cran: ggplot2 | Projects | Ecosyste.ms: Papers

10.1038/s41598-021-94329-8

Combined detection of peripheral blood VEGF and inflammation biomarkers to evaluate the clinical response and prognostic prediction of non-operative ESCC
Cited by: 4
Author(s): Yuanyuan Ma, Xinyu Su, Xin Li, Xiaohui Zhi, Kan Jiang, Jianhong Xia, Hongliang Li, Yan Chen, Lixin Zhou
Software Mentions: 10
Published: over 3 years ago

10.1186/s12864-015-2356-9

QuickRNASeq lifts large-scale RNA-seq data analyses to the next level of automation and interactive visualization
Cited by: 33
Author(s): Shanrong Zhao, Li Xi, Jie Quan, Hualin Simon Xi, Ying Zhang, David von Schack, Michael S. Vincent, Baohong Zhang
Software Mentions: 10
Published: almost 9 years ago

10.1371/journal.pone.0209331

Rethomics: An R framework to analyse high-throughput behavioural data
Cited by: 66
Author(s): Quentin Geissmann, Luis García Rodríguez, Esteban J. Beckwith, Giorgio F. Gilestro
Software Mentions: 10
Published: almost 6 years ago

10.1093/gigascience/giaa060

SnpHub: an easy-to-set-up web server framework for exploring large-scale genomic variation data in the post-genomic era with applications in wheat
Cited by: 35
Author(s): Wenxi Wang, Zihao Wang, Xintong Li, Zhongfu Ni, Zhaorong Hu, Mingming Xin, Huiru Peng, Yingyin Yao, Qixin Sun, Weilong Guo
Software Mentions: 10
Published: over 4 years ago

10.1186/s12864-015-2250-5

Leveraging global gene expression patterns to predict expression of unmeasured genes
Cited by: 3
Author(s): James Rudd, René A. Zelaya, Eugene Demidenko, Ellen L. Goode, Casey S. Greene, Jennifer A. Doherty
Software Mentions: 10
Published: almost 9 years ago

10.1155/2017/7457131

NFP: An R Package for Characterizing and Comparing of Annotated Biological Networks
Cited by: 0
Author(s): Yang Cao, Wenjian Xu, Chao Niu, Xiaochen Bo, Fēi Li
Software Mentions: 10
Published: almost 8 years ago

10.1038/s41598-021-89904-y

Feasibility of predicting allele specific expression from DNA sequencing using machine learning
Cited by: 5
Author(s): Zhenhua Zhang, Freerk van Dijk, Nigel Klein, Mariëlle van Gijn, Lude Franke, Richard J. Sinke, Morris A. Swertz, K. Joeri van der Velde
Software Mentions: 10
Published: over 3 years ago

10.1038/s41598-020-78228-y

Gastrointestinal adenocarcinoma analysis identifies promoter methylation-based cancer subtypes and signatures
Cited by: 7
Author(s): Renshen Xiang, Tao Fu
Software Mentions: 10
Published: almost 4 years ago

10.1007/s00253-021-11449-x

Assessment of Biolog EcoplateTM method for functional metabolic diversity of aerotolerant pig fecal microbiota
Cited by: 6
Author(s): Alice Checcucci, Diana Luise, Monica Marianna Modesto, Federico Correa, Paolo Bosi, Paola Mattarelli, Paolo Trevisi
Software Mentions: 10
Published: over 3 years ago

10.3389/fimmu.2021.622563

9-Gene Signature Correlated With CD8+ T Cell Infiltration Activated by IFN-γ: A Biomarker of Immune Checkpoint Therapy Response in Melanoma
Cited by: 17
Author(s): Kexin Yan, Yuxiu Lu, Zhangyong Yan, Yutao Wang
Software Mentions: 10
Published: over 3 years ago

10.1038/s41598-020-76103-4

Phenotypic variation, functional traits repeatability and core collection inference in Synsepalum dulcificum (Schumach & Thonn.) Daniell reveals the Dahomey Gap as a centre of diversity
Cited by: 3
Author(s): Dèdéou Apocalypse Tchokponhoué, Enoch G. Achigan‐Dako, Sognigbé N’Danikou, Daniel Nyadanu, Rémi Kahane, Jacob S Houéto, V.N. Fassinou Hotegni, Alfred Odindo, Julia Sibiya
Software Mentions: 10
Published: about 4 years ago

10.1038/s41598-020-74909-w

Multi-strain volatile profiling of pathogenic and commensal cutaneous bacteria
Cited by: 19
Author(s): Shane Fitzgerald, Emer Duffy, Linda Holland, Aoife Morrin
Software Mentions: 10
Published: about 4 years ago

10.1186/s12916-020-01595-w

Serum metabolite profiles are associated with the presence of advanced liver fibrosis in Chinese patients with chronic hepatitis B viral infection
Cited by: 30
Author(s): Guoxiang Xie, Xiaoning Wang, Runmin Wei, Jingye Wang, Aihua Zhao, Tianlu Chen, Yixing Wang, Hua Zhang, Zhun Xiao, Xin-Zhu Liu, Youping Deng, Linda L. Wong, Cynthia Rajani, Sandi A. Kwee, Hua Bian, Xin Gao, Ping Liu, Jia Wang
Software Mentions: 10
Published: over 4 years ago

