10.3389/fmicb.2020.01022

Phytopathogenic Rhodococcus Have Diverse Plasmids With Few Conserved Virulence Functions
Cited by: 14
Author(s): Elizabeth A. Savory, Alexandra J. Weisberg, Danielle M. Stevens, Allison Creason, Skylar L Fuller, Emma M Pearce, Jeff H. Chang
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-019-53599-z

Effects of sampling strategy and DNA extraction on human skin microbiome investigations
Cited by: 67
Author(s): Rie Dybboe Bjerre, Luisa W. Hugerth, Fredrik Boulund, Maike Seifert, Jeanne Duus Johansen, Lars Engstrand
Software Mentions: 4
Published: over 6 years ago

10.3389/fnbot.2021.648374

Robot Communication: Network Traffic Classification Based on Deep Neural Network
Cited by: 1
Author(s): Ming Ge, Xiangzhan Yu, Likun Liu
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2019.01384

Genomic Diversity Evaluation of Populus trichocarpa Germplasm for Rare Variant Genetic Association Studies
Cited by: 10
Author(s): Anthony Piot, Julien Prunier, Nathalie Isabel, Jaroslav Klápště, Yousry A. El‐Kassaby, Juan Carlos Villarreal Aguilar, Ilga Porth
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0225368

Computational analysis of functional single nucleotide polymorphisms associated with SLC26A4 gene
Cited by: 18
Author(s): Mirza Jawad ul Hasnain, Muhammad Shoaib, Salman Qadri, Bakhtawar Afzal, Tehreem Anwar, Syed Hassan Abbas, Amina Sarwar, Hafiz Muhammad Talha Malik, Muhammad Tariq Pervez
Software Mentions: 4
Published: over 6 years ago

10.1128/mSystems.00299-20

Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms
Cited by: 44
Author(s): Elizabeth A. McDaniel, Brittany F. Peterson, Sarah Stevens, Patricia Q. Tran, Karthik Anantharaman, Katherine D. McMahon
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0165705

Propensity Scoring after Multiple Imputation in a Retrospective Study on Adjuvant Radiation Therapy in Lymph-Node Positive Vulvar Cancer
Cited by: 15
Author(s): Christine zu Eulenburg, Anna Suling, Petra Neuser, Alexander Reuß, Ulrich Canzler, Tanja Fehm, Alexander Luyten, Martin Hellriegel, Linn Woelber, Sven Mahner
Software Mentions: 4
Published: almost 10 years ago

10.1186/1471-2105-13-S17-S22

Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package
Cited by: 20
Author(s): Mohamed El‐Kalioby, Mohamed Abouelhoda, Jan Walters Kruger, Robert Giegerich, Alexander Sczyrba, Dennis P. Wall, Peter J. Tonellato
Software Mentions: 4
Published: over 13 years ago

10.1136/ard.2008.096172

Is the blood B-cell subset profile diagnostic for Sjögren syndrome?
Cited by: 72
Author(s): Aymeric Binard, Laëtitia Le Pottier, Valérie Devauchelle‐Pensec, Alain Saraux, Pierre Youinou, Jacques‐Olivier Pers
Software Mentions: 4
Published: almost 18 years ago

10.1371/journal.pone.0138139

Patterns of Lynx Predation at the Interface between Protected Areas and Multi-Use Landscapes in Central Europe
Cited by: 18
Author(s): Elisa Belotti, Nicole Weder, Luděk Bufka, Arne Kaldhusdal, Helmut Küchenhoff, Heidi Seibold, Benno Woelfing, Marco Heurich
Software Mentions: 4
Published: almost 11 years ago

10.1002/ece3.6952

Different landscape effects on the genetic structure of two broadly distributed woody legumes,<i>Acacia salicina</i>and<i>A. stenophylla</i>(Fabaceae)
Cited by: 2
Author(s): Francisco Encinas‐Viso, Christiana McDonald‐Spicer, Nunzio Knerr, Peter H. Thrall, Linda Broadhurst
Software Mentions: 4
Published: almost 6 years ago

10.7717/peerj.8544

SpeciesPrimer: a bioinformatics pipeline dedicated to the design of qPCR primers for the quantification of bacterial species
Cited by: 9
Author(s): Matthias Dreier, Hélène Berthoud, Noam Shani, Daniel Wechsler, Pilar Junier
Software Mentions: 4
Published: over 6 years ago

