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: custom

https://packages.ecosyste.ms/registries/pypi.org/packages/custom

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Latest release: about 8 years ago
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Papers Mentioning custom 1,363

10.1371/journal.pone.0122928
GeneSippr: A Rapid Whole-Genome Approach for the Identification and Characterization of Foodborne Pathogens such as Priority Shiga Toxigenic Escherichia coli
Cited by: 27
Author(s): Dominic Lambert, Catherine D. Carrillo, Adam Koziol, Paul Manninger, Burton W. Blais
Software Mentions: 2
Published: over 9 years ago
10.1093/gigascience/giaa034
CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes
Cited by: 3
Author(s): Heiner Kuhl, Ling Li, Sven Wuertz, Matthias Stöck, Xu‐Fang Liang, Christophe Klopp
Software Mentions: 2
Published: over 4 years ago
10.1099/mgen.0.000177
Expanding an expanded genome: long-read sequencing of Trypanosoma cruzi
Cited by: 87
Author(s): Luisa Berná, Matías Rodriguez, María Laura Chiribao, Adriana Parodi-Talice, Sebastián Pita, Gastón Rijo, Fernando Álvarez-Valín, Carlos Robello
Software Mentions: 2
Published: over 6 years ago
10.1016/j.heares.2020.108068
Effects of age on electrophysiological measures of cochlear synaptopathy in humans
Cited by: 13
Author(s): Samuele Carcagno, Christopher J. Plack
Software Mentions: 2
Published: about 4 years ago
10.1111/1751-7915.12735
Exploring bacterial interspecific interactions for discovery of novel antimicrobial compounds
Cited by: 47
Author(s): Olaf Tyc, Victor C. L. de Jager, Marlies van den Berg, Saskia Gerards, Thierry Janssens, Niels Zaagman, Marco Kai, Aleš Svatoš, Hans Zweers, C.A. Hordijk, Harrie Besselink, Wietse de Boer, Paolina Garbeva
Software Mentions: 2
Published: over 7 years ago
10.1371/journal.pone.0101607
Tandem Repeats and G-Rich Sequences Are Enriched at Human CNV Breakpoints
Cited by: 42
Author(s): Promita Bose, Karen Hermetz, Karen N. Conneely, M. Katharine Rudd
Software Mentions: 2
Published: over 10 years ago
10.1111/acel.12785
Extracellular <scp>RNA</scp> profiles with human age
Cited by: 23
Author(s): Douglas F. Dluzen, Nicole Noren Hooten, Supriyo De, William H. Wood, Yongqing Zhang, Kevin G. Becker, Alan B. Zonderman, Toshiko Tanaka, Luigi Ferrucci, Michele K. Evans
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pone.0122074
Comparative Genomic Analysis of Two Novel Sporadic Shiga Toxin-Producing Escherichia coli O104:H4 Strains Isolated 2011 in Germany
Cited by: 12
Author(s): Erhard Tietze, Piotr Wojtek Dabrowski, Rita Prager, Aleksandar Radonić, Angelika Fruth, Philipp Auraß, Andreas Nitsche, Martin Mielke, Antje Flieger
Software Mentions: 2
Published: over 9 years ago
10.1038/s41438-018-0021-6
Genotyping-by-sequencing application on diploid rose and a resulting high-density SNP-based consensus map
Cited by: 23
Author(s): Muqing Yan, David Byrne, Patricia E. Klein, Jianping Yang, Qianni Dong, Natalie Anderson
Software Mentions: 2
Published: over 6 years ago
10.1016/j.jbc.2021.101031
Epistatic interactions promote persistence of NS3-Q80K in HCV infection by compensating for protein folding instability
Cited by: 1
Author(s): G. Dultz, Sanjay Kumar Srikakulam, Michael Konetschnik, Tetsuro Shimakami, Nadezhda T. Doncheva, Julia Dietz, Christoph Sarrazin, Ricardo M. Biondi, Stefan Zeuzem, Robert Tampé, Olga Kalinina, Christoph Welsch
Software Mentions: 2
Published: about 3 years ago
10.1038/srep27040
Homoeologue expression insights into the basis of growth heterosis at the intersection of ploidy and hybridity in Cyprinidae
Cited by: 22
Author(s): Li Ren, Wuhui Li, Min Tao, Qinbo Qin, Jing Luo, Jing Chai, Chenchen Tang, Jun Xiao, Xiaojun Tang, Guoliang Lin, Chun Zhang, Wei Duan, Yunhan Hong, Shaojun Liu
Software Mentions: 2
Published: over 8 years ago
10.1007/s11306-016-1120-8
Loss of ncm5 and mcm5 wobble uridine side chains results in an altered metabolic profile
Cited by: 11
Author(s): Tony Karlsborn, A. K. M. Firoj Mahmud, Hasan Tükenmez, Andeŕs S. Byström
Software Mentions: 2
Published: about 8 years ago
10.1186/s13059-017-1385-x
A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers
Cited by: 34