10.7717/peerj.7907

motoRneuron: an open-source R toolbox for time-domain motor unit analyses
Cited by: 0
Author(s): Andrew J. Tweedell, Matthew S. Tenan
Software Mentions: 10
Published: almost 5 years ago

10.1371/journal.pone.0215142

Mathematical modeling for the prediction of cerebral white matter lesions based on clinical examination data
Cited by: 7
Author(s): Yuya Shinkawa, Takashi Yoshida, Yohei Onaka, Makoto Ichinose, Kazuo Ishii
Software Mentions: 10
Published: over 5 years ago

10.3389/fimmu.2021.641495

Mitochondrial Reactive Oxygen Species Regulate Immune Responses of Macrophages to Aspergillus fumigatus
Cited by: 15
Author(s): Rémi Hatinguais, Arnab Pradhan, Gordon D. Brown, Alistair J. P. Brown, Adilia Warris, Elena Shekhova
Software Mentions: 10
Published: over 3 years ago

10.3389/fimmu.2016.00372

SONAR: A High-Throughput Pipeline for Inferring Antibody Ontogenies from Longitudinal Sequencing of B Cell Transcripts
Cited by: 52
Author(s): Chaim A. Schramm, Zizhang Sheng, Zhenhai Zhang, John R. Mascola, Peter D. Kwong, Lawrence Shapiro
Software Mentions: 10
Published: about 8 years ago

10.1038/s41598-020-62453-6

Patterns of Rift Valley fever virus seropositivity in domestic ruminants in central South Africa four years after a large outbreak
Cited by: 19
Author(s): Yusuf B. Ngoshe, Alida Avenant, Melinda K. Rostal, William B. Karesh, Janusz T. Pawęska, Whitney Bagge, Petrus Jansen van Vuren, Alan C. Kemp, Claudia Cordel, Veerle Msimang, Peter N. Thompson
Software Mentions: 10
Published: over 4 years ago

10.1186/s13073-020-0710-2

Interactions between the gut microbiome and host gene regulation in cystic fibrosis
Cited by: 65
Author(s): Gargi Dayama, Sambhawa Priya, David Niccum, Alexander Khoruts, Ran Blekhman
Software Mentions: 10
Published: almost 5 years ago

10.7717/peerj.10118

High-throughput analysis of adaptation using barcoded strains ofSaccharomyces cerevisiae
Cited by: 8
Author(s): Vincent J. Fasanello, Ping Liu, Carlos A. Botero, Justin C. Fay
Software Mentions: 10
Published: about 4 years ago

10.1371/journal.pone.0114749

FindFoci: A Focus Detection Algorithm with Automated Parameter Training That Closely Matches Human Assignments, Reduces Human Inconsistencies and Increases Speed of Analysis
Cited by: 88
Author(s): Alex Herbert, Antony Carr, Eva R. Hoffmann
Software Mentions: 10
Published: almost 10 years ago

10.3389/fimmu.2021.602539

Single-Cell Transcriptomic Analyses Define Distinct Peripheral B Cell Subsets and Discrete Development Pathways
Cited by: 60
Author(s): Alexander Stewart, Joseph C.F. Ng, Gillian A. Wallis, Vasiliki Tsioligka, Franca Fraternali, Deborah K. Dunn‐Walters
Software Mentions: 10
Published: over 3 years ago

10.1038/s41422-021-00467-z

Dissecting human embryonic skeletal stem cell ontogeny by single-cell transcriptomic and functional analyses
Cited by: 44
Author(s): Jian He, Yan Jing, Jianfang Wang, Liangyu Zhao, Xin Qian, Yang Zeng, Yuxi Sun, Han Zhang, Zhijie Bai, Zongcheng Li, Yanli Ni, Yandong Gong, Yunqiao Li, Han He, Zhilei Bian, Yu Lan, Chunyu Ma, Lihong Bian, Heng Zhu, Bing Liu, Rui Yue
Software Mentions: 10
Published: almost 4 years ago

10.1038/s41598-020-65160-4

Influence of climate variation on phenolic composition and antioxidant capacity of Medicago minima populations
Cited by: 45
Author(s): Souhir Kabtni, Dorra Sdouga, Ines Bettaib Rebey, Mattew Save, Neïla Trifi-Farah, Marie‐Laure Fauconnier, Sonia Marghali
Software Mentions: 10
Published: over 4 years ago

10.1002/cam4.4117

A comprehensive analysis of immune infiltration in the tumor microenvironment of osteosarcoma
Cited by: 17
Author(s): Hao Yang, Liang Zhao, Yang Zhang, Fangfang Li
Software Mentions: 10
Published: over 3 years ago

10.3389/fmicb.2020.00037

FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies
Cited by: 164
Author(s): Arkadiy I. Garber, Kenneth H. Nealson, Akimitsu Okamoto, Sean M. McAllister, Clara S. Chan, Roman A. Barco, Nancy Merino
Software Mentions: 10
Published: almost 5 years ago

10.1186/s13059-018-1432-2

FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer–promoter map
Cited by: 57
Author(s): Tom Aharon Hait, David Amar, Ron Shamir, Ran Elkon
Software Mentions: 10
Published: over 6 years ago

