10.1371/journal.pone.0179613

A data analysis framework for biomedical big data: Application on mesoderm differentiation of human pluripotent stem cells
Cited by: 7
Author(s): Benjamin Ulfenborg, Alexander Karlsson, Maria Riveiro, Caroline Améen, Karolina Åkesson, Christian X. Andersson, Peter Sartipy, Jane Synnergren
Software Mentions: 5
Published: about 9 years ago

10.1038/s41598-018-22977-4

Analysis of the neurotoxic effects of neuropathic organophosphorus compounds in adult zebrafish
Cited by: 11
Author(s): Melissa Faria, Inmaculada Fuertes, Eva Prats, José Luı́s Abad, Francesc Padrós, Cristian Gómez‐Canela, Josefina Casas, Jorge Estévez, Eugenio Vilanova, Benjamı́n Piña, Demetrio Raldúa
Software Mentions: 5
Published: over 8 years ago

10.7554/eLife.15657

An integrative transcriptomic atlas of organogenesis in human embryos
Cited by: 55
Author(s): Dave T. Gerrard, Andrew Berry, Rachel Jennings, Karen Piper Hanley, Nicoletta Bobola, Neil A. Hanley
Software Mentions: 5
Published: almost 10 years ago

10.1186/s40168-020-00907-9

Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial
Cited by: 33
Author(s): Suryang Kwak, Joo-Hee Choi, Tiffany Hink, Kimberly A. Reske, Kenneth Blount, Courtney Jones, Margaret H. Bost, Xiaoqing Sun, Carey-Ann D. Burnham, Erik R. Dubberke, Gautam Dantas
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pone.0048990

A Phylogenomic Approach to Vertebrate Phylogeny Supports a Turtle-Archosaur Affinity and a Possible Paraphyletic Lissamphibia
Cited by: 58
Author(s): Jonathan J. Fong, Jeremy M. Brown, Matthew K. Fujita, Bastien Boussau
Software Mentions: 5
Published: over 13 years ago

10.1371/journal.pone.0078120

Effective Population Size, Genetic Variation, and Their Relevance for Conservation: The Bighorn Sheep in Tiburon Island and Comparisons with Managed Artiodactyls
Cited by: 20
Author(s): Jaime Gasca-Pineda, Ivonne Cassaigne, Ricardo Alonso, Luis E. Eguiarte
Software Mentions: 5
Published: almost 13 years ago

10.1038/s41598-018-28107-4

A selective high affinity MYC-binding compound inhibits MYC:MAX interaction and MYC-dependent tumor cell proliferation
Cited by: 73
Author(s): Alina Castell, Qinzi Yan, Karin Fawkner, Per Hydbring, Fan Zhang, Vasiliki Verschut, Marcela Franco, Siti Mariam Zakaria, Wesam Bazzar, Jacob Goodwin, Giovanna Zinzalla, Lars Larsson
Software Mentions: 5
Published: about 8 years ago

10.1038/s41598-019-55357-7

Exploring genetic architecture of grain yield and quality traits in a 16-way indica by japonica rice MAGIC global population
Cited by: 26
Author(s): Hein Zaw, Chitra Raghavan, Arnel E. Pocsedio, B. P. Mallikarjuna Swamy, Mona Liza Jubay, Rakesh Kumar Singh, Justine Bonifacio, Ramil Mauleon, Jose E. Hernandez, Merlyn S. Mendioro, Glenn B. Gregorio, Hei Leung
Software Mentions: 5
Published: over 6 years ago

10.7717/peerj.9777

Generalized Linear Models outperform commonly used canonical analysis in estimating spatial structure of presence/absence data
Cited by: 4
Author(s): Lélis Antonio Carlos-Júnior, Joel Christopher Creed, Rob H. Marrs, Rob J. Lewis, Timothy P. Moulton, Rafael Feijó‐Lima, Matthew Spencer
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12864-020-6746-2

Genetic differentiation and intrinsic genomic features explain variation in recombination hotspots among cocoa tree populations
Cited by: 13
Author(s): Enrique J. Schwarzkopf, Juan Carlos Motamayor, Omar E. Cornejo
Software Mentions: 5
Published: about 6 years ago

10.1038/s41598-017-01767-4

Systems Immunology of Diabetes-Tuberculosis Comorbidity Reveals Signatures of Disease Complications
Cited by: 78
Author(s): César Augusto Prada-Medina, Kiyoshi F. Fukutani, Nathella Pavan Kumar, Leonardo Gil-Santana, Subash Babu, Flávio Lichtenstein, Kim West, Sivakumar Shanmugam, Pradeep A. Menon, Vijay Viswanathan, Bruno B. Andrade, Hidehiko Nakaya, Hardy Kornfeld
Software Mentions: 5
Published: about 9 years ago

10.1038/s41598-021-91058-w

Vulnerability to climate change of a microendemic lizard species from the central Andes
Cited by: 4
Author(s): Alejandro Laspiur, Juan Carlos Santos, Susana Marlin Medina, Jesús E Pizarro, Eduardo Alfredo Sanabria, Barry Sinervo, Nora R. Ibargüengoytía
Software Mentions: 5
Published: about 5 years ago