Author(s): Enrique Martín‐Gayo, Michael B. Cole, Kellie E. Kolb, Zhengyu Ouyang, Jacqueline Cronin, Samuel W. Kazer, José Ordovás-Montañés, Mathias Lichterfeld, Bruce D. Walker, Nir Yosef, Alex K. Shalek, Xu G. Yu
Software Mentions: 2
Published: almost 7 years ago
10.1371/journal.pone.0061521
Stratified Whole Genome Linkage Analysis of Chiari Type I Malformation Implicates Known Klippel-Feil Syndrome Genes as Putative Disease Candidates
Cited by: 39
Author(s): Christina A. Markunas, Karen Soldano, Kaitlyn Dunlap, Heidi Cope, Edgar Asiimwe, Jeffrey M. Stajich, David S. Enterline, Gerald A. Grant, Herbert E. Fuchs, Simon G. Gregory, Allison E. Ashley-Koch
Software Mentions: 2
Published: over 11 years ago
10.1186/s13059-015-0727-9
Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution
Cited by: 107
Author(s): Pelin Sahlén, Ilgar Abdullayev, Daniel Ramsköld, Liudmila Matskova, Nemanja Rilakovic, Britta Lötstedt, Thomas Albert, Joakim Lundeberg, Rickard Sandberg
Software Mentions: 2
Published: over 9 years ago
10.1186/s12864-020-07192-8
Integrated analysis of lncRNAs and mRNAs reveals key trans-target genes associated with ETEC-F4ac adhesion phenotype in porcine small intestine epithelial cells
Cited by: 9
Author(s): Serafino M. A. Augustino, Qiang Xu, Xueqin Liu, Siyuan Mi, Liangyu Shi, Yibing Liu, Hui Wen, Di Wang, Lei Liu, Qin Zhang, Ying Yu
Software Mentions: 2
Published: about 4 years ago
10.1093/gbe/evv126
A Novel Terminal-Repeat Retrotransposon in Miniature (TRIM) Is Massively Expressed in<i>Echinococcus multilocularis</i>Stem Cells
Cited by: 18
Author(s): Uriel Koziol, Santiago Radío, Pablo Smircich, Magdalena Zarowiecki, Cecilia Fernández, Klaus Brehm
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0097568
Genome-Wide Quantitative Analysis of Histone H3 Lysine 4 Trimethylation in Wild House Mouse Liver: Environmental Change Causes Epigenetic Plasticity
Cited by: 12
Author(s): Angelika Börsch-Haubold, Inka Montero, Kathryn Konrad, Bernhard Haubold
Software Mentions: 2
Published: over 10 years ago
10.1007/s10126-020-10001-8
Genomic and Transcriptomic Analyses of Bioluminescence Genes in the Enope Squid Watasenia scintillans
Cited by: 3
Author(s): Masa‐aki Yoshida, Junichi Imoto, Yuri Kawai, Shigenobu Funahashi, Ryuhei Minei, Yuki Akizuki, Atsushi Ogura, Kazuhiko Nakabayashi, Kei Yura, Kazuho Ikeo
Software Mentions: 2
Published: about 4 years ago
10.1371/journal.pone.0189654
Facultative parthenogenesis validated by DNA analyses in the green anaconda (Eunectes murinus)
Cited by: 13
Author(s): Hiroki Shibata, Shuichi Sakata, Yuzo Hirano, Eiji Nitasaka, Ai Sakabe
Software Mentions: 2
Published: almost 7 years ago
10.1186/gb-2013-14-12-r142
The draft genome of a socially polymorphic halictid bee, Lasioglossum albipes
Cited by: 74
Author(s): Sarah D. Kocher, Li Cai, Wei Yang, Hao Tan, Soojin V. Yi, Xingyu Yang, Hopi E. Hoekstra, Guojie Zhang, Naomi E. Pierce, Douglas W. Yu
Software Mentions: 2
Published: almost 12 years ago
10.1371/journal.pone.0043350
Strand-Specific RNA-Seq Reveals Ordered Patterns of Sense and Antisense Transcription in Bacillus anthracis
Cited by: 23
Author(s): Karla D. Passalacqua, Anjana Varadarajan, Charlotte Weist, Brian D. Ondov, Benjamin Byrd, Timothy D. Read, Nicholas H. Bergman
Software Mentions: 2
Published: over 12 years ago
10.1186/s12864-015-1996-0
Transcriptome profiling of wheat glumes in wild emmer, hulled landraces and modern cultivars
Cited by: 14
Author(s): Hongda Zou, Raanan Tzarfati, Sariel Hübner, Tamar Krugman, Tzion Fahima, Shahal Abbo, Yehoshua Saranga, Abraham B. Korol
Software Mentions: 2
Published: about 9 years ago
10.1186/gb-2013-14-8-r92
A global profiling of uncapped mRNAs under cold stress reveals specific decay patterns and endonucleolytic cleavages in Brachypodium distachyon
Cited by: 22
Author(s): Jingyu Zhang, Zhiwei Mao, Kang Chong
Software Mentions: 2
Published: almost 12 years ago
10.1186/gb-2014-15-5-r74
SoxNeuro orchestrates central nervous system specification and differentiation in Drosophila and is only partially redundant with Dichaete
Cited by: 32
Author(s): Enrico Ferrero, Bettina Fischer, Steven Russell
Software Mentions: 2
Published: almost 11 years ago
10.1186/s12862-017-0973-4
Phylogenomic analyses of Crassiclitellata support major Northern and Southern Hemisphere clades and a Pangaean origin for earthworms
