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
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Papers Mentioning bwa 989

10.1186/s13073-021-00882-2
Profiling SARS-CoV-2 mutation fingerprints that range from the viral pangenome to individual infection quasispecies
Cited by: 17
Author(s): Billy T. Lau, Dmitri S. Pavlichin, Anna C Hooker, Alison Almeda, Giwon Shin, Jiamin Chen, Malaya K. Sahoo, Chun Huang, Benjamin A. Pinsky, Ho‐Joon Lee, Hanlee P. Ji
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pgen.1002849
Variation of BMP3 Contributes to Dog Breed Skull Diversity
Cited by: 142
Author(s): Jeffrey J. Schoenebeck, Sarah A. Hutchinson, Alexandra M. Byers, Holly C. Beale, Blake Carrington, Daniel L. Faden, Maud Rimbault, Brennan Decker, Jeffrey M. Kidd, Raman Sood, Adam R. Boyko, John W. Fondon, Robert K. Wayne, Carlos D. Bustamante, Brian Ciruna, Elaine A. Ostrander
Software Mentions: 2
Published: over 12 years ago
10.1371/journal.pgen.1006455
Extremely Rare Polymorphisms in Saccharomyces cerevisiae Allow Inference of the Mutational Spectrum
Cited by: 13
Author(s): Yuan Zhu, Gavin Sherlock, Dmitri A. Petrov
Software Mentions: 2
Published: almost 8 years ago
10.1186/s12864-019-6211-2
The genomic diversification of grapevine clones
Cited by: 60
Author(s): Amanda M. Vondras, Andrea Minio, Barbara Blanco‐Ulate, Rosa Figueroa‐Balderas, Michael A. Penn, Yongfeng Zhou, Danelle Seymour, Zirou Ye, Dingren Liang, Lucero K. Espinoza, Michael M. Anderson, M. Andrew Walker, Dario Cantu
Software Mentions: 2
Published: almost 5 years ago
10.1371/journal.pgen.1008085
Mitochondrial fusion is required for regulation of mitochondrial DNA replication
Cited by: 99
Author(s): Eduardo Silva Ramos, Elisa Motori, Christian Brüser, Inge Kühl, Assa Yeroslaviz, Benedetta Ruzzenente, Johanna H.K. Kauppila, Jakob D. Busch, Kjell Hultenby, Bianca Habermann, Stefan Jakobs, Nils‐Göran Larsson, Arnaud Mourier
Software Mentions: 2
Published: over 5 years ago
10.1186/s13073-021-00868-0
The global dissemination of hospital clones of Enterococcus faecium
Cited by: 30
Author(s): Sebastiaan J. van Hal, Rob J. L. Willems, Theodore Gouliouris, Susan A Ballard, Teresa M. Coque, Anette M. Hammerum, Kristin Hegstad, Hendrik T. Westh, Benjamin P Howden, Surbhi Malhotra-Kumar, Guido Werner, Katsunori Yanagihara, Ashlee M. Earl, Katherine E. Raven, Jukka Corander, Rory Bowden
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pgen.1004362
Meiotic Drive Impacts Expression and Evolution of X-Linked Genes in Stalk-Eyed Flies
Cited by: 34
Author(s): Josephine A. Reinhardt, Cara L. Brand, Kimberly A. Paczolt, Philip M. Johns, Richard H. Baker, Gerald S. Wilkinson
Software Mentions: 2
Published: over 10 years ago
10.1186/s12920-021-00904-3
Sequential filtering for clinically relevant variants as a method for clinical interpretation of whole exome sequencing findings in glioma
Cited by: 0
Author(s): Ege Ülgen, Özge Çan, Kaya Bilgüvar, Cemaliye Akyerli Boylu, Şirin Yüksel, Ayça Erşen Danyeli, Osman Uğur Sezerman, Mustafa Cengiz Yakıcıer, M. Necmettin Pamir, Koray Özduman
Software Mentions: 2
Published: over 3 years ago
10.1186/s12864-021-07508-2
Comparing low-pass sequencing and genotyping for trait mapping in pharmacogenetics
Cited by: 27
Author(s): Kaja A. Wasik, Tomaz Berisa, Joseph K. Pickrell, Jeremiah H. Li, Dana J. Fraser, Karen S. King, Charles Cox
Software Mentions: 2
Published: over 3 years ago
10.1186/s12920-016-0220-7
Immunoseq: the identification of functionally relevant variants through targeted capture and sequencing of active regulatory regions in human immune cells
Cited by: 24
Author(s): Andréanne Morin, Tony Kwan, Bing Ge, Louis Létourneau, Masashi Ban, Karolina Tandre, Maxime Caron, Johanna K. Sandling, Jonas Carlsson, Guillaume Bourque, Catherine Laprise, Alexandre Montpetit, Ann‐Christine Syvänen, Lars Rönnblom, Stephen Sawcer, Mark Lathrop, Tomi Pastinen
Software Mentions: 2
Published: about 8 years ago
10.1186/s13073-018-0562-1
Epigenomic profiling of non-small cell lung cancer xenografts uncover LRP12 DNA methylation as predictive biomarker for carboplatin resistance
Cited by: 36
Author(s): Sabrina Grasse, Matthias Lienhard, Steffen Frese, Martin Kerick, Anne Steinbach, Christina Grimm, Michelle Hussong, Jana Rolff, Michael W. Becker, Felix Dreher, Uwe Schirmer, Stefan Boerno, Anna Ramisch, Gunda Leschber, Bernd Timmermann, Christian Grohé, H Lüders, Martin Vingron, Iduna Fichtner, Sebastian Klein, Margarete Odenthal, Reinhard Büttner, Hans Lehrach, Holger Sültmann, Ralf Herwig, Michal R. Schweiger
