Ecosyste.ms: Papers

10.1371/journal.pgen.1007588

Numerous recursive sites contribute to accuracy of splicing in long introns in flies
Cited by: 17
Author(s): Athma A. Pai, Joseph M. Paggi, Paul Yan, Karen Adelman, Christopher B. Burge
Software Mentions: 4
Published: about 6 years ago

10.1016/j.immuni.2020.08.004

Osteopontin Expression Identifies a Subset of Recruited Macrophages Distinct from Kupffer Cells in the Fatty Liver
Cited by: 243
Author(s): Anneleen Remmerie, Liesbet Martens, Tinne Thoné, Ângela Castoldi, Ruth Seurinck, Benjamin Pavie, Joris Roels, Bavo Vanneste, Sofie De Prijck, Mathias Vanhockerhout, Mushida Binte Abdul Latib, Lindsey Devisscher, Anne Hoorens, Johnny Bonnardel, Niels Vandamme, Anna Kremer, Peter Borghgraef, Hans Van Vlierberghe, Saskia Lippens, Edward J. Pearce, Yvan Saeys, Charlotte Scott
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pcbi.1009105

Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis
Cited by: 40
Author(s): Cecilia Wieder, Clément Frainay, Nathalie Poupin, Pablo Rodríguez-Mier, Florence Vinson, Juliette Cooke, Rachel Lai, Jacob G. Bundy, Fabien Jourdan, Timothy M. D. Ebbels
Software Mentions: 4
Published: about 3 years ago

10.1371/journal.pone.0140829

Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud
Cited by: 99
Author(s): Enis Afgan, Clare Sloggett, Nuwan Goonasekera, Igor V. Makunin, Derek Benson, Mark L. Crowe, Simon Gladman, Yousef Kowsar, Michael Pheasant, Ron Horst, Andrew Lonie
Software Mentions: 4
Published: about 9 years ago

10.1186/s13059-021-02333-y

Genomic insights into the origin, domestication and genetic basis of agronomic traits of castor bean
Cited by: 28
Author(s): Wei Xu, Di Wu, Tianquan Yang, Chao Sun, Zaiqing Wang, Bing Han, Shibo Wu, Anmin Yu, Mark A. Chapman, Sammy Muraguri, Qing Tan, Wenbo Wang, Zhigui Bao, Aizhong Liu, Li D
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pbio.2005359

Comparative genomics and the nature of placozoan species
Cited by: 63
Author(s): Michael Eitel, Warren R. Francis, Frédérique Varoqueaux, Jean Daraspe, Hans-Jürgen Osigus, Stefan Krebs, Sergio Vargas, Helmut Blum, Gray A. Williams, Bernd Schierwater, Gert Wörheide
Software Mentions: 4
Published: over 6 years ago

10.1126/sciadv.aaw3095

GWAS on longitudinal growth traits reveals different genetic factors influencing infant, child, and adult BMI
Cited by: 76
Author(s): Alexessander Couto Alves, N. Maneka G. De Silva, Ville Karhunen, Ulla Sovio, Shikta Das, H. Rob Taal, Nicole M. Warrington, Arie Y. Lewin, Marika Kaakinen, Diana L. Cousminer, Elisabeth Thiering, Nicholas J. Timpson, Tom A Bond, Estelle Lowry, Christopher D. Brown, Xavier Estivill, Virpi Lindi, Jonathan P. Bradfield, Frank Geller, Doug Speed, Lachlan Coin, Marie Loh, Sheila J. Barton, Lawrence J. Beilin, Hans Bisgaard, Klaus Bønnelykke, Rohia Alili, Ida J. Hatoum, Katharina Schramm, Rufus Cartwright, Charles Munier, Vincenzo Salerno, Karine Clément, Annique Claringbould, Cornelia M. van Duijn, Elena Moltchanova, Johan G. Eriksson, Cathy E. Elks, Bjarke Feenstra, Claudia Flexeder, Stephen Franks, Timothy M. Frayling, Rachel M. Freathy, Paul Elliott, Elisabeth Widén, Hákon Hákonarson, Andrew T. Hattersley, Alina Rodriguez, Marco Banterle, Joachim Heinrich, Barbara Heude, John W. Holloway, Albert Hofman, Elina Hyppönen, Hazel Inskip, Lee M. Kaplan, Åsa K. Hedman, Esa Läärä, Holger Prokisch, Harald Grallert, Timo A. Lakka, Debbie A. Lawlor, Mads Melbye, Tarunveer S. Ahluwalia, M. Marinelli, Iona Y. Millwood, Lyle J. Palmer, Craig E. Pennell, John Perry, Susan M. Ring, Markku J. Savolainen, Fernando Rivadeneira, Marie Standl, Jordi Sunyer, Carla M. T. Tiesler, André G. Uitterlinden, William Schierding, Justin M. O’Sullivan, Inga Prokopenko, Karl‐Heinz Herzig, George Davey Smith, Paul O’Reilly, Janine F. Felix, Jessica L. Buxton, Alexandra I. F. Blakemore, Ken K. Ong, Vincent W. V. Jaddoe, Struan F.A. Grant, Sylvain Sebért, Mark McCarthy, Marjo‐Riitta Järvelin
Software Mentions: 4
Published: about 5 years ago