Cited by: 26
Author(s): Frank E. Anderson, Bronwyn W. Williams, Kevin M. Horn, Christer Erséus, Kenneth M. Halanych, Scott R. Santos, Samuel W. James
Software Mentions: 2
Published: over 7 years ago
10.1186/gb-2007-8-12-r262
Transcriptional profiling of MnSOD-mediated lifespan extension in Drosophila reveals a species-general network of aging and metabolic genes
Cited by: 121
Author(s): Christina Curtis, Gary N. Landis, Donna G. Folk, Nancy B. Wehr, Nicholas Hoe, Morris Waskar, Diana Abdueva, Dmitriy Skvortsov, Daniel Ford, Allan Luu, Ananth Badrinath, Rodney L. Levine, Timothy J. Bradley, Simon Tavaré, John Tower
Software Mentions: 2
Published: almost 18 years ago
10.1371/journal.pntd.0000658
The Genome Sequence of Trypanosoma brucei gambiense, Causative Agent of Chronic Human African Trypanosomiasis
Cited by: 128
Author(s): Andrew P. Jackson, Mandy Sanders, Andrew Berry, Jacqueline A. McQuillan, Martin Aslett, Michael A. Quail, Bridget Chukualim, Paul Capewell, Annette MacLeod, Sara E. Melville, Wendy Gibson, J. David Barry, Matthew Berriman, Christiane Hertz‐Fowler
Software Mentions: 2
Published: over 14 years ago
10.1038/s41375-018-0092-2
Mutation, methylation, and gene expression profiles in dup(1q)-positive pediatric B-cell precursor acute lymphoblastic leukemia
Cited by: 5
Author(s): R Gunnarsson, Sebastian DiLorenzo, Kristina B. Lundin-Ström, Linda Olsson, Andrea Biloglav, Henrik Lilljebjörn, Marianne Rissler, Per Wahlberg, Anders Lundmark, Anders Castor, Mikael Behrendtz, Thoas Fioretos, Kajsa Paulsson, Anders Isaksson, Bertil Johansson
Software Mentions: 2
Published: over 6 years ago
10.1186/1471-2164-10-379
High throughput sequencing in mice: a platform comparison identifies a preponderance of cryptic SNPs
Cited by: 23
Author(s): Nicole A.R. Walter, Daniel Bottomly, Ted Laderas, Michael A. Mooney, Priscila Darakjian, Robert P. Searles, Christina A. Harrington, Shannon K. McWeeney, Robert Hitzemann, Kari J. Buck
Software Mentions: 2
Published: over 15 years ago
10.1371/journal.pgen.1005493
The Dynamic Genome and Transcriptome of the Human Fungal Pathogen Blastomyces and Close Relative Emmonsia
Cited by: 57
Author(s): José F. Muñoz, Gregory M. Gauthier, Christopher A. Desjardins, Juan Esteban Gallo, Jason W. Holder, Thomas D. Sullivan, Amber J. Marty, John C. Carmen, Zehua Chen, Ding Li, Sharvari Gujja, Vincent Magrini, Elizabeth Misas, Makedonka Mitreva, Margaret Priest, Sakina Saif, Emily Whiston, Sarah Young, Qiandong Zeng, William E. Goldman, Elaine R. Mardis, John W. Taylor, Juan G. McEwen, Oliver Clay, Bruce S. Klein, Christina A. Cuomo
Software Mentions: 2
Published: about 9 years ago
10.1186/s40575-015-0029-2
Evaluation of whole-genome sequencing of four Chinese crested dogs for variant detection using the ion proton system
Cited by: 5
Author(s): Agnese Viļuma, Shumaila Sayyab, Sofia Mikko, Gerhard Andersson, Tomas F. Bergström
Software Mentions: 2
Published: about 9 years ago
10.1534/genetics.117.300448
Assessing the Relationship of Ancient and Modern Populations
Cited by: 16
Author(s): Joshua G. Schraiber
Software Mentions: 2
Published: almost 7 years ago
10.1186/gb-2010-11-4-r38
Phylogenetic detection of numerous gene duplications shared by animals, fungi and plants
Cited by: 20
Author(s): Xin Zhou, Zhenguo Lin, Hong Mā
Software Mentions: 2
Published: almost 15 years ago
10.1371/journal.pgen.1005887
Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback
Cited by: 194
Author(s): David Alexander Marques, Kay Lucek, Joana I. Meier, Salome Mwaiko, Catherine E. Wagner, Laurent Excoffier, Ole Seehausen
Software Mentions: 2
Published: over 8 years ago
10.1186/s12864-016-3030-6
Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler
Cited by: 125
Author(s): Samuel S. Shepard, Sarah Meno, Justin Bahl, Malania M. Wilson, John Barnes, Elizabeth B. Neuhaus
Software Mentions: 2
Published: about 8 years ago
10.1093/g3journal/jkab076
Evidence of gene nucleotide composition favoring replication and growth in a fastidious plant pathogen
Cited by: 5
Author(s): Andreína I. Castillo, Rodrigo P. P. Almeida
Software Mentions: 2
Published: over 3 years ago
10.1093/g3journal/jkab154