Software Mentions: 2
Published: over 6 years ago
10.1186/s12859-015-0682-1
Odintifier - A computational method for identifying insertions of organellar origin from modern and ancient high-throughput sequencing data based on haplotype phasing
Cited by: 5
Author(s): José Alfredo Samaniego Castruita, Marie Lisandra Zepeda Mendoza, Ross Barnett, Nathan Wales, M. Thomas P. Gilbert
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pntd.0007222
Frequent expansion of Plasmodium vivax Duffy Binding Protein in Ethiopia and its epidemiological significance
Cited by: 23
Author(s): Eugenia Lo, Jessica B. Hostetler, Delenasaw Yewhalaw, Richard D. Pearson, Muzamil Mahdi Abdel Hamid, Karthigayan Gunalan, Daniel Kepple, Anthony M. Ford, Daniel Janies, Julian C. Rayner, Louis H. Miller, Guiyun Yan
Software Mentions: 2
Published: about 5 years ago
10.1186/1471-2164-13-477
In depth comparison of an individual’s DNA and its lymphoblastoid cell line using whole genome sequencing
Cited by: 35
Author(s): Dorothee Nickles, Lohith Madireddy, Shan Yang, Pouya Khankhanian, Steve Lincoln, Stephen L. Hauser, Jorge R. Oksenberg, Sergio E. Baranzini
Software Mentions: 2
Published: about 12 years ago
10.1371/journal.pone.0187617
Identification of a t(3;4)(p1.3;q1.5) translocation breakpoint in pigs using somatic cell hybrid mapping and high-resolution mate-pair sequencing
Cited by: 2
Author(s): Katia Fève, Sylvain Foissac, Alain Pinton, Florence Mompart, Diane Esquerré, Thomas Faraut, Martine M. Yerle, Juliette Riquet
Software Mentions: 2
Published: about 7 years ago
10.1186/s12915-021-01017-0
Rat PRDM9 shapes recombination landscapes, duration of meiosis, gametogenesis, and age of fertility
Cited by: 10
Author(s): Ondřej Mihola, V. Landa, Florencia Pratto, Kevin Brick, Tatyana Kobets, Fitore Kusari, Srdjan Gasic, Fátima Smagulova, Corinne Grey, Petr Flachs, Václav Gergelits, Karel Tresnak, Jan Šilhavý, Petr Mlejnek, R. Daniel Camerini‐Otero, Michal Pravenec, Galina V. Petukhova, Zdeněk Trachtulec
Software Mentions: 2
Published: over 3 years ago
10.1186/1755-8794-6-50
ChIP-seq in steatohepatitis and normal liver tissue identifies candidate disease mechanisms related to progression to cancer
Cited by: 8
Author(s): Madhu Sudhan Reddy Bysani, Ola Wallerman, Susanne Bornelöv, Kurt Zatloukal, Jan Komorowski, Claes Wadelius
Software Mentions: 2
Published: about 11 years ago
10.3390/jpm6010012
Bioinformatics Workflow for Clinical Whole Genome Sequencing at Partners HealthCare Personalized Medicine
Cited by: 21
Author(s): Ellen Tsai, Rimma Shakbatyan, Jonathan D. Evans, Peter Rossetti, Chet Graham, Himanshu Sharma, Chiao‐Feng Lin, Matthew S. Lebo
Software Mentions: 2
Published: over 8 years ago
10.1186/s40360-020-00446-x
A phase I study of a dual PI3-kinase/mTOR inhibitor BEZ235 in adult patients with relapsed or refractory acute leukemia
Cited by: 20
Author(s): Fabian Lang, Lydia Wunderle, Susanne Badura, Eberhard Schleyer, Monika Brüggemann, Hubert Serve, Susanne Schnittger, Nicola Gökbuget, Heike Pfeifer, Sebastian Wagner, Kevin E. Ashelford, Gesine Bug, Oliver G. Ottmann
Software Mentions: 2
Published: about 4 years ago
10.1111/acel.13468
Inhibition of the cGAS‐STING pathway ameliorates the premature senescence hallmarks of Ataxia‐Telangiectasia brain organoids
Cited by: 28
Author(s): Julio Aguado, Harman Chaggar, Cecilia Gómez-Inclán, Mohammed R. Shaker, Hannah C Leeson, Alan Mackay‐Sim, Ernst J. Wolvetang
Software Mentions: 2
Published: about 3 years ago
10.1371/journal.pone.0067461
High-Throughput miRNA and mRNA Sequencing of Paired Colorectal Normal, Tumor and Metastasis Tissues and Bioinformatic Modeling of miRNA-1 Therapeutic Applications
Cited by: 52
Author(s): Christina Röhr, Martin Kerick, Axel Fischer, Alexander Kühn, Karl Kashofer, Bernd Timmermann, Andriani Daskalaki, Thomas Meinel, Dmitriy Drichel, Stefan T. Börno, Anja Nowka, Sylvia Krobitsch, Alice C. McHardy, Christina Kratsch, Tim Becker, Andrea Wunderlich, Christian Barmeyer, Christian Viertler, Kurt Zatloukal, Christoph Wierling, Hans Lehrach, Michal R. Schweiger
Software Mentions: 2
Published: over 11 years ago
10.1371/journal.pone.0104405
An Improved Method for Including Upper Size Range Plasmids in Metamobilomes
Cited by: 31
Author(s): Anders Norman, Leise Riber, Wenting Luo, L i Li Li, Lars Hestbjerg Hansen, Søren J. Sørensen
Software Mentions: 2
Published: over 10 years ago
10.3389/fmicb.2019.02556
Comparative Genomics of Pandoraea, a Genus Enriched in Xenobiotic Biodegradation and Metabolism
Cited by: 79