10.3389/fmicb.2018.03243

Dead or Alive; or Does It Really Matter? Level of Congruency Between Trophic Modes in Total and Active Fungal Communities in High Arctic Soil
Cited by: 22
Author(s): Magdalena Wutkowska, Anna Vader, Sunil Mundra, Elisabeth J. Cooper, Pernille Bronken Eidesen
Software Mentions: 5
Published: over 7 years ago

10.3389/fimmu.2020.01636

Immune and Metabolic Signatures of COVID-19 Revealed by Transcriptomics Data Reuse
Cited by: 101
Author(s): Luiz Gustavo Gardinassi, Camila Oliveira Silva Souza, Helioswilton Sales‐Campos, Simone Gonçalves Fonseca
Software Mentions: 5
Published: about 6 years ago

10.3389/fmicb.2018.00897

Lactobacillus frumenti Facilitates Intestinal Epithelial Barrier Function Maintenance in Early-Weaned Piglets
Cited by: 54
Author(s): Jun Hu, Lingli Chen, Wenyong Zheng, Min Shi, Liu Liu, Chunlin Xie, Xinkai Wang, Youguo Niu, Qiliang Hou, Xichen Xu, Baoyang Xu, Yimei Tang, Shengqian Zhou, Yiqin Yan, Tao Yang, Libao Ma, Xianghua Yan
Software Mentions: 5
Published: about 8 years ago

10.1111/pbi.12852

The transcriptome, extracellular proteome and active secretome of agroinfiltrated<i>Nicotiana benthamiana</i>uncover a large, diverse protease repertoire
Cited by: 52
Author(s): Friederike Grosse‐Holz, Steven L. Kelly, Svenja Blaskowski, Farnusch Kaschani, Markus Kaiser, Renier A. L. van der Hoorn
Software Mentions: 5
Published: over 8 years ago

10.1002/ece3.6535

Trophic level and basal resource use of soil animals are hardly affected by local plant associations in abandoned arable land
Cited by: 0
Author(s): Jörg‐Alfred Salamon, Janet Wissuwa, Thomas Frank, Stefan Scheu, Anton Potapov
Software Mentions: 5
Published: about 6 years ago

10.1186/s12864-021-07517-1

Transcriptomic analysis of the trade-off between endurance and burst-performance in the frog Xenopus allofraseri
Cited by: 1
Author(s): Valérie Ducret, Adam Richards, Mathieu Videlier, Thibault Scalvenzi, Karen Moore, Konrad Paszkiewicz, Camille Bonneaud, Nicolas Pollet, Anthony Herrel
Software Mentions: 5
Published: over 5 years ago

10.1002/ece3.3216

Influence of density‐dependent competition on foraging and migratory behavior of a subtropical colonial seabird
Cited by: 36
Author(s): Juliet S. Lamb, Yvan G. Satgé, Patrick G. R. Jodice
Software Mentions: 5
Published: about 9 years ago

10.1371/journal.pone.0239486

BioPETsurv: Methodology and open source software to evaluate biomarkers for prognostic enrichment of time-to-event clinical trials
Cited by: 3
Author(s): Siyuan Cheng, Kathleen F. Kerr, Heather Thiessen-Philbrook, Steven G. Coca, Chirag R. Parikh
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-020-67362-2

Integrated metabolomics and gut microbiome to the effects and mechanisms of naoxintong capsule on type 2 diabetes in rats
Cited by: 22
Author(s): Zenghao Yan, Hao Wu, Haokui Zhou, Shuo Chen, Yan He, Weijian Zhang, Taobin Chen, Hongliang Yao, Weiwei Su
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0081415

Dispersion Estimation and Its Effect on Test Performance in RNA-seq Data Analysis: A Simulation-Based Comparison of Methods
Cited by: 29
Author(s): Will Landau, Peng Liu
Software Mentions: 5
Published: over 12 years ago

10.3389/fgene.2021.652623

Construction of Condition-Specific Gene Regulatory Network Using Kernel Canonical Correlation Analysis
Cited by: 2
Author(s): Dabin Jeong, Sangsoo Lim, Sangseon Lee, Minsik Oh, Changyun Cho, Hyeju Seong, Wi Hoon Jung, Sun Kim
Software Mentions: 5
Published: about 5 years ago

10.1002/aps3.11295

An empirical assessment of a single family‐wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae
Cited by: 24
Author(s): K. Jones, Tomáš Fér, Roswitha Schmickl, Rebecca B. Dikow, Vicki A. Funk, Sonia Herrando‐Moraira, Paul R. Johnston, Norbert Kilian, Carolina M. Siniscalchi, Alfonso Susanna, Marek Slovák, Ramhari Thapa, Linda E. Watson, Jennifer R. Mandel
Software Mentions: 5
Published: almost 7 years ago