Genomic patterns of structural variation among diverse genotypes of <i>Sorghum bicolor</i> and a potential role for deletions in local adaptation
Cited by: 6
Author(s): Kittikun Songsomboon, Zachary Brenton, James Heuser, Stephen Kresovich, Nadia Shakoor, Todd C. Mockler, Elizabeth A. Cooper
Software Mentions: 2
Published: over 3 years ago
10.1186/gb-2011-12-10-r103
Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer
Cited by: 176
Author(s): Wigard P. Kloosterman, Marlous Hoogstraat, Oscar Paling, Masoumeh Tavakoli-Yaraki, Ivo Renkens, Joost S.P. Vermaat, Markus J. van Roosmalen, Stef van Lieshout, Isaäc J Nijman, Wijnand M. Roessingh, Ruben van ‘t Slot, José van de Belt, Victor Guryev, Marco J. Koudijs, Emile E. Voest, Edwin Cuppen
Software Mentions: 2
Published: almost 14 years ago
10.1534/g3.119.400930
High-Quality Genome Assembly and Annotation of the Big-Eye Mandarin Fish (<i>Siniperca knerii</i>)
Cited by: 14
Author(s): Liang Lu, Jianmin Zhao, Chenhong Li
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pgen.1003772
Cell Interactions and Patterned Intercalations Shape and Link Epithelial Tubes in C. elegans
Cited by: 25
Author(s): Jeffrey P. Rasmussen, Jessica L. Feldman, Sowmya Somashekar Reddy, James R Priess
Software Mentions: 2
Published: about 11 years ago
10.1371/journal.pgen.1002316
Identification of Genomic Regions Associated with Phenotypic Variation between Dog Breeds using Selection Mapping
Cited by: 330
Author(s): Amaury Vaysse, Abhirami Ratnakumar, Thomas Derrien, Erik Axelsson, Gerli Pielberg, Snaevar Sigurðsson, Tove Fall, Eija H. Seppälä, Mark Hansen, Cindy Lawley, Elinor K. Karlsson, Danika Bannasch, Carles Vilà, Hannes Lohi, Francis Galibert, Merete Fredholm, Jens Häggström, Åke Hedhammar, Catherine André, Kerstin Lindblad‐Toh, Christophe Hitte, Matthew T. Webster
Software Mentions: 2
Published: about 13 years ago
10.1371/journal.pgen.1006245
The Contribution of Mosaic Variants to Autism Spectrum Disorder
Cited by: 96
Author(s): Donald Freed, Jonathan Pevsner
Software Mentions: 2
Published: about 8 years ago
10.3390/brainsci11020145
Transcranial Evoked Potentials Can Be Reliably Recorded with Active Electrodes
Cited by: 26
Author(s): Marco Mancuso, Valerio Sveva, Alessandro Cruciani, Katlyn E. Brown, Jaime Ibáñez, Vishal Rawji, Elias Paolo Casula, Isabella Premoli, Sasha D’Ambrosio, John C. Rothwell, Lorenzo Rocchi
Software Mentions: 2
Published: almost 4 years ago
10.1186/1471-2148-12-217
Protein evolution in two co-occurring types of Symbiodinium: an exploration into the genetic basis of thermal tolerance in Symbiodinium clade D
Cited by: 104
Author(s): Jason T. Ladner, Daniel J. Barshis, Stephen R. Palumbi
Software Mentions: 2
Published: almost 13 years ago
10.1371/journal.pgen.1003464
Breakpoint Analysis of Transcriptional and Genomic Profiles Uncovers Novel Gene Fusions Spanning Multiple Human Cancer Types
Cited by: 101
Author(s): Craig P. Giacomini, Steven Sun, Sushama Varma, A. Hunter Shain, Marilyn M. Giacomini, Jay Michael S. Balagtas, Robert T. Sweeney, Everett Lai, Catherine A. Del Vecchio, Andrew D. Forster, Nicole Clarke, Kelli Montgomery, Shirley Zhu, Albert J. Wong, Matt van de Rijn, Robert B. West, Jonathan R. Pollack
Software Mentions: 2
Published: over 11 years ago
10.1371/journal.pgen.1003056
Population Genomics of Inversion Polymorphisms in Drosophila melanogaster
Cited by: 173
Author(s): Russell Corbett-Detig, Daniel L. Hartl
Software Mentions: 2
Published: almost 12 years ago
10.1534/g3.116.032797
Comparative Analysis Highlights Variable Genome Content of Wheat Rusts and Divergence of the Mating Loci
Cited by: 107
Author(s): Christina A. Cuomo, Guus Bakkeren, H. M. Khalil, Vinay Panwar, David L. Joly, Rob Linning, Sharadha Sakthikumar, Xiao Ping Song, Xian Adiconis, Fan Lin, Jonathan M. Goldberg, Joshua Z. Levin, Sarah Young, Qiandong Zeng, Y. Anikster, Myron Bruce, Meinan Wang, Chuntao Yin, Brent D. McCallum, Les J. Szabo, Scot H. Hulbert, Xianming Chen, John P. Fellers
Software Mentions: 2
Published: almost 8 years ago
10.1186/1471-2164-11-499
Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites
Cited by: 73
Author(s): Paul Hunt, Axel Martinelli, Katarzyna Modrzynska, Sofia Trindade Borges, Alison M. Creasey, Louise Rodrigues, Dario Beraldi, Laurence Loewe, R.H. Fawcett, Sujai Kumar, Marian Thomson, Urmi Trivedi, Thomas D. Otto, Arnab Pain, Mark Blaxter, Pedro Vitor Lemos Cravo
