Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: cran: UpSetR

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/UpSetR

A More Scalable Alternative to Venn and Euler Diagrams for Visualizing Intersecting Sets
18 versions
Latest release: over 5 years ago
15 dependent packages
15,935 downloads last month

Papers Mentioning UpSetR 319

10.1186/s13395-017-0144-8
Comparison of multiple transcriptomes exposes unified and divergent features of quiescent and activated skeletal muscle stem cells
Cited by: 29
Author(s): Natalia Pietrosemoli, Sébastien Mella, Siham Yennek, Meryem B. Baghdadi, Hiroshi Sakai, Ramkumar Sambasivan, Francesca Pala, Daniela Di Girolamo, Shahragim Tajbakhsh
Software Mentions: 5
Published: almost 7 years ago
10.1155/2021/6641838
Analysis of Molecular Mechanism of Erxian Decoction in Treating Osteoporosis Based on Formula Optimization Model
Cited by: 22
Author(s): Lang Yang, Liuyi Fan, Kexin Wang, Yu-peng Chen, Liuqin Liang, Xuemei Qin, Aiping Lü, Peng Cao, Bin Yu, Daogang Guan, Junxiang Peng
Software Mentions: 5
Published: over 3 years ago
10.1093/jxb/erz546
Transcriptional and biochemical analyses of gibberellin expression and content in germinated barley grain
Cited by: 16
Author(s): Natalie S. Betts, Christoph Dockter, Oliver Berkowitz, Helen Collins, Michelle Hooi, Qiongxian Lu, Rachel A. Burton, Vincent Bulone, Birgitte Skadhauge, James Whelan, Geoffrey B. Fincher
Software Mentions: 5
Published: almost 5 years ago
10.1073/pnas.2110758118
TET2 as a tumor suppressor and therapeutic target in T-cell acute lymphoblastic leukemia
Cited by: 22
Author(s): Maike Bensberg, Olof Rundquist, Aida Selimović, Cathrine Lagerwall, Mikael Benson, Mika Gustafsson, Hartmut Vogt, Antonio Lentini, Colm E. Nestor
Software Mentions: 5
Published: over 3 years ago
10.1126/sciimmunol.abe4782
Severely ill patients with COVID-19 display impaired exhaustion features in SARS-CoV-2–reactive CD8 <sup>+</sup> T cells
Cited by: 163
Author(s): Anthony Kusnadi, Ciro Ramírez-Suástegui, Vicente Fajardo, Serena Chee, Benjamin J Meckiff, Hayley Simon, Emanuela Pelosi, Grégory Seumois, Ferhat Ay, Pandurangan Vijayanand, Christian Ottensmeier
Software Mentions: 5
Published: almost 4 years ago
10.1038/s41598-020-69672-x
A footprint of plant eco-geographic adaptation on the composition of the barley rhizosphere bacterial microbiota
Cited by: 39
Author(s): Rodrigo Alegria Terrazas, Katharin Balbirnie-Cumming, Jenny Morris, Pete E. Hedley, Joanne Russell, Eric Paterson, Elizabeth M. Baggs, Eyal Fridman, Davide Bulgarelli
Software Mentions: 5
Published: over 4 years ago
10.1038/s41598-021-81447-6
Acetyl-CoA flux from the cytosol to the ER regulates engagement and quality of the secretory pathway
Cited by: 16
Author(s): Inca A. Dieterich, Yusi Cui, Megan M. Braun, Alexis J. Lawton, Nicklaus H. Robinson, Jennifer L. Peotter, Qing Yu, Jason C. Casler, Benjamin S. Glick, Anjon Audhya, John M. Denu, Lingjun Li, Luigi Puglielli
Software Mentions: 5
Published: almost 4 years ago
10.1002/btm2.10198
Transcriptomic response of brain tissue to focused <scp>ultrasound‐mediated blood–brain</scp> barrier disruption depends strongly on anesthesia
Cited by: 12
Author(s): Alexander S. Mathew, Catherine M. Gorick, E. Andrew Thim, William J. Garrison, Alexander L. Klibanov, G. Wilson Miller, Natasha D. Sheybani, Richard J. Price
Software Mentions: 5
Published: almost 4 years ago
10.1093/bioinformatics/btx364
UpSetR: an R package for the visualization of intersecting sets and their properties
Cited by: 1,808
Author(s): Jake R. Conway, Alexander Lex, Nils Gehlenborg
Software Mentions: 5
Published: over 7 years ago
10.1186/s13068-021-01915-z
Physiological and transcriptional response to drought stress among bioenergy grass Miscanthus species
Cited by: 10
Author(s): Jose J De Vega, Abel Teshome, Manfred Klaas, Jim Grant, John Finnan, Susanne Barth
Software Mentions: 5
Published: over 3 years ago
10.1186/s12859-018-2252-9
npInv: accurate detection and genotyping of inversions using long read sub-alignment
Cited by: 26
Author(s): Haojing Shao, Devika Ganesamoorthy, Tânia Duarte, Minh Duc Cao, Clive Hoggart, Lachlan Coin