Author(s): Charlotte Peeters, Evelien De Canck, Margo Cnockaert, Evie De Brandt, Cindy Snauwaert, Bart Verheyde, Eliza Depoorter, Theodore Spilker, John J. LiPuma, Peter Vandamme
Software Mentions: 2
Published: about 5 years ago
10.1186/s12870-014-0289-0
A precise chloroplast genome of Nelumbo nucifera (Nelumbonaceae) evaluated with Sanger, Illumina MiSeq, and PacBio RS II sequencing platforms: insight into the plastid evolution of basal eudicots
Cited by: 78
Author(s): Zhihua Wu, Songtao Gui, Zhiwu Quan, Lei Pan, Shuzhen Wang, Weidong Ke, Dequan Liang, Yi Ding
Software Mentions: 2
Published: about 10 years ago
10.1186/s12864-019-5874-z
Arctic charr brain transcriptome strongly affected by summer seasonal growth but only subtly by feed deprivation
Cited by: 6
Author(s): Anja Striberny, Even H. Jørgensen, Christophe Klopp, Élodie Magnanou
Software Mentions: 2
Published: over 5 years ago
10.1186/1471-2164-15-190
Immunomic, genomic and transcriptomic characterization of CT26 colorectal carcinoma
Cited by: 263
Author(s): John C. Castle, Martin Löewer, Sebastian Boegel, Jos de Graaf, Christian Bender, Arbel D. Tadmor, Valesca Boisguérin, Thomas Bukur, Patrick Sorn, Claudia Paret, Mustafa Diken, Sebastian Kreiter, Özlem Türeci, Uğur Şahin
Software Mentions: 2
Published: almost 11 years ago
10.1371/journal.pone.0163059
Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics’ GemCode Sequencing Data
Cited by: 28
Author(s): Lauren Coombe, Warren Rm, Shaun D. Jackman, Chen Yang, Benjamin P. Vandervalk, Richard A. Moore, Stephen Pleasance, Robin Coope, Jöerg Bohlmann, Robert A. Holt, Steven J.M. Jones, İnanç Birol
Software Mentions: 2
Published: about 8 years ago
10.1186/s12915-020-0748-z
Contaminant DNA in bacterial sequencing experiments is a major source of false genetic variability
Cited by: 45
Author(s): Galo A. Goig, Silvia Blanco, Alberto L. García‐Basteiro, Iñaki Comas
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pgen.1006971
Fine scale mapping of genomic introgressions within the Drosophila yakuba clade
Cited by: 82
Author(s): David A. Turissini, Daniel R. Matute
Software Mentions: 2
Published: about 7 years ago
10.18632/oncotarget.25188
The critical role that STAT3 plays in glioma-initiating cells: STAT3 addiction in glioma
Cited by: 41
Author(s): Debolina Ganguly, Meiyun Fan, Chuan Yang, Blazej Zbytek, David Finkelstein, Martine F. Roussel, Lawrence M. Pfeffer
Software Mentions: 2
Published: over 6 years ago
10.18632/oncotarget.24305
Unbiased compound-protein interface mapping and prediction of chemoresistance loci through forward genetics in haploid stem cells
Cited by: 15
Author(s): Moritz Horn, Virginia Kroef, Kira Allmeroth, Nicole Schuller, Stephan Miethe, Martin Peifer, Josef Penninger, Ulrich Elling, Martin S. Denzel
Software Mentions: 2
Published: almost 7 years ago
10.1186/s12915-018-0581-9
Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences
Cited by: 38
Author(s): Cesare de Filippo, Matthias Meyer, Kay Prüfer
Software Mentions: 2
Published: about 6 years ago
10.1111/j.1365-294X.2012.05731.x
Genome‐wide patterns of latitudinal differentiation among populations of <i><scp>D</scp>rosophila melanogaster</i> from <scp>N</scp>orth <scp>A</scp>merica
Cited by: 241
Author(s): Daniel K. Fabian, Martin Kapun, Viola Nolte, Robert Kofler, Paul S. Schmidt, Christian Schlötterer, Thomas Flatt
Software Mentions: 2
Published: over 12 years ago
10.18632/oncotarget.14150
AML associated oncofusion proteins PML-RARA, AML1-ETO and CBFB-MYH11 target RUNX/ETS-factor binding sites to modulate H3ac levels and drive leukemogenesis
Cited by: 23
Author(s): Abhishek A. Singh, Amit Mandoli, K.H.M. Prange, Marko Laakso, Joost H.A. Martens
Software Mentions: 2
Published: almost 8 years ago
10.1371/journal.pone.0083012
Elucidating Emergence and Transmission of Multidrug-Resistant Tuberculosis in Treatment Experienced Patients by Whole Genome Sequencing
Cited by: 66
Author(s): Taane G. Clark, Kim Mallard, Francesc Español i Coll, Mark D. Preston, Samuel Assefa, David Harris, Sam Ogwang, Francis Mumbowa, Bruce Kirenga, Denise M O’Sullivan, Alphonse Okwera, Kathleen D. Eisenach, Moses Joloba, Stephen D. Bentley, Jerrold J. Ellner, Julian Parkhill, Edward C. Jones-López, Ruth McNerney
Software Mentions: 2
Published: almost 11 years ago
10.1186/s12864-015-1570-9
Comparative genome analysis of Pseudogymnoascus spp. reveals primarily clonal evolution with small genome fragments exchanged between lineages
Cited by: 12
Author(s): Evgeny Leushkin, Maria D. Logacheva, Aleksey A. Penin, Roman A. Sutormin, Evgeny S. Gerasimov, Г. А. Кочкина, N. E. Ivanushkina, O. V. Vasilenko, Alexey S. Kondrashov, S. M. Ozerskaya