10.1016/j.cels.2020.06.005

PertInInt: An Integrative, Analytical Approach to Rapidly Uncover Cancer Driver Genes with Perturbed Interactions and Functionalities
Cited by: 7
Author(s): Shilpa Nadimpalli Kobren, Bernard Chazelle, Mona Singh
Software Mentions: 5
Published: about 6 years ago

10.1186/s12862-016-0758-1

Molecular phylogeny and timing of diversification in Alpine Rhithrogena (Ephemeroptera: Heptageniidae)
Cited by: 15
Author(s): Laurent Vuataz, Sereina Rutschmann, Michael T. Monaghan, Michel Sartori
Software Mentions: 5
Published: almost 10 years ago

10.3389/fmicb.2019.02143

The Bacterial Microbiome Associated With Arid Biocrusts and the Biogeochemical Influence of Biocrusts Upon the Underlying Soil
Cited by: 37
Author(s): Benjamin Moreira‐Grez, Kang Tam, Adam T. Cross, Jean Wan Hong Yong, Deepak Kumaresan, Paul Nevill, Mark Farrell, Andrew S. Whiteley
Software Mentions: 5
Published: almost 7 years ago

10.1186/s12889-017-4994-0

A novel integrative procedure for identifying and integrating three-dimensions of objectively measured free-living sedentary behaviour
Cited by: 10
Author(s): Anna Myers, Catherine Gibbons, Edward Butler, Michelle Dalton, Nicola J. Buckland, John Blundell, Graham Finlayson
Software Mentions: 5
Published: over 8 years ago

10.1099/mgen.0.000341

An assessment of genome annotation coverage across the bacterial tree of life
Cited by: 44
Author(s): Briallen Lobb, Benjamin Tremblay, Gabriel Moreno–Hagelsieb, Andrew C. Doxey
Software Mentions: 5
Published: over 6 years ago

10.1186/s12859-019-3008-x

An equivalence approach to the integrative analysis of feature lists
Cited by: 1
Author(s): Álex Sánchez-Pla, Miquel Salicrú, Jordi Ocaña
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pgen.1008502

Ancestral male recombination in Drosophila albomicans produced geographically restricted neo-Y chromosome haplotypes varying in age and onset of decay
Cited by: 26
Author(s): Kevin H.-C. Wei, Doris Bachtrog
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0129074

Making Large-Scale Networks from fMRI Data
Cited by: 16
Author(s): Verena D. Schmittmann, Sara Jahfari, Denny Borsboom, Alexander Olof Savi, Lourens J. Waldorp
Software Mentions: 5
Published: almost 11 years ago

10.1098/rsos.201010

Biomechanical properties of a buzz-pollinated flower
Cited by: 14
Author(s): Vinícius Lourenço Garcia de Brito, Carlos Eduardo Pereira Nunes, Caíque Rocha Resende, Fernando Montealegre‐Z, Mario Vallejo‐Marín
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12859-021-04121-8

Euler diagrams drawn with ellipses area-proportionally (Edeap)
Cited by: 6
Author(s): Michael Wybrow, Peter Rodgers, Fadi K. Dib
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pntd.0007876

Microsatellite analysis reveals connectivity among geographically distant transmission zones of Plasmodium vivax in the Peruvian Amazon: A critical barrier to regional malaria elimination
Cited by: 11
Author(s): Paulo Manrique, Julio Miranda-Alban, Jhonatan Alarcon-Baldeon, Roberson Ramirez, Gabriel Carrasco-Escobar, Henry Herrera, Mitchel Guzmán-Guzmán, Ángel Rosas Aguirre, Alejandro Llanos‐Cuentas, Joseph M. Vinetz, Ananías A. Escalante, Dionicia Gamboa
Software Mentions: 5
Published: over 6 years ago

10.7717/peerj.4936

Assessment of the ecotoxicity of urban estuarine sediment using benthic and pelagic copepod bioassays
Cited by: 5
Author(s): Maria P. Charry, Vaughan Keesing, Mark J. Costello, Louis A. Tremblay
Software Mentions: 5
Published: about 8 years ago

10.3390/foods10061431

Synergistic Effects of the Jackfruit Seed Sourced Resistant Starch and Bifidobacterium pseudolongum subsp. globosum on Suppression of Hyperlipidemia in Mice
Cited by: 8
Author(s): Zhen Zeng, Yuanyuan Wang, Yanjun Zhang, Kaining Chen, Haibo Chang, Chenchen Ma, Shuaiming Jiang, Dongxue Huo, Wenjun Liu, Rajesh Jha, Jiachao Zhang
Software Mentions: 5
Published: about 5 years ago

10.3389/fgene.2020.00214

The Identification of Metal Ion Ligand-Binding Residues by Adding the Reclassified Relative Solvent Accessibility
Cited by: 5
Author(s): Xiuzhen Hu, Zhenxing Feng, Xiaojin Zhang, Liu Liu, Shan Wang
Software Mentions: 5
Published: over 6 years ago