Software Mentions: 5
Published: over 6 years ago
10.1186/s13229-020-00369-8
Chd8 haploinsufficiency impairs early brain development and protein homeostasis later in life
Cited by: 18
Author(s): Jessica A. Jiménez, Travis Ptacek, Alex H. Tuttle, Ralf S. Schmid, Sheryl S. Moy, Jeremy M. Simon, Mark J. Zylka
Software Mentions: 5
Published: about 4 years ago
10.7717/peerj.6448
The draft genome of strain <i>c</i>Cpun from biting midges confirms insect <i>Cardinium</i> are not a monophyletic group and reveals a novel gene family expansion in a symbiont
Cited by: 10
Author(s): Stefanos Siozios, Jack Pilgrim, Alistair C. Darby, Matthew Baylis, Gregory D. D. Hurst
Software Mentions: 5
Published: over 5 years ago
10.7717/peerj.9174
Identification of potential biomarkers and their clinical significance in gastric cancer using bioinformatics analysis methods
Cited by: 4
Author(s): Jie Liu, Miao Zhou, Yangyang Ouyang, Laifeng Du, Lingbo Xu, Hongyun Liu
Software Mentions: 5
Published: over 4 years ago
10.7717/peerj.7171
Identification of diagnostic markers for major depressive disorder by cross-validation of data from whole blood samples
Cited by: 10
Author(s): Huimei Wang, Mingwei Zhang, Qiqi Xie, Yu Jin, Qi Yan, Qiuyuan Yue
Software Mentions: 5
Published: over 5 years ago
10.1371/journal.pntd.0008671
Novel small RNAs expressed by Bartonella bacilliformis under multiple conditions reveal potential mechanisms for persistence in the sand fly vector and human host
Cited by: 6
Author(s): Shaun Wachter, Linda D. Hicks, Rahul Raghavan, Michael F. Minnick
Software Mentions: 5
Published: about 4 years ago
10.3389/fbioe.2019.00229
The White-Rot Basidiomycete Dichomitus squalens Shows Highly Specific Transcriptional Response to Lignocellulose-Related Aromatic Compounds
Cited by: 21
Author(s): Joanna E. Kowalczyk, Mao Peng, Megan Pawlowski, Anna Lipzen, Vivian Ng, Vasanth Singan, Mei Wang, Igor V. Grigoriev, Miia Mäkelä
Software Mentions: 5
Published: about 5 years ago
10.3389/fgene.2019.01333
A Novel Prognostic Index Based on Alternative Splicing in Papillary Renal Cell Carcinoma
Cited by: 2
Author(s): Zhipeng Wu, Jinhui Liu, Rui Sun, Dongming Chen, Kai Wang, Changchun Cao, Xianlin Xu
Software Mentions: 5
Published: almost 5 years ago
10.3389/fgene.2021.589160
Gene and Transposable Element Expression Evolution Following Recent and Past Polyploidy Events in Spartina (Poaceae)
Cited by: 9
Author(s): Delphine Giraud, Oscar Lima, Mathieu Rousseau‐Gueutin, Armel Salmon, Malika L. Aïnouche
Software Mentions: 5
Published: over 3 years ago
10.3389/fgene.2020.522383
Survival-Associated Alternative Splicing Events and Prognostic Signatures in Pancreatic Cancer
Cited by: 5
Author(s): Lichao Xu, Jianji Pan, Yanni Ding, Hongda Pan
Software Mentions: 5
Published: about 4 years ago
10.1038/s41396-018-0263-1
In situ development of a methanotrophic microbiome in deep-sea sediments
Cited by: 56
Author(s): S. Emil Ruff, Janine Felden, Harald R. Gruber‐Vodicka, Yann Marcon, Katrin Knittel, Alban Ramette, Antje Boetius
Software Mentions: 5
Published: about 6 years ago
10.3389/fgene.2018.00491
Dynamic Changes in the Global MicroRNAome and Transcriptome Identify Key Nodes Associated With Ovarian Development in Chickens
Cited by: 12
Author(s): Wenwen Wang, Keliang Wu, Meiting Jia, Siyuan Sun, Kang Li, Qin Zhang, Hui Tang
Software Mentions: 5
Published: about 6 years ago
10.3389/fimmu.2021.640837
Transcriptomic Analysis of Inflammatory Cardiomyopathy Identifies Molecular Signatures of Disease and Informs in silico Prediction of a Network-Based Rationale for Therapy
Cited by: 1
Author(s): Khushboo Singh, Hai Fang, Graham Davies, Benjamin Wright, Helen Lockstone, Richard O. Williams, Daniela Čiháková, Julian C. Knight, Shoumo Bhattacharya
Software Mentions: 5
Published: over 3 years ago
10.3389/fimmu.2021.670309
Comparative Immunogenomics of Canine Natural Killer Cells as Immunotherapy Target
Cited by: 7
Author(s): Alicia A. Gingrich, Taylor Reiter, Sean J Judge, Daniel York, Mio Yanagisawa, Aryana Razmara, Ian R. Sturgill, Ugur Nur Basmaci, Rachel Brady, Kevin Stoffel, William J. Murphy, Robert B. Rebhun, C. Titus Brown, Robert J. Canter