10.3390/plants10020364

A Systems Biology Approach to Identify Essential Epigenetic Regulators for Specific Biological Processes in Plants
Cited by: 5
Author(s): Rachel M. McCoy, Russell Julian, Shoban R V Kumar, Rajeev Ranjan, Kranthi Varala, Ying Liu
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0090706

A Bulk Segregant Gene Expression Analysis of a Peach Population Reveals Components of the Underlying Mechanism of the Fruit Cold Response
Cited by: 36
Author(s): Clara Pons, Cristina Martí, Javier Forment, Carlos H. Crisosto, Abhaya M. Dandekar, Antonio Granell
Software Mentions: 4
Published: over 10 years ago

10.1186/s12711-021-00668-5

A near complete genome for goat genetic and genomic research
Cited by: 11
Author(s): Ran Li, Peng Yang, Xuelei Dai, Hojjat Asadollahpour Nanaei, Wenwen Fang, Zhirui Yang, Yi Cai, Zhuqing Zheng, Xihong Wang, Yu Jiang
Software Mentions: 4
Published: about 3 years ago

10.1111/pbi.13516

Genome‐wide association coupled gene to gene interaction studies unveil novel epistatic targets among major effect loci impacting rice grain chalkiness
Cited by: 23
Author(s): Gopal Misra, Saurabh Badoni, Sabiha Parween, Rakesh Kumar Singh, Hei Leung, Olufunmilayo Ladejobi, Richard Mott, Nese Sreenivasulu
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12864-019-6384-8

Chicken adaptive response to low energy diet: main role of the hypothalamic lipid metabolism revealed by a phenotypic and multi-tissue transcriptomic approach
Cited by: 6
Author(s): Frédéric Jehl, Colette Désert, Christophe Klopp, M. Brenet, Andrea Rau, Sophie Leroux, Morgane Boutin, Laëtitia Lagoutte, Kévin Muret, Yuna Blum, Diane Esquerré, David Gourichon, Thierry Burlot, Anne Collin, Frédérique Pitel, Alexandre Bénani, Tatiana Zerjal, Sandrine Lagarrigue
Software Mentions: 4
Published: almost 5 years ago

10.1534/g3.117.039396

Comparative Genomics of the Ectomycorrhizal Sister Species <i>Rhizopogon vinicolor</i> and <i>Rhizopogon vesiculosus</i> (Basidiomycota: Boletales) Reveals a Divergence of the Mating Type <i>B</i> Locus
Cited by: 16
Author(s): Alija B. Mujic, Alan Kuo, Andrew Tritt, Anna Lipzen, Cindy Chen, Jenifer Johnson, Aarti Sharma, Kerrie Barry, Igor V. Grigoriev, Joseph W. Spatafora
Software Mentions: 4
Published: over 7 years ago

10.3390/genes12010044

Re-Evaluating the Internal Phylogenetic Relationships of Collembola by Means of Mitogenome Data
Cited by: 12
Author(s): Claudio Cucini, Pietro Paolo Fanciulli, Francesco Frati, Peter Convey, Francesco Nardi, Antonio Carapelli
Software Mentions: 4
Published: almost 4 years ago

10.3389/fpls.2016.01651

Modeling the Morphometric Evolution of the Maize Shoot Apical Meristem
Cited by: 10
Author(s): Samuel Leiboff, Christopher K. DeAllie, Michael J. Scanlon
Software Mentions: 4
Published: about 8 years ago

10.3389/fpls.2017.00184

Analysis of Plant Pan-Genomes and Transcriptomes with GET_HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species
Cited by: 60
Author(s): Bruno Contreras‐Moreira, Carlos Pérez Cantalapiedra, María Jesús García-Pereira, Sean P. Gordon, John P. Vogel, Ernesto Igartua, Ana M. Casas, Pablo Vinuesa
Software Mentions: 4
Published: over 7 years ago

10.3389/fmolb.2021.648012

Artificial Intelligence in Epigenetic Studies: Shedding Light on Rare Diseases
Cited by: 10
Author(s): Sandra Brasil, Cátia J. Neves, Tatiana Rijoff, Marta Falcão, Gonçalo Valadão, Paula A. Videira, Vanessa Ferreira
Software Mentions: 4
Published: over 3 years ago

10.1186/s12860-019-0241-0

Prediction of novel mouse TLR9 agonists using a random forest approach
Cited by: 4
Author(s): Varun Khanna, Lei Li, Johnson Fung, Shoba Ranganathan, Nikolai Petrovsky
Software Mentions: 4
Published: almost 5 years ago