10.1186/s12915-017-0359-5

Low-cell-number, single-tube amplification (STA) of total RNA revealed transcriptome changes from pluripotency to endothelium
Cited by: 5
Author(s): Yi‐Hsuan Lee, Ya Wen Hsueh, Yunyan Peng, Kung Chao Chang, Kuen‐Jer Tsai, Han Sun, Ih Jen Su, Po Min Chiang
Software Mentions: 5
Published: over 9 years ago

10.1186/s40168-021-01119-5

Metapangenomics reveals depth-dependent shifts in metabolic potential for the ubiquitous marine bacterial SAR324 lineage
Cited by: 16
Author(s): Dominique Le Bœuf, John M. Eppley, Daniel Mende, Rex R. Malmstrom, Tanja Woyke, Edward F. DeLong
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12870-019-1771-5

Early consequences of allopolyploidy alter floral evolution in Nicotiana (Solanaceae)
Cited by: 8
Author(s): Elizabeth W. McCarthy, Jacob B. Landis, Amelda Kurti, Amber J. Lawhorn, Mark W. Chase, Sandra Knapp, Steven C. Le Comber, Andrew R. Leitch, Amy Litt
Software Mentions: 5
Published: about 7 years ago

10.1093/bioinformatics/btw311

PERMANOVA-S: association test for microbial community composition that accommodates confounders and multiple distances
Cited by: 94
Author(s): Zheng-Zheng Tang, Guanhua Chen, Alexander V. Alekseyenko
Software Mentions: 5
Published: about 10 years ago

10.1002/ece3.7212

Genetic studies of various<i>Prosopis</i>species (Leguminosae, Section<i>Algarobia</i>) co‐occurring in oases of the Atacama Desert (northern Chile)
Cited by: 2
Author(s): Cecilia Bessega, Carolina Luciana Pometti, Renée H. Fortunato, Francisca Greene, Calógero M. Santoro, Virginia McRostie
Software Mentions: 5
Published: over 5 years ago

10.7717/peerj.7177

Population-, sex- and individual level divergence in life-history and activity patterns in an annual killifish
Cited by: 15
Author(s): Eli S.J. Thoré, Arnout Grégoir, Bart Adriaenssens, Charlotte Philippe, Robby Stoks, Luc Brendonck, Tom Pinceel
Software Mentions: 5
Published: about 7 years ago

10.3389/fmicb.2018.02784

The Influence of Viable Cells and Cell-Free Extracts of Lactobacillus casei on Volatile Compounds and Polyphenolic Profile of Elderberry Juice
Cited by: 17
Author(s): Annalisa Ricci, Alessia Levante, Martina Cirlini, Luca Calani, Valentina Bernini, Daniele Del Rio, Gianni Galaverna, Erasmo Neviani, Camilla Lazzi
Software Mentions: 5
Published: over 7 years ago

10.3389/fpsyg.2020.00945

Introducing a Computerized Figural Memory Test Based on Automatic Item Generation: An Analysis With the Rasch Poisson Counts Model
Cited by: 3
Author(s): David Jendryczko, Laura Berkemeyer, Heinz Holling
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0153160

SWATH2stats: An R/Bioconductor Package to Process and Convert Quantitative SWATH-MS Proteomics Data for Downstream Analysis Tools
Cited by: 39
Author(s): Peter Blattmann, Moritz Heusel, Ruedi Aebersold
Software Mentions: 5
Published: over 10 years ago

10.3390/microorganisms9020229

Arbuscular Mycorrhizal Fungal Communities in the Soils of Desert Habitats
Cited by: 15
Author(s): Martti Vasar, John Davison, Siim‐Kaarel Sepp, Maarja Öpik, Mari Moora, Kadri Koorem, Yiming Meng, Jane Oja, Asem A. Akhmetzhanova, Saleh Al‐Quraishy, В. Г. Онипченко, Juan José Cantero, Sydney I. Glassman, Wael N. Hozzein, Martin Zobel
Software Mentions: 5
Published: over 5 years ago

10.1155/2016/8409183

Azocasein Substrate for Determination of Proteolytic Activity: Reexamining a Traditional Method Using Bromelain Samples
Cited by: 60
Author(s): D. Coelho, Thais Peron Saturnino, Fernanda Freitas Fernandes, Priscila Gava Mazzola, Edgar Silveira, Elias Basile Tambourgi
Software Mentions: 5
Published: over 10 years ago

10.1186/1471-2164-15-687

Species and gene divergence in Littorina snails detected by array comparative genomic hybridization
Cited by: 20
Author(s): Marina Panova, Tomas Johansson, Björn Canbäck, Johan Bentzer, Magnus Alm Rosenblad, Kerstin Johannesson, Anders Tunlid, Carl André
Software Mentions: 5
Published: over 12 years ago