10.1111/pbi.13299

Learning from methylomes: epigenomic correlates ofPopulus balsamiferatraits based on deep learning models of natural DNA methylation
Cited by: 9
Author(s): Marc J. Champigny, Faride Unda, Oleksandr Skyba, Raju Soolanayakanahally, Shawn D. Mansfield, Malcolm M. Campbell
Software Mentions: 10
Published: almost 5 years ago

10.3389/fneur.2021.683051

An Externally Validated Dynamic Nomogram for Predicting Unfavorable Prognosis in Patients With Aneurysmal Subarachnoid Hemorrhage
Cited by: 8
Author(s): Ping Hu, Yang Xu, Yangfan Liu, Yuntao Li, Liguo Ye, Si Zhang, Xinyi Zhu, Yangzhi Qi, Huikai Zhang, Qian Sun, Yixuan Wang, Gang Deng, Qianxue Chen
Software Mentions: 10
Published: over 3 years ago

10.1186/s12918-015-0169-8

Increased robustness of early embryogenesis through collective decision-making by key transcription factors
Cited by: 8
Author(s): Ali Sharifi-Zarchi, Mehdi Totonchi, Keynoush Khaloughi, Razieh Karamzadeh, Marcos J. Araúzo-Bravo, Hossein Baharvand, Ruzbeh Tusserkani, Hamid Pezeshk, Hamidreza Chitsaz, Mehdi Sadeghi
Software Mentions: 10
Published: over 9 years ago

10.3389/fmolb.2021.692530

Ferroptosis-Related Gene Signature and Patterns of Immune Infiltration Predict the Overall Survival in Patients With Lung Adenocarcinoma
Cited by: 5
Author(s): Yuxuan Wang, Weikang Chen, Minqi Zhu, Lei Xian
Software Mentions: 10
Published: over 3 years ago

10.1172/jci.insight.138970

Hypoxia acts as an environmental cue for the human tissue-resident memory T cell differentiation program
Cited by: 21
Author(s): Farah Hasan, Yulun Chiu, Rebecca Shaw, Junmei Wang, Cassian Yee
Software Mentions: 10
Published: over 3 years ago

10.3390/ijms21051754

MiR&moRe2: A Bioinformatics Tool to Characterize microRNAs and microRNA-Offset RNAs from Small RNA-Seq Data
Cited by: 10
Author(s): Enrico Gaffo, Michele Bortolomeazzi, Andrea Bisognin, Piero Di Battista, Federica Lovisa, Lara Mussolin, Stefania Bortoluzzi
Software Mentions: 10
Published: over 4 years ago

10.3389/pore.2021.594649

Bcl-2 Associated Athanogene 2 (BAG2) is Associated With Progression and Prognosis of Hepatocellular Carcinoma: A Bioinformatics-Based Analysis
Cited by: 7
Author(s): Xi Zhang, Junjun Zhang, Yang Liu, Jie Li, Juan Tan, Zewen Song
Software Mentions: 10
Published: over 3 years ago

10.1038/s41598-020-72369-w

Connectivity and population structure of albacore tuna across southeast Atlantic and southwest Indian Oceans inferred from multidisciplinary methodology
Cited by: 10
Author(s): Natacha Nikolic, Iratxe Montes, Maxime Lalire, Alexis Puech, Nathalie Bodin, Sophie Arnaud‐Haond, Sven E. Kerwath, Emmanuel Corse, Philippe Gaspar, Stéphanie Hollanda, Jérôme Bourjea, Wendy West, Sylvain Bonhommeau
Software Mentions: 10
Published: about 4 years ago

10.3389/fgene.2021.682475

Genomic and Chemical Diversity of Commercially Available High-CBD Industrial Hemp Accessions
Cited by: 10
Author(s): Matthew Johnson, Jason Wallace
Software Mentions: 10
Published: over 3 years ago

10.3390/cancers13133371

Meta-Analysis of Microdissected Breast Tumors Reveals Genes Regulated in the Stroma but Hidden in Bulk Analysis
Cited by: 7
Author(s): Aurora Savino, Niccolò De Marzo, Paolo Provero, Valeria Poli
Software Mentions: 10
Published: over 3 years ago

10.7717/peerj.11222

The postcranial skeleton of Cerrejonisuchus improcerus (Crocodyliformes: Dyrosauridae) and the unusual anatomy of dyrosaurids
Cited by: 1
Author(s): Isaure Scavezzoni, Valentin Fischer
Software Mentions: 10
Published: over 3 years ago

10.1007/s00228-020-03052-2

Potentially inappropriate prescribing in older hospitalized Dutch patients according to the STOPP/START criteria v2: a longitudinal study
Cited by: 9
Author(s): Birgit A. Damoiseaux-Volman, Stephanie Medlock, Kimmy Raven, Danielle Sent, Johannes A. Romijn, Nathalie van der Velde, Ameen Abu‐Hanna
Software Mentions: 10
Published: almost 4 years ago

10.1038/s41598-021-96236-4

A novel prognostic signature of immune-related lncRNA pairs in lung adenocarcinoma
Cited by: 5
Author(s): Yang Liu, Qiuhong Wu, Xuejiao Fan, Wen Li, Yong Li, Hui Zhu, Qinghua Zhou, Jinming Yu
Software Mentions: 10
Published: over 3 years ago