Software Mentions: 2
Published: over 9 years ago
10.1186/s12864-018-5403-5
Probe-based association analysis identifies several deletions associated with average daily gain in beef cattle
Cited by: 17
Author(s): Lingyang Xu, Yang Liu, Lei Wang, Bo Zhu, Yan Chen, Huijiang Gao, Xue Gao, Lupei Zhang, George E. Liu, Junya Li
Software Mentions: 2
Published: almost 6 years ago
10.3390/ijms22147583
Comprehensive Genomic and Transcriptomic Analysis of Three Synchronous Primary Tumours and a Recurrence from a Head and Neck Cancer Patient
Cited by: 3
Author(s): Luisa Bresadola, D. F. Weber, Christoph Ritzel, Martin Löwer, Valesca Bukur, Özlem Akilli-Öztürk, Julia Powers Becker, Hisham Mehanna, Barbara Schrörs, Fulvia Vascotto, Uğur Şahin, Anthony Kong
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pone.0028171
Dual Function of Histone H3 Lysine 36 Methyltransferase ASH1 in Regulation of Hox Gene Expression
Cited by: 43
Author(s): Yujiro Tanaka, Koji Kawahashi, Zen-ichiro Katagiri, Yasuhiro Nakayama, Milind Mahajan, Dimitris Kioussis
Software Mentions: 2
Published: almost 13 years ago
10.3390/ijms22073617
Construction of Whole Genomes from Scaffolds Using Single Cell Strand-Seq Data
Cited by: 6
Author(s): Matthew J. Hills, Ester Falconer, Kieran O’Neill, Ashley D. Sanders, Kerstin Howe, Victor Guryev, Peter M. Lansdorp
Software Mentions: 2
Published: over 3 years ago
10.3389/fmicb.2020.01055
Impact of RNase E and RNase J on Global mRNA Metabolism in the Cyanobacterium Synechocystis PCC6803
Cited by: 19
Author(s): Marina Cavaiuolo, Carine Chagneau, Soumaya Laalami, Harald Putzer
Software Mentions: 2
Published: over 4 years ago
10.3389/fmicb.2020.00149
PromA Plasmids Are Instrumental in the Dissemination of Linuron Catabolic Genes Between Different Genera
Cited by: 7
Author(s): Johannes Werner, Eman Nour, Boyke Bunk, Cathrin Spröer, Kornelia Smalla, Dirk Springael, Başak Öztürk
Software Mentions: 2
Published: almost 5 years ago
10.1186/s12896-020-00604-3
Integration, abundance, and transmission of mutations and transgenes in a series of CRISPR/Cas9 soybean lines
Cited by: 14
Author(s): Jean Michel Michno, Kamaldeep S. Virdi, Adrian O. Stec, Junqi Liu, Xiaobo Wang, Yer Xiong, Robert M. Stupar
Software Mentions: 2
Published: over 4 years ago
10.3390/ijms21072414
Development and Proof-of-Concept Application of Genome-Enabled Selection for Pea Grain Yield under Severe Terminal Drought
Cited by: 14
Author(s): Paolo Annicchiarico, Nelson Espinoza N., Meriem Laouar, Imane Thami-Alami, Massimo Romani, L. Pecetti
Software Mentions: 2
Published: over 4 years ago
10.1128/JVI.01039-16
NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses
Cited by: 34
Author(s): Marta L. DeDiego, Aitor Nogales, Kris Lambert-Emo, Luis Martinez‐Sobrido, David J. Topham
Software Mentions: 1
Published: about 8 years ago
10.1186/s40478-020-01085-3
Frequent SLC35A2 brain mosaicism in mild malformation of cortical development with oligodendroglial hyperplasia in epilepsy (MOGHE)
Cited by: 57
Author(s): Thomas Bonduelle, Till Hartlieb, Sara Baldassari, Nam Suk Sim, Se Hoon Kim, Hoon Chul Kang, Katja Kobow, Roland Coras, Mathilde Chipaux, Georg Dorfmüller, Homa Adle‐Biassette, Eleonora Aronica, Jehee Lee, Ingmar Blümcke, Stéphanie Baulac
Software Mentions: 1
Published: almost 4 years ago
10.1002/ajpa.23753
Evaluating macroscopic sex estimation methods using genetically sexed archaeological material: The medieval skeletal collection from St John's Divinity School, Cambridge
Cited by: 28
Author(s): Sarah Inskip, Christiana L. Scheib, Anthony Wilder Wohns, Xin Ge, Toomas Kivisild, John Robb
Software Mentions: 1
Published: almost 6 years ago
10.4269/ajtmh.19-0383
Oxford Nanopore MinION Sequencing Enables Rapid Whole Genome Assembly of Rickettsia typhi in a Resource-Limited Setting
Cited by: 21
Author(s): Ivo Elliott, Elizabeth M. Batty, Damien Ming, Matthew T. Robinson, Pruksa Nawtaisong, Mariateresa de Cesare, Paul N. Newton, Rory Bowden
Software Mentions: 1
Published: almost 5 years ago
10.3390/antiox9121265
Xenopus gpx3 Mediates Posterior Development by Regulating Cell Death during Embryogenesis
Cited by: 5
Author(s): Hongchan Lee, Tayaba Ismail, Youni Kim, Shinhyeok Chae, Hong‐Yeoul Ryu, Dong‐Seok Lee, Taeg Kyu Kwon, Tae Joo Park, Taejoon Kwon, Hyun‐Shik Lee
Software Mentions: 1
Published: almost 4 years ago
10.1186/s12859-020-3349-5
Accurately estimating the length distributions of genomic micro-satellites by tumor purity deconvolution