10.1186/s12864-021-07906-6

Genome analyses of four Wolbachia strains and associated mitochondria of Rhagoletis cerasi expose cumulative modularity of cytoplasmic incompatibility factors and cytoplasmic hitchhiking across host populations
Cited by: 2
Author(s): Jennifer L. Morrow, Markus Riegler
Software Mentions: 5
Published: almost 5 years ago

10.3390/microorganisms8060905

First Detection of Paralytic Shellfish Toxins from Alexandrium pacificum above the Regulatory Limit in Blue Mussels (Mytilus galloprovincialis) in New South Wales, Australia
Cited by: 8
Author(s): Abanti Barua, Penelope Ajani, Rendy Ruvindy, H. Farrell, A. Zammit, Steve Brett, David R. Hill, Chowdhury Sarowar, Mona Hoppenrath, Shauna A. Murray
Software Mentions: 5
Published: about 6 years ago

10.1186/s40168-017-0261-y

Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome
Cited by: 127
Author(s): Dorottya Nagy‐Szakal, Brent L. Williams, Nischay Mishra, Xiaoyu Che, Bohyun Lee, Lucinda Bateman, Nancy G. Klimas, Anthony L. Komaroff, Susan Levine, José G. Montoya, Daniel L. Peterson, Devi Ramanan, Komal Jain, M L Eddy, Mady Hornig, W. Ian Lipkin
Software Mentions: 5
Published: about 9 years ago

10.7717/peerj.11944

Herbivory and misidentification of target habitat constrain region-wide restoration success of spekboom (Portulacaria afra) in South African subtropical succulent thicket
Cited by: 3
Author(s): Marius L. van der Vyver, Anthony Mills, Mark Difford, Richard M. Cowling
Software Mentions: 5
Published: almost 5 years ago

10.1186/s13567-021-00972-4

Transcriptomic analysis of equine chorioallantois reveals immune networks and molecular mechanisms involved in nocardioform placentitis
Cited by: 8
Author(s): Hesham A. Ali, Shavahn C. Loux, Laura Kennedy, Kirsten E. Scoggin, Pouya Dini, Carleigh E. Fedorka, Theodore S. Kalbfleisch, A. Esteller-Vico, David W. Horohov, Erdal Erol, Craig N. Carter, Jon J. Smith, Barry A. Ball
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0165252

Environmental DNA from Seawater Samples Correlate with Trawl Catches of Subarctic, Deepwater Fishes
Cited by: 250
Author(s): Philip Francis Thomsen, Peter Rask Møller, Eva Egelyng Sigsgaard, Steen Wilhelm Knudsen, Ole A Jørgensen, Eske Willerslev
Software Mentions: 5
Published: over 9 years ago

10.1093/molbev/msz114

The Legacy of Sexual Ancestors in Phenotypic Variability, Gene Expression, and Homoeolog Regulation of Asexual Hybrids and Polyploids
Cited by: 20
Author(s): Oldřich Bartoš, Jan Röslein, Jan Kotusz, Jan Pačes, Ladislav Pekárik, Miloslav Petrtýl, Karel Halačka, Eva Kašparová, Jan Mendel, Alicja Boroń, Dorota Juchno, Anna Leska, Olga Jabłońska, Vladimı́r Beneš, Monika Šídová, Karel Janko
Software Mentions: 5
Published: about 7 years ago

10.1186/s12864-015-1540-2

Gene expression associated with white syndromes in a reef building coral, Acropora hyacinthus
Cited by: 185
Author(s): Rachel M. Wright, Galina V. Aglyamova, Eli Meyer, Mikhail V. Matz
Software Mentions: 5
Published: about 11 years ago

10.7717/peerj.5812

Home sick: impacts of migratory beekeeping on honey bee (<i>Apis mellifera</i>) pests, pathogens, and colony size
Cited by: 24
Author(s): Samantha A. Alger, P. Alexander Burnham, Zachary S. Lamas, Alison K. Brody, Leif L. Richardson
Software Mentions: 5
Published: over 7 years ago

10.1038/s42003-021-01985-7

Global climate and nutrient controls of photosynthetic capacity
Cited by: 18
Author(s): Yunke Peng, Keith J. Bloomfield, Lucas A. Cernusak, Tomas F. Domingues, Iain Colin Prentice
Software Mentions: 5
Published: over 5 years ago

10.1002/ece3.2469

Emissions of methane from northern peatlands: a review of management impacts and implications for future management options
Cited by: 106
Author(s): Mohamed Abdalla, Astley Hastings, Jaak Truu, Mikk Espenberg, Ülo Mander, Pete Smith
Software Mentions: 5
Published: almost 10 years ago

10.7554/eLife.55305

Unexplained repeated pregnancy loss is associated with altered perceptual and brain responses to men’s body-odor
Cited by: 11
Author(s): Liron Rozenkrantz, Reut Weissgross, Tali Weiss, Inbal Ravreby, Idan Frumin, Sagit Shushan, Lior Gorodisky, Netta Reshef, Yael Holzman, Liron Pinchover, Yaara Endevelt‐Shapira, Eva Mishor, Timna Soroka, Maya Finkel, Liav Tagania, Aharon Ravia, Ofer Perl, Edna Furman‐Haran, Howard Carp, Noam Sobel
Software Mentions: 5
Published: almost 6 years ago

