cran: heatmaply | Projects | Ecosyste.ms: Papers

10.1038/s41598-020-78469-x

Cerina: systematic circRNA functional annotation based on integrative analysis of ceRNA interactions
Cited by: 14
Author(s): Jacob Cardenas, Uthra Balaji, Jin Gu
Software Mentions: 23
Published: about 4 years ago

10.1186/s13104-019-4179-2

TCC-GUI: a Shiny-based application for differential expression analysis of RNA-Seq count data
Cited by: 75
Author(s): Wei Su, Jianqiang Sun, Kentaro Shimizu, Koji Kadota
Software Mentions: 20
Published: almost 6 years ago

10.1186/s12859-020-03577-4

NASQAR: a web-based platform for high-throughput sequencing data analysis and visualization
Cited by: 38
Author(s): Ayman Yousif, Nizar Drou, Jillian Rowe, Mohammed Khalfan, Kristin C. Gunsalus
Software Mentions: 17
Published: over 4 years ago

10.1038/s41598-021-81200-z

MuSA: a graphical user interface for multi-OMICs data integration in radiogenomic studies
Cited by: 11
Author(s): Mario Zanfardino, Rossana Castaldo, Katia Pane, Ornella Affinito, Marco Aiello, Marco Salvatore, Monica Franzese
Software Mentions: 15
Published: almost 4 years ago

10.1093/bioinformatics/btx657

heatmaply: an R package for creating interactive cluster heatmaps for online publishing
Cited by: 334
Author(s): Tal Galili, Alan O’Callaghan, Jonathan Savage, Carson Sievert
Software Mentions: 14
Published: about 7 years ago

10.1186/s13073-021-00904-z

An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility
Cited by: 33
Author(s): Liuyang Wang, Thomas J Balmat, Alejandro L. Antonia, Florica J. Constantine, Ricardo Henao, Thomas W. Burke, Andy Ingham, Micah T. McClain, Ephraim L. Tsalik, Emily R Ko, Geoffrey S. Ginsburg, Mark DeLong, Xiling Shen, Christopher W. Woods, Elizabeth R. Hauser, Dennis C. Ko
Software Mentions: 13
Published: over 3 years ago

10.3389/fgene.2019.01079

HiCeekR: A Novel Shiny App for Hi-C Data Analysis
Cited by: 13
Author(s): Lucio Di Filippo, Dario Righelli, Miriam Gagliardi, Maria R. Matarazzo, Claudia Angelini
Software Mentions: 12
Published: about 5 years ago

10.1038/s41598-018-33986-8

Identification of Novel Genes in Human Airway Epithelial Cells associated with Chronic Obstructive Pulmonary Disease (COPD) using Machine-Based Learning Algorithms
Cited by: 24
Author(s): Shayan Mostafaei, Anoshirvan Kazemnejad, Sadegh Azimzadeh Jamalkandi, Soroush Amirhashchi, Seamas C. Donnelly, Michelle E. Armstrong, Mohammad Doroudian
Software Mentions: 11
Published: about 6 years ago

10.1186/s12859-020-3360-x

ShinyOmics: collaborative exploration of omics-data
Cited by: 11
Author(s): Defne Surujon, Tim van Opijnen
Software Mentions: 11
Published: almost 5 years ago

10.1186/s11689-021-09360-7

Modeling familial predictors of proband outcomes in neurogenetic disorders: initial application in XYY syndrome
Cited by: 3
Author(s): Kathleen Wilson, Ari M. Fish, Catherine Mankiw, Anastasia Xenophontos, Allysa Warling, Ethan T. Whitman, Liv S. Clasen, Erin Torres, Jonathan D. Blumenthal, Armin Raznahan
Software Mentions: 10
Published: almost 4 years ago

10.1186/s12864-021-07388-6

Phenotype and multi-omics comparison of Staphylococcus and Streptococcus uncovers pathogenic traits and predicts zoonotic potential
Cited by: 3
Author(s): Niels A. Zondervan, Vítor A. P. Martins dos Santos, María Suárez-Diez, Edoardo Saccenti
Software Mentions: 10
Published: almost 4 years ago

10.3390/v11121085

Evolution of BACON Domain Tandem Repeats in crAssphage and Novel Gut Bacteriophage Lineages
Cited by: 19
Author(s): Patrick A. de Jonge, F. A. Bastiaan von Meijenfeldt, Laura E van Rooijen, Stan J. J. Brouns, Bas E. Dutilh
Software Mentions: 7
Published: about 5 years ago

10.1371/journal.pone.0176334

shinyheatmap: Ultra fast low memory heatmap web interface for big data genomics
Cited by: 97
Author(s): Bohdan B. Khomtchouk, John L. Hennessy, Claes Wahlestedt
Software Mentions: 7
Published: over 7 years ago