Cited by: 3
Author(s): Yixuan Wang, Xuanping Zhang, Xiao Xiao, Feiran Zhang, Xinxing Yan, Xuan Feng, Zhongmeng Zhao, Yanfang Guan, Jiayin Wang
Software Mentions: 1
Published: over 4 years ago
10.1186/s12915-018-0508-5
Genomics analysis of Aphanomyces spp. identifies a new class of oomycete effector associated with host adaptation
Cited by: 35
Author(s): Elodie Gaulin, Michiel J. C. Pel, Laurent Camborde, Hélène San-Clemente, Sarah Courbier, Marie-Alexane Dupouy, Juliette Lengellé, Marine Veyssière, Aurélie Le Ru, Frédéric Grandjean, Richard Cordaux, Bouziane Moumen, Clément Gilbert, Liliana Cano, Jean‐Marc Aury, Julie Guy, Patrick Wincker, Olivier Bouchez, Christophe Klopp, Bernard Dumas
Software Mentions: 1
Published: over 6 years ago
10.1186/1741-7007-12-46
ABCC transporters mediate insect resistance to multiple Bt toxins revealed by bulk segregant analysis
Cited by: 140
Author(s): Youngjin Park, Rosa M. González-Martínez, Gloria Navarro-Cerrillo, Maissa Chakroun, Yonggyun Kim, Peio Ziarsolo, José Blanca, Joaquı́n Cañizares, Juan Ferré, Salvador Herrero
Software Mentions: 1
Published: over 10 years ago
10.1186/s12885-016-2820-1
Aldehyde dehydrogenase activity plays a Key role in the aggressive phenotype of neuroblastoma
Cited by: 39
Author(s): Marjorie Flahaut, Nicolas Jauquier, Nadja Chevalier, Katya Nardou, Katia Balmas Bourloud, Jean-Marc Joseph, David Barras, Christian Widmann, Nicole Groß, Raffaele Renella, Annick Mühlethaler-Mottet
Software Mentions: 1
Published: about 8 years ago
10.1186/s12885-020-6597-x
Clinical value of next generation sequencing of plasma cell-free DNA in gastrointestinal stromal tumors
Cited by: 30
Author(s): César Serrano, Ana Vivancos, Antonio López‐Pousa, Judit Matito, Francesco Mancuso, Claudia Valverde, Sergi Quiroga, Stefania Landolfi, Sandra Castro, Cristina Dopazo, Ana Sebio, Anna Virgili, Maria Magdalena Menso, Javier Martín-Broto, Miriam Sansó, Alfonso García-Valverde, Jordi Rosell, Jonathan A. Fletcher, Suzanne George, Joan Carles, Joaquı́n Arribas
Software Mentions: 1
Published: almost 5 years ago
10.1186/s12885-016-2209-1
Clinical application of genomic profiling to find druggable targets for adolescent and young adult (AYA) cancer patients with metastasis
Cited by: 30
Author(s): Seung-Do Cha, Jeongeun Lee, Jong Yeon Shin, Ji Yeon Kim, Sung Hoon Sim, Bhumsuk Keam, Tae Min Kim, Dong Wan Kim, Dae Seog Heo, Se‐Hoon Lee, Jong‐Il Kim
Software Mentions: 1
Published: over 8 years ago
10.1186/s12901-018-0064-1
Staphylococcus aureus from patients with chronic rhinosinusitis show minimal genetic association between polyp and non-polyp phenotypes
Cited by: 6
Author(s): Jake Jervis Bardy, Derek S. Sarovich, Erin P. Price, Eike J. Steinig, Steven Y. C. Tong, Amanda Drilling, Judy Ou, Sarah Vreugde, Peter John Wormald, Alkis J. Psaltis
Software Mentions: 1
Published: about 6 years ago
10.1186/s12862-016-0650-z
Evolutionary history of endemic Sulawesi squirrels constructed from UCEs and mitogenomes sequenced from museum specimens
Cited by: 35
Author(s): Melissa T. R. Hawkins, Jennifer A. Leonard, Kristofer M. Helgen, Molly M. McDonough, Larry L. Rockwood, Jésus E. Maldonado
Software Mentions: 1
Published: over 8 years ago
10.1186/s12862-020-01652-1
Genetic legacy of cultures indigenous to the Northeast Asian coast in mitochondrial genomes of nearly extinct maritime tribes
Cited by: 4
Author(s): Stanislav Dryomov, Elena B. Starikovskaya, Azhar M Nazhmidenova, И. В. Морозов, Rem I. Sukernik
Software Mentions: 1
Published: over 4 years ago
10.1186/s12862-016-0825-7
A core phylogeny of Dictyostelia inferred from genomes representative of the eight major and minor taxonomic divisions of the group
Cited by: 18
Author(s): Reema Singh, Christina Schilde, Pauline Schaap
Software Mentions: 1
Published: about 8 years ago
10.1186/s12863-015-0202-3
Loci associated with adult stature also affect calf birth survival in cattle
Cited by: 26
Author(s): Goutam Sahana, Johanna Höglund, Bernt Guldbrandtsen, Mogens Sandø Lund
Software Mentions: 1
Published: over 9 years ago
10.1186/s12863-015-0269-x
Genome-wide association study for female fertility in Nordic Red cattle
Cited by: 34
Author(s): Johanna Höglund, Bart Buitenhuis, Bernt Guldbrandtsen, Mogens Sandø Lund, Goutam Sahana
Software Mentions: 1
Published: about 9 years ago
10.1186/s12864-015-1796-6
Comparison and evaluation of two exome capture kits and sequencing platforms for variant calling
Cited by: 16
Author(s): Guoqiang Zhang, Jianfeng Wang, Jin Yang, Wenjie Li, Yutian Deng, Jing Li, Jun Huang, Songnian Hu, Bing Zhang