10.3389/fmicb.2016.00427

Proteogenomic Analysis of Mycobacterium smegmatis Using High Resolution Mass Spectrometry
Cited by: 16
Author(s): Potgieter Mg, Kehilwe C. Nakedi, Jon Ambler, Andrew J. M. Nel, Shaun Garnett, Nelson C. Soares, Nicola Mulder, Jonathan M. Blackburn
Software Mentions: 4
Published: over 8 years ago

10.3389/fpsyg.2020.02154

HIIT the Road Jack: An Exploratory Study on the Effects of an Acute Bout of Cardiovascular High-Intensity Interval Training on Piano Learning
Cited by: 3
Author(s): Dana Swarbrick, Alex Kiss, Sandra E. Trehub, Luc Tremblay, David A. Alter, Joyce L. Chen
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0167715

Cultivar-Based Introgression Mapping Reveals Wild Species-Derived Pm-0, the Major Powdery Mildew Resistance Locus in Squash
Cited by: 26
Author(s): William L. Holdsworth, Kyle E. LaPlant, Duane C. Bell, Molly M. Jahn, Michael Mazourek
Software Mentions: 4
Published: almost 8 years ago

10.3389/fmicb.2020.00490

Genomic Investigation of the Strawberry Pathogen Phytophthora fragariae Indicates Pathogenicity Is Associated With Transcriptional Variation in Three Key Races
Cited by: 12
Author(s): Thomas M. Adams, Andrew D. Armitage, Maria K. Sobczyk, Helen Bates, Javier F. Tabima, Brent Kronmiller, Brett M. Tyler, Niklaus J. Grünwald, Jim M. Dunwell, Charlotte F. Nellist, Richard J. Harrison
Software Mentions: 4
Published: over 4 years ago

10.3389/fmicb.2019.02886

Microbial Communities in Human Milk Relate to Measures of Maternal Weight
Cited by: 26
Author(s): Sara Lundgren, Juliette C. Madan, Margaret R. Karagas, Hilary G. Morrison, Anne G. Hoen, Brock C. Christensen
Software Mentions: 4
Published: almost 5 years ago

10.3389/fgene.2020.00194

Quantifying RNA Editing in Deep Transcriptome Datasets
Cited by: 26
Author(s): Claudio Lo Giudice, Domenico Alessandro Silvestris, Shalom Hillel Roth, Eli Eisenberg, Graziano Pesole, Angela Gallo, Ernesto Picardi
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0199132

Effects of low dose silver nanoparticle treatment on the structure and community composition of bacterial freshwater biofilms
Cited by: 23
Author(s): Alexandra Grün, Constantin Benjamin App, Andreas Breidenbach, Jutta Meier, George Metreveli, Gabriele E. Schaumann, Werner Manz
Software Mentions: 4
Published: over 6 years ago

10.15252/msb.20167456

A photoconversion model for full spectral programming and multiplexing of optogenetic systems
Cited by: 29
Author(s): Evan J. Olson, Constantine N. Tzouanas, Jeffrey J. Tabor
Software Mentions: 4
Published: over 7 years ago

10.1038/s41597-021-00905-y

A resource to explore the discovery of rare diseases and their causative genes
Cited by: 5
Author(s): Friederike Ehrhart, Egon Willighagen, Martina Kutmon, Max van Hoften, Leopold Curfs, Chris T. Evelo
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.49002

Dynamic turnover of centromeres drives karyotype evolution in Drosophila
Cited by: 57
Author(s): Ryan Bracewell, Kamalakar Chatla, Matthew J. Nalley, Doris Bachtrog
Software Mentions: 4
Published: about 5 years ago

10.1128/mSystems.00179-21

Gut Microbiome Structure and Association with Host Factors in a Korean Population
Cited by: 10
Author(s): Mi Young Lim, Seungpyo Hong, So-Jung Bang, Won‐Hyong Chung, Ji-Hee Shin, Jung-Ha Kim
Software Mentions: 3
Published: about 3 years ago

10.1038/s41389-019-0146-y

RelB acts as a molecular switch driving chronic inflammation in glioblastoma multiforme
Cited by: 33
Author(s): Michael R. Waters, Angela Gupta, Karli Mockenhaupt, LaShardai N. Brown, Debolina D. Biswas, Tomasz Kordula
Software Mentions: 3
Published: over 5 years ago

10.3390/toxins12040248

Phylogenomic Analysis of Secondary Metabolism in the Toxic Cyanobacterial Genera Anabaena, Dolichospermum and Aphanizomenon
Cited by: 28
Author(s): Julia Österholm, Rafael Vicentini Popin, David P. Fewer, Kaarina Sivonen
Software Mentions: 3
Published: over 4 years ago

10.1111/eva.12599

Genomewide association analyses of fitness traits in captive‐reared Chinook salmon: Applications in evaluating conservation strategies
Cited by: 22
Author(s): Charles Waters, Jeffrey J. Hard, Marine S. O. Brieuc, David E. Fast, Kenneth I. Warheit, Curtis M. Knudsen, William J. Bosch, Kerry A. Naish
Software Mentions: 3
Published: over 6 years ago