10.1186/s12882-018-0870-0

Effects of dialysate to serum sodium (Na+) alignment in chronic hemodialysis (HD) patients: retrospective cohort study from a quality improvement project
Cited by: 9
Author(s): Jochen G. Raimann, Linda H. Ficociello, Len Usvyat, Hanjie Zhang, Lisa Pacelli, Sandi Moore, Penny Sheppard, Qingqing Xiao, Yuedong Wang, Claudy Mullon, Paul Balter, Theodore Sullivan, Peter Kotanko
Software Mentions: 4
Published: over 8 years ago

10.1186/s12859-019-2626-7

Partition-based optimization model for generative anatomy modeling language (POM-GAML)
Cited by: 4
Author(s): Doga Demirel, Berk Çetinsaya, Tansel Halic, Sinan Kockara, Shahryar Ahmadi
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0187150

RNA-seq transcriptome analysis of formalin fixed, paraffin-embedded canine meningioma
Cited by: 13
Author(s): Jennifer K. Grenier, Polly Foureman, Erica A. Sloma, Andrew D. Miller
Software Mentions: 4
Published: almost 9 years ago

10.3389/fpls.2020.00496

Chromosome-Scale Assembly of Winter Oilseed Rape Brassica napus
Cited by: 55
Author(s): HueyTyng Lee, Harmeet Singh Chawla, Christian Obermeier, Felix Dreyer, Amine Abbadi, Rod J. Snowdon
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0177750

Inflammatory and apoptotic remodeling in autonomic nervous system following myocardial infarction
Cited by: 23
Author(s): Chen Gao, Kimberly Howard‐Quijano, Christoph Rau, Tatsuo Takamiya, Yang Song, Kalyanam Shivkumar, Yibin Wang, Aman Mahajan
Software Mentions: 4
Published: about 9 years ago

10.7554/eLife.24836

Minimal-assumption inference from population-genomic data
Cited by: 21
Author(s): Daniel B. Weissman, Oskar Hallatschek
Software Mentions: 4
Published: about 9 years ago

10.1155/2019/3869825

A Novel Clinical Six-Flavoprotein-Gene Signature Predicts Prognosis in Esophageal Squamous Cell Carcinoma
Cited by: 6
Author(s): Peng Liu, Jincheng Guo, Li-Wen Lin, Feng Pan, Jian Zhao, Li–Yan Xu, En‐Min Li
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13072-016-0070-8

Changes of 5-hydroxymethylcytosine distribution during myeloid and lymphoid differentiation of CD34+ cells
Cited by: 18
Author(s): Xavier Tekpli, Alfonso Urbanucci, Adnan Hashim, Cathrine Broberg Vågbø, Robert Lyle, Marianne Kristiansen Kringen, Anne Cathrine Staff, Ingunn Dybedal, Ian G. Mills, Arne Klungland, Judith Staerk
Software Mentions: 4
Published: about 10 years ago

10.3390/s18124125

Model Driven Development Applied to Complex Event Processing for Near Real-Time Open Data
Cited by: 6
Author(s): Pedro J. Clemente, Adolfo Lozano-Tello
Software Mentions: 4
Published: over 7 years ago

10.1186/s12915-021-00991-9

Long-term persistence of supernumerary B chromosomes in multiple species of Astyanax fish
Cited by: 6
Author(s): Duílio Mazzoni Zerbinato de Andrade Silva, Francisco J. Ruíz-Ruano, Ricardo Utsunomia, María Martín-Peciña, Jonathan Pena Castro, Paula Paccielli Freire, Robson Francisco Carvalho, Diogo Teruo Hashimoto, Alexander Suh, Cláudio Oliveira, Fábio Porto‐Foresti, Roberto Ferreira Artoni, Fausto Foresti, Juan Pedro M. Camacho
Software Mentions: 4
Published: over 5 years ago

10.1002/humu.23765

Heterozygosity mapping for human dominant trait variants
Cited by: 2
Author(s): Atsuko Imai‐Okazaki, Yang Li, Sukanya Horpaopan, Yasser Riazalhosseini, Masoud Garshasbi, Yaël P. Mossé, Di Zhang, Isabelle Schrauwen, Aarushi Sharma, Cathy S.J. Fann, Suzanne M. Leal, Mark Lathrop, Jürg Ott
Software Mentions: 4
Published: over 7 years ago

10.1186/s12889-021-11790-w

Electronic data collection, management and analysis tools used for outbreak response in low- and middle-income countries: a systematic review and stakeholder survey
Cited by: 4
Author(s): Patrick Keating, Jillian Murray, Karl Schenkel, Laura Merson, Anna C. Seale
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-020-61678-9

