cran: igraph | Projects | Ecosyste.ms: Papers

10.1093/beheco/araa104

Sequential organization of birdsong: relationships with individual quality and fitness
Cited by: 8
Author(s): Sándor Zsebők, Gábor Herczeg, Miklós Laczi, Gergely Nagy, Éva Vaskúti, Rita Hargitai, Gergely Hegyi, Márton Herényi, Gábor Markó, Balázs Rosivall, Eszter Szász, Eszter Szöllősi, János Török, László Zsolt Garamszegi
Software Mentions: 11
Published: over 3 years ago

10.3389/fbioe.2020.00034

A Guide to Conquer the Biological Network Era Using Graph Theory
Cited by: 129
Author(s): Mikaela Koutrouli, Evangelos Karatzas, David Páez-Espino, Georgios A. Pavlopoulos
Software Mentions: 11
Published: over 4 years ago

10.1186/s12859-017-1579-y

metaX: a flexible and comprehensive software for processing metabolomics data
Cited by: 402
Author(s): Bo Wen, Zhanlong Mei, Chunwei Zeng, Siqi Liu
Software Mentions: 11
Published: about 7 years ago

10.1016/j.xpro.2021.100397

Protocol for comprehensive RNA sequencing analysis of murine long non-coding RNAs during aging
Cited by: 0
Author(s): Xinyue Lu, Qi Zhou, Jin Liu, Li Sun
Software Mentions: 11
Published: almost 3 years ago

10.3389/fmicb.2020.619226

Terroir Is the Main Driver of the Epiphytic Bacterial and Fungal Communities of Mango Carposphere in Reunion Island
Cited by: 4
Author(s): Ahmed Taïbi, Ronan Rivallan, Véronique Broussolle, Dominique Pallet, Sylvie Lortal, Jean-Christophe Meile, Florentin Constancias
Software Mentions: 11
Published: over 3 years ago

10.3389/fpubh.2021.649190

Shifting From Sectoral to Integrated Surveillance by Changing Collaborative Practices: Application to West Nile Virus Surveillance in a Small Island State of the Caribbean
Cited by: 2
Author(s): Mariana Geffroy, Nonito Pagès, David Chavernac, Alexis Dereeper, L. Aubert, Cécile Herrmann-Storck, Anubis Vega-Rúa, Sylvie Lecollinet, Jennifer Pradel
Software Mentions: 11
Published: almost 3 years ago

10.1128/mBio.02699-19

The Toxoplasma gondii Cyst Wall Interactome
Cited by: 24
Author(s): Vincent Tu, Tadakimi Tomita, Tatsuki Sugi, Joshua Mayoral, Bing Han, Rama R. Yakubu, Tere Williams, Aline Luciano Horta, Yanfen Ma, Louis M. Weiss
Software Mentions: 11
Published: about 4 years ago

10.7717/peerj.4152

Population structure and phenotypic variation ofSclerotinia sclerotiorumfrom dry bean (Phaseolus vulgaris) in the United States
Cited by: 28
Author(s): Zhian N. Kamvar, Bimal S. Amaradasa, Rachana Jhala, Serena McCoy, James R. Steadman, Sydney E. Everhart
Software Mentions: 11
Published: over 6 years ago

10.3389/fimmu.2019.00827

Quantitative Prediction of the Landscape of T Cell Epitope Immunogenicity in Sequence Space
Cited by: 60
Author(s): Masato Ogishi, Hiroshi Yotsuyanagi
Software Mentions: 11
Published: about 5 years ago

10.1016/j.cell.2018.08.067

Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease
Cited by: 396
Author(s): James Kinchen, Hannah H. Chen, Kaushal Parikh, Agne Antanaviciute, Marta Jagielowicz, David Fawkner-Corbett, Neil Ashley, Laura Cubitt, Esther Mellado-Gomez, Moustafa Attar, Eshita Sharma, Quin F. Wills, Rory Bowden, Felix Clemens Richter, David Ahern, Kamal D. Puri, Jill Hénault, François G. Gervais, Hashem Koohy, Alison Simmons
Software Mentions: 11
Published: over 5 years ago