10.1002/ece3.6645

Power of a dual‐use SNP panel for pedigree reconstruction and population assignment
Cited by: 13
Author(s): Samuel A. May, Garrett J. McKinney, Ray Hilborn, Lorenz Hauser, Kerry A. Naish
Software Mentions: 3
Published: about 4 years ago

10.1002/evl3.8

Direct estimation of the spontaneous mutation rate by short-term mutation accumulation lines in <i>Chironomus riparius</i>
Cited by: 54
Author(s): Ann-Marie Oppold, Markus Pfenninger
Software Mentions: 3
Published: over 7 years ago

10.1186/s40168-016-0209-7

Microbiota fingerprints lose individually identifying features over time
Cited by: 72
Author(s): David E. Wilkins, Marcus H. Y. Leung, Patrick K. H. Lee
Software Mentions: 3
Published: almost 8 years ago

10.1186/s40168-019-0676-8

Unprecedented bacterial community richness in soybean nodules vary with cultivar and water status
Cited by: 44
Author(s): Hazem Sharaf, Richard R. Rodrigues, Jin-Young Moon, Bo Zhang, Kerri Mills, Mark A. Williams
Software Mentions: 3
Published: over 5 years ago

10.3390/s19153246

RPAS Forensic Validation Analysis Towards a Technical Investigation Process: A Case Study of Yuneec Typhoon H
Cited by: 16
Author(s): Fahad E. Salamh, Umit Karabiyik, Marcus Rogers
Software Mentions: 3
Published: over 5 years ago

10.1002/ece3.2097

A phylogenetic analysis of macroevolutionary patterns in fermentative yeasts
Cited by: 15
Author(s): Rocío Paleo‐López, Julian Quintero-Galvis, Jaiber J. Solano‐Iguaran, Ángela M. Sánchez-Salazar, Juan Diego Gaitán‐Espitía, Roberto F. Nespolo
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-021-86087-4

Microdroplet-based one-step RT-PCR for ultrahigh throughput single-cell multiplex gene expression analysis and rare cell detection
Cited by: 13
Author(s): Jennifer Ma, Gary Tran, Alwin M. D. Wan, Elton T. Young, Eugenia Kumacheva, Norman N. Iscove, Peter W. Zandstra
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-86395-9

Integrated transcription factor profiling with transcriptome analysis identifies L1PA2 transposons as global regulatory modulators in a breast cancer model
Cited by: 1
Author(s): Jiayue-Clara Jiang, Joseph A. Rothnagel, Kyle R. Upton
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-016-3083-6

De-novo transcriptome assembly for gene identification, analysis, annotation, and molecular marker discovery in Onobrychis viciifolia
Cited by: 30
Author(s): Marina Mora-Ortiz, Martin Swain, Martin Vickers, Matthew J. Hegarty, Rhys Kelly, Lydia Smith, Leif Skøt
Software Mentions: 3
Published: about 8 years ago

10.1186/s12936-019-2665-6

Aminoacyl tRNA synthetases as malarial drug targets: a comparative bioinformatics study
Cited by: 21
Author(s): Dorothy Wavinya Nyamai, Özlem Tastan Bishop
Software Mentions: 3
Published: almost 6 years ago

10.1002/ece3.3173

Historic changes in length distributions of three Baltic cod (<i>Gadus morhua</i>) stocks: Evidence of growth retardation
Cited by: 19
Author(s): Henrik Svedäng, Sara Hornborg
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-021-90325-0

Genome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America
Cited by: 6
Author(s): Kyung Seok Kim, Kevin J. Roe
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-018-23931-0

Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience
Cited by: 98
Author(s): Dinka Mandaković, Claudia Rojas, Jonathan Maldonado, Mauricio Latorre, Dante Travisany, Erwan Delage, Audrey Bihouée, Géraldine Jean, Francisco Javier Mato Díaz, Beatriz Fernández-Gómez, Pablo J. Cabrera, Alexis Gaete, Claudio Latorre, Rodrigo A. Gutiérrez, Alejandro Maass, Verónica Cambiazo, Sergio A. Navarrete, Damien Eveillard, Maurício González
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-017-16633-6

A meta-proteomics approach to study the interspecies interactions affecting microbial biofilm development in a model community
Cited by: 45
Author(s): Jakob Herschend, Zacharias Brimnes Visby Damholt, Andrea Marion Marquard, Birte Svensson, Søren J. Sørensen, Per Hägglund, Mette Burmølle
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12915-020-00899-w

Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection
Cited by: 18
Author(s): Peter D. Olson, Alan S. Tracey, Andrew Baillie, Katherine James, Stephen R. Doyle, Sarah Kay Buddenborg, Faye H. Rodgers, Nancy Holroyd, Matthew Berriman
Software Mentions: 3
Published: about 4 years ago

10.1111/evo.13217

Developmental mechanisms of macroevolutionary change in the tetrapod axis: A case study of Sauropterygia
Cited by: 20
Author(s): Laura C. Soul, Roger Benson
Software Mentions: 3
Published: over 7 years ago