Software Mentions: 5
Published: about 3 years ago
10.3389/fmicb.2020.603692
Shift and Metabolic Potentials of Microbial Eukaryotic Communities Across the Full Depths of the Mariana Trench
Cited by: 3
Author(s): Xiaoyu Zhu, Jiwen Liu, Chun-Xu Xue, Jiwei Tian, Xiao‐Hua Zhang
Software Mentions: 5
Published: almost 4 years ago
10.1128/mSystems.00323-18
Gut Microbiota Has a Widespread and Modifiable Effect on Host Gene Regulation
Cited by: 62
Author(s): Allison L. Richards, Amanda L. Muehlbauer, Adnan Alazizi, Michael B. Burns, Anthony Findley, Francesco Messina, Trevor Gould, Camilla Cascardo, Roger Piqué-Regi, Ran Blekhman, Francesca Luca
Software Mentions: 5
Published: about 5 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: over 3 years ago
10.3389/fonc.2021.640272
Identification of Novel Alternative Splicing Events Associated With Tumorigenesis, Protein Modification, and Immune Microenvironment in Early-Onset Gastric Cancer
Cited by: 4
Author(s): Jian Zhang, Ajay Goel, Lin Zhu
Software Mentions: 5
Published: over 3 years ago
10.1186/s12864-020-07114-8
Predicting and clustering plant CLE genes with a new method developed specifically for short amino acid sequences
Cited by: 12
Author(s): Zhe Zhang, Lei Liu, Melis Kücükoglu, Dongdong Tian, Robert M. Larkin, Xueping Shi, Bo Zheng
Software Mentions: 5
Published: about 4 years ago
10.3389/fpls.2019.00223
Infection Strategies Deployed by Botrytis cinerea, Fusarium acuminatum, and Rhizopus stolonifer as a Function of Tomato Fruit Ripening Stage
Cited by: 56
Author(s): Stefan Petrasch, Christian J. Silva, Saskia D Mesquida-Pesci, Karina Gallegos, Casper van den Abeele, Victor Papin, Francisco Javier Fernández-Acero, Steven J. Knapp, Bárbara Blanco-Ulate
Software Mentions: 5
Published: over 5 years ago
10.1186/s42523-019-0017-z
Development of the duodenal, ileal, jejunal and caecal microbiota in chickens
Cited by: 36
Author(s): Laura Glendinning, Kellie Watson, Michael Watson
Software Mentions: 5
Published: about 5 years ago
10.3390/genes11020227
Alternative Splicing Events as Indicators for the Prognosis of Uveal Melanoma
Cited by: 15
Author(s): Qi Wan, Xuan Sang, Lin Jin, Zhichong Wang
Software Mentions: 5
Published: over 4 years ago
10.1186/s12711-021-00602-9
Expression quantitative trait loci in sheep liver and muscle contribute to variations in meat traits
Cited by: 12
Author(s): Zehu Yuan, Sunduimijid Bolormaa, Ruidong Xiang, R. Behrendt, Matthew I. Knight, Brett Mason, Coralie M. Reich, Claire P. Prowse-Wilkins, Christy J. Vander Jagt, Amanda J. Chamberlain, Iona M. MacLeod, Fadi Li, Xiangpeng Yue, Hans D. Daetwyler
Software Mentions: 5
Published: almost 4 years ago
10.1534/genetics.120.303038
Genetic Associations in Four Decades of Multienvironment Trials Reveal Agronomic Trait Evolution in Common Bean
Cited by: 22
Author(s): Alice MacQueen, Jeffrey W. White, Rian Lee, Juan M. Osorno, Jeremy Schmutz, Phillip N. Miklas, James R. Myers, Phillip E. McClean, Thomas E. Juenger
Software Mentions: 5
Published: over 4 years ago
10.3389/fpls.2020.01075
Populations of the Parasitic Plant Phelipanche ramosa Influence Their Seed Microbiota
Cited by: 23
Author(s): Sarah Huet, Jean‐Bernard Pouvreau, Erwan Delage, Sabine Delgrange, Coralie Marais, Muriel Bahut, Philippe Delavault, Philippe Simier, Lucie Poulin
Software Mentions: 4
Published: over 4 years ago
10.3389/fgene.2020.00796
Genome-Wide Profiling of Alternative Splicing Signature Reveals Prognostic Predictor for Esophageal Carcinoma
Cited by: 5
Author(s): Jian-Rong Sun, Chen-Fan Kong, Yanni Lou, Ran Yu, Xiang-Ke Qu, Liqun Jia
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pgen.1009221
Short-range template switching in great ape genomes explored using pair hidden Markov models
Cited by: 10
Author(s): Conor R Walker, Aylwyn Scally, Nicola De Maio, Nick Goldman
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pcbi.1007603
SuperFreq: Integrated mutation detection and clonal tracking in cancer
Cited by: 34
Author(s): Christoffer Flensburg, Tobias Sargeant, Alicia Oshlack, Ian J. Majewski
Software Mentions: 4
Published: almost 5 years ago
10.1371/journal.pcbi.1006484
Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties
Cited by: 68
Author(s): Ling Chen, Alexandra E. Fish, John A. Capra
Software Mentions: 4
Published: about 6 years ago
10.1038/s41598-021-94701-8
Integrative analysis reveals the prognostic value and functions of splicing factors implicated in hepatocellular carcinoma
Cited by: 7
Author(s): Yue Wang, Fan Yang, Jiaqi Shang, Hai‐Tao He, Qing Yang
Software Mentions: 4
Published: over 3 years ago
10.3390/plants10040765
Proteomic Identification and Meta-Analysis in Salvia hispanica RNA-Seq de novo Assemblies
Cited by: 1
Author(s): Ashwil Klein, Lizex Husselmann, Achmat Williams, Liam Bell, Bret Cooper, Brent Ragar, David L. Tabb
Software Mentions: 4
Published: over 3 years ago
10.7717/peerj.11956
Small-scale variation in a pristine montane cloud forest: evidence on high soil fungal diversity and biogeochemical heterogeneity
Cited by: 1
Author(s): Patricia Vélez, Yunuen Tapia-Torres, Felipe Garcı́a-Oliva, Jaime Gasca-Pineda
Software Mentions: 4
Published: over 3 years ago
10.3389/fgene.2018.00412
Network, Transcriptomic and Genomic Features Differentiate Genes Relevant for Drug Response
Cited by: 14
Author(s): Janet Piñero, Abel González-Pérez, Emre Güney, Joaquim Aguirre‐Plans, Ferrán Sanz, Baldo Oliva, Laura I. Furlong
Software Mentions: 4
Published: about 6 years ago
10.1186/s12864-019-6126-y
Comparative genomics of Leishmania (Mundinia)
Cited by: 24
Author(s): Anzhelika Butenko, Alexei Y. Kostygov, Jovana Sádlová, Yuliya Kleschenko, Tomáš Bečvář, Lucie Podešvová, Diego H. Macedo, David Žihala, Julius Lukeš, Paul A. Bates, Petr Volf, Frederik Opperdoes, Vyacheslav Yurchenko
Software Mentions: 4
Published: about 5 years ago
10.1186/s12931-018-0932-7
Inflammatory pathways are upregulated in the nasal epithelium in patients with idiopathic pulmonary fibrosis
Cited by: 13
Author(s): Marc A. Sala, Yalbi I. Balderas-Martínez, Ivette Buendía-Roldán, Hiam Abdala‐Valencia, Ki-Won Nam, Manu Jain, Sangeeta Bhorade, Ankit Bharat, Paul A. Reyfman, Karen M. Ridge, Annie Pardo, Jacob I. Sznajder, G. R. Scott Budinger, Alexander V. Misharin, Moisés Selman
Software Mentions: 4
Published: almost 6 years ago
10.1016/j.gpb.2020.06.004
The mRNA Binding Proteome of Proliferating and Differentiated Muscle Cells
Cited by: 4
Author(s): Monika Hiller, M Geissler, George M.C. Janssen, Peter A. van Veelen, Annemieke Aartsma‐Rus, Pietro Spitali
Software Mentions: 4
Published: over 4 years ago
10.3389/fmicb.2021.701067
Nitrogen Supply and Host-Plant Genotype Modulate the Transcriptomic Profile of Plasmodiophora brassicae
Cited by: 3
Author(s): Kévin Gazengel, Yoann Aigu, Christine Lariagon, Mathilde Humeau, Antoine Gravot, Maria Manzanares-Dauleux, Stéphanie Daval
Software Mentions: 4
Published: over 3 years ago
10.3389/fmicb.2021.628437
Volatile Compounds From Bacillus, Serratia, and Pseudomonas Promote Growth and Alter the Transcriptional Landscape of Solanum tuberosum in a Passively Ventilated Growth System
Cited by: 8
Author(s): Darren Heenan-Daly, Simone Coughlan, Eileen Dillane, Barbara Doyle Prestwich
Software Mentions: 4
Published: over 3 years ago
10.1007/s12035-020-02128-5
Molecular Regulatory Mechanism and Toxicology of Neurodegenerative Processes in MPTP/Probenecid-Induced Progressive Parkinson’s Disease Mice Model Revealed by Transcriptome
Cited by: 12
Author(s): Weiwei Yang, Wenwen Hao, Zhen Meng, Shuizi Ding, Xiaodi Li, Tao Zhang, Weixiao Huang, Liang Xu, Yu Zhang, Jian Yang, Xiaosong Gu
Software Mentions: 4
Published: about 4 years ago
10.3389/fmicb.2019.00715
Response of Lactobacillus plantarum WCFS1 to the Gram-Negative Pathogen-Associated Quorum Sensing Molecule N-3-Oxododecanoyl Homoserine Lactone
Cited by: 16
Author(s): Joseph R. Spangler, Scott N. Dean, Dagmar H. Leary, Scott A. Walper
Software Mentions: 4
Published: over 5 years ago
10.1186/s12967-019-2029-6
Determining the prognostic significance of alternative splicing events in soft tissue sarcoma using data from The Cancer Genome Atlas
Cited by: 11
Author(s): Xia Yang, Wenting Huang, Rong‐Quan He, Jie Ma, Peng Lin, Zucheng Xie, Fuchao Ma, Gang Chen
Software Mentions: 4
Published: about 5 years ago