Software Mentions: 2
Published: almost 15 years ago
10.1534/g3.116.030486
Head Transcriptomes of Two Closely Related Species of Fruit Flies of the<i>Anastrepha fraterculus</i>Group Reveals Divergent Genes in Species with Extensive Gene Flow
Cited by: 14
Author(s): Victor Borges Rezende, Carlos Congrains, André Luís A. Lima, Emeline Boni Campanini, Aline Minali Nakamura, Janaína Lima de Oliveira, Samira Chahad‐Ehlers, Iderval Sobrinho, Reinaldo Alves de Brito
Software Mentions: 2
Published: about 8 years ago
10.1093/brain/awaa045
In vivo CRISPRa decreases seizures and rescues cognitive deficits in a rodent model of epilepsy
Cited by: 67
Author(s): Gaia Colasante, Yichen Qiu, Luca Massimino, Claudia Di Berardino, Jonathan Cornford, Albert Snowball, Mikail Weston, Steffan P. Jones, Serena Giannelli, Andreas Lieb, Stephanie Schorge, Dimitri M. Kullmann, Vania Broccoli, Gabriele Lignani
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pgen.1005706
Trm9-Catalyzed tRNA Modifications Regulate Global Protein Expression by Codon-Biased Translation
Cited by: 78
Author(s): Wenjun Deng, I. Ramesh Babu, Dan Su, Shanye Yin, Thomas J. Begley, Peter C. Dedon
Software Mentions: 2
Published: almost 9 years ago
10.1186/s12862-018-1137-x
Phylogeny with introgression in Habronattus jumping spiders (Araneae: Salticidae)
Cited by: 27
Author(s): Geneviève Leduc-Robert, Wayne P. Maddison
Software Mentions: 2
Published: over 6 years ago
10.1093/brain/awv222
Early maturation and distinct tau pathology in induced pluripotent stem cell-derived neurons from patients with<i>MAPT</i>mutations
Cited by: 107
Author(s): Mariangela Iovino, Sylvia Agathou, Ana González‐Rueda, Martín Del Castillo Velasco-Herrera, Barbara Borroni, Antonella Alberici, Timothy Lynch, Seán O’Dowd, Imbisaat Geti, Daniel J. Gaffney, Ludovic Vallier, Ole Paulsen, Ragnhildur Thóra Káradóttir, Maria Grazia Spillantini
Software Mentions: 2
Published: over 9 years ago
10.1186/1471-2164-14-653
HANDS: a tool for genome-wide discovery of subgenome- specific base-identity in polyploids
Cited by: 9
Author(s): Aziz Mithani, Eric J. Belfield, C. Titus Brown, Caifu Jiang, Lindsey Leach, Nicholas P. Harberd
Software Mentions: 2
Published: about 11 years ago
10.3389/fnsys.2014.00004
Back to front: cerebellar connections and interactions with the prefrontal cortex
Cited by: 117
Author(s): Thomas C. Watson, Nadine Becker, Richard Apps, Matthew W. Jones
Software Mentions: 2
Published: almost 11 years ago
10.1371/journal.pgen.1005050
Complex Genomic Rearrangements at the PLP1 Locus Include Triplication and Quadruplication
Cited by: 52
Author(s): Christine R. Beck, Claudia M.B. Carvalho, Linda Banser, Tomasz Gambin, Danielle Stubbolo, Bo Yuan, Karen Sperle, Suzanne M. McCahan, Marco Henneke, Pavel Seeman, James Garbern, Grace M. Hobson, James R. Lupski
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pgen.1007367
Patterns of chromatin accessibility along the anterior-posterior axis in the early Drosophila embryo
Cited by: 39
Author(s): Jenna E. Haines, Michael B. Eisen
Software Mentions: 2
Published: over 6 years ago
10.3390/biom10111491
Development of Methods Derived from Iodine-Induced Specific Cleavage for Identification and Quantitation of DNA Phosphorothioate Modifications
Cited by: 4
Author(s): Sucheng Zhu, Tao Zheng, Lingxin Kong, Jinli Li, Bo Cao, Michael S. DeMott, Yihua Sun, Ying Chen, Zixin Deng, Peter C. Dedon, Delin You
Software Mentions: 2
Published: about 4 years ago
10.3390/biom11040560
Identification and Characterization of a Novel Genomic Island Harboring Cadmium and Arsenic Resistance Genes in Listeria welshimeri
Cited by: 6
Author(s): Sangmi Lee, Cameron Parsons, Yi Chen, Zahra Hanafy, Eric W. Brown, Sophia Kathariou
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pgen.1004161
Insights into the Dekkera bruxellensis Genomic Landscape: Comparative Genomics Reveals Variations in Ploidy and Nutrient Utilisation Potential amongst Wine Isolates
Cited by: 81
Author(s): Anthony R. Borneman, Ryan Zeppel, Paul J. Chambers, Chris Curtin
Software Mentions: 2
Published: almost 11 years ago
10.1128/AEM.02765-19