Software Mentions: 1
Published: over 9 years ago
10.1186/s12864-016-2827-7
Bioinformatic analysis of genotype by sequencing (GBS) data with NGSEP
Cited by: 43
Author(s): Claudia Perea, Juan Fernando de la Hoz, Daniel Felipe Cruz, Juan David Lobaton, Paulo Izquierdo, Juan Camilo Quintero, Bodo Raatz, Jorge Duitama
Software Mentions: 1
Published: over 8 years ago
10.1186/1471-2164-15-728
Strategies for imputation to whole genome sequence using a single or multi-breed reference population in cattle
Cited by: 93
Author(s): Rasmus Froberg Brøndum, Bernt Guldbrandtsen, Goutam Sahana, Mogens Sandø Lund, Guosheng Su
Software Mentions: 1
Published: almost 11 years ago
10.1186/1471-2164-13-142
A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy
Cited by: 81
Author(s): Kankshita Swaminathan, Won Byoung Chae, Therese Mitros, Kranthi Varala, Liang Xie, Adam Barling, Nitsan Lugassi, Mark E. Hall, S. Jeżowski, Ray Ming, Matthew E. Hudson, John A. Juvik, Daniel S. Rokhsar, Stephen P. Moose
Software Mentions: 1
Published: over 12 years ago
10.1186/s12864-018-5308-3
Perturbation of IIS/TOR signaling alters the landscape of sex-differential gene expression in Drosophila
Cited by: 21
Author(s): Rita M. Graze, Ruei-Ying Tzeng, Tiffany Howard, Michelle N. Arbeitman
Software Mentions: 1
Published: almost 6 years ago
10.1186/s12864-015-1476-6
Extensive intra-phylotype diversity in lactobacilli and bifidobacteria from the honeybee gut
Cited by: 106
Author(s): Kirsten Ellegaard, Daniel Tamarit, Emelie Javelind, Tobias Olofsson, Siv G. E. Andersson, Alejandra Vásquez
Software Mentions: 1
Published: over 9 years ago
10.1186/1471-2164-15-740
Genotyping by sequencing for genomic prediction in a soybean breeding population
Cited by: 163
Author(s): Diego Jarquín, Kyle Kocak, Luis Posadas, Katie E. Hyma, Joseph Jedlicka, George L. Graef, Aaron J. Lorenz
Software Mentions: 1
Published: about 10 years ago
10.1186/1471-2164-15-973
Comparative genomics of first available bovine Anaplasma phagocytophilum genome obtained with targeted sequence capture
Cited by: 14
Author(s): Thibaud Dugat, Valentin Loux, Sylvain Marthey, Marco Moroldo, Anne-Claire Lagrée, Henri-Jean Boulouis, Nadia Haddad, Renaud Maillard
Software Mentions: 1
Published: about 10 years ago
10.1186/s12864-015-2134-8
A genomic approach to understand interactions between Streptococcus pneumoniae and its bacteriophages
Cited by: 15
Author(s): Philippe Leprohon, Hélène Gingras, Siham Ouennane, Sylvain Moineau, Marc Ouellette
Software Mentions: 1
Published: about 9 years ago
10.1186/s12864-017-3603-z
Genome analysis following a national increase in Scarlet Fever in England 2014
Cited by: 58
Author(s): Victoria J. Chalker, Aleksey Jironkin, Juliana Coelho, Ali Al‐Shahib, Steve Platt, Georgia Kapatai, Roger Daniel, Chenchal Dhami, Marisa Laranjeira, Timothy E. Chambers, Rebecca Guy, Theresa Lamagni, Timothy G. Harrison, Meera Chand, Alan P. Johnson, Anthony Underwood
Software Mentions: 1
Published: over 7 years ago
10.1186/s12864-021-07591-5
Population and subspecies diversity at mouse centromere satellites
Cited by: 11
Author(s): Uma P. Arora, Caleigh Charlebois, Raman Akinyanju Lawal, Beth L. Dumont
Software Mentions: 1
Published: over 3 years ago
10.1186/s12864-015-1488-2
Pan-genome dynamics of Pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite
Cited by: 15
Author(s): Anukriti Sharma, Naseer Sangwan, Vivek Negi, Puneet Kohli, Jitendra P. Khurana, D. L. N. Rao, Rup Lal
Software Mentions: 1
Published: over 9 years ago
10.1186/1471-2164-14-615
Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy
Cited by: 42
Author(s): Ting Ni, Yanqin Yang, Dina Hafez, Wenjing Yang, Kurtis Kiesewetter, Yoshi Wakabayashi, Uwe Ohler, Weiqun Peng, Jun Zhu
Software Mentions: 1
Published: almost 12 years ago
10.1186/1471-2164-12-59
Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence
Cited by: 134
Author(s): Frank M. You, Naxin Huo, Karin R. Deal, Yong Gu, Ming Luo, Patrick E. McGuire, Jan Dvořák, Olin D. Anderson
Software Mentions: 1
Published: almost 14 years ago
10.1186/s12864-014-1210-9
A medium density genetic map and QTL for behavioral and production traits in Japanese quail
Cited by: 23
Author(s): Julien Recoquillay, Frédérique Pitel, Cécile Arnould, Sophie Leroux, Patrice Déhais, Carole Moréno, Ludovic Calandreau, Aline Bertin, David Gourichon, Olivier Bouchez, Alain Vignal, María Inés Fariello, Francis Minvielle, Catherine Beaumont, Christine Leterrier, Elisabeth Le Bihan‐Duval
Software Mentions: 1
Published: almost 10 years ago
10.1186/s12864-016-3177-1