Systematic alteration of ATAC-seq for profiling open chromatin in cryopreserved nuclei preparations from livestock tissues
Cited by: 23
Author(s): Michelle M. Halstead, Colin Kern, Perot Saelao, Ganrea Chanthavixay, Y. Wang, Mary E. Delany, Huaijun Zhou, Pablo J. Ross
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-017-17975-x

Functional redundancy and sensitivity of fish assemblages in European rivers, lakes and estuarine ecosystems
Cited by: 31
Author(s): Nils Teichert, Mario Lepage, Alban Sagouis, Ángel Borja, Guillem Chust, Maria Teresa Ferreira, Stéphanie Pasquaud, Rafaela Schinegger, Pedro Segurado, Christine Argillier
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0148028

Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis
Cited by: 198
Author(s): Adam G. Clooney, Fiona Fouhy, Roy D. Sleator, Aisling O’ Driscoll, Catherine Stanton, Paul D. Cotter, Marcus J. Claesson
Software Mentions: 4
Published: over 10 years ago

10.1002/ece3.2819

Outlier analyses to test for local adaptation to breeding grounds in a migratory arctic seabird
Cited by: 26
Author(s): Anna Tigano, Allison J. Shultz, Scott V. Edwards, Gregory J. Robertson, Vicki L. Friesen
Software Mentions: 4
Published: over 9 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 5 years ago

10.1038/srep37680

Molecular Insight into Affinities of Gallated and Nongallated Proanthocyanidins Dimers to Lipid Bilayers
Cited by: 13
Author(s): Wei Zhu, Le Xiong, Jinming Peng, Xin Deng, Jun Gao, Chunmei Li
Software Mentions: 4
Published: over 9 years ago

10.1186/1471-2105-11-598

Initial steps towards a production platform for DNA sequence analysis on the grid
Cited by: 8
Author(s): Angela C. M. Luyf, Barbera D.C. van Schaik, Michèl de Vries, Frank Baas, Antoine H. C. van Kampen, Sílvia D. Olabarriaga
Software Mentions: 4
Published: over 15 years ago

10.1186/s13321-017-0228-9

chemalot and chemalot_knime: Command line programs as workflow tools for drug discovery
Cited by: 12
Author(s): Man-Ling Lee, Ignacio Aliagas, Jianwen Feng, Thomas R. Gabriel, TJ O'Donnell, Benjamin D. Sellers, Bernd Wiswedel, A. Gobbi
Software Mentions: 4
Published: about 9 years ago

10.1038/sdata.2018.55

Massively parallel recordings in macaque motor cortex during an instructed delayed reach-to-grasp task
Cited by: 41
Author(s): Thomas Brochier, Lyuba Zehl, Yaoyao Hao, Margaux Duret, Julia Sprenger, Michael Denker, Sonja Grün, Alexa Riehle
Software Mentions: 4
Published: over 8 years ago

10.1186/s12915-021-01122-0

Single-cell analysis of cell fate bifurcation in the chordate Ciona
Cited by: 4
Author(s): Konner Winkley, Wendy Reeves, Michael Veeman
Software Mentions: 4
Published: almost 5 years ago

10.1534/g3.118.200521

Identification of Candidate Genes Controlling Black Seed Coat and Pod Tip Color in Cowpea (<i>Vigna unguiculata</i>[L.] Walp)
Cited by: 31
Author(s): Ira A. Herniter, María Muñoz‐Amatriaín, Sassoum Lo, Yi‐Ning Guo, Timothy J. Close
Software Mentions: 4
Published: almost 8 years ago

10.1186/s13059-020-01986-5

HiNT: a computational method for detecting copy number variations and translocations from Hi-C data
Cited by: 43
Author(s): Wang Su, Soohyun Lee, Chong Chu, Dhawal Jain, Peter Kerpedjiev, Geoffrey M. Nelson, Jennifer Walsh, B. Alver, Peter J. Park
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-018-26239-1

A 2-transcript host cell signature distinguishes viral from bacterial diarrhea and it is influenced by the severity of symptoms
Cited by: 19
Author(s): Ruth Barral-Arca, Jacobo Pardo‐Seco, Federico Martinón‐Torres, Antonio Salas
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pone.0023581

Strategy to Find Molecular Signatures in a Small Series of Rare Cancers: Validation for Radiation-Induced Breast and Thyroid Tumors
Cited by: 16
Author(s): Nicolas Ugolin, Catherine Ory, Emilie Lefèvre, Nora Benhabilès, Paul Hofman, Martin Schlumberger, Sylvie Chevillard
Software Mentions: 4
Published: almost 15 years ago