10.7717/peerj.10941

Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture
Cited by: 59
Author(s): Rachel Gilroy, Anuradha Ray, María Getino, Isabella Pursley, Daniel L. Horton, Nabil-Fareed Alikhan, Dave Baker, Karim Gharbi, Neil Hall, Mick Watson, Evelien M. Adriaenssens, Ebenezer Foster-Nyarko, Sheikh Jarju, Arss Secka, Martín Antonio, Aharon Oren, Roy R. Chaudhuri, Roberto La Ragione, Falk Hildebrand, Mark J. Pallen
Software Mentions: 5
Published: over 5 years ago

10.1038/srep19244

Evaluation of the 2b-RAD method for genomic selection in scallop breeding
Cited by: 57
Author(s): Jun Dou, Xue Li, Qiang Fu, Wenqian Jiao, Yangping Li, Tianqi Li, Yangfan Wang, Xiaoli Hu, Shi Wang, Zhenmin Bao
Software Mentions: 5
Published: over 10 years ago

10.1186/s12862-019-1479-z

Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa (Rosaceae)
Cited by: 16
Author(s): Kévin Debray, Jordan Marie‐Magdelaine, Tom Ruttink, Jérémy Clotault, Fabrice Foucher, Valéry Malécot
Software Mentions: 5
Published: almost 7 years ago

10.3390/ani8100182

Investigating Home Range, Movement Pattern, and Habitat Selection of Bar-headed Geese during Breeding Season at Qinghai Lake, China
Cited by: 1
Author(s): Ruobing Zheng, Lacy M. Smith, Diann J. Prosser, John Y. Takekawa, Scott H. Newman, Jeffery D. Sullivan, Ze Luo, Binbin Yan
Software Mentions: 5
Published: over 7 years ago

10.7717/peerj.8094

The influence of ecological infrastructures adjacent to crops on their carabid assemblages in intensive agroecosystems
Cited by: 10
Author(s): Emilie Pécheur, Julien Piqueray, Arnaud Monty, Marc Dufrêne, Grégory Mahy
Software Mentions: 5
Published: over 6 years ago

10.3389/fmicb.2016.01727

Gradual Changes of Gut Microbiota in Weaned Miniature Piglets
Cited by: 123
Author(s): Jun Hu, Yangfan Nie, Jian Wei Chen, Yong Zhang, Zhi‐Chang Wang, Qi-Wen Fan, Xianghua Yan
Software Mentions: 5
Published: over 9 years ago

10.1074/mcp.O115.050229

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets
Cited by: 129
Author(s): Yasset Perez‐Riverol, Qing Wei Xu, Rui Wang, Julian Uszkoreit, Johannes Griss, Aniel Sánchez, Florian Reisinger, Attila Csordás, Tobias Ternent, Noemi del-Toro, José A. Dianes, Martin Eisenacher, Henning Hermjakob, Juan Antonio Vizcaíno
Software Mentions: 5
Published: over 10 years ago

10.1002/ece3.3012

No evidence for adaptation to local rhizobial mutualists in the legume<i>Medicago lupulina</i>
Cited by: 23
Author(s): Tia L. Harrison, Corlett W. Wood, Isabela L. Borges, John R. Stinchcombe
Software Mentions: 5
Published: about 9 years ago

10.3390/microorganisms8081152

Population Structure of Non-ST6 Listeria monocytogenes Isolated in the Red Meat and Poultry Value Chain in South Africa
Cited by: 11
Author(s): Itumeleng Matle, Thendo Mafuna, Evelyn Madoroba, Khanyisile R. Mbatha, Kudakwashe Magwedere, Rian Pierneef
Software Mentions: 5
Published: almost 6 years ago

10.18383/j.tom.2016.00172

Dynamic Susceptibility Contrast-MRI Quantification Software Tool: Development and Evaluation
Cited by: 7
Author(s): Panagiotis Korfiatis, Timothy L. Kline, Zachary S. Kelm, Rickey E. Carter, Leland Hu, Bradley J. Erickson
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pgen.1009260

TDP-43 mutations link Amyotrophic Lateral Sclerosis with R-loop homeostasis and R loop-mediated DNA damage
Cited by: 43
Author(s): Marta Gianini, Aleix Bayona-Feliú, Daisy Sproviero, Sónia Barroso, Cristina Cereda, Andrés Aguilera
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0072238

Effect of Doxorubicin/Pluronic SP1049C on Tumorigenicity, Aggressiveness, DNA Methylation and Stem Cell Markers in Murine Leukemia
Cited by: 73
Author(s): Daria Y. Alakhova, Yi Zhao, Shu Li, Alexander V. Kabanov
Software Mentions: 5
Published: almost 13 years ago