10.1016/j.cell.2013.06.040

Genome Sequencing Reveals Loci under Artificial Selection that Underlie Disease Phenotypes in the Laboratory Rat
Cited by: 148
Author(s): Santosh S. Atanur, Ana García Díaz, Klio Maratou, Allison B. Sarkis, Maxime Rotival, Laurence Gamé, Michael Tschannen, Pamela J. Kaisaki, G. Otto, Man Chun John, Thomas M. Keane, Oliver Hummel, Kathrin Saar, Weiwei Chen, Victor Guryev, Kathirvel Gopalakrishnan, Michael R. Garrett, Bina Joe, Lorena Citterio, Giuseppe Bianchi, Martin W. McBride, Anna F. Dominiczak, David J. Adams, Tadao Serikawa, Paul Flicek, Edwin Cuppen, Norbert Hübner, Enrico Petretto, Dominique Guyader, Anne E. Kwitek, Howard J. Jacob, Timothy J. Aitman
Software Mentions: 3
Published: over 11 years ago

10.1038/s41598-017-03528-9

Genetic Determinants of Crop Timing and Quality Traits in Two Interspecific Petunia Recombinant Inbred Line Populations
Cited by: 8
Author(s): Yufang Guo, Wei Kuang Lin, Qiuxia Chen, Verónica Vallejo, Ryan M. Warner
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pgen.1009735

Chromoanagenesis from radiation-induced genome damage in Populus
Cited by: 8
Author(s): Weier Guo, Luca Comai, Isabelle Henry
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pgen.0030022

Transition-Transversion Bias Is Not Universal: A Counter Example from Grasshopper Pseudogenes
Cited by: 138
Author(s): Irene Keller, Douda Bensasson, Richard A. Nichols
Software Mentions: 3
Published: almost 18 years ago

10.1002/ece3.3121

Disentangling the genetic and morphological structure of <i>Patella candei</i> complex in Macaronesia (NE Atlantic)
Cited by: 10
Author(s): João Faria, Gustavo M. Martins, Alfonso Pita, Pedro A. Ribeiro, Stephen J. Hawkins, Pablo Presa, Ana I. Neto
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-017-10488-7

Massive transcriptome sequencing of human spinal cord tissues provides new insights into motor neuron degeneration in ALS
Cited by: 89
Author(s): Anna Maria D’Erchia, Angela Gallo, Caterina Manzari, Susanna Raho, David S. Horner, Matteo Chiara, Alessio Valletti, Italia Aiello, Francesca Mastropasqua, Loredana Ciaccia, Franco Locatelli, Francesco Pisani, Grazia Paola Nicchia, María Svelto, Graziano Pesole, Ernesto Picardi
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pgen.1009242

Accurate mapping of mitochondrial DNA deletions and duplications using deep sequencing
Cited by: 36
Author(s): Swaraj Basu, Xie Xie, Jay P. Uhler, Carola Hedberg‐Oldfors, Dusanka Milenkovic, Olivier Baris, Sammy Kimoloi, Stanka Matic, James B. Stewart, Nils-Göran Larsson, Rudolf J. Wiesner, Anders Oldfors, Claes M. Gustafsson, Maria Falkenberg, Erik Larsson
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12931-020-01364-6

Increased mortality of acute respiratory distress syndrome was associated with high levels of plasma phenylalanine
Cited by: 17
Author(s): Jing Xu, Tingting Pan, Xiaoling Qi, Ruoming Tan, Xiaoli Wang, Zhaojun Liu, Zheying Tao, Yi Zhang, Hong Chen, Yihui Wang, Jingjing Zhang, Jie Wang, Jialin Liu
Software Mentions: 3
Published: over 4 years ago

10.1093/gigascience/giz041

Bioportainer Workbench: a versatile and user-friendly system that integrates implementation, management, and use of bioinformatics resources in Docker environments
Cited by: 6
Author(s): Fabiano Bezerra Menegídio, David Aciole Barbosa, Rafael Dos S Gonçalves, Marcio M Nishime, Daniela Jabés, Regina Costa de Oliveira, Luiz R. Nunes
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-020-06778-6

Impacts of local population history and ecology on the evolution of a globally dispersed pathogen
Cited by: 18
Author(s): Andreína I. Castillo, Carlos Chacón-Díaz, Neysa Rodríguez-Murillo, Helvécio Della Coletta-Filho, Rodrigo P. P. Almeida
Software Mentions: 3
Published: over 4 years ago

10.1186/s13059-021-02449-1

Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection
Cited by: 12
Author(s): Deepak Thirunavukarasu, Lauren Y. Cheng, Ping Song, Sherry X. Chen, Mitesh J. Borad, Lawrence N. Kwong, Phillip James, Daniel J. Turner, David Y. Zhang
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0130891