Polygenic sex determination in the cichlid fish Astatotilapia burtoni
Cited by: 58
Author(s): Natalie B. Roberts, Scott A. Juntti, Kaitlin P. Coyle, Bethany L. Dumont, M. Kaitlyn Stanley, Allyson Q. Ryan, Russell D. Fernald, Reade B. Roberts
Software Mentions: 1
Published: about 8 years ago
10.1186/s12864-018-5009-y
Analysis of porcine body size variation using re-sequencing data of miniature and large pigs
Cited by: 11
Author(s): Christian Reimer, Carl-Johan Rubin, Ahmad Sharifi, Ngoc Thuy Ha, Steffen Weigend, K.-H. Waldmann, O. Distl, Sameer D. Pant, Merete Fredholm, Martin Schlather, Henner Simianer
Software Mentions: 1
Published: about 6 years ago
10.1186/1471-2164-15-790
Fine mapping QTL for female fertility on BTA04 and BTA13 in dairy cattle using HD SNP and sequence data
Cited by: 37
Author(s): Johanna Höglund, Goutam Sahana, Rasmus Froberg Brøndum, Bernt Guldbrandtsen, Bart Buitenhuis, Mogens Sandø Lund
Software Mentions: 1
Published: almost 11 years ago
10.1186/s12879-020-05599-y
Genomic and phenotypic characterisation of invasive neonatal and colonising group B Streptococcus isolates from Slovenia, 2001–2018
Cited by: 7
Author(s): Tina Perme, Daniel Golparian, Maja Bombek Ihan, Andrej Rojnik, Miha Lučovnik, Lilijana Kornhauser Cerar, Petja Fister, Jana Lozar Krivec, Štefan Grosek, Alojz Ihan, Samo Jeverica, Magnus Unemo
Software Mentions: 1
Published: almost 4 years ago
10.1186/s12881-015-0265-z
Enhanced diagnostic yield in Meckel-Gruber and Joubert syndrome through exome sequencing supplemented with split-read mapping
Cited by: 49
Author(s): Christopher M. Watson, Laura A. Crinnion, Ian Berry, Sally M. Harrison, Carolina Lascelles, Agne Antanaviciute, Ruth Charlton, Angus Dobbie, Ian Carr, David T. Bonthron
Software Mentions: 1
Published: almost 9 years ago
10.1186/s12881-020-01121-y
A de novo synonymous variant in EFTUD2 disrupts normal splicing and causes mandibulofacial dysostosis with microcephaly: case report
Cited by: 6
Author(s): Arthur Jacob, Jennifer Pasquier, Raphaël Carapito, Frédéric Auradé, Anne Molitor, Philippe Froguel, Khalid Fakhro, Najeeb Halabi, Géraldine Viot, Seiamak Bahram, Arash Rafii
Software Mentions: 1
Published: about 4 years ago
10.1186/1755-8794-7-20
Analytical validation of whole exome and whole genome sequencing for clinical applications
Cited by: 96
Author(s): Michael D. Linderman, Tracy Brandt, Lisa Edelmann, Omar Jabado, Yumi Kasai, Ruth Kornreich, Milind Mahajan, Hardik Shah, Andrew Kasarskis, Eric E. Schadt
Software Mentions: 1
Published: over 10 years ago
10.1186/1755-8794-4-68
Targeted high throughput sequencing in clinical cancer Settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity
Cited by: 155
Author(s): Martin Kerick, Melanie Isau, Bernd Timmermann, Holger Sültmann, Ralf Herwig, Sylvia Krobitsch, Georg Schaefer, Irmgard Verdorfer, Georg Bartsch, Helmut Klocker, Hans Lehrach, Michal R. Schweiger
Software Mentions: 1
Published: about 13 years ago
10.1186/s12870-020-02796-4
Bruchid beetle ovipositioning mediated defense responses in black gram pods
Cited by: 4
Author(s): Debajit Das, Indrani Baruah, Debashis Panda, Ricky Raj Paswan, Sumita Acharjee, B. C. Sarmah
Software Mentions: 1
Published: almost 4 years ago
10.1186/1753-6561-5-S7-O17
High-throughput targeted SNP discovery using Next Generation Sequencing (NGS) in few selected candidate genes in Eucalyptus camaldulensis
Cited by: 2
Author(s): Prasad Suresh Hendre, R. Kamalakannan, Rajkumar Rathinavelu, M. Varghese
Software Mentions: 1
Published: about 13 years ago
10.1186/s13104-021-05793-4
Improved library preparation protocols for amplicon sequencing-based noninvasive fetal genotyping for RHD-positive D antigen-negative alleles
Cited by: 0
Author(s): Asuka Hori, Hiroko Ogata‐Kawata, Akira Sasaki, Ken Takahashi, Kosuke Taniguchi, Ohsuke Migita, Akitsugu Kawashima, Aikou Okamoto, Akihiko Sekizawa, Haruhiko Sago, Fumio Takada, Kazuhiko Nakabayashi, Kenichiro Hata
Software Mentions: 1
Published: about 3 years ago
10.1186/s12917-017-1035-2
Illumina MiSeq 16S amplicon sequence analysis of bovine respiratory disease associated bacteria in lung and mediastinal lymph node tissue
Cited by: 37
Author(s): Dayle Johnston, Bernadette Earley, Paul Cormican, Gerard Murray, David A. Kenny, Sinéad M. Waters, M. McGee, A. K. Kelly, Matthew S. McCabe
Software Mentions: 1
Published: over 7 years ago
10.1186/s13040-019-0209-9
SEQdata-BEACON: a comprehensive database of sequencing performance and statistical tools for performance evaluation and yield simulation in BGISEQ-500
Cited by: 7