10.1186/s12864-020-07132-6
Progress in quickly finding orthologs as reciprocal best hits: comparing blast, last, diamond and MMseqs2
Cited by: 35
Author(s): Julie E. Hernández-Salmerón, Gabriel Moreno‐Hagelsieb
Software Mentions: 4
Published: about 4 years ago
10.1111/mec.15699
Diversity of gut microbiomes in marine fishes is shaped by host‐related factors
Cited by: 43
Author(s): Qi Huang, Ronia Chung-tin Sham, Yu Deng, Yanping Mao, Chunxiao Wang, Tong Zhang, Kenneth M.Y. Leung
Software Mentions: 4
Published: about 4 years ago
10.3389/fmicb.2017.01808
Gene Expression Analysis of Zobellia galactanivorans during the Degradation of Algal Polysaccharides Reveals both Substrate-Specific and Shared Transcriptome-Wide Responses
Cited by: 36
Author(s): François Thomas, Philippe Bordron, Damien Eveillard, Gurvan Michel
Software Mentions: 4
Published: about 7 years ago
10.3389/fmicb.2021.705724
New Estimation of Antibiotic Resistance Genes in Sediment Along the Haihe River and Bohai Bay in China: A Comparison Between Single and Successive DNA Extraction Methods
Cited by: 0
Author(s): Chao Wu, Guicheng Zhang, Wenzhe Xu, Shan Jian, Liyin Peng, Dai Jia, Jun Sun
Software Mentions: 4
Published: about 3 years ago
10.3389/fmicb.2020.542742
Testing the Two-Step Model of Plant Root Microbiome Acquisition Under Multiple Plant Species and Soil Sources
Cited by: 14
Author(s): Hugo R. Barajas, Shamayim Martínez-Sánchez, Miguel Romero, Cristóbal Hernández Álvarez, Luis Servı́n‐González, Mariana Peimbert, Rocío Cruz-Ortega, Felipe Garcı́a-Oliva, Luis David Alcaraz
Software Mentions: 4
Published: about 4 years ago
10.1186/s12967-020-02454-1
Comprehensive analysis and establishment of a prediction model of alternative splicing events reveal the prognostic predictor and immune microenvironment signatures in triple negative breast cancer
Cited by: 11
Author(s): Shanshan Yu, Chuan Hu, Lixiao Liu, Luya Cai, Xuedan Du, Qiongjie Yu, Fan Lin, Jinduo Zhao, Ye Zhao, Cheng Zhang, Xuan Li, Wenfeng Li
Software Mentions: 4
Published: over 4 years ago
10.3389/fmicb.2019.02371
The Bacterial Communities of Little Cigars and Cigarillos Are Dynamic Over Time and Varying Storage Conditions
Cited by: 10
Author(s): Eoghan M. Smyth, Suhana Chattopadhyay, Kelsey R. Babik, Molly C. Reid, Jessica Chopyk, Leena Malayil, Prachi Kulkarni, Lauren E. Hittle, Pamela I. Clark, Amy R. Sapkota, Emmanuel F. Mongodin
Software Mentions: 4
Published: about 5 years ago
10.1002/cam4.3977
Identification of prognostic and bone metastasis​‐related alternative splicing signatures in mesothelioma
Cited by: 1
Author(s): Runzhi Huang, Zixuan Zheng, Sijia Liu, Penghui Yan, Dianwen Song, Huabin Yin, Peng Hu, Xiaolong Zhu, Zhengyan Chang, Yihan Liu, Juanwei Zhuang, Tong Meng, Zongqiang Huang, Jie Zhang
Software Mentions: 4
Published: over 3 years ago
10.1186/s12915-020-00802-7
A chromosome-level assembly of the cat flea genome uncovers rampant gene duplication and genome size plasticity
Cited by: 25
Author(s): Timothy Driscoll, Victoria I. Verhoeve, Joseph J. Gillespie, J. Spencer Johnston, Mark L. Guillotte, Kristen E. Rennoll-Bankert, M. Sayeedur Rahman, Darren E. Hagen, Christine G. Elsik, Kevin R. Macaluso, Abdu F. Azad
Software Mentions: 4
Published: over 4 years ago
10.1186/s13059-020-02018-y
CircAtlas: an integrated resource of one million highly accurate circular RNAs from 1070 vertebrate transcriptomes
Cited by: 217
Author(s): Wanying Wu, Peifeng Ji, Fangqing Zhao
Software Mentions: 4
Published: over 4 years ago
10.1128/mSystems.00640-20
Stability of the Virome in Lab- and Field-Collected Aedes albopictus Mosquitoes across Different Developmental Stages and Possible Core Viruses in the Publicly Available Virome Data of <i>Aedes</i> Mosquitoes
Cited by: 34
Author(s): Chengying Shi, Lu Zhao, Evans Atoni, Weihua Zeng, Xiaomin Hu, Jelle Matthijnssens, Zhiming Yuan, Han Xia
Software Mentions: 4
Published: about 4 years ago
10.1186/s12859-017-1708-7
Intervene: a tool for intersection and visualization of multiple gene or genomic region sets
Cited by: 322
Author(s): Aziz Khan, Anthony Mathelier
Software Mentions: 4
Published: over 7 years ago
10.1155/2020/4251761
