExperimentsCited by: 24
Author(s): Susanne Tilk, Alan O. Bergland, Aaron J. Goodman, Paul S. Schmidt, Dmitri A. Petrov, Sharon Greenblum
Software Mentions: 1
Published: almost 5 years ago
10.1534/g3.119.400846
De Novo Assembly of a High-Quality Reference Genome for the Horned Lark (Eremophila alpestris)Cited by: 7
Author(s): Nicholas A. Mason, Paulo C. Pulgarín, Carlos Daniel Cadena, Irby J. Lovette
Software Mentions: 1
Published: almost 5 years ago
10.1534/g3.120.401559
Identification and Characterization of Breakpoints and Mutations on<i>Drosophila melanogaster</i>Balancer ChromosomesCited by: 13
Author(s): Danny E. Miller, Lily Kahsai, Kasun Buddika, Michael J. Dixon, Bernard Kim, Brian R. Calvi, Nicholas S. Sokol, R. Scott Hawley, Kevin R. Cook
Software Mentions: 1
Published: about 4 years ago
10.1093/g3journal/jkaa051
Independent evolution toward larger body size in the distinctive Faroe Island miceCited by: 0
Author(s): Ricardo Wilches, William Beluch, Ellen McConnell, Diethard Tautz, Yingguang Frank Chan
Software Mentions: 1
Published: almost 4 years ago
10.1093/g3journal/jkaa022
Forward genetic screens identified mutants with defects in trap morphogenesis in the nematode-trapping fungus <i>Arthrobotrys oligospora</i>Cited by: 4
Author(s): Tsung-Yu Huang, Yi-Yun Lee, Guillermo Vidal-Diez de Ulzurrun, Yu-Ting Hsueh
Software Mentions: 1
Published: almost 4 years ago
10.1093/g3journal/jkab144
<b>QTL</b> × <b>environment interactions underlie ionome divergence in switchgrass</b>Cited by: 6
Author(s): Li Zhang, Alice MacQueen, Jason Bonnette, Felix B. Fritschi, David B. Lowry, Thomas E. Juenger
Software Mentions: 1
Published: over 3 years ago
10.1093/g3journal/jkab213
Chromosome assembled and annotated genome sequence of <i>Aspergillus flavus</i> NRRL 3357Cited by: 18
Author(s): Jeffrey M. Skerker, Kaila M. Pianalto, Stephen J. Mondo, Kunlong Yang, Adam P. Arkin, Nancy P. Keller, Igor V. Grigoriev, N. Louise Glass
Software Mentions: 1
Published: over 3 years ago
10.3390/genes12010091
Targeted Sequencing of Mitochondrial Genes Reveals Signatures of Molecular Adaptation in a Nearly Panmictic Small Pelagic Fish SpeciesCited by: 9
Author(s): Miguel Baltazar‐Soares, André Ricardo de Araújo Lima, Gonçalo Silva
Software Mentions: 1
Published: almost 4 years ago
10.3390/genes12020310
Rare Recurrent Variants in Noncoding Regions Impact Attention-Deficit Hyperactivity Disorder (ADHD) Gene Networks in Children of both African American and European American AncestryCited by: 8
Author(s): Yichuan Liu, Xiao Chang, Hui‐Qi Qu, Lifeng Tian, Joseph Glessner, Jingchun Qu, Dong Liu, Haijun Qiu, Patrick Sleiman, Hákon Hákonarson
Software Mentions: 1
Published: over 3 years ago
10.1534/genetics.119.301970
Necessity and Contingency in Developmental Genetic Screens: EGF, Wnt, and Semaphorin Pathways in Vulval Induction of the Nematode <i>Oscheius tipulae</i>Cited by: 9
Author(s): Amhed Missael Vargas Velazquez, Fabrice Besnard, Marie‐Anne Félix
Software Mentions: 1
Published: almost 6 years ago
10.1128/genomeA.00899-14
Draft Genome Sequence of Brachybacterium phenoliresistens Strain W13A50, a Halotolerant Hydrocarbon-Degrading BacteriumCited by: 4
Author(s): Xinxin Wang, Zhuo Zhang, Decai Jin, Lisha Zhou, Liang Wu, Chen Li, Long Zhao, Wei An, Yu Chen
Software Mentions: 1
Published: about 10 years ago
10.1128/genomeA.01245-14
Complete Genome Sequence of Haemophilus influenzae Strain 375 from the Middle Ear of a Pediatric Patient with Otitis MediaCited by: 14
Author(s): Joshua Chang Mell, Sunita Sinha, Sergey Balashov, Cristina Viadas, Christopher J. Grassa, Garth D. Ehrlich, Corey Nislow, Rosemary J. Redfield, Junkal Garmendía
Software Mentions: 1
Published: almost 10 years ago