Integrative Transcriptome Profiling of Cognitive Aging and Its Preservation through Ser/Thr Protein Phosphatase Regulation
Cited by: 4
Author(s): C. Sehwan Park, Amandine Valomon, Hans Welzl
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0143811

The Clinical Significance and Molecular Features of the Spatial Tumor Shapes in Breast Cancers
Cited by: 14
Author(s): Hyeong‐Gon Moon, Namshin Kim, Seongmun Jeong, Min-Ju Lee, Hyunhye Moon, Jong-Jin Kim, Tae-Kyung Yoo, Han‐Byoel Lee, Ji Sun Kim, Dong‐Young Noh, Wonshik Han
Software Mentions: 3
Published: almost 9 years ago

10.3762/bjoc.16.105

Anthelmintic drug discovery: target identification, screening methods and the role of open science
Cited by: 28
Author(s): Frederick A. Partridge, Ruth Forman, Carole J. R. Bataille, Graham M. Wynne, Marina Nick, Angela J. Russell, Kathryn J. Else, David B. Sattelle
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0048231

Proteomic Properties Reveal Phyloecological Clusters of Archaea
Cited by: 1
Author(s): Nela Nikolić, Zlatko Smole, Anita Kriško
Software Mentions: 3
Published: about 12 years ago

10.3390/plants9010063

Comparative Analysis between Wild and Cultivated Cucumbers Reveals Transcriptional Changes during Domestication Process
Cited by: 6
Author(s): Eslam M. Abdel-Salam, Abdulrahman A. Alatar, Quaiser Saquib, Hend A. Alwathnani
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12864-018-5228-2

DAWN: a resource for yielding insights into the diversity among wheat genomes
Cited by: 18
Author(s): Nathan S. Watson-Haigh, Radosław Suchecki, Elena Kalashyan, Melissa Garcia, Ute Baumann
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0164047

Molecular Models for the Core Components of the Flagellar Type-III Secretion Complex
Cited by: 13
Author(s): William R. Taylor, Teige R. S. Matthews-Palmer, Morgan Beeby
Software Mentions: 3
Published: almost 8 years ago

10.1186/s13059-019-1849-2

Impact of mouse contamination in genomic profiling of patient-derived models and best practice for robust analysis
Cited by: 13
Author(s): Se-Young Jo, Eun Young Kim, Sang Woo Kim
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0194938

Widespread domain-like perturbations of DNA methylation in whole blood of Down syndrome neonates
Cited by: 22
Author(s): Peter Henneman, Arjan Bouman, Adri N. Mul, Lia Knegt, Anne-Marie van der Kevie-Kersemaekers, Nitash Zwaveling-Soonawala, Hanne Meijers-Heijboer, A S Paul van Trotsenburg, Marcel M.A.M. Mannens
Software Mentions: 3
Published: over 6 years ago

10.1534/g3.119.400392

<i>De Novo</i> Genome Sequence Assemblies of <i>Gossypium raimondii</i> and <i>Gossypium turneri</i>
Cited by: 65
Author(s): Joshua A. Udall, Evan Long, Chris Hanson, Daojun Yuan, Thiruvarangan Ramaraj, Justin L. Conover, Lei Gong, Mark A. Arick, Corrinne E. Grover, Daniel G. Peterson, Jonathan F. Wendel
Software Mentions: 3
Published: about 5 years ago

10.1002/advs.201900721

Circulating DNA‐Based Sequencing Guided Anlotinib Therapy in Non‐Small Cell Lung Cancer
Cited by: 28
Author(s): Jun Lü, Hua Zhong, Jun Wu, Tianqing Chu, Lele Zhang, Hua Li, Qiming Wang, Rong Li, Yupei Zhao, Aiqin Gu, Huimin Wang, Chunlei Shi, Liwen Xiong, Xueyan Zhang, Wei Zhang, Yu‐Qing Lou, Bo Yan, Yu Dong, Yanwei Zhang, Baolan Li, Li Zhang, Xiaodong Zhao, Kai Li, Baohui Han
Software Mentions: 3
Published: about 5 years ago

10.1111/pbi.12772

A toolkit for <i>Nannochloropsis oceanica </i><scp>CCMP</scp>1779 enables gene stacking and genetic engineering of the eicosapentaenoic acid pathway for enhanced long‐chain polyunsaturated fatty acid production
Cited by: 101
Author(s): Eric Poliner, Jane A. Pulman, Krzysztof Zienkiewicz, Kevin L. Childs, Christoph Benning, Eva M. Farré
Software Mentions: 3
Published: over 7 years ago

10.1186/s13059-020-01976-7

Smarcad1 mediates microbiota-induced inflammation in mouse and coordinates gene expression in the intestinal epithelium
Cited by: 10
Author(s): Juri Kazakevych, Jérémy Denizot, Anke Liebert, Mariana Portovedo, Mia Mosavie, Payal Jain, Claudia Stellato, Claire M. Fraser, Renan Oliveira Corrêa, Marina Célestine, Raphaël Mattiuz, Hanneke Okkenhaug, Jim Miller, Marco Aurélio Ramirez Vinolo, Marc Veldhoen, Patrick Varga‐Weisz
Software Mentions: 3
Published: over 4 years ago