10.3389/fgene.2020.589881

The Toolbox for Fiber Flax Breeding: A Pipeline From Gene Expression to Fiber Quality
Cited by: 8
Author(s): Dmitry Galinousky, Natalia Mokshina, Tsimafei Padvitski, Marina Ageeva, Victor Bogdan, A. V. Kilchevsky, Т. А. Горшкова
Software Mentions: 6
Published: about 4 years ago

10.3390/plants10061149

QTL Mapping and Phenotypic Variation for Seedling Vigour Traits in Barley (Hordeum vulgare L.)
Cited by: 7
Author(s): Ludovic J. A. Capo-chichi, Sharla Eldridge, Ammar Elakhdar, Takahiko Kubo, Robert Brueggeman, Anthony O. Anyia
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.ppat.1008477

Immunosuppressive FK506 treatment leads to more frequent EBV-associated lymphoproliferative disease in humanized mice
Cited by: 15
Author(s): Nicole Caduff, Donal McHugh, Anita Murer, Patrick C. Rämer, Ana Raykova, Vanessa Landtwing, Lisa Rieble, Christian W. Keller, Michael Prummer, Laurent Hoffmann, Janice K. P. Lam, Aks Chiang, Friedrich Raulf, Tarik Azzi, Christoph Berger, Tina Rubic-Schneider, Elisabetta Traggiai, Jan D. Lünemann, Michael Kammüller, Christian Münz
Software Mentions: 5
Published: over 4 years ago

10.1186/s12859-017-1790-x

Bayesian Unidimensional Scaling for visualizing uncertainty in high dimensional datasets with latent ordering of observations
Cited by: 13
Author(s): Linh P. Nguyen, Susan Holmes
Software Mentions: 4
Published: over 7 years ago

10.3390/ani11071849

Environmental Streptococcus uberis Associated with Clinical Mastitis in Dairy Cows: Virulence Traits, Antimicrobial and Biocide Resistance, and Epidemiological Typing
Cited by: 10
Author(s): Norhan K. Abd El-Aziz, Ahmed M. Ammar, Hend M. El Damaty, Rehab A. Abd Elkader, Hosam A. Saad, Waleed El-Kazzaz, Eman Khalifa
Software Mentions: 4
Published: over 3 years ago

10.1128/AEM.00853-19

Generation of a Prophage-Free Variant of the Fast-Growing Bacterium Vibrio natriegens
Cited by: 25
Author(s): Eugen Pfeifer, Slawomir Michniewski, Cornelia Gätgens, Eugenia Münch, Felix L. Müller, Tino Polen, Andrew Millard, Bastian Blombach, Julia Frunzke
Software Mentions: 4
Published: over 5 years ago

10.1099/mgen.0.000426

Symbiosis islands of Loteae-nodulating Mesorhizobium comprise three radiating lineages with concordant nod gene complements and nodulation host-range groupings
Cited by: 4
Author(s): Benjamin J. Perry, John T. Sullivan, Elena Colombi, Riley Murphy, Joshua P. Ramsay, Clive W. Ronson
Software Mentions: 4
Published: over 4 years ago

10.3389/fimmu.2021.691725

Severe COVID-19 Recovery Is Associated with Timely Acquisition of a Myeloid Cell Immune-Regulatory Phenotype
Cited by: 29
Author(s): A.C. Trombetta, Guilherme B. Farias, André M. C. Gomes, Ana Godinho‐Santos, Pedro Rosmaninho, Carolina M. Conceição, Joel Laia, Diana Santos, Afonso R. M. Almeida, Catarina Mota, Andréia Gomes, María Luisa Madueño Serrano, Marc Veldhoen, Ana E. Sousa, S. Fernandes
Software Mentions: 4
Published: over 3 years ago

10.3389/fmicb.2020.01721

Alpine Snow Algae Microbiome Diversity in the Coast Range of British Columbia
Cited by: 19
Author(s): Kurt M. Yakimovich, Casey B. Engstrom, Lynne M. Quarmby
Software Mentions: 4
Published: over 4 years ago

10.1002/ece3.6348

Genetic structure among morphotypes of the endangered Brazilian palm<i>Euterpe edulis</i>Mart (Arecaceae)
Cited by: 9
Author(s): Gislaine Mendes Coelho, Alesandro Souza Santos, Ivandilson Pessoa Pinto de Menezes, Roberto Tarazi, Fernanda Maria Oliveira Souza, Maria das Graças Conceição Parada Costa Silva, Fernanda Amato Gaiotto
Software Mentions: 3
Published: over 4 years ago

10.7717/peerj.10121

The Bacteria Genome Pipeline (BAGEP): an automated, scalable workflow for bacteria genomes with Snakemake
Cited by: 8
Author(s): Idowu B. Olawoye, Simon D. W. Frost, Christian Happi
Software Mentions: 3
Published: about 4 years ago