10.1038/s41598-019-46168-x

Cytotoxic unsaturated electrophilic compounds commonly target the ubiquitin proteasome system
Cited by: 16
Author(s): Karthik Selvaraju, Arjan Mofers, Paola Pellegrini, Johannes Salomonsson, Alexandra Ahlner, Vivian Morad, Ellin-Kristina Hillert, Belén Espinosa, Elias S.J. Arnér, Lasse Jensen, Jonas Malmström, Maria V. Turkina, Pádraig D’Arcy, Michael A. Walters, Maria Sunnerhagen, Stig Linder
Software Mentions: 10
Published: over 5 years ago

10.1186/s13059-014-0413-3

A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription factors are positive regulators
Cited by: 19
Author(s): Laurence D. Hurst, Oxana Sachenkova, Carsten O. Daub, Alistair R.R. Forrest, Łukasz Huminiecki
Software Mentions: 10
Published: over 10 years ago

10.1186/s13059-019-1647-x

Dynamic inosinome profiles reveal novel patient stratification and gender-specific differences in glioblastoma
Cited by: 48
Author(s): Domenico Alessandro Silvestris, Ernesto Picardi, Valeriana Cesarini, Bruno Fosso, Nicolò Mangraviti, Luca Massimi, Maurizio Martini, Graziano Pesole, Franco Locatelli, Angela Gallo
Software Mentions: 10
Published: almost 6 years ago

10.1038/s41396-020-00862-1

Fungal sporocarps house diverse and host-specific communities of fungicolous fungi
Cited by: 21
Author(s): Sundy Maurice, Gontran Arnault, Jenni Nordén, Synnøve Smebye Botnen, Otto Miettinen, Håvard Kauserud
Software Mentions: 10
Published: almost 4 years ago

10.1038/s41598-017-09303-0

The impact of immigration on microbial community composition in full-scale anaerobic digesters
Cited by: 111
Author(s): Rasmus Hansen Kirkegaard, Simon Jon McIlroy, Jannie Munk Kristensen, Marta Nierychlo, Søren Michael Karst, Morten Simonsen Dueholm, Mads Albertsen, Per Halkjær Nielsen
Software Mentions: 10
Published: over 7 years ago

10.1242/dev.193060

Extensive nuclear gyration and pervasive non-genic transcription during primordial germ cell development in zebrafish
Cited by: 4
Author(s): Stefan Redl, António Miguel de Jesus Domingues, Edoardo Caspani, Stefanie Möckel, Willi Salvenmoser, María Méndez-Lago, René F. Ketting
Software Mentions: 10
Published: almost 5 years ago

10.1172/jci.insight.147535

The relationship between cytokine and neutrophil gene network distinguishes SARS-CoV-2–infected patients by sex and age
Cited by: 12
Author(s): Paula Paccielli Freire, Amélia Pasqual Marques, G. Baiocchi, Lena F. Schimke, Dennyson Leandro M. Fonseca, Ranieri Coelho Salgado, Igor Salerno Filgueiras, Sarah M.S. Napoleao, Desirée Rodrigues Plaça, Karen Tiemi Akashi, Thiago Dominguez Crespo Hirata, Nadia El Khawanky, Lasse Melvær Giil, Gustavo Cabral-Miranda, Robson Francisco Carvalho, Luís Carlos S. Ferreira, Antônio Condino‐Neto, Helder I. Nakaya, Igor Jurišica, Hans D. Ochs, Niels Olsen Saraiva Câmara, Vera Lúcia Garcia Calich, Otávio Cabral-Marques
Software Mentions: 10
Published: over 3 years ago

10.1371/journal.pone.0216723

A metadata approach to evaluate the state of ocean knowledge: Strengths, limitations, and application to Mexico
Cited by: 10
Author(s): Juliano Palacios‐Abrantes, Andrés M. Cisneros‐Montemayor, Miguel Á. Cisneros-Mata, Laura Rodríguez, Francisco Arreguı́n-Sánchez, Verónica Aguilar, Santiago Domínguez-Sánchez, Stuart Fulton, Raquel López-Sagástegui, Héctor Reyes‐Bonilla, Rocío Rivera-Campos, Silvia Salas, Nuno Simões, William W. L. Cheung
Software Mentions: 10
Published: over 5 years ago

10.3389/fmicb.2020.597745

Impact of Long-Term Organic and Mineral Fertilization on Rhizosphere Metabolites, Root–Microbial Interactions and Plant Health of Lettuce
Cited by: 15
Author(s): Saskia Windisch, Loreen Sommermann, Doreen Babin, Soumitra Paul Chowdhury, Rita Grosch, Narges Moradtalab, Frank Walker, Birgit Höglinger, Abbas El‐Hasan, Wolfgang Armbruster, Joseph Nesme, Søren J. Sørensen, Ingo Schellenberg, Joerg Geistlinger, Kornelia Smalla, Michael Rothballer, Uwe Ludewig, Günter Neumann
Software Mentions: 10
Published: almost 4 years ago