Identification of Potential Hub Genes Related to Diagnosis and Prognosis of Hepatitis B Virus-Related Hepatocellular Carcinoma via Integrated Bioinformatics Analysis
Cited by: 28
Author(s): Yuqin Tang, Yongqiang Zhang, Xun Hu
Software Mentions: 4
Published: almost 4 years ago
10.1038/s41598-021-85733-1
High-intensity leg cycling alters the molecular response to resistance exercise in the arm muscles
Cited by: 4
Author(s): Marcus Moberg, William Apró, Igor Červenka, Björn Ekblom, Gerrit van Hall, Hans-Christer Holmberg, Jorge L. Ruas, Eva Blomstrand
Software Mentions: 4
Published: over 3 years ago
10.3389/fonc.2021.652063
Machine Learning Applicability for Classification of PAD/VCD Chemotherapy Response Using 53 Multiple Myeloma RNA Sequencing Profiles
Cited by: 15
Author(s): Nicolas Borisov, Anna Sergeeva, Maria Suntsova, Mikhail Raevskiy, Нуршат Гайфуллин, Л. П. Менделеева, Alexander Gudkov, Maria Nareiko, Andrew Garazha, Victor Tkachev, Xinmin Li, Maxim Sorokin, В. Л. Сурин, Anton Buzdin
Software Mentions: 4
Published: over 3 years ago
10.1038/s41598-021-84044-9
Identification of candidate repurposable drugs to combat COVID-19 using a signature-based approach
Cited by: 18
Author(s): Sinead M. O’Donovan, Ali Sajid Imami, Hunter M. Eby, Nicholas Henkel, Justin Creeden, Sophie Asah, Xiaolu Zhang, Xiaojun Wu, Rawan Alnafisah, R. Travis Taylor, James Reigle, Alexander W. Thorman, Behrouz Shamsaei, Jarek Meller, Robert E. McCullumsmith
Software Mentions: 4
Published: over 3 years ago
10.1038/s41598-020-61633-8
MicroRNA hsa-mir-3923 serves as a diagnostic and prognostic biomarker for gastric carcinoma
Cited by: 11
Author(s): Xiaohui Yang, Ze Zhang, Lichao Zhang, Li Zhou
Software Mentions: 4
Published: over 4 years ago
10.1186/s13059-019-1842-9
Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods
Cited by: 318
Author(s): Brian J. Haas, Alexander Dobin, Bo Li, Nicolas Stransky, Nathalie Pochet, Aviv Regev
Software Mentions: 4
Published: about 5 years ago
10.1111/imb.12688
Jekyll or Hyde? The genome (and more) of <i>Nesidiocoris tenuis</i>, a zoophytophagous predatory bug that is both a biological control agent and a pest
Cited by: 11
Author(s): Kim Ferguson, Sako Visser, Martina Dalíková, Irena Provazníková, Alberto Urbaneja, František Marec, John H. Werren, Bas J. Zwaan, Bart A. Pannebakker, Eveline C. Verhulst
Software Mentions: 4
Published: almost 4 years ago
10.1534/g3.117.300550
Genetic Loci Governing Androgenic Capacity in Perennial Ryegrass (<i>Lolium perenne</i> L.)
Cited by: 8
Author(s): Rachel F. Begheyn, Steven Yates, Timothy Sykes, Bruno Studer
Software Mentions: 4
Published: over 6 years ago
10.1371/journal.pone.0198191
Early responses to dehydration in contrasting wild Arachis species
Cited by: 21
Author(s): C. C. Vinson, Ana Paula Zotta Mota, Thais Nicolini Oliveira, Larissa Arrais Guimarães, Soraya C. M. Leal‐Bertioli, Thomas Christopher Rhys Williams, Alexandre Lima Nepomuceno, Mario Alfredo Passos Saraiva, Ana Cláudia Guerra Araújo, P. M. Guimarães, Ana Cristina Miranda Brasileiro
Software Mentions: 4
Published: over 6 years ago
10.1093/dnares/dsz002
A siphonous macroalgal genome suggests convergent functions of homeobox genes in algae and land plants
Cited by: 32
Author(s): Asuka Arimoto, Koki Nishitsuji, Yoshimi Higa, Nana Arakaki, Kanako Hisata, Chuya Shinzato, Noriyuki Satoh, Eiichi Shoguchi
Software Mentions: 4
Published: over 5 years ago
10.3390/ijms21218333
Transcriptional Effects of Psychoactive Drugs on Genes Involved in Neurogenesis
Cited by: 7
Author(s): Chiara C. Bortolasci, Briana Spolding, Srisaiyini Kidnapillai, Timothy Connor, Trang T. T. Truong, Zoe Liu, Bruna Panizzutti, Mark F. Richardson, Laura J. Gray, Michael Berk, Olivia Dean, Ken Walder
Software Mentions: 4
Published: about 4 years ago
10.1371/journal.pone.0230566
Genetic compensation in a stable slc25a46 mutant zebrafish: A case for using F0 CRISPR mutagenesis to study phenotypes caused by inherited disease
Cited by: 35
Author(s): Elena Buglo, Evan Sarmiento, Nicole Belliard Martuscelli, David W. Sant, Matt C. Danzi, A. Jeanine Abrams, Julia E. Dallman, Stephan Züchner
Software Mentions: 4
Published: over 4 years ago