Emergence of Fluoroquinolone-Resistant <i>Campylobacter jejuni</i> and <i>Campylobacter coli</i> among Australian Chickens in the Absence of Fluoroquinolone Use
Cited by: 35
Author(s): Sam Abraham, Shafi Sahibzada, Kylie Hewson, Tanya Laird, Rebecca Abraham, Anthony Pavic, Alec Truswell, Terence Lee, Mark O’Dea, David Jordan
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pgen.1000445
Meta-Analysis of Genome-Wide Scans for Human Adult Stature Identifies Novel Loci and Associations with Measures of Skeletal Frame Size
Cited by: 241
Author(s): Nicole Soranzo, Fernando Rivadeneira, Usha Chinappen-Horsley, Ida Malkina, J. Brent Richards, Naomi Hammond, Lisette Stolk, Alexandra C. Nica, Michael Inouye, Albert Hofman, Jonathan Stephens, Eleanor Wheeler, Pascal P. Arp, Rhian Gwilliam, P. Mila Jhamai, Simon Potter, Amy Chaney, Mohammed J. R. Ghori, Radhi Ravindrarajah, Sergey Ermakov, Karol Estrada, Huibert A. P. Pols, Frances Williams, Wendy L. McArdle, Joyce B. J. van Meurs, Ruth J.F. Loos, Emmanouil T. Dermitzakis, Kourosh R. Ahmadi, Deborah Hart, Willem H. Ouwehand, Nicholas J. Wareham, Inês Barroso, Manjinder S. Sandhu, David P. Strachan, Gregory Livshits, Timothy D. Spector, André G. Uitterlinden, Panos Deloukas
Software Mentions: 2
Published: over 15 years ago
10.1155/2014/675158
Defining Loci in Restriction-Based Reduced Representation Genomic Data from Nonmodel Species: Sources of Bias and Diagnostics for Optimal Clustering
Cited by: 84
Author(s): Daniel C. Ilut, Marie L. Nydam, Matthew P. Hare
Software Mentions: 2
Published: almost 11 years ago
10.1155/2016/8285428
Next Generation Sequencing Identifies Five Major Classes of Potentially Therapeutic Enzymes Secreted by<i>Lucilia sericata</i>Medical Maggots
Cited by: 19
Author(s): Zdeněk Franta, Heiko Vogel, Rüdiger Lehmann, Oliver Rupp, Alexander Goesmann, Andreas Vilcinskas
Software Mentions: 2
Published: almost 9 years ago
10.3389/fpls.2013.00362
Facile mutant identification via a single parental backcross method and application of whole genome sequencing based mapping pipelines
Cited by: 30
Author(s): Robert S. Allen, Kenlee Nakasugi, Rachel L. Doran, Anthony A. Millar, Peter M. Waterhouse
Software Mentions: 2
Published: almost 12 years ago
10.1534/g3.115.024349
The Effects of Both Recent and Long-Term Selection and Genetic Drift Are Readily Evident in North American Barley Breeding Populations
Cited by: 20
Author(s): Ana M. Poets, Mohsen Mohammadi, Kiran Seth, Hongyun Wang, Thomas J. Y. Kono, Zhou Fang, Gary J. Muehlbauer, Kevin P. Smith, Peter L. Morrell
Software Mentions: 2
Published: over 8 years ago
10.3389/fpls.2018.00893
Comparative Aerial and Ground Based High Throughput Phenotyping for the Genetic Dissection of NDVI as a Proxy for Drought Adaptive Traits in Durum Wheat
Cited by: 101
Author(s): Giuseppe Emanuele Condorelli, Marco Maccaferri, Maria Newcomb, Pedro Andrade-Sánchez, Jeffrey W. White, Andrew N. French, Giuseppe Notarbartolo di Sciara, Roxanne Ward, Roberto Tuberosa
Software Mentions: 2
Published: over 6 years ago
10.3389/fpls.2017.00654
Grapevine Grafting: Scion Transcript Profiling and Defense-Related Metabolites Induced by Rootstocks
Cited by: 65
Author(s): Walter Chitarra, Irene Perrone, C. Avanzato, Andrea Minio, Deborah Santini, G. Gilardi, Ilenia Siciliano, M. L. Gullino, Massimo Delledonne, F. Mannini, Giorgio Gambino
Software Mentions: 2
Published: over 7 years ago
10.1371/journal.pgen.1004782
ARTIST: High-Resolution Genome-Wide Assessment of Fitness Using Transposon-Insertion Sequencing
Cited by: 132
Author(s): Justin R. Pritchard, Michael C. Chao, Sören Abel, Brigid M. Davis, Catherine Baranowski, Yanjia J. Zhang, Eric J. Rubín, Matthew K. Waldor
Software Mentions: 2
Published: about 10 years ago
10.1371/journal.pgen.1009429
A loss-of-function mutation in RORB disrupts saltatorial locomotion in rabbits
Cited by: 7
Author(s): Miguel Carneiro, Jennifer Vieillard, Pedro Andrade, Samuel Boucher, Sandra Afonso, José Antonio Blanco‐Aguiar, Nuno Santos, João Branco, Pedro J. Esteves, Nathalie Ferrand, Klas Kullander, Leif Andersson
Software Mentions: 2
Published: over 3 years ago
10.1186/s40478-019-0826-z
Mapping actionable pathways and mutations in brain tumours using targeted RNA next generation sequencing