10.1093/gbe/evz003

Repeated Evolution Versus Common Ancestry: Sex Chromosome Evolution in the Haplochromine CichlidPseudocrenilabrus philander
Cited by: 25
Author(s): Astrid Böhne, Alexandra Anh‐Thu Weber, Jelena Rajkov, Michael Rechsteiner, Andrin Riss, Bernhard Egger, Walter Salzburger
Software Mentions: 10
Published: almost 6 years ago

10.1186/s13059-021-02484-y

Revisiting genetic artifacts on DNA methylation microarrays exposes novel biological implications
Cited by: 5
Author(s): Benjamin Planterose Jiménez, Manfred Kayser, Athina Vidaki
Software Mentions: 10
Published: about 3 years ago

10.3389/fgene.2020.00260

IntAssoPlot: An R Package for Integrated Visualization of Genome-Wide Association Study Results With Gene Structure and Linkage Disequilibrium Matrix
Cited by: 20
Author(s): Fengyu He, Shuangcheng Ding, Hongwei Wang, Feng Qin
Software Mentions: 10
Published: over 4 years ago

10.3390/ijms22083975

Mapping Astrocyte Transcriptional Signatures in Response to Neuroactive Compounds
Cited by: 11
Author(s): Debosmita Sardar, Brittney Lozzi, Junsung Woo, Teng-Wei Huang, Caroline Cvetkovic, Chad J. Creighton, Robert Krencik, Benjamin Deneen
Software Mentions: 10
Published: over 3 years ago

10.3390/cancers13020230

A Set of Cell Lines Derived from a Genetic Murine Glioblastoma Model Recapitulates Molecular and Morphological Characteristics of Human Tumors
Cited by: 10
Author(s): Bárbara Costa, Michael Fletcher, Pavle Boskovic, Ekaterina Ivanova, Tanja Eisemann, Sabrina Lohr, Lukas Bunse, Martin Löwer, Stefanie Burchard, Andrey Korshunov, Nadia Coltella, Melania Cusimano, Luigi Naldini, Hai-Kun Liu, Michael Platten, Bernhard Radlwimmer, Peter Angel, Heike Peterziel
Software Mentions: 10
Published: almost 4 years ago

10.1172/jci.insight.145854

Cell-autonomous retinoic acid receptor signaling has stage-specific effects on mouse enteric nervous system
Cited by: 6
Author(s): Tao Gao, Elizabeth C. Wright-Jin, Rajarshi Sengupta, Jessica B. Anderson, Robert O. Heuckeroth
Software Mentions: 10
Published: over 3 years ago

10.1186/s12940-021-00693-3

Examining the role of wind in human illness due to pesticide drift in Washington state, 2000–2015
Cited by: 3
Author(s): Edward J. Kasner, Joanne Bonnar Prado, Michael G. Yost, Richard A. Fenske
Software Mentions: 10
Published: over 3 years ago

10.1128/mSystems.00571-21

Pathogenic Vibrio Species Are Associated with Distinct Environmental Niches and Planktonic Taxa in Southern California (USA) Aquatic Microbiomes
Cited by: 11
Author(s): Rachel E. Diner, Drishti Kaul, Ariel Rabines, Hong Zheng, Joshua A. Steele, John F. Griffith, Andrew E. Allen
Software Mentions: 10
Published: about 3 years ago

10.1186/s13071-020-04319-4

Retrospective analysis of feline intestinal parasites: trends in testing positivity by age, USA geographical region and reason for veterinary visit
Cited by: 7
Author(s): Sarah Sweet, Donald Szlosek, Donald J. McCrann, Michael J. Coyne, David Kincaid, Evan Hegarty
Software Mentions: 10
Published: about 4 years ago

10.3389/fgene.2018.00461

TEsmall Identifies Small RNAs Associated With Targeted Inhibitor Resistance in Melanoma
Cited by: 4
Author(s): Kathryn O’Neill, Wen‐Wei Liao, Asmita Patel, Molly Gale Hammell
Software Mentions: 10
Published: about 6 years ago

10.3389/fpls.2020.00136

The Bacterial Microbiome of Meloidogyne-Based Disease Complex in Coffee and Tomato
Cited by: 17
Author(s): Araceli Lamelas, Damaris Desgarennes, Daniel López-Lima, Luc Villain, Alexandro Alonso-Sánchez, Alejandro Artacho, Amparo Latorre, Andrés Moya, Gloria Carrión
Software Mentions: 10
Published: over 4 years ago

10.1038/s41598-020-70722-7

Active and social life is associated with lower non-social fearfulness in pet dogs
Cited by: 15
Author(s): Emma Hakanen, Salla Mikkola, Milla Salonen, Jenni Puurunen, Sini Sulkama, Cynthia Gobbi Alves Araújo, Hannes Lohi
Software Mentions: 10
Published: over 4 years ago

10.3390/ijerph17218164

Differences in the Estimation of Wildfire-Associated Air Pollution by Satellite Mapping of Smoke Plumes and Ground-Level Monitoring
Cited by: 9
Author(s): Raj P. Fadadu, John R. Balmes, Stephanie M. Holm
Software Mentions: 10
Published: about 4 years ago

10.1038/s41396-020-00777-x

A network approach to elucidate and prioritize microbial dark matter in microbial communities
Cited by: 71
Author(s): Tatyana Zamkovaya, Jamie S. Foster, Valérie de Crécy‐Lagard, Ana Conesa
Software Mentions: 10
Published: about 4 years ago