10.1128/mSystems.00876-19

Initial Mapping of the New York City Wastewater Virome
Cited by: 24
Author(s): Kristen M. Gulino, Jahan Rahman, Michelle Badri, James T. Morton, Richard Bonneau, Elodie Ghedin
Software Mentions: 3
Published: over 4 years ago

10.3390/antibiotics9100667

Promising Antibiofilm Agents: Recent Breakthrough against Biofilm Producing Methicillin-Resistant Staphylococcus aureus
Cited by: 43
Author(s): Marwa I. Abd El-Hamid, El-Sayed Y El-Naenaeey, Toka M Kandeel, Wael A. H. Hegazy, Rasha Mosbah, Majed S. Nassar, Muhammed A Bakhrebah, Wesam H. Abdulaal, Nabil A. Alhakamy, Mahmoud M. Bendary
Software Mentions: 3
Published: about 4 years ago

10.3389/fpls.2017.00564

Modular Design of Picroside-II Biosynthesis Deciphered through NGS Transcriptomes and Metabolic Intermediates Analysis in Naturally Variant Chemotypes of a Medicinal Herb, Picrorhiza kurroa
Cited by: 19
Author(s): Varun Kumar, Ankush Bansal, Rajinder Singh Chauhan
Software Mentions: 3
Published: over 7 years ago

10.3389/fpls.2021.722802

Effect and Response of Quercus ilex subsp. ballota [Desf.] Samp. Seedlings From Three Contrasting Andalusian Populations to Individual and Combined Phytophthora cinnamomi and Drought Stresses
Cited by: 18
Author(s): Bonoso San-Eufrasio, María Ángeles Castillejo, Mónica Labella-Ortega, Francisco J. Ruíz-Gómez, Rafael M. Navarro-Cerrillo, Marta Tienda-Parrilla, Jesús V. Jorrín‐Novo, María‐Dolores Rey
Software Mentions: 3
Published: over 3 years ago

10.3390/ani10112067

First Report of aacC5-aadA7Δ4 Gene Cassette Array and Phage Tail Tape Measure Protein on Class 1 Integrons of Campylobacter Species Isolated from Animal and Human Sources in Egypt
Cited by: 10
Author(s): Norhan K. Abd El-Aziz, Ahmed M. Ammar, Mona Hamdy, Adil A. Gobouri, Ehab Azab, Alaa H Sewid
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-021-99097-z

Uncovering the transcriptional response of popcorn (Zea mays L. var. everta) under long-term aluminum toxicity
Cited by: 2
Author(s): Vitor Batista Pinto, Patrícia Rodrigues Ferreira, Pedro Marcus Pereira Vidigal, Tiago Mendes, Maximiller Dal-Bianco, J. V. de Magalhães, José Marcelo Soriano Viana
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0215332

Azospirillum brasilense promotes increases in growth and nitrogen use efficiency of maize genotypes
Cited by: 101
Author(s): Douglas Mariani Zeffa, Luiz Júnior Perini, Mayara Barbosa Silva, Nicholas Vieira de Sousa, Carlos Alberto Scapim, André Luíz Martinez de Oliveira, Antônio Teixeira do Amaral Júnior, Leandro Simões Azeredo Gonçalves
Software Mentions: 3
Published: over 5 years ago

10.1038/s42003-021-01946-0

Diapause vs. reproductive programs: transcriptional phenotypes in a keystone copepod
Cited by: 14
Author(s): Petra H. Lenz, Vittoria Roncalli, Matthew Cieslak, Ann M. Tarrant, Ann M. Castelfranco, Daniel K. Hartline
Software Mentions: 3
Published: over 3 years ago

10.1186/s13104-021-05624-6

Effects of FUdR on gene expression in the C. elegans bacterial diet OP50
Cited by: 3
Author(s): Grace McIntyre, Justin Wright, Hoi Tong Wong, Regina Lamendella, Jason P. Chan
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2020.573335

Riboflavin Biosynthesis and Overproduction by a Derivative of the Human Gut Commensal Bifidobacterium longum subsp. infantis ATCC 15697
Cited by: 14
Author(s): Ana Solopova, Francesca Bottacini, Elena Venturi Degli Esposti, Alberto Amaretti, Stefano Raimondi, Maddalena Rossi, Douwe van Sinderen
Software Mentions: 2
Published: over 4 years ago

10.1186/s12859-021-04100-z

Strain-specific behavior of Mycobacterium tuberculosis in A549 lung cancer cell line
Cited by: 4
Author(s): Shima Hadifar, Shayan Mostafaei, Ava Behrouzi, Abolfazl Fateh, Parisa Riahi, Seyed Davar Siadat, Farzam Vaziri
Software Mentions: 2
Published: over 3 years ago