10.1186/1471-2148-13-233

True lemurs…true species - species delimitation using multiple data sources in the brown lemur complex
Cited by: 31
Author(s): Matthias Markolf, Hanitriniaina Rakotonirina, Claudia Fichtel, Phillip von Grumbkow, Markus Brameier, Peter M. Kappeler
Software Mentions: 5
Published: over 13 years ago

10.1080/23802359.2021.1966334

Aln2tbl: building a mitochondrial features table from a assembly alignment in fasta format
Cited by: 0
Author(s): Joan Pons, Juan José Ensenyat, Pere Rosselló Bover, M. Serra, Francesco Nardi
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41598-021-87564-6

The ANTsX ecosystem for quantitative biological and medical imaging
Cited by: 56
Author(s): Nicholas J. Tustison, Philip A. Cook, Andrew J. Holbrook, Hans J. Johnson, John Muschelli, Gabriel A. Devenyi, Jeffrey T. Duda, Sandhitsu R. Das, Nicholas Cullen, Daniel L. Gillen, Michael A. Yassa, James L. Stone, James C. Gee, Brian Avants
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0256554

Is it easier to use one language variety at a time, or mix them? An investigation of voluntary language switching with bidialectals
Cited by: 1
Author(s): Mathieu Declerck, Neil W. Kirk
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41598-020-63919-3

Increased Prediction Accuracy Using Combined Genomic Information and Physiological Traits in A Soft Wheat Panel Evaluated in Multi-Environments
Cited by: 12
Author(s): Jia Guo, Sumit Pradhan, Dipendra Shahi, Jahangir Khan, Jordan C. McBreen, Guihua Bai, J. Paul Murphy, Ali Babar
Software Mentions: 5
Published: about 6 years ago

10.1016/j.chom.2018.03.007

Chromatin Accessibility-Based Characterization of the Gene Regulatory Network Underlying Plasmodium falciparum Blood-Stage Development
Cited by: 122
Author(s): Christa Geeke Toenhake, Sabine Anne‐Kristin Fraschka, M. Vijayabaskar, David R. Westhead, Simon J. van Heeringen, Richárd Bártfai
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pone.0210347

EMBL2checklists: A Python package to facilitate the user-friendly submission of plant and fungal DNA barcoding sequences to ENA
Cited by: 6
Author(s): Michael Gruenstaeudl, Yannick Hartmaring
Software Mentions: 5
Published: over 7 years ago

10.1038/s41598-020-61192-y

Diet influences the functions of the human intestinal microbiome
Cited by: 104
Author(s): Maria De Angelis, Ilario Ferrocino, Francesco Maria Calabrese, Francesca De Filippis, Noemi Cavallo, Sonya Siragusa, Simone Rampelli, Raffaella Di Cagno, Kalliopi Rantsiou, Lucia Vannini, Nicoletta Pellegrini, Camilla Lazzi, Silvia Turroni, Nicola Lorusso, Mario Ventura, Marcello Chieppa, Erasmo Neviani, Patrizia Brigidi, Paul W. O’Toole, Marco Gobbetti, Luca Simone Cocolin
Software Mentions: 5
Published: over 6 years ago

10.7717/peerj.11950

Rephine.r: a pipeline for correcting gene calls and clusters to improve phage pangenomes and phylogenies
Cited by: 2
Author(s): Jason W. Shapiro, Catherine Putonti
Software Mentions: 5
Published: almost 5 years ago

10.1002/ece3.5720

Ocean acidification during prefertilization chemical communication affects sperm success
Cited by: 8
Author(s): Rowan A. Lymbery, W. Jason Kennington, Christopher E. Cornwall, Jonathan P. Evans
Software Mentions: 5
Published: over 6 years ago

10.3390/cancers13112592

Identification of Candidate Protein Biomarkers for CIN2+ Lesions from Self-Sampled, Dried Cervico–Vaginal Fluid Using LC-MS/MS
Cited by: 6
Author(s): Ariadna Lara Gutiérrez, Julia Hedlund Lindberg, Ganna Shevchenko, Inger Gustavsson, Jonas Bergquist, Ulf Gyllensten, Stefan Enroth
Software Mentions: 5
Published: about 5 years ago

10.7717/peerj.7647

Interspecific variation in the limb long bones among modern rhinoceroses—extent and drivers
Cited by: 25
Author(s): Christophe Mallet, Raphaël Cornette, Guillaume Billet, Alexandra Houssaye
Software Mentions: 5
Published: almost 7 years ago

10.7717/peerj.2038

PhySortR: a fast, flexible tool for sorting phylogenetic trees in R
Cited by: 16
Author(s): Timothy G. Stephens, Debashish Bhattacharya, Mark A. Ragan, Cheong Xin Chan
Software Mentions: 5
Published: about 10 years ago

10.1371/journal.pone.0229807

Microhabitat and ectomycorrhizal effects on the establishment, growth and survival of Quercus ilex L. seedlings under drought
Cited by: 20
Author(s): Laura García de Jalón, Jean‐Marc Limousin, Franck Richard, Arthur Geßler, Martina Peter, Stephan Hättenschwiler, Alexandru Milcu
Software Mentions: 5
Published: about 6 years ago