10.1038/sdata.2019.2

Qresp, a tool for curating, discovering and exploring reproducible scientific papers
Cited by: 22
Author(s): Marco Govoni, Milson Munakami, Aditya Tanikanti, Jonathan H. Skone, Hakizumwami Birali Runesha, Federico Giberti, Juan Pablo, Giulia Galli
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0226481

Connectivity differences between Gulf War Illness (GWI) phenotypes during a test of attention
Cited by: 4
Author(s): Tomas Clarke, Jessie D. Jamieson, Patrick S. Malone, Rakib U. Rayhan, Stuart D. Washington, John W. VanMeter, James N. Baraniuk
Software Mentions: 3
Published: almost 5 years ago

10.3389/fpls.2021.703283

Lens orientalis Contributes Quantitative Trait Loci and Candidate Genes Associated With Ascochyta Blight Resistance in Lentil
Cited by: 10
Author(s): Rama Harinath Reddy Dadu, Ido Bar, Rebecca Ford, Prabhakaran Thanjavur Sambasivam, Janine Croser, Federico M. Ribalta, Sukhjiwan Kaur, Shimna Sudheesh, Dorin Gupta
Software Mentions: 3
Published: about 3 years ago

10.3389/fphys.2018.01568

Transcriptional Signatures in Liver Reveal Metabolic Adaptations to Seasons in Migratory Blackheaded Buntings
Cited by: 15
Author(s): Devraj Singh, Vivek Swarup, Hiep D. Le, Vinod Kumar
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-017-3721-7

Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples
Cited by: 19
Author(s): Jake Lin, Lenka Kramná, Reija Autio, Heikki Hyöty, Matti Nykter, Ondřej Cinek
Software Mentions: 3
Published: over 7 years ago

10.3389/fphys.2020.00954

Fine-Tuning of Energy Levels Regulates SUC2 via a SNF1-Dependent Feedback Loop
Cited by: 8
Author(s): Sebastian Persson, Niek Welkenhuysen, Sviatlana Shashkova, Marija Cvijović
Software Mentions: 3
Published: about 4 years ago

10.3389/fmicb.2020.581660

The Effect of Iodine-Containing Nano-Micelles, FS-1, on Antibiotic Resistance, Gene Expression and Epigenetic Modifications in the Genome of Multidrug Resistant MRSA Strain Staphylococcus aureus ATCC BAA-39
Cited by: 9
Author(s): Oleg N. Reva, Ilya S. Korotetskiy, Monique Joubert, Sergey V. Shilov, Ardak B. Jumagaziyeva, Natalya A. Suldina, А. И. Ильин
Software Mentions: 3
Published: about 4 years ago

10.3389/fpls.2015.01246

A De novo Transcriptomic Approach to Identify Flavonoids and Anthocyanins “Switch-Off” in Olive (Olea europaea L.) Drupes at Different Stages of Maturation
Cited by: 30
Author(s): Domenico Iaria, Adriana Chiappetta, Innocenzo Muzzalupo
Software Mentions: 3
Published: almost 9 years ago

10.7717/peerj.8088

Warm temperatures, cool sponges: the effect of increased temperatures on the Antarctic sponge<i>Isodictya</i>sp.
Cited by: 11
Author(s): Marcelo González-Aravena, Nathan J. Kenny, Magdalena Osorio, Alejandro Font, Ana Riesgo, César Cárdenas
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12864-016-2488-6

Genome-wide polymorphism and signatures of selection in the symbiotic sea anemone Aiptasia
Cited by: 24
Author(s): Emily S. Bellis, Dana K. Howe, Dee R. Denver
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0083504

RNA Sequencing of the Exercise Transcriptome in Equine Athletes
Cited by: 43
Author(s): Stefano Capomaccio, Nicola Vitulo, Andrea Verini-Supplizi, Gianni Barcaccia, Alessandro Albiero, Michela D’Angelo, Davide Campagna, Giorgio Valle, Michela Felicetti, Maurizio Silvestrelli, Katia Cappelli
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0216233

A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set
Cited by: 37
Author(s): Boas Pucker, Daniela Holtgräwe, Kai Bernd Stadermann, Karl Frey, Bruno Huettel, Richard Reinhardt, Bernd Weißhaar
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2020.01430

A Hopeful Sea-Monster: A Very Large Homologous Recombination Event Impacting the Core Genome of the Marine Pathogen Vibrio anguillarum
Cited by: 6
Author(s): Nicola M. Coyle, Kerry L. Bartie, Sion C. Bayliss, Michaël Bekaert, Alexandra Adams, Stuart McMillan, David W. Verner–Jeffreys, Andrew P. Desbois, Edward J. Feil
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2105-15-S15-S7