10.1128/genomeA.01675-15
Draft Genome Sequence of Pannonibacter phragmitetus Strain CGMCC9175, a Halotolerant Polycyclic Aromatic Hydrocarbon-Degrading BacteriumCited by: 4
Author(s): Xinxin Wang, Decai Jin, Lisha Zhou, Zhuo Zhang
Software Mentions: 1
Published: over 8 years ago
10.1128/genomeA.00123-16
Complete Genome Sequence of Vancomycin-Intermediate Staphylococcus aureus Strain MI (HIP5827)Cited by: 0
Author(s): Tomomi Hishinuma, Yuki Katayama, Miki Matsuo, Takashi Sasaki, Kazumasa Hiramatsu
Software Mentions: 1
Published: over 8 years ago
10.1128/genomeA.01343-15
Complete Genome Sequence of the Drug-Naive Classical Staphylococcus aureus Strain FDA209PCited by: 9
Author(s): Madhuri Singh, Takashi Sasaki, Miki Matsuo, Yuichi Morimoto, Yoshifumi Aiba, Kazumasa Hiramatsu
Software Mentions: 1
Published: almost 9 years ago
10.1128/genomeA.00062-17
Draft Genome Sequence of Streptomyces sp. Strain IB2014011-1, Isolated from Trichoptera sp. Larvae of Lake BaikalCited by: 1
Author(s): Denis V. Axenov-Gribanov, Bogdan Tokovenko, Yuriy Rebets, Irina V. Voytsekhovskaya, Z. M. Shatilina, E S Protasov, Andriy Luzhetskyy, Maxim A. Timofeyev
Software Mentions: 1
Published: over 7 years ago
10.1128/genomeA.01091-17
Complete Genome Sequence of Peste des Petits Ruminants Virus from Georgia, 2016Cited by: 10
Author(s): Paulina Rajko-Nenow, Tabitha G. Cunliffe, John Flannery, Honorata M. Ropiak, Lasha Avaliani, Marina Donduashvili, Michael D. Baron, Carrie Batten
Software Mentions: 1
Published: about 7 years ago
10.1186/gb-2010-11-6-r69
Estimating enrichment of repetitive elements from high-throughput sequence dataCited by: 90
Author(s): Daniel S. Day, Lovelace J. Luquette, Peter J. Park, Peter V. Kharchenko
Software Mentions: 1
Published: almost 15 years ago
10.1186/gb-2010-11-9-r91
Sequencing and analysis of an Irish human genomeCited by: 41
Author(s): Pin Tong, James Prendergast, Amanda J. Lohan, Susan M. Farrington, Simon Cronin, Nial Friel, Daniel G. Bradley, Orla Hardiman, A.C.O. Evans, James F. Wilson, Brendan J. Loftus
Software Mentions: 1
Published: almost 15 years ago
10.1186/gb-2012-13-8-r69
Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylaseCited by: 210
Author(s): Eun Ang Raiber, Dario Beraldi, Gabriella Ficz, Heather E. Burgess, Miguel R. Branco, Pierre Murat, David Oxley, Michael J. Booth, Wolf Reik, Shankar Balasubramanian
Software Mentions: 1
Published: almost 13 years ago
10.1186/gb-2013-14-9-r96
An ENU mutagenesis screen identifies novel and known genes involved in epigenetic processes in the mouseCited by: 72
Author(s): Lucia Daxinger, Sarah K. Harten, Harald Oey, Trevor Epp, Luke Isbel, Edward Huang, Nadia C Whitelaw, Anwyn Apedaile, Anabel Sorolla, Joan Yong, Vandhana Bharti, Joanne Sutton, Alyson Ashe, Zhenyi Pang, Nathan Wallace, Daniel J. Gerhardt, Marnie E. Blewitt, Jeffrey A. Jeddeloh, Emma Whitelaw
Software Mentions: 1
Published: almost 12 years ago
10.1186/gb-2013-14-8-r90
Virmid: accurate detection of somatic mutations with sample impurity inferenceCited by: 59
Author(s): Sangwoo Kim, Kyowon Jeong, Kunal Bhutani, Jehee Lee, Amit K. Patel, Eric Scott, Hojung Nam, Hayan Lee, Joseph G. Gleeson, Vineet Bafna
Software Mentions: 1
Published: almost 12 years ago
10.1186/s13059-014-0566-0
Causes and consequences of crossing-over evidenced via a high-resolution recombinational landscape of the honey beeCited by: 58
Author(s): Haoxuan Liu, Xiaohui Zhang, Ju Huang, Jian Qun Chen, Dacheng Tian, Laurence D. Hurst, Sihai Yang
Software Mentions: 1
Published: almost 10 years ago
10.1186/s13059-018-1452-y
Diversification and independent domestication of Asian and European pearsCited by: 124