10.1371/journal.pntd.0004626

Reproductive Incompatibility Involving Senegalese Aedes aegypti (L) Is Associated with Chromosome Rearrangements
Cited by: 21
Author(s): Laura B. Dickson, Maria V. Sharakhova, Vladimir A. Timoshevskiy, Karen Fleming, Alex Caspary, Massamba Sylla, William C. Black
Software Mentions: 4
Published: over 10 years ago

10.34133/2019/2591849

Easy MPE: Extraction of Quality Microplot Images for UAV-Based High-Throughput Field Phenotyping
Cited by: 24
Author(s): Léa Tresch, Yun Mu, Atsushi Itoh, Akito Kaga, Kazunori Taguchi, Masayuki Hirafuji, S. Ninomiya, Wei Guo
Software Mentions: 4
Published: over 7 years ago

10.7554/eLife.60498

Genome-wide alterations of uracil distribution patterns in human DNA upon chemotherapeutic treatments
Cited by: 11
Author(s): Hajnalka Laura Pálinkás, Angéla Békési, Gergely Róna, Lőrinc Sándor Pongor, Gábor Papp, Gergely Tihanyi, Eszter Holub, Ádám Póti, Carolina Gemma, Simak Ali, Michael J. Morten, Eli Rothenberg, Michele Pagano, Dávid Szűts, Balázs Győrffy, Beáta G. Vértessy
Software Mentions: 4
Published: almost 6 years ago

10.1038/bcj.2016.77

lncRNA profiling in early-stage chronic lymphocytic leukemia identifies transcriptional fingerprints with relevance in clinical outcome
Cited by: 40
Author(s): Domenica Ronchetti, Martina Manzoni, Luca Agnelli, Cristina Vinci, Sonia Fabris, Giovanna Cutrona, Serena Matis, Monica Colombo, S. Galletti, Elisa Taìana, Anna Grazia Recchia, Sabrina Bossio, Massimo Gentile, Caterina Musolino, Francesco Di Raimondo, Andrea Grilli, Silvio Bicciato, Agostino Cortelezzi, Pierfrancesco Tassone, Fortunato Morabito, Manlio Ferrarini, Antonino Neri
Software Mentions: 4
Published: almost 10 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 6 years ago

10.1038/s41597-021-00823-z

Collegiate athlete brain data for white matter mapping and network neuroscience
Cited by: 3
Author(s): Bradley Caron, Ricardo Stuck, Brent McPherson, Daniel Bullock, Lindsey Kitchell, Joshua Faskowitz, Derek Kellar, Hu Cheng, Sharlene D. Newman, Nicholas Port, Franco Pestilli
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0256729

Sociodemographic risk factors of under-five stunting in Bangladesh: Assessing the role of interactions using a machine learning method
Cited by: 4
Author(s): Mohaimen Mansur, Awan Afiaz, Md. Saddam Hossain
Software Mentions: 4
Published: almost 5 years ago

10.7554/eLife.19760

Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation
Cited by: 551
Author(s): Max A. Horlbeck, Luke A. Gilbert, Jacqueline E. Villalta, Brittany Susan Adamson, Ryan A. Pak, Yu‐Wen Chen, Alexander P. Fields, Chong Yon Park, Jacob E. Corn, Martin Kampmann, Jonathan S. Weissman
Software Mentions: 4
Published: almost 10 years ago

10.1186/1471-2105-12-184

SuiteMSA: visual tools for multiple sequence alignment comparison and molecular sequence simulation
Cited by: 19
Author(s): Catherine L. Anderson, Cory L. Strope, Etsuko N. Moriyama
Software Mentions: 4
Published: about 15 years ago

10.1186/1471-2105-14-S7-S14

Examples of sequence conservation analyses capture a subset of mouse long non-coding RNAs sharing homology with fish conserved genomic elements
Cited by: 16
Author(s): Swaraj Basu, Ferenc Müller, Remo Sanges
Software Mentions: 4
Published: over 13 years ago

10.3389/fmicb.2012.00293

Millimeter-scale patterns of phylogenetic and trait diversity in a salt marsh microbial mat
Cited by: 30
Author(s): David Armitage, Kimberley L. Gallagher, Nicholas D. Youngblut, Daniel H. Buckley, Stephen H. Zinder
Software Mentions: 4
Published: over 14 years ago