10.1002/ece3.6946
Genomic analysis of Asian honeybee populations in China reveals evolutionary relationships and adaptation to abiotic stress
Cited by: 6
Author(s): Peng Shi, Jun Zhou, Huali Song, Yujuan Wu, Lan Lan, Xiangyou Tang, Zhengang Ma, Charles R. Vossbrinck, Bettina Vossbrinck, Zeyang Zhou, Jianlong Xu
Software Mentions: 4
Published: about 4 years ago
10.1186/s13072-018-0190-4
“Same difference”: comprehensive evaluation of four DNA methylation measurement platforms
Cited by: 26
Author(s): Thadeous J. Kacmarczyk, Mame P. Fall, Xihui Zhang, Xin Yuan, Yushan Li, Alicia Alonso, Doron Betel
Software Mentions: 4
Published: over 6 years ago
10.1186/s12864-020-06899-y
The wheat pathogen Zymoseptoria tritici senses and responds to different wavelengths of light
Cited by: 7
Author(s): Cassandra B. McCorison, Stephen B. Goodwin
Software Mentions: 4
Published: over 4 years ago
10.1186/s12864-019-5709-y
Improved annotation of the domestic pig genome through integration of Iso-Seq and RNA-seq data
Cited by: 53
Author(s): Hamid Beiki, Haibo Li, Jinrong Huang, Nancy Manchanda, D. Nonneman, Timothy P. L. Smith, James M. Reecy, Christopher K. Tuggle
Software Mentions: 4
Published: over 5 years ago
10.1038/s41598-018-31072-7
Transcriptional shifts account for divergent resource allocation in feed efficient broiler chickens
Cited by: 12
Author(s): Henry Reyer, Barbara U. Metzler‐Zebeli, Nares Trakooljul, Michael Oster, Eduard Muráni, Siriluck Ponsuksili, Frieder Hadlich, Klaus Wimmers
Software Mentions: 4
Published: about 6 years ago
10.1371/journal.pntd.0008237
Comprehensive analysis of the secreted proteome of adult Necator americanus hookworms
Cited by: 20
Author(s): Jayden Logan, Mark S. Pearson, Srikanth S. Manda, Young Jun Choi, Matthew A. Field, Ramon M. Eichenberger, Jason Mulvenna, Shivashankar H. Nagaraj, Ricardo Toshio Fujiwara, Pedro Henrique Gazzinelli-Guimarães, Lilian Lacerda Bueno, Vitor Luís Tenório Mati, Jeffrey M. Bethony, Makedonka Mitreva, Javier Sotillo, Alex Loukas
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pgen.1008452
Transcriptional and genomic parallels between the monoxenous parasite Herpetomonas muscarum and Leishmania
Cited by: 12
Author(s): Megan A. Sloan, Karen Brooks, Thomas D. Otto, Mandy Sanders, James A. Cotton, Petros Ligoxygakis
Software Mentions: 4
Published: about 5 years ago
10.1371/journal.pgen.1009713
Multitrait GWAS to connect disease variants and biological mechanisms
Cited by: 12
Author(s): Hanna Julienne, Vincent Laville, Zachary R. McCaw, Zihuai He, Vincent Guillemot, Carla Lasry, Andrey Ziyatdinov, Cyril Nerin, Amaury Vaysse, Pierre Lechat, Hervé Ménager, Wilfried Le Goff, Marie‐Pierre Dubé, Peter Kraft, Iuliana Ionita‐Laza, Bjarni J. Vilhjálmsson, Hugues Aschard
Software Mentions: 4
Published: about 3 years ago
10.3389/fcimb.2020.608020
Investigating Major Recurring Campylobacter jejuni Lineages in Luxembourg Using Four Core or Whole Genome Sequencing Typing Schemes
Cited by: 12
Author(s): Morgane Nennig, Ann-Katrin Llarena, Malte Herold, Joël Mossong, Christian Penny, Serge Losch, Odile Tresse, Catherine Ragimbeau
Software Mentions: 4
Published: almost 4 years ago
10.3389/fcimb.2020.00086
Methodological Insight Into Mosquito Microbiome Studies
Cited by: 12
Author(s): Sonia M. Rodríguez‐Ruano, Eliška Juhaňáková, Jakub Vávra, Eva Nováková
Software Mentions: 4
Published: over 4 years ago
10.1093/g3journal/jkab072
Photoperiod-dependent developmental reprogramming of the transcriptional response to seawater entry in Atlantic salmon (Salmo salar)
Cited by: 2
Author(s): Marianne Iversen, Teshome Dagne Mulugeta, Alexander C. West, Even H. Jørgensen, Samuel Martín, Simen Rød Sandve, David G. Hazlerigg
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pone.0242550
Are papers addressing certain diseases perceived where these diseases are prevalent? The proposal to use Twitter data as social-spatial sensors
Cited by: 7
Author(s): Lutz Bornmann, Robin Haunschild, Vishal Patel
Software Mentions: 3
Published: about 4 years ago
10.3389/fcell.2021.642773
Juvenile Huntington’s Disease and Other PolyQ Diseases, Update on Neurodevelopmental Character and Comparative Bioinformatic Review of Transcriptomic and Proteomic Data