Author(s): Yanqiu Zhou, Chen Liu, Rongfang Zhou, Anzhi Lu, Biao Huang, Liling Liu, Ling Chen, Bei Luo, Jin Huang, Zhijian Tian
Software Mentions: 1
Published: about 5 years ago
10.3390/biology9110392
Global Picture of Genetic Relatedness and the Evolution of Humankind
Cited by: 2
Author(s): Gennady V. Khvorykh, Oleh A Mulyar, Larisa Fedorova, Andrey Khrunin, Svetlana A. Limborska, Alexei Fedorov
Software Mentions: 1
Published: about 4 years ago
10.3390/biomedicines9081030
Prenatal Diagnosis of Small Supernumerary Marker Chromosome 10 by Array-Based Comparative Genomic Hybridization and Microdissected Chromosome Sequencing
Cited by: 3
Author(s): I. N. Lebedev, Т. В. Карамышева, Eugeny A. Elisaphenko, Alex Makunin, Д. И. Жигалина, М. Е. Лопаткина, Г.В. Дроздов, А Д Черемных, Natalia B. Torkhova, Г. Н. Сеитова, S. A. Vasilyev, А. А. Кашеварова, Л. П. Назаренко, N. B. Rubtsov
Software Mentions: 1
Published: over 3 years ago
10.1093/braincomms/fcab002
Evidence that autosomal recessive spastic cerebral palsy-1 (CPSQ1) is caused by a missense variant in <i>HPDL</i>
Cited by: 5
Author(s): Neil V. Morgan, Bryndís Yngvadóttir, Mary O’Driscoll, Graeme R. Clark, Diana Walsh, Ezequiel Martín, Louise Tee, Evan Reid, Hannah Titheradge, Eamonn R. Maher
Software Mentions: 1
Published: almost 4 years ago
10.1093/bib/bbaa223
<i>In silico</i> tools for accurate HLA and KIR inference from clinical sequencing data empower immunogenetics on individual-patient and population scales
Cited by: 10
Author(s): Jieming Chen, Shravan Madireddi, Deepti R. Nagarkar, Maciej Migdał, Jason A. Vander Heiden, Diana Chang, Kiran Mukhyala, S. Selvaraj, Edward E. Kadel, Matthew J. Brauer, Sanjeev Mariathasan, Julie Hunkapiller, Suchit Jhunjhunwala, Matthew L. Albert, Christian Hammer
Software Mentions: 1
Published: about 4 years ago
10.1186/s12935-019-0725-1
Markers of MEK inhibitor resistance in low-grade serous ovarian cancer: EGFR is a potential therapeutic target
Cited by: 30
Author(s): Marta Llauradó Fernández, Amy Dawson, Joshua Hoenisch, Hannah Kim, Sylvia Bamford, Clara Salamanca, Gabriel E. DiMattia, Trevor G. Shepherd, Mattia Cremona, Bryan T. Hennessy, Shawn Anderson, Stanislav V. Volik, Colin C. Collins, David G. Huntsman, Mark Carey
Software Mentions: 1
Published: almost 6 years ago
10.1002/cam4.2458
Targeted deep sequencing from multiple sources demonstrates increased NOTCH1 alterations in lung cancer patient plasma
Cited by: 7
Author(s): Yuwei Liao, Zhaokui Ma, Yu Zhang, Dan Li, Dekang Lv, Zhisheng Chen, Peiying Li, Aisha Mohammed AI-Dherasi, Feng Zhao, Jichao Tian, Kun Zou, Yue Wang, Dongxia Wang, Miguel Córdova, Huan Zhou, Xiuhua Li, Dan Liú, Ruofei Yu, Qingzheng Zhang, Xiaolong Zhang, Jian Zhang, Xuehong Zhang, Xia Zhang, Yulong Li, Yanyan Shao, Limei Song, Ruimei Liu, Yichen Wang, Sufiyan Sufiyan, Quentin Liu, Gareth I. Owen, Chi Kong Li, Jun Chen
Software Mentions: 1
Published: over 5 years ago
10.3390/life10090174
Over Expression of the Cyanobacterial Pgr5-Homologue Leads to Pseudoreversion in a Gene Coding for a Putative Esterase in Synechocystis 6803
Cited by: 7
Author(s): Ketty Margulis, Hagit Zer, Hagar Lis, Hanan Schoffman, Omer Murik, Ginga Shimakawa, Anja Krieger‐Liszkay, Nir Keren
Software Mentions: 1
Published: about 4 years ago
10.1186/1475-2875-12-64
Mitochondrial genome sequences reveal deep divergences among Anopheles punctulatus sibling species in Papua New Guinea
Cited by: 34
Author(s): Kyle Logue, E. Ricky Chan, Tenisha Phipps, Scott T. Small, Lisa J. Reimer, Cara N. Halldin, Jetsumon Sattabongkot, Peter Siba, Peter A. Zimmerman, David Serre
Software Mentions: 1
Published: almost 12 years ago
10.1186/s12934-015-0382-6
Deletion of the 2-acyl-glycerophosphoethanolamine cycle improve glucose metabolism in Escherichia coli strains employed for overproduction of aromatic compounds
Cited by: 6
Author(s): César Aguilar, Noemí Flores, Fernando Riveros-Mckay, Diana X. Sahonero‐Canavesi, Susy Beatriz Carmona, Otto Geiger, Adelfo Escalante, Francisco Bolívar
Software Mentions: 1
Published: almost 9 years ago
10.1099/mgen.0.000326
Comparative genomics confirms a rare melioidosis human-to-human transmission event and reveals incorrect phylogenomic reconstruction due to polyclonality
Cited by: 16
Author(s): Ammar Aziz, Bart J. Currie, Mark Mayo, Derek S. Sarovich, Erin P. Price
Software Mentions: 1
Published: almost 5 years ago
10.1099/mgen.0.000434
Read trimming has minimal effect on bacterial SNP-calling accuracy
Cited by: 5
Author(s): Stephen J. Bush
Software Mentions: 1
Published: almost 4 years ago