10.1186/s13059-020-02007-1

Influenza infection elicits an expansion of gut population of endogenous Bifidobacterium animalis which protects mice against infection
Cited by: 62
Author(s): Qiang Zhang, Jin Hu, Jia-Wu Feng, Xiaoru Hu, Wang Ting, Wenxiao Gong, Kun Huang, Yi-Xiong Guo, Zhong Zou, Xian Lin, Run Zhou, Yuqi Yuan, Anding Zhang, Hong Wei, Gang Cao, Chen Liu, Lingling Chen, Meilin Jin
Software Mentions: 4
Published: over 6 years ago

10.3389/fonc.2021.630432

High Expression of microRNA-223 Indicates a Good Prognosis in Triple-Negative Breast Cancer
Cited by: 10
Author(s): Li Chen, Xiao Li Zhu, Bin Han, Lei Ji, Ling Yao, Zhonghua Wang
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.ppat.1009272

Nucleosome landscape reflects phenotypic differences in Trypanosoma cruzi life forms
Cited by: 10
Author(s): Alex Ranieri Jerônimo Lima, Christiane B. de Araujo, Saloê Bispo, José Salvatore Leister Patané, Ariel Mariano Silber, Maria Carolina Elias, Júlia Pinheiro Chagas da Cunha
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0170540

Avian Species and Functional Diversity in Agricultural Landscapes: Does Landscape Heterogeneity Matter?
Cited by: 33
Author(s): Myung Bok Lee, James A. Martin
Software Mentions: 4
Published: over 9 years ago

10.3389/fpls.2016.01924

Transcriptome Analysis Reveals Candidate Genes Involved in Gibberellin-Induced Fruit Setting in Triploid Loquat (Eriobotrya japonica)
Cited by: 25
Author(s): Shuang Jiang, Luo Jun, Fanjie Xu, Xueying Zhang
Software Mentions: 4
Published: over 9 years ago

10.1534/g3.120.401824

A Novel Mapping Strategy Utilizing Mouse Chromosome Substitution Strains Identifies Multiple Epistatic Interactions That Regulate Complex Traits
Cited by: 3
Author(s): Anna Miller, Anlu Chen, Jacquelaine Bartlett, Li Wang, Scott M. Williams, David A. Buchner
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0237749

A systematic review of fuzzing based on machine learning techniques
Cited by: 26
Author(s): Yan Wang, Peng Jia, Luping Liu, Cheng Huang, Zhonglin Liu
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0214311

ukbtools: An R package to manage and query UK Biobank data
Cited by: 33
Author(s): Ken B. Hanscombe, Jonathan R. I. Coleman, Matthew Traylor, Cathryn M. Lewis
Software Mentions: 4
Published: about 7 years ago

10.1128/mBio.02257-16

Selective Whole-Genome Amplification Is a Robust Method That Enables Scalable Whole-Genome Sequencing of <i>Plasmodium vivax</i> from Unprocessed Clinical Samples
Cited by: 54
Author(s): Annie N. Cowell, Dorothy E. Loy, Sesh A. Sundararaman, Hugo O. Valdivia, Kathleen Fisch, Andrés G. Lescano, G. Christian Baldeviano, Salomón Durand, Vincent R. Gerbasi, Colin J. Sutherland, Debbie Nolder, Joseph M. Vinetz, Beatrice H. Hahn, Elizabeth A. Winzeler
Software Mentions: 4
Published: over 9 years ago

10.1038/s41598-020-69925-9

Comparative assessment of genetic diversity matrices and clustering methods in white Guinea yam (Dioscorea rotundata) based on morphological and molecular markers
Cited by: 27
Author(s): Kwabena Darkwa, Paterne A. Agre, Bunmi Olasanmi, Kazuo Iseki, Ryo Matsumoto, Adrian F. Powell, Guillaume Bauchet, David De Koeyer, Satoru Muranaka, Patrick Adebola, Robert Asiedu, Ryohei Terauchi, Asrat Asfaw
Software Mentions: 4
Published: about 6 years ago

10.1186/1476-072X-12-39

A cross-sectional analysis of light at night, neighborhood sociodemographics and urinary 6-sulfatoxymelatonin concentrations: implications for the conduct of health studies
Cited by: 21
Author(s): Susan Hurley, David Nelson, Erika Garcia, Robert B. Gunier, Andrew Hertz, Peggy Reynolds
Software Mentions: 4
Published: over 13 years ago

10.1186/1471-2105-15-76

Metavir 2: new tools for viral metagenome comparison and assembled virome analysis
Cited by: 185
Author(s): Simon Roux, Jérémy Tournayre, Antoine Mahul, Didier Debroas, François Enault
Software Mentions: 4
Published: over 12 years ago