10.3390/ijms22031190

Genome-Wide DNA Methylation Analysis of a Cohort of 41 Patients Affected by Oculo-Auriculo-Vertebral Spectrum (OAVS)
Cited by: 12
Author(s): Valentina Guida, Luciano Calzari, Maria Teresa Fadda, Francesca Piceci‐Sparascio, María Cristina Digilio, Laura Bernardini, Francesco Brancati, Teresa Mattina, Daniela Melis, Francesca Forzano, Silvana Briuglia, Tommaso Mazza, Sebastiano Bianca, Enza Maria Valente, Leila Bagherjad Salehi, Paolo Prontera, Mario Pagnoni, Romano Tenconi, Bruno Dallapiccola, Giorgio Iannetti, Luigi Corsaro, Alessandro De Luca, Davide Gentilini
Software Mentions: 10
Published: almost 4 years ago

10.1038/s41598-017-05505-8

Machine Learning Algorithms for Risk Prediction of Severe Hand-Foot-Mouth Disease in Children
Cited by: 15
Author(s): Bin Zhang, Xiang Wan, Fu Ouyang, Yu Dong, Dehui Luo, Jing Liu, Long Liang, Wen Bo Chen, Xiao Luo, Xiao Mo, Lu Zhang, Wen Hui Huang, Shu Fang Pei, Bao Liang Guo, Chun Liang, Long Zhou, Shui Xing Zhang
Software Mentions: 10
Published: over 7 years ago

10.1186/s40360-021-00505-x

Causal inference multiple imputation investigation of the impact of cannabinoids and other substances on ethnic differentials in US testicular cancer incidence
Cited by: 26
Author(s): Albert Stuart Reece, Gary Kenneth Hulse
Software Mentions: 10
Published: over 3 years ago

10.1038/srep43932

Implications of the cattle trade network in Cameroon for regional disease prevention and control
Cited by: 60
Author(s): Paolo Carlo Motta, Thibaud Porphyre, Ian Handel, Saidou M. Hamman, Victor Ngu Ngwa, Vincent N. Tanya, K. L. Morgan, Rob Christley, Barend M. deC. Bronsvoort
Software Mentions: 10
Published: over 7 years ago

10.1097/MD.0000000000026068

MiRNA-based model for predicting the TMB level in colon adenocarcinoma based on a LASSO logistic regression method
Cited by: 1
Author(s): Zhengtian Li, Lingling Jiang, Rong Zhao, Jun Huang, Weibo Yang, Zhenpei Wen, Bo Zhang, Gang Du
Software Mentions: 10
Published: over 3 years ago

10.1038/s41598-020-71663-x

Discovering the indigenous microbial communities associated with the natural fermentation of sap from the cider gum Eucalyptus gunnii
Cited by: 12
Author(s): Cristián Varela, Joanna F. Sundstrom, Kathleen Cuijvers, Vladimir Jiranek, Anthony R. Borneman
Software Mentions: 10
Published: about 4 years ago

10.1017/S0950268820000746

Risk of bacteremia in patients presenting with shaking chills and vomiting - a prospective cohort study
Cited by: 2
Author(s): Madlene Holmqvist, Malin Inghammar, Lisa I. Påhlman, John H. Boyd, Per Åkesson, Adam Linder, Fredrik Kahn
Software Mentions: 10
Published: almost 5 years ago

10.3389/fgene.2019.00279

Integrative Differential Expression Analysis for Multiple EXperiments (IDEAMEX): A Web Server Tool for Integrated RNA-Seq Data Analysis
Cited by: 46
Author(s): Verónica Jiménez-Jacinto, Alejandro Sánchez-Flores, Leticia Vega‐Alvarado
Software Mentions: 10
Published: over 5 years ago

10.1111/jcmm.16619

Systematic profiling of invasion‐related gene signature predicts prognostic features of lung adenocarcinoma
Cited by: 17
Author(s): Ping Yu, L. Tong, Yujia Song, Hui Qü, Ying Chen
Software Mentions: 10
Published: over 3 years ago

10.1128/mSystems.00541-20

Evidence for Succession and Putative Metabolic Roles of Fungi and Bacteria in the Farming Mutualism of the Ambrosia Beetle Xyleborus affinis
Cited by: 17
Author(s): Luis A. Ibarra-Juárez, Maureen Burton, Peter H. W. Biedermann, Luisa F. Cruz, Damaris Desgarennes, Enrique Ibarra-Laclette, Amparo Latorre, Alexandro Alonso-Sánchez, Emanuel Villafán, Greta Hanako-Rosas, Loredana Lopez, Mirna Vázquez-Rosas-Landa, Gloria Carrión, Daniel Carrillo, Andrés Moya, Araceli Lamelas
Software Mentions: 10
Published: about 4 years ago

10.1038/s41598-019-45491-7

The future of coffee and cocoa agroforestry in a warmer Mesoamerica
Cited by: 58
Author(s): Kauê de Sousa, Maarten van Zonneveld, Milena Holmgren, Roeland Kindt, Jenny C. Ordóñez
Software Mentions: 10
Published: over 5 years ago