EasyCluster2: an improved tool for clustering and assembling long transcriptome reads
Cited by: 3
Author(s): Vitoantonio Bevilacqua, Nicola Pietroleonardo, Ely Ignazio Giannino, Fabio Stroppa, Domenico Simone, Graziano Pesole, Ernesto Picardi
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0236684

Distinct patterns of activity in individual cortical neurons and local networks in primary somatosensory cortex of mice evoked by square-wave mechanical limb stimulation
Cited by: 2
Author(s): Mischa V Bandet, Bin Dong, Ian R. Winship
Software Mentions: 3
Published: over 3 years ago

10.3390/v12050510

Asian Zika Virus Isolate Significantly Changes the Transcriptional Profile and Alternative RNA Splicing Events in a Neuroblastoma Cell Line
Cited by: 21
Author(s): Gaston Bonenfant, Ryan Meng, Carl Shotwell, Pheonah Badu, Anne F. Payne, Alexander T. Ciota, Morgan A. Sammons, J. Andrew Berglund, Cara T. Pager
Software Mentions: 3
Published: over 4 years ago

10.3390/v11110988

Evolution of a Landscape Phage Library in a Mouse Xenograft Model of Human Breast Cancer
Cited by: 10
Author(s): James W. Gillespie, Liping Yang, Laura M. De Plano, Murray Stackhouse, Valery A. Petrenko
Software Mentions: 3
Published: about 5 years ago

10.1186/s12863-021-00981-4

Transcriptome profiling provides insights into the molecular mechanisms of maize kernel and silk development
Cited by: 0
Author(s): Ting Li, Yapeng Wang, Ying Shi, Xiaonan Gou, Bingpeng Yang, Jianzhou Qu, Xinghua Zhang, Jiquan Xue, Shutu Xu
Software Mentions: 3
Published: about 3 years ago

10.3389/fgene.2018.00332

A Gene-Based Positive Selection Detection Approach to Identify Vaccine Candidates Using Toxoplasma gondii as a Test Case Protozoan Pathogen
Cited by: 17
Author(s): Stephen J. Goodswen, Paul J. Kennedy, John Ellis
Software Mentions: 3
Published: about 6 years ago

10.1186/s12985-016-0592-5

Functional prediction of differentially expressed lncRNAs in HSV-1 infected human foreskin fibroblasts
Cited by: 15
Author(s): Benxia Hu, Yongxia Huo, Guijun Chen, Liping Yang, Dong‐Dong Wu, Jumin Zhou
Software Mentions: 3
Published: over 8 years ago

10.1186/1743-422X-5-160

Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences
Cited by: 35
Author(s): Nobubelo K. Ngandu, Konrad Scheffler, Penny L. Moore, Zenda Woodman, Darren P. Martin, Cathal Seoighe
Software Mentions: 3
Published: almost 16 years ago

10.1186/s40478-020-01037-x

Network analysis of the progranulin-deficient mouse brain proteome reveals pathogenic mechanisms shared in human frontotemporal dementia caused by GRN mutations
Cited by: 38
Author(s): Meixiang Huang, Erica Modeste, Eric B. Dammer, Paola Merino, Georgia Taylor, Duc M. Duong, Qiudong Deng, Christopher J. Holler, Marla Gearing, Dennis W. Dickson, Nicholas T. Seyfried, Thomas Kukar
Software Mentions: 3
Published: about 4 years ago

10.15252/msb.20198982

Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome
Cited by: 98
Author(s): Ines Thiele, Swagatika Sahoo, Almut Heinken, Johannes Hertel, Laurent Heirendt, Maike Kathrin Aurich, Ronan M. T. Fleming
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0059831

Construction of Customized Sub-Databases from NCBI-nr Database for Rapid Annotation of Huge Metagenomic Datasets Using a Combined BLAST and MEGAN Approach
Cited by: 48
Author(s): Ke Yu, Tong Zhang
Software Mentions: 3
Published: over 11 years ago

10.1186/1471-2164-14-670

An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome
Cited by: 135
Author(s): Marco Ferrarini, Marco Moretto, J. A. Ward, Nada Šurbanovski, Vladimir D. Stevanović, L. Giongo, Roberto Viola, Duccio Cavalieri, Riccardo Velasco, Alessandro Cestaro, Daniel J. Sargent
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0043554

A Mitogenomic Re-Evaluation of the Bdelloid Phylogeny and Relationships among the Syndermata
Cited by: 17
Author(s): Erica Lasek‐Nesselquist
Software Mentions: 3
Published: about 12 years ago

10.3389/fgene.2017.00205

Adaptive Evolution of Energy Metabolism-Related Genes in Hypoxia-Tolerant Mammals
Cited by: 29
Author(s): Ran Tian, Daiqing Yin, Yanzhi Liu, Inge Seim, Shixia Xu
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0029696

Broad Phylogenomic Sampling and the Sister Lineage of Land Plants
Cited by: 234
Author(s): Ruth Timme, Tsvetan R. Bachvaroff, Charles F. Delwiche
Software Mentions: 3
Published: almost 13 years ago