10.1093/molbev/msw161

Characterization of the Poplar Pan-Genome by Genome-Wide Identification of Structural Variation
Cited by: 82
Author(s): Sara Pinosio, Stefania Giacomello, Patricia Faivre-Rampant, Gail Taylor, Véronique Jorge, Marie Christine Le Paslier, Giusi Zaina, Catherine Bastien, Federica Cattonaro, Fabio Marroni, Michèle Morgante
Software Mentions: 4
Published: about 10 years ago

10.3390/ijerph15051048

Reconciling the Entomological Hazard and Disease Risk in the Lyme Disease System
Cited by: 17
Author(s): Max McClure, Maria A. Diuk‐Wasser
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pbio.3000187

Single-cell RNA sequencing reveals regulatory mechanism for trophoblast cell-fate divergence in human peri-implantation conceptuses
Cited by: 49
Author(s): Bo Lv, Qin An, Qiao Zeng, Xunyi Zhang, Ping Lü, Yanqiu Wang, Xianmin Zhu, Yao Ji, Guoping Fan, Zhigang Xue
Software Mentions: 4
Published: almost 7 years ago

10.1155/2021/6679661

Fraudulent News Headline Detection with Attention Mechanism
Cited by: 1
Author(s): Hankun Liu, Daojing He, Sammy Chan
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-65322-4

Genomic analysis of the natural history of attention-deficit/hyperactivity disorder using Neanderthal and ancient Homo sapiens samples
Cited by: 17
Author(s): Paula Esteller-Cucala, Iago Maceda, Anders Børglum, Ditte Demontis, Stephen V. Faraone, Bru Cormand, Oscar Lao
Software Mentions: 4
Published: about 6 years ago

10.1038/s41416-021-01335-8

The amino acid metabolism is essential for evading physical plasma-induced tumour cell death
Cited by: 9
Author(s): Rajesh Kumar Gandhirajan, Dorothee Meyer, Sanjeev Kumar Sagwal, Klaus‐Dieter Weltmann, Thomas von Woedtke, Sander Bekeschus
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1005510

Good enough practices in scientific computing
Cited by: 240
Author(s): Greg Wilson, Jenny Bryan, Karen Cranston, Justin Kitzes, Alexander J. Nederbragt, Tracy K. Teal
Software Mentions: 4
Published: about 9 years ago

10.3389/fpls.2019.01346

Seed Coat Pattern QTL and Development in Cowpea (Vigna unguiculata [L.] Walp.)
Cited by: 30
Author(s): Ira A. Herniter, Ryan Lo, María Muñoz‐Amatriaín, Sassoum Lo, Yi‐Ning Guo, Bao‐Lam Huynh, Mitchell R. Lucas, Zhenyu Jia, Philip A. Roberts, Stefano Lonardi, Timothy J. Close
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0230799

The SIESTA (SEAAV Integrated evaluation sedation tool for anaesthesia) project: Initial development of a multifactorial sedation assessment tool for dogs
Cited by: 11
Author(s): Fernando Martínez-Taboada, J. I. Redondo
Software Mentions: 4
Published: over 6 years ago

10.1186/s40246-015-0042-2

Performance evaluation of indel calling tools using real short-read data
Cited by: 76
Author(s): Mohammad Shabbir Hasan, Xiaowei Wu, Liqing Zhang
Software Mentions: 4
Published: almost 11 years ago

10.3389/fonc.2021.621993

Ultrasound-Based Radiomics Analysis for Predicting Disease-Free Survival of Invasive Breast Cancer
Cited by: 21
Author(s): Lang Xiong, Haolin Chen, Xiaofeng Tang, Biyun Chen, Xinhua Jiang, Lizhi Liu, Yanqiu Feng, Longzhong Liu, Li Li
Software Mentions: 4
Published: over 5 years ago

10.1186/s13321-021-00550-y

GenUI: interactive and extensible open source software platform for de novo molecular generation and cheminformatics
Cited by: 7
Author(s): Martin Šícho, Xuhan Liu, Daniel Svozil, Gerard J. P. van Westen
Software Mentions: 4
Published: almost 5 years ago

10.1186/1471-2105-15-246

Rapid screening for phenotype-genotype associations by linear transformations of genomic evaluations
Cited by: 55
Author(s): José Luis Gualdrón Duarte, Rodolfo Juan Carlos Cantet, R. O. Bates, Catherine W. Ernst, Nancy E. Raney, Juan P. Steibel
Software Mentions: 4
Published: about 12 years ago