Cited by: 7
Author(s): Krissie Lenting, Corina N. A. M. van den Heuvel, Anne van Ewijk, Duaa Elmelik, R. de Boer, Elizabeth A. Tindall, Wei Ge, Benno Küsters, Maarten te Dorsthorst, Mark ter Laan, Martijn Huynen, William P. J. Leenders
Software Mentions: 2
Published: about 5 years ago
10.3389/fpls.2017.02081
microRNAs and Their Targets in Apple (Malus domestica cv. “Fuji”) Involved in Response to Infection of Pathogen Valsa mali
Cited by: 13
Author(s): Feng Hu, Ming Xu, Zheng Xiang, Tongyi Zhu, Xiaoning Gao, Lili Huang
Software Mentions: 2
Published: almost 7 years ago
10.1371/journal.pgen.1009200
A spectrum of verticality across genes
Cited by: 17
Author(s): Falk S. P. Nagies, Julia Brueckner, Fernando D. K. Tria, William Martin
Software Mentions: 2
Published: about 4 years ago
10.3389/fpls.2013.00456
Transcriptome analysis of poplar rust telia reveals overwintering adaptation and tightly coordinated karyogamy and meiosis processes
Cited by: 27
Author(s): Stéphane Hacquard, Christine Delaruelle, Pascal Frey, Émilie Tisserant, Annegret Kohler, Sébastien Duplessis
Software Mentions: 2
Published: almost 12 years ago
10.1371/journal.pgen.1005206
Accounting for Experimental Noise Reveals That mRNA Levels, Amplified by Post-Transcriptional Processes, Largely Determine Steady-State Protein Levels in Yeast
Cited by: 157
Author(s): Gábor Csárdi, Alexander Franks, David Choi, Edoardo M. Airoldi, D. Allan Drummond
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pgen.1005631
GBStools: A Statistical Method for Estimating Allelic Dropout in Reduced Representation Sequencing Data
Cited by: 28
Author(s): Thomas F. Cooke, Muh-Ching Yee, Marina Muzzio, Alexandra Sockell, Ryan T. Bell, Omar E. Cornejo, Joanna L. Kelley, Graciela Bailliet, Cláudio M. Bravi, Carlos D. Bustamante, Eimear E. Kenny
Software Mentions: 2
Published: almost 9 years ago
10.1371/journal.pgen.1002835
Brain-Specific Rescue of Clock Reveals System-Driven Transcriptional Rhythms in Peripheral Tissue
Cited by: 94
Author(s): Michael Hughes, Hee Kyung Hong, Jason Chong, Alejandra A. Indacochea, Samuel S. Lee, Michael Han, Joseph S. Takahashi, John B. Hogenesch
Software Mentions: 2
Published: over 12 years ago
10.1186/1745-6150-7-18
Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics
Cited by: 390
Author(s): Dapeng Zhang, Robson Francisco de Souza, Vivek Anantharaman, Lakshminarayan M. Iyer, L. Aravind
Software Mentions: 2
Published: over 12 years ago
10.1371/journal.pgen.1008389
Chromosome-wide co-fluctuation of stochastic gene expression in mammalian cells
Cited by: 20
Author(s): Mengyi Sun, Jianzhi Zhang
Software Mentions: 2
Published: about 5 years ago
10.3389/fphar.2018.01427
Mid-Latency Auditory Evoked Potentials Differentially Predict Sedation and Drug Level Under Opioid and Hypnotic Agents
Cited by: 7
Author(s): Gernot G. Supp, Focko L. Higgen, Joerg F. Hipp, Andreas K. Engel, Markus Siegel
Software Mentions: 2
Published: almost 6 years ago
10.1371/journal.pcbi.1002404
Epitope Flexibility and Dynamic Footprint Revealed by Molecular Dynamics of a pMHC-TCR Complex
Cited by: 54
Author(s): Cyril Reboul, Grischa R. Meyer, Benjamin T. Porebski, Natalie A. Borg, Ashley M. Buckle
Software Mentions: 2
Published: over 12 years ago
10.1371/journal.pcbi.1007226
Energy-efficient information transfer at thalamocortical synapses
Cited by: 22
Author(s): Julia J. Harris, Elisabeth Engl, David Attwell, Renaud Jolivet
Software Mentions: 2
Published: over 5 years ago
10.3389/fnins.2019.01407
Temporal Profile of Brain Gene Expression After Prey Catching Conditioning in an Anuran Amphibian
Cited by: 3
Author(s): Vern Lewis, Frédéric Laberge, Andreas Heyland
Software Mentions: 2
Published: almost 5 years ago
10.1371/journal.pcbi.1006838
Finding the balance between model complexity and performance: Using ventral striatal oscillations to classify feeding behavior in rats
Cited by: 10
Author(s): Lucas L. Dwiel, Jibran Y. Khokhar, Michael Connerney, Alan I. Green, Wilder T. Doucette
Software Mentions: 2
Published: over 5 years ago
10.1186/s12864-015-1219-8
Impacts of low coverage depths and post-mortem DNA damage on variant calling: a simulation study
Cited by: 18
Author(s): Matthew Parks, David M. Lambert
Software Mentions: 2
Published: almost 10 years ago