10.1111/jcmm.15848

m6A RNA methylation regulators could contribute to the occurrence of chronic obstructive pulmonary disease
Cited by: 43
Author(s): Xinwei Huang, Dongjin Lv, Yao Xiao, Min Li, Hong Zhang
Software Mentions: 10
Published: about 4 years ago

10.1093/database/bay033

The tragedy of the biodiversity data commons: a data impediment creeping nigher?
Cited by: 11
Author(s): Nora Escribano, David Galicia, Arturo H. Ariño
Software Mentions: 10
Published: almost 7 years ago

10.1186/s13071-020-04461-z

Oviposition of Aedes japonicus japonicus (Diptera: Culicidae) and associated native species in relation to season, temperature and land use in western Germany
Cited by: 12
Author(s): Linus Früh, Helge Kampen, Marcel B. Koban, Nadja Pernat, Günter A. Schaub, Doreen Werner
Software Mentions: 10
Published: almost 4 years ago

10.1007/s00125-018-4641-z

Multiplex proteomics for prediction of major cardiovascular events in type 2 diabetes
Cited by: 38
Author(s): Christoph Nowak, Axel C. Carlsson, Carl Johan Östgren, Fredrik Nyström, Moudud Alam, Tobias Feldreich, Johan Sundström, Juan-Jesús Carrero, Jerzy Leppert, Pär Hedberg, Egil Henriksen, A. C. C. Cordeiro, Vilmantas Giedraitis, Lars Lind, Erik Ingelsson, Tove Fall, Johan Ärnlöv
Software Mentions: 10
Published: over 6 years ago

10.3390/ijerph18168271

Cluster Analysis of Urban Acoustic Environments on Barcelona Sensor Network Data
Cited by: 10
Author(s): Antonio Pita, Francisco Javier Iglesias Rodríguez, Juan M. Navarro
Software Mentions: 10
Published: over 3 years ago

10.1038/s41598-019-46290-w

GeneHunt for rapid domain-specific annotation of glycoside hydrolases
Cited by: 14
Author(s): SC Nguyen, A. Flores, D. Talamantes, Furqan Dar, Adrian Roy L. Valdez, Jason P. Schwans, Renaud Berlemont
Software Mentions: 10
Published: over 5 years ago

10.1038/s41598-020-72047-x

Light intensity regulates flower visitation in Neotropical nocturnal bees
Cited by: 11
Author(s): Rodolfo Liporoni, Guaraci Duran Cordeiro, Paulo Inácio Prado, Clemens Schlindwein, Eric J. Warrant, Isabel Alves‐dos‐Santos
Software Mentions: 10
Published: about 4 years ago

10.1038/s41598-020-72272-4

Video-assisted thoracoscopic lobectomy is feasible for selected patients with clinical N2 non-small cell lung cancer
Cited by: 7
Author(s): Jae Kwang Yun, Geun Dong Lee, Sehoon Choi, Hyeong Ryul Kim, Yong Hee Kim, Seung-Il Park, Dong Kwan Kim
Software Mentions: 10
Published: about 4 years ago

10.1186/s13007-021-00795-6

Open source 3D phenotyping of chickpea plant architecture across plant development
Cited by: 6
Author(s): William T. Salter, Arjina Shrestha, Margaret M. Barbour
Software Mentions: 9
Published: about 3 years ago

10.1186/s13059-021-02374-3

The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle
Cited by: 18
Author(s): Mayra Furlan-Magaril, Masami Ando-Kuri, Rodrigo G. Arzate-Mejía, Jörg Morf, Jonathan Cairns, Abraham Román-Figueroa, Luis Tenorio-Hernández, Augusto César Poot-Hernández, Simon Andrews, Csilla Várnai, Boo Virk, Steven Wingett, Peter Fraser
Software Mentions: 9
Published: over 3 years ago

10.1534/genetics.119.302662

Polygenic Adaptation to an Environmental Shift: Temporal Dynamics of Variation Under Gaussian Stabilizing Selection and Additive Effects on a Single Trait
Cited by: 47
Author(s): Kevin R. Thornton
Software Mentions: 9
Published: almost 5 years ago

10.1038/s41396-019-0416-x

Variability in snake skin microbial assemblages across spatial scales and disease states
Cited by: 19
Author(s): Donald M. Walker, Jacob E. Leys, Matthew Grisnik, Alejandro Grajal-Puche, Christopher M. Murray, Matthew C. Allender
Software Mentions: 9
Published: over 5 years ago

10.1038/s41396-019-0546-1

Spatial and temporal axes impact ecology of the gut microbiome in juvenile European lobster (Homarus gammarus)
Cited by: 29
Author(s): Corey C. Holt, Mark van der Giezen, Carly L. Daniels, Grant D. Stentiford, David Bass
Software Mentions: 9
Published: about 5 years ago

10.3389/fgene.2021.663617

Multi-Omics Data Analyses Construct a Six Immune-Related Genes Prognostic Model for Cervical Cancer in Tumor Microenvironment
Cited by: 10
Author(s): Fangfang Xu, Jiacheng Shen, Shaohua Xu
Software Mentions: 9
Published: over 3 years ago