Author(s): Jun Wu, Yingtao Wang, Jiabao Xu, Schuyler S. Korban, Zhangjun Fei, Shutian Tao, Ray Ming, Shuaishuai Tai, Awais Khan, Joseph D. Postman, Chao Gu, Hong Yin, Dandan Zheng, Kaijie Qi, Yong Li, Runze Wang, Cecilia Deng, Satish Kumar, David Chagné, Xiaosan Huang, Huping Zhang, Zhihua Xie, Xiao Li, Mingyue Zhang, Yanhong Li, Zhen Yue, Xiaodong Fang, Jiaming Li, Leiting Li, Can Jin, Mengfan Qin, Jiaying Zhang, Xiao Wu, Ya-Qi Ke, Jian Wang, Huanmimg Yang
Software Mentions: 1
Published: over 6 years ago
10.1186/s13059-020-02254-2
SequencErr: measuring and suppressing sequencer errors in next-generation sequencing dataCited by: 12
Author(s): Eric M. Davis, Yu Sun, Yanling Liu, Pandurang Kolekar, Ying Shao, Karol Szlachta, Heather L. Mulder, Dongren Ren, Stephen V. Rice, Zhaoming Wang, Joy Nakitandwe, Alexander M. Gout, Bridget Shaner, Salina Hall, Leslie L. Robison, Stanley Pounds, Jeffery M. Klco, John Easton, Xiaotu Ma
Software Mentions: 1
Published: almost 4 years ago
10.1093/gbe/evx137
Brucella Genetic Variability in Wildlife Marine Mammals Populations Relates to Host Preference and Ocean DistributionCited by: 25
Author(s): Marcela Suárez-Esquivel, Kate S. Baker, Nazareth Ruíz-Villalobos, Gabriela Hernández-Mora, Elías Barquero-Calvo, Rocío González-Barrientos, Amanda Castillo-Zeledón, César Jiménez-Rojas, Carlos Chacón-Díaz, Axel Cloeckaert, Esteban Chaves-Olarte, Nicholas R. Thomson, Edgardo Moreno, Caterina Guzmán-Verri
Software Mentions: 1
Published: over 7 years ago
10.1093/gbe/evy202
Thermosipho spp. immune system differences affect variation in genome size and geographical distributionsCited by: 2
Author(s): Thomas Haverkamp, Claire Geslin, Julien Lossouarn, Olga A. Podosokorskaya, Ilya V. Kublanov, Camilla Nesbø
Software Mentions: 1
Published: about 6 years ago
10.1093/gbe/evz194
Genetics of Adaptation of the Ascomycetous Fungus Podospora anserina to Submerged CultivationCited by: 1
Author(s): Olga Kudryavtseva, Ksenia R Safina, Olga A. Vakhrusheva, Maria D. Logacheva, Aleksey A. Penin, Tatyana V. Neretina, Viktoria N Moskalenko, Elena S. Glagoleva, Georgii A. Bazykin, Alexey S. Kondrashov
Software Mentions: 1
Published: about 5 years ago
10.1093/gbe/evz224
Interspecific Gene Exchange Introduces High Genetic Variability in Crop PathogenCited by: 24
Author(s): Alice Feurtey, Danielle M. Stevens, Wolfgang Stephan, Eva H. Stukenbrock
Software Mentions: 1
Published: about 5 years ago
10.1093/gbe/evaa019
An Ancient Baboon Genome Demonstrates Long-Term Population Continuity in Southern AfricaCited by: 11
Author(s): Iain Mathieson, Federico Abascal, Lasse Vinner, Pontus Skoglund, Cristina Pomilla, Peter Mitchell, Charles Arthur, Deepti Gurdasani, Eske Willerslev, Manj S. Sandhu, Genevieve Dewar
Software Mentions: 1
Published: almost 5 years ago
10.1093/gbe/evaa102
Genome Assembly of the Ragweed Leaf Beetle: A Step Forward to Better Predict Rapid Evolution of a Weed Biocontrol Agent to Environmental NoveltiesCited by: 9
Author(s): Sarah Bouchemousse, Laurent Falquet, Heinz Müller‐Schärer
Software Mentions: 1
Published: over 4 years ago
10.1093/gbe/evaa234
Selective Sweeps in a Nutshell: The Genomic Footprint of Rapid Insecticide Resistance Evolution in the Almond AgroecosystemCited by: 17
Author(s): Bernarda Calla, Mark Demkovich, Joel P. Siegel, João Paulo Gomes Viana, Kimberly K. O. Walden, Hugh M. Robertson, May R. Berenbaum
Software Mentions: 1
Published: about 4 years ago
10.1093/gbe/evab134
Genome Assembly of the Cold-Tolerant Leaf Beetle <i>Gonioctena quinquepunctata</i>, an Important Resource for Studying Its Evolution and Reproductive Barriers between SpeciesCited by: 1
Author(s): Svitlana Lukicheva, Jean‐François Flot, Patrick Mardulyn
Software Mentions: 1
Published: over 3 years ago