10.1186/1471-2105-6-216

JACOP: A simple and robust method for the automated classification of protein sequences with modular architecture
Cited by: 22
Author(s): Peter Sperisen, Marco Pagni
Software Mentions: 4
Published: almost 21 years ago

10.3390/ani11030627

Comparative Transcriptome Profile between Iberian Pig Varieties Provides New Insights into Their Distinct Fat Deposition and Fatty Acids Content
Cited by: 6
Author(s): Ana Villaplana-Velasco, J. L. Noguera, Ramona N. Pena, María Ballester, Lourdes Gaitán Muñoz, Elena González, J.F. Tejeda, Noelia Ibáñez‐Escriche
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.40292

Is it possible to reconstruct an accurate cell lineage using CRISPR recorders?
Cited by: 62
Author(s): Irepan Salvador-Martínez, Marco Grillo, Michalis Averof, Maximilian J. Telford
Software Mentions: 4
Published: over 7 years ago

10.1097/MD.0000000000016829

The effectiveness of moxibustion for stable angina pectoris
Cited by: 0
Author(s): Yili Zhang, Yuan Li, Juan Wang, Nannan Tan, Junjie Liu, Kangjia Du, Miao Zhang, Yong Wang, Huihui Zhao, Wei Wang
Software Mentions: 4
Published: about 7 years ago

10.1186/s13059-021-02364-5

scSNV: accurate dscRNA-seq SNV co-expression analysis using duplicate tag collapsing
Cited by: 6
Author(s): Gavin Wilson, Mathieu Derouet, Gail Darling, Jonathan C. Yeung
Software Mentions: 4
Published: over 5 years ago

10.3390/diagnostics10121113

Deep Learning Assisted Localization of Polycystic Kidney on Contrast-Enhanced CT Images
Cited by: 15
Author(s): Djeane Debora Onthoni, Ting-Wen Sheng, Prasan Kumar Sahoo, Li-Jen Wang, Pushpanjali Gupta
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-45236-6

In-silico Prediction of Synergistic Anti-Cancer Drug Combinations Using Multi-omics Data
Cited by: 55
Author(s): Remzi Çelebi, Oliver Bear Don't Walk, Rajiv Movva, Semih Alpsoy, Michel Dumontier
Software Mentions: 4
Published: about 7 years ago

10.3390/jcm8081158

Role of MYC-miR-29-B7-H3 in Medulloblastoma Growth and Angiogenesis
Cited by: 29
Author(s): Ian J. Purvis, Avilala Janardhan, Maheedhara R. Guda, Sujatha Venkataraman, Rajeev Vibhakar, Andrew J. Tsung, Kiran Kumar Velpula, Swapna Asuthkar
Software Mentions: 4
Published: about 7 years ago

10.18632/aging.202365

Transcriptomic characterization reveals prognostic molecular signatures of sorafenib resistance in hepatocellular carcinoma
Cited by: 7
Author(s): Wei Yuan, Ran Tao, Da Huang, Weiming Yan, Shen Gao, Qin Ning
Software Mentions: 4
Published: over 5 years ago

10.1038/s41437-018-0177-8

MHC class I diversity predicts non-random mating in Chinese alligators (Alligator sinensis)
Cited by: 8
Author(s): Quan Han, Ru-Na Sun, Hai-Qiong Yang, Zhenwei Wang, Qiu‐Hong Wan, Sheng‐Guo Fang
Software Mentions: 4
Published: over 7 years ago

10.3390/cancers12102918

Time-Resolved Profiling Reveals ATF3 as a Novel Mediator of Endocrine Resistance in Breast Cancer
Cited by: 8
Author(s): Simone Borgoni, Emre Sofyalı, Maryam Soleimani, Heike Wilhelm, Karin Müller‐Decker, Rainer Will, Ashish Noronha, Lukas Beumers, Pernette J. Verschure, Yosef Yarden, Luca Magnani, Antoine H. C. van Kampen, Perry D. Moerland, Stefan Wiemann
Software Mentions: 4
Published: almost 6 years ago

10.1186/s13007-021-00747-0

Maize-IAS: a maize image analysis software using deep learning for high-throughput plant phenotyping
Cited by: 17
Author(s): Shuo Zhou, Xiujuan Chai, Zixuan Yang, Hongwu Wang, Chenxue Yang, Tan Sun
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2021.693608