10.1186/s13059-020-02141-w

Improved reference genome of the arboviral vector Aedes albopictus
Cited by: 61
Author(s): Umberto Palatini, Reem A. Masri, Luciano V. Cosme, Sergey Koren, Françoise Thibaud‐Nissen, James K. Biedler, Flávia Krsticevic, J. Spencer Johnston, Rebecca Halbach, Jacob E. Crawford, Igor Antoshechkin, Anna‐Bella Failloux, Elisa Pischedda, Michele Marconcini, Jay Ghurye, Arang Rhie, Atashi Sharma, Д. А. Карагодин, James Jenrette, Stephanie Gamez, Pascal Miesen, Patrick Masterson, Adalgisa Caccone, Maria V. Sharakhova, Zhijian Tu, Philippos Aris Papathanos, Ronald P. van Rij, Omar S. Akbari, Jeffrey R. Powell, Adam M. Phillippy, Mariangela Bonizzoni
Software Mentions: 9
Published: over 4 years ago

10.1186/s12918-016-0349-1

DGCA: A comprehensive R package for Differential Gene Correlation Analysis
Cited by: 156
Author(s): Andrew McKenzie, Igor Katsyv, Won Min Song, Minghui Wang, Bin Zhang
Software Mentions: 9
Published: about 8 years ago

10.3390/metabo11040211

gcProfileMakeR: An R Package for Automatic Classification of Constitutive and Non-Constitutive Metabolites
Cited by: 3
Author(s): Fernando Pérez-Sánz, Victoria Ruiz-Hernández, Marta I. Terry, Sara Arce-Gallego, Julia Weiß, Pedro J. Navarro, Marcos Egea‐Cortines
Software Mentions: 9
Published: over 3 years ago

10.7150/jca.47559

Preoperative Splenic Density for the Prediction of Survival and Adjuvant Chemotherapy Benefits in Gastric Cancer
Cited by: 1
Author(s): Weiteng Zhang, Ce Zhu, Xiang Wang, Sujun Wang, Xiao Chen, Xiaolei Chen, Xian Shen
Software Mentions: 9
Published: almost 5 years ago

10.3390/pathogens9080628

Comparative Analysis of the Bacterial and Fungal Communities in the Gut and the Crop of Aedes albopictus Mosquitoes: A Preliminary Study
Cited by: 10
Author(s): Morgane Guégan, Edwige Martin, Claire Valiente Moro
Software Mentions: 9
Published: over 4 years ago

10.2196/10076

Key Elements of mHealth Interventions to Successfully Increase Physical Activity: Meta-Regression
Cited by: 56
Author(s): Lisa V. Eckerstorfer, Norbert K. Tanzer, Claudia Vogrincic-Haselbacher, Gayannée Kedia, Hilmar Brohmer, Isabelle Dinslaken, Katja Corcoran
Software Mentions: 9
Published: about 6 years ago

10.1016/j.comppsych.2019.152143

Longitudinal population subgroups of CRP and risk of depression in the ALSPAC birth cohort
Cited by: 11
Author(s): Emanuele F. Osimo, Jan S̆tochl, Stanley Zammit, Glyn Lewis, Peter B. Jones, Golam M. Khandaker
Software Mentions: 9
Published: almost 5 years ago

10.1371/journal.pone.0247790

Parasitism and host behavior in the context of a changing environment: The Holocene record of the commercially important bivalve Chamelea gallina, northern Italy
Cited by: 3
Author(s): John Warren Huntley, Daniele Scarponi
Software Mentions: 9
Published: over 3 years ago

10.3390/metabo10030086

Local Phenomena Shape Backyard Soil Metabolite Composition
Cited by: 9
Author(s): Tra D Nguyen, Mahbobeh Lesani, Ines Forrest, Yunpeng Lan, Danya A. Dean, Quentin M. R. Gibaut, Yanting Guo, Ekram Hossain, Marcela Olvera, Hannah Panlilio, Adwaita R. Parab, Chao‐Yi Wu, Jean A. Bernatchez, Robert H. Cichewicz, Laura-Isobel McCall
Software Mentions: 9
Published: over 4 years ago

10.3389/fgene.2021.691465

ARG2, MAP4K5 and TSTA3 as Diagnostic Markers of Steroid-Induced Osteonecrosis of the Femoral Head and Their Correlation With Immune Infiltration
Cited by: 10
Author(s): Rongguo Yu, Jiayu Zhang, Youguang Zhuo, Hong Xu, Jie Ye, Susu Tang, Nannan Liu, Yiyuan Zhang
Software Mentions: 9
Published: over 3 years ago

10.1371/journal.pone.0254356

Endpoint PCR coupled with capillary electrophoresis (celPCR) provides sensitive and quantitative measures of environmental DNA in singleplex and multiplex reactions
Cited by: 7
Author(s): Bettina Thalinger, Yannick Pütz, Michael Traugott
Software Mentions: 9
Published: over 3 years ago

10.3389/fgene.2020.00192

Integrated Analysis Identifies a Nine-microRNA Signature Biomarker for Diagnosis and Prognosis in Colorectal Cancer
Cited by: 31
Author(s): Ziyang Di, Maojun Di, Weihua Fu, Qiang Tang, Yanwei Liu, Peijie Lei, Xinsheng Gu, Tong Liu, Min Sun
Software Mentions: 9
Published: over 4 years ago

Projects: cran: ggplot2

Papers Mentioning ggplot2 11,441