10.1038/s41598-017-12559-1

The neural representation of personally familiar and unfamiliar faces in the distributed system for face perception
Cited by: 75
Author(s): Matteo Visconti di Oleggio Castello, Yaroslav O. Halchenko, J. Swaroop Guntupalli, Jason Gors, M. Ida Gobbini
Software Mentions: 5
Published: almost 9 years ago

10.1186/s13059-019-1857-2

eIF4A2 drives repression of translation at initiation by Ccr4-Not through purine-rich motifs in the 5′UTR
Cited by: 34
Author(s): Ania Wilczynska, Sarah L. Gillen, Tobias Schmidt, Hedda A. Meijer, Rebekah Jukes-Jones, Claudia Langlais, Kari Kopra, Wei-Ting Lu, Jack D. Godfrey, Ben R Hawley, Kelly Hodge, Sara Zanivan, Kelvin Cain, John Le Quesne, Martin Bushell
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0180007

Diversity of fruit-feeding butterflies in a mountaintop archipelago of rainforest
Cited by: 18
Author(s): Geanne Carla Novais Pereira, Marcel Serra Coelho, Marina do Vale Beirão, Rodrigo Fagundes Braga, Geraldo Wilson Fernandes
Software Mentions: 5
Published: about 9 years ago

10.1111/eva.12960

Genomic insights into historical population dynamics, local adaptation, and climate change vulnerability of the East Asian Tertiary relict <i>Euptelea</i> (Eupteleaceae)
Cited by: 12
Author(s): Yanan Cao, Shanshan Zhu, Jun Chen, Hans Peter Comes, Ian Wang, Luyao Chen, Shota Sakaguchi, Ying‐Xiong Qiu
Software Mentions: 5
Published: over 6 years ago

10.3389/fpsyg.2021.673535

Equal Opportunity Interference: Both L1 and L2 Influence L3 Morpho-Syntactic Processing
Cited by: 2
Author(s): Nawras Abbas, Tamar Degani, Anat Prior
Software Mentions: 5
Published: about 5 years ago

10.3390/cancers12061531

Mass Spectrometric Comparison of HPV-Positive and HPV-Negative Oropharyngeal Cancer
Cited by: 6
Author(s): M. Wurlitzer, Nikolaus Möckelmann, Malte Kriegs, Maren Vens, Maryam Omidi, Konstantin Hoffer, Clara von Bargen, Christina Möller‐Koop, Melanie Witt, Conrad Droste, Agnes Oetting, Hannes Petersen, Chia‐Jung Busch, Adrian Münscher, Hartmut Schlüter, Till S. Clauditz, Thorsten Rieckmann
Software Mentions: 5
Published: about 6 years ago

10.1186/s12859-017-1462-x

Comparative network stratification analysis for identifying functional interpretable network biomarkers
Cited by: 5
Author(s): Chuanchao Zhang, Juan Liu, Qianqian Shi, Tao Zeng, Luonan Chen
Software Mentions: 5
Published: over 9 years ago

10.1002/ece3.3673

Rapid song divergence leads to discordance between genetic distance and phenotypic characters important in reproductive isolation
Cited by: 21
Author(s): Emmanuel C. Nwankwo, Chryso Th. Pallari, Louis Hadjioannou, Andreas L. Ioannou, Ronald K. Mulwa, Alexander N. G. Kirschel
Software Mentions: 5
Published: over 8 years ago

10.1186/s13100-019-0190-3

Stowaway miniature inverted repeat transposable elements are important agents driving recent genomic diversity in wild and cultivated carrot
Cited by: 6
Author(s): Alicja Macko-Podgórni, Katarzyna Stelmach, Kornelia Kwolek, Dariusz Grzebelus
Software Mentions: 5
Published: over 6 years ago

10.1186/1471-2202-10-81

A toolbox for the fast information analysis of multiple-site LFP, EEG and spike train recordings
Cited by: 200
Author(s): Cesare Magri, Kevin Whittingstall, Vanessa Singh, Nikos K. Logothetis, Stefano Panzeri
Software Mentions: 5
Published: almost 17 years ago

10.1371/journal.pbio.2004356

Antibiotic combination efficacy (ACE) networks for a Pseudomonas aeruginosa model
Cited by: 68
Author(s): Camilo Barbosa, Robert Beardmore, Hinrich Schulenburg, Gunther Jansen
Software Mentions: 5
Published: about 8 years ago

10.1371/journal.pcbi.1008735

From heterogeneous healthcare data to disease-specific biomarker networks: A hierarchical Bayesian network approach
Cited by: 9
Author(s): Ann‐Kristin Becker, Marcus Dörr, Stephan B. Felix, Fabian Frost, Hans J. Grabe, Markus M. Lerch, Matthias Nauck, Uwe Völker, Henry Völzke, Lars Kaderali
Software Mentions: 5
Published: over 5 years ago