Single-Cell RNA Sequencing Reveals the Immunological Profiles of Renal Allograft Rejection in Mice
Cited by: 11
Author(s): Qixia Shen, Yucheng Wang, Jiaoyi Chen, Lifeng Ma, Xiao‐Ru Huang, Sydney C. W. Tang, Hui‐Yao Lan, Hong Jiang, Jianghua Chen
Software Mentions: 4
Published: about 5 years ago

10.1186/s12859-019-2781-x

Computational enhancer prediction: evaluation and improvements
Cited by: 10
Author(s): Hasiba Asma, Marc S. Halfon
Software Mentions: 4
Published: over 7 years ago

10.3389/frai.2021.711467

DICE: A Drug Indication Classification and Encyclopedia for AI-Based Indication Extraction
Cited by: 2
Author(s): Arjun Bhatt, Ruth Roberts, Xi Chen, Ting Li, Skylar Connor, Qais Hatim, Mike Mikailov, Weida Tong, Zhichao Liu
Software Mentions: 4
Published: about 5 years ago

10.2196/16117

Predicting Adverse Outcomes for Febrile Patients in the Emergency Department Using Sparse Laboratory Data: Development of a Time Adaptive Model
Cited by: 3
Author(s): Sungjoo Lee, Sungchul Hong, Won Chul, Kyunga Kim
Software Mentions: 4
Published: over 6 years ago

10.7717/peerj-cs.353

Joint embedding VQA model based on dynamic word vector
Cited by: 116
Author(s): Zhiyang Ma, Wenfeng Zheng, Xiaobing Chen, Lirong Yin
Software Mentions: 4
Published: over 5 years ago

10.3390/metabo11070441

Hyperpolarized Dihydroxyacetone Is a Sensitive Probe of Hepatic Gluconeogenic State
Cited by: 7
Author(s): Mukundan Ragavan, Marc McLeod, Anthony Giacalone, Matthew E. Merritt
Software Mentions: 4
Published: about 5 years ago

10.1186/1471-2431-13-152

The swiss neonatal quality cycle, a monitor for clinical performance and tool for quality improvement
Cited by: 6
Author(s): Mark Adams, Tjade Claus Hoehre, Hans Ulrich Bucher
Software Mentions: 4
Published: almost 13 years ago

10.18632/aging.202258

Therapeutic potential of targeting HSPA5 through dual regulation of two candidate prognostic biomarkers ANXA1 and PSAT1 in osteosarcoma
Cited by: 6
Author(s): Xiaojun Tang, Lingli Luo, Yukun Li, Hailong Wu, Qing Hu, Haiyan Yue, Xueling He, Juan Zou, Shaoxiong Min
Software Mentions: 4
Published: over 5 years ago

10.1186/s40168-020-00909-7

Hill-based dissimilarity indices and null models for analysis of microbial community assembly
Cited by: 21
Author(s): Oskar Modin, Raquel Liébana, Soroush Saheb-Alam, Britt‐Marie Wilén, Carolina Suarez, Malte Hermansson, Frank Persson
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12859-020-03682-4

NEDD: a network embedding based method for predicting drug-disease associations
Cited by: 22
Author(s): Renyi Zhou, Zhangli Lu, Huimin Luo, Xu Ju, Min Zeng, Min Li
Software Mentions: 4
Published: almost 6 years ago

10.1186/1471-2105-15-180

PBHoney: identifying genomic variants via long-read discordance and interrupted mapping
Cited by: 135
Author(s): Adam C. English, William Salerno, Jeffrey G. Reid
Software Mentions: 4
Published: about 12 years ago

10.1371/journal.pgen.1002658

Dynamic Deposition of Histone Variant H3.3 Accompanies Developmental Remodeling of the Arabidopsis Transcriptome
Cited by: 113
Author(s): Heike Wollmann, Sarah Holec, Keith Alden, Neil D. Clarke, Pierre-Étienne Jacques, Frédéric Berger
Software Mentions: 4
Published: over 14 years ago

10.1371/journal.pone.0220976

Word2vec convolutional neural networks for classification of news articles and tweets
Cited by: 95
Author(s): Beakcheol Jang, In-Hwan Kim, Jong Wook Kim
Software Mentions: 4
Published: almost 7 years ago

10.7554/eLife.62207

Thalamus and claustrum control parallel layer 1 circuits in retrosplenial cortex
Cited by: 21
Author(s): Ellen Brennan, Izabela Jedrasiak‐Cape, Sameer Kailasa, Sharena P Rice, S Sudhakar, Omar J. Ahmed
Software Mentions: 4
Published: about 5 years ago