10.3389/fonc.2021.606820
Interpreting Sequence Variation in PDAC-Predisposing Genes Using a Multi-Tier Annotation Approach Performed at the Gene, Patient, and Cohort Level
Cited by: 3
Author(s): Michael T. Zimmermann, Angela Mathison, Tim Stodola, Douglas B. Evans, Jenica Abrudan, Wendy Demos, Michael Tschannen, Mohammed Aldakkak, Jennifer L. Geurts, Gwen Lomberk, Susan Tsai, Raúl Urrutia
Software Mentions: 2
Published: over 3 years ago
10.1186/1752-0509-5-202
A chemokine gene expression signature derived from meta-analysis predicts the pathogenicity of viral respiratory infections
Cited by: 18
Author(s): Stewart T. Chang, Nicolas Tchitchek, Debashis Ghosh, Arndt Benecke, Michael G. Katze
Software Mentions: 2
Published: almost 13 years ago
10.1371/journal.pcbi.1004862
Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes
Cited by: 131
Author(s): Amit A. Upadhyay, Aaron D. Fleetwood, Ogün Adebali, Alex Bateman, Igor B. Zhulin
Software Mentions: 2
Published: over 8 years ago
10.3389/fninf.2021.596443
A Quick and Easy Way to Estimate Entropy and Mutual Information for Neuroscience
Cited by: 10
Author(s): Mickaël Zbili, Sylvain Rama
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pcbi.1007205
Bayesian hypothesis testing and experimental design for two-photon imaging data
Cited by: 6
Author(s): Luke Edward Rogerson, Zhijian Zhao, Katrin Franke, Thomas Euler, Philipp Berens
Software Mentions: 2
Published: over 5 years ago
10.3389/fncir.2016.00032
Feed-Forward Propagation of Temporal and Rate Information between Cortical Populations during Coherent Activation in Engineered In Vitro Networks
Cited by: 24
Author(s): Thomas B. DeMarse, Longfa Pan, Sankaraleengam Alagapan, Gregory J. Brewer, Bruce C. Wheeler
Software Mentions: 2
Published: over 8 years ago
10.3389/fnins.2018.00351
Partially Overlapping Brain Networks for Singing and Cello Playing
Cited by: 27
Author(s): Melanie Segado, Avrum Hollinger, Joseph Thibodeau, Virginia B. Penhune, Robert J. Zatorre
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pcbi.1001102
Accurate and Fast Simulation of Channel Noise in Conductance-Based Model Neurons by Diffusion Approximation
Cited by: 70
Author(s): Daniele Linaro, Marco Storace, Michèle Giugliano
Software Mentions: 2
Published: over 13 years ago
10.3389/fmolb.2020.00179
A Workflow for Protein Structure Determination From Thin Crystal Lamella by Micro-Electron Diffraction
Cited by: 20
Author(s): Emma V. Beale, David Waterman, Corey W. Hecksel, Jason M. van Rooyen, James B. Gilchrist, James M. Parkhurst, Felix de Haas, Bart Buijsse, Gwyndaf Evans, Peijun Zhang
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pcbi.1004780
4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments
Cited by: 84
Author(s): Ramya Raviram, Pedro P. Rocha, Christian L. Müller, Emily R. Miraldi, Sana Badri, Yi Fu, Emily Swanzey, Charlotte Proudhon, Valentina Snetkova, Richard Bonneau, Jane A. Skok
Software Mentions: 2
Published: over 8 years ago
10.3389/fpls.2016.00525
Population Genomic Analysis Reveals Differential Evolutionary Histories and Patterns of Diversity across Subgenomes and Subpopulations of Brassica napus L.
Cited by: 24
Author(s): Élodie Gazave, Erica E. Tassone, Daniel C. Ilut, Megan Wingerson, Erwin Datema, H. Witsenboer, James B. Davis, David Grant, John M. Dyer, Matthew A. Jenks, J. Brown, Michael A. Gore
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pcbi.1007627
The role of adaptation in generating monotonic rate codes in auditory cortex
Cited by: 6
Author(s): Jong Hoon Lee, Xiaoqin Wang, Daniel Bendor
Software Mentions: 2
Published: almost 5 years ago
10.1186/s12900-016-0064-6
Conservation of the C-type lectin fold for accommodating massive sequence variation in archaeal diversity-generating retroelements
Cited by: 15
Author(s): Sumit Handa, Blair G. Paul, Jeffery F. Miller, David L. Valentine, Partho Ghosh
Software Mentions: 2
Published: about 8 years ago
10.3389/fmicb.2019.01011
Regional and Microenvironmental Scale Characterization of the Zostera muelleri Seagrass Microbiome
Cited by: 45
Author(s): Valentina Hurtado-McCormick, Tim Kahlke, Katherina Petrou, Thomas C. Jeffries, Peter J. Ralph, Justin R. Seymour
Software Mentions: 2
Published: over 5 years ago