10.3390/toxins12090561

Insight into Unprecedented Diversity of Cyanopeptides in Eutrophic Ponds Using an MS/MS Networking Approach
Cited by: 23
Author(s): Andreja Kust, Klára Řeháková, Jaroslav Vrba, Vincent Maicher, Jan Mareš, Pavel Hrouzek, Cecilia Chiriac, Zdeňka Benedová, Blanka Tesařová, Kumar Saurav
Software Mentions: 2
Published: over 4 years ago

10.7717/peerj.6577

Genome-wide analysis of long non-coding RNA expression profile in porcine circovirus 2-infected intestinal porcine epithelial cell line by RNA sequencing
Cited by: 10
Author(s): Manxin Fang, Yi Yang, Naidong Wang, Aibing Wang, Yanfeng He, Jiaoshun Wang, Jing You, Zhibang Deng
Software Mentions: 2
Published: almost 6 years ago

10.34133/2020/3194308

A Deep Learning-Based Phenotypic Analysis of Rice Root Distribution from Field Images
Cited by: 20
Author(s): Shota Teramoto, Yusaku Uga
Software Mentions: 2
Published: almost 5 years ago

10.1016/j.gpb.2020.12.004

Large-scale Proteomic and Phosphoproteomic Analyses of Maize Seedling Leaves During De-etiolation
Cited by: 11
Author(s): Zili Gao, Zhuo Shen, Qing Chao, Zhen Yan, Xuan-Liang Ge, Tian-Cong Lu, Haiyan Zheng, Chunrong Qian, Bai-Chen Wang
Software Mentions: 2
Published: over 4 years ago

10.1186/s12864-017-3918-9

Assembling metagenomes, one community at a time
Cited by: 83
Author(s): A.J. van der Walt, Marc W. Van Goethem, Jean‐Baptiste Ramond, Thulani P. Makhalanyane, Oleg N. Reva, Don A. Cowan
Software Mentions: 2
Published: over 7 years ago

10.3389/fimmu.2021.674279

A Virus-Specific Immune Rheostat in the Immunome of Patients Recovering From Mild COVID-19
Cited by: 4
Author(s): Joo Guan Yeo, Jing Yao Leong, Tay Sh, Karen Donceras Nadua, Danielle E. Anderson, Amanda Jin Mei Lim, Xiang Wen Ng, Su Li Poh, D. Guo, Katherine Nay Yaung, Pavanish Kumar, Martin Wasser, Sharifah Nur Hazirah, Nursyuhadah Sutamam, Camillus Chua, Martin Qui, Randy Foo, Akshamal M Gamage, Kee Thai Yeo, Lakshmi Ramakrishna, Thaschawee Arkachaisri, Barnaby Edward Young, David C. Lye, Lin‐Fa Wang, Chia Yin Chong, Natalie Woon Hui Tan, Jiahui Li, Kai Qian Kam, Florent Ginhoux, Koh Cheng Thoon, Jerry Kok Yen Chan, Chee Fu Yung, Salvatore Albani
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-017-08073-z

Global temporal dynamic landscape of pathogen-mediated subversion of Arabidopsis innate immunity
Cited by: 30
Author(s): Bharat Mishra, Yali Sun, Hadia Ahmed, Xiaoyu Liu, M. Shahid Mukhtar
Software Mentions: 1
Published: over 7 years ago

10.3389/fchem.2020.00443

In silico Druggability Assessment of the NUDIX Hydrolase Protein Family as a Workflow for Target Prioritization
Cited by: 15
Author(s): Maurice Michel, Evert Homan, Elisée Wiita, Kia Pedersen, Ingrid Almlöf, Anna‐Lena Gustavsson, Thomas Lundbäck, Thomas Helleday, Ulrika Warpman Berglund
Software Mentions: 1
Published: over 4 years ago

10.3390/genes11040432

The Peptidoglycan Biosynthesis Gene murC in Frankia: Actinorhizal vs. Plant Type
Cited by: 4
Author(s): Fede Berckx, Daniel Wibberg, Joern Kalinowski, Katharina Pawlowski
Software Mentions: 1
Published: over 4 years ago

10.1002/sctm.19-0392

Lowering the increased intracellular pH of human-induced pluripotent stem cell-derived endothelial cells induces formation of mature Weibel-Palade bodies
Cited by: 8
Author(s): Gesa L. Tiemeier, Rozemarijn de Koning, Gangqi Wang, Sarantos Kostidis, Rosalie G.J. Rietjens, Wendy Sol, Sébastien J. Dumas, Martin Giera, Cathelijne W. van den Berg, Jeroen Eikenboom, Bernard M. van den Berg, Peter Carmeliet, Ton J. Rabelink
Software Mentions: 1
Published: almost 5 years ago

Projects: cran: heatmaply

Papers Mentioning heatmaply 45