Cited by: 7
Author(s): Karolina Świtońska-Kurkowska, Bart Krist, Joanna Delimata, Maciej Figiel
Software Mentions: 3
Published: over 3 years ago
10.3389/fcell.2021.706375
Structural Variations of the 3D Genome Architecture in Cervical Cancer Development
Cited by: 19
Author(s): Muhammad Muzammal Adeel, Hao Jiang, Yibeltal Arega, Kai Cao, Dazhen Lin, Canhui Cao, Gang Cao, Peng Wu, Guoliang Li
Software Mentions: 3
Published: over 3 years ago
10.3389/fpls.2021.647035
Single and Double Mutations in Tomato Ripening Transcription Factors Have Distinct Effects on Fruit Development and Quality Traits
Cited by: 14
Author(s): Jaclyn A Adaskaveg, Christian J. Silva, Peng Huang, Bárbara Blanco-Ulate
Software Mentions: 3
Published: over 3 years ago
10.1186/s13059-020-1938-2
Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice
Cited by: 69
Author(s): Jae Young Choi, Zoe N. Lye, Simon C. Groen, Xiaofeng Dai, Priyesh Rughani, Sophie Zaaijer, Eoghan Harrington, Sissel Juul, Michael D. Purugganan
Software Mentions: 3
Published: almost 5 years ago
10.1038/s41598-019-40955-2
Draft genome of the brown alga, Nemacystus decipiens, Onna-1 strain: Fusion of genes involved in the sulfated fucan biosynthesis pathway
Cited by: 28
Author(s): Koki Nishitsuji, Asuka Arimoto, Yoshimi Higa, Munekazu Mekaru, Mayumi Kawamitsu, Noriyuki Satoh, Eiichi Shoguchi
Software Mentions: 3
Published: over 5 years ago
10.1186/s12864-020-07287-2
Ion channel profiling of the Lymnaea stagnalis ganglia via transcriptome analysis
Cited by: 8
Author(s): Nancy Dong, Julia Bandura, Zhaolei Zhang, Yan Wang, Karine Labadie, Benjamin Noël, Angus Davison, Joris M. Koene, Hong Sun, Marie Agnès Coutellec, Feng Zhang
Software Mentions: 3
Published: almost 4 years ago
10.3389/fcimb.2020.00217
Extracellular Vesicle-Contained microRNA of C. elegans as a Tool to Decipher the Molecular Basis of Nematode Parasitism
Cited by: 9
Author(s): Thomas Duguet, Julien Soichot, Rostyslav Kuzyakiv, Lars Malmström, Lucienne Tritten
Software Mentions: 3
Published: over 4 years ago
10.1186/s12864-021-07457-w
Dynamic expression of Ralstonia solanacearum virulence factors and metabolism-controlling genes during plant infection
Cited by: 27
Author(s): Roger de Pedro Jové, Marina Puigvert, Pau Sebastià, Alberto P. Macho, Jhonatas Sirino Monteiro, Núria S. Coll, João Carlos Setúbal, Marc Valls
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pone.0222921
Computational identification of key genes that may regulate gene expression reprogramming in Alzheimer’s patients
Cited by: 20
Author(s): Judith A. Potashkin, Virginie Bottero, José A. Santiago, James P. Quinn
Software Mentions: 3
Published: about 5 years ago
10.3389/fmolb.2021.686770
NMR Metabolite Profiles of the Bivalve Mollusc Mytilus galloprovincialis Before and After Immune Stimulation With Vibrio splendidus
Cited by: 8
Author(s): Riccardo Frizzo, Enrico Bortoletto, Tobia Riello, Luigi Leanza, Elisabetta Schievano, Paola Venier, Stefano Mammi
Software Mentions: 3
Published: about 3 years ago
10.3389/fgene.2018.00294
Multi-omic Directed Networks Describe Features of Gene Regulation in Aged Brains and Expand the Set of Genes Driving Cognitive Decline
Cited by: 23
Author(s): Shinya Tasaki, Chris Gaiteri, Sara Mostafavi, Lei Yu, Yanling Wang, Philip L. De Jager, David A. Bennett
Software Mentions: 3
Published: over 6 years ago
10.1038/s41598-018-37442-5
Wnt/β-catenin signaling pathway safeguards epigenetic stability and homeostasis of mouse embryonic stem cells
Cited by: 28
Author(s): Ilda Theka, Francesco Sottile, Marco Cammisa, Sarah Bonnin, Marta Sánchez-Delgado, Umberto Di Vicino, Maria Victoria Neguembor, Karthik Arumugam, Francesco Aulicino, David Gabriel Monk, Andrea Riccio, María Pía Cosma
Software Mentions: 3
Published: almost 6 years ago
10.1093/braincomms/fcab083
Defining functional variants associated with Alzheimer’s disease in the induced immune response
Cited by: 13
Author(s): Janet Harwood, Ganna Leonenko, Rebecca Sims, Valentina Escott‐Price, Julie Williams, Peter Holmans
Software Mentions: 3
Published: over 3 years ago