10.3390/jcm9082591

Risk of Adverse Drug Events Following the Virtual Addition of COVID-19 Repurposed Drugs to Drug Regimens of Frail Older Adults with Polypharmacy
Cited by: 14
Author(s): Sweilem B. Al Rihani, Matt K. Smith, Ravil Bikmetov, Malavika Deodhar, Pamela Dow, Jacques Turgeon, Véronique Michaud
Software Mentions: 11
Published: almost 4 years ago

10.1016/j.celrep.2020.107908

Meta-Analysis of the Alzheimer’s Disease Human Brain Transcriptome and Functional Dissection in Mouse Models
Cited by: 174
Author(s): Ying-Wooi Wan, Rami Al‐Ouran, Carl Grant Mangleburg, Thanneer M. Perumal, Tom V. Lee, Katherine S. Allison, Vivek Swarup, Cory C. Funk, Chris Gaiteri, Mariet Allen, Minghui Wang, Sarah M. Neuner, Catherine C. Kaczorowski, Vivek Philip, Gareth R. Howell, Heidi Martini‐Stoica, Hui Zheng, Hongkang Mei, Xiaoyan Zhong, Jungwoo Wren Kim, Valina L. Dawson, Ted M. Dawson, Ping‐Chieh Pao, Li‐Huei Tsai, Jean‐Vianney Haure‐Mirande, Michelle E. Ehrlich, Paramita Chakrabarty, Yona Levites, Xue Wang, Eric B. Dammer, Gyan Srivastava, Sumit Mukherjee, Solveig K. Sieberts, Larsson Omberg, Kristen K. Dang, James A. Eddy, Phil Snyder, Yooree Chae, Sandeep Amberkar, Wenbin Wei, Winston Hide, Christoph Preuß, Ayla Ergün, Philip J. Ebert, David Airey, Sara Mostafavi, Lei Yu, Hans‐Ulrich Klein, Gregory W. Carter, David A. Collier, Todd E. Golde, Aĺlan I. Levey, David A. Bennett, Karol Estrada, T. Matthew Townsend, Bin Zhang, Eric E. Schadt, Philip L. De Jager, Nathan D. Price, Nilüfer Ertekin-Taner, Zhandong Liu, Zhandong Liu, Lara M. Mangravite, Benjamin A. Logsdon
Software Mentions: 11
Published: almost 4 years ago

10.3389/fvets.2017.00002

Using Machine Learning to Predict Swine Movements within a Regional Program to Improve Control of Infectious Diseases in the US
Cited by: 28
Author(s): Pablo Valdes–Donoso, Kimberly VanderWaal, Lovell S. Jarvis, Spencer Wayne, Andres Pérez
Software Mentions: 11
Published: over 7 years ago

10.7554/eLife.65372

Image3C, a multimodal image-based and label-independent integrative method for single-cell analysis
Cited by: 6
Author(s): Alice Accorsi, Andrew Box, Robert Peuß, Christopher J. Wood, Alejandro Sánchez Alvarado, Nicolas Rohner
Software Mentions: 11
Published: almost 3 years ago

10.3390/genes12020293

G2PMineR: A Genome to Phenome Literature Review Approach
Cited by: 2
Author(s): John M. A. Wojahn, Stephanie J. Galla, Anthony E. Melton, Sven Buerki
Software Mentions: 10
Published: about 3 years ago

10.1002/ece3.7907

Inventory of the benthic eukaryotic diversity in the oldest European lake
Cited by: 2
Author(s): Benjamin Wilden, Walter Traunspurger, Stefan Geisen
Software Mentions: 10
Published: almost 3 years ago

10.1093/gigascience/giz064

TuBA: Tunable biclustering algorithm reveals clinically relevant tumor transcriptional profiles in breast cancer
Cited by: 6
Author(s): Amartya Singh, Gyan Bhanot, Hossein Khiabanian
Software Mentions: 10
Published: almost 5 years ago

10.1093/gigascience/giy014

Bipartite graphs in systems biology and medicine: a survey of methods and applications
Cited by: 116
Author(s): Georgios A. Pavlopoulos, Panagiota I. Kontou, Athanasia Pavlopoulou, Costas Bouyioukos, Evripides Markou, Pantelis G. Bagos
Software Mentions: 10
Published: about 6 years ago

10.3390/genes11060677

Predicting Functions of Uncharacterized Human Proteins: From Canonical to Proteoforms
Cited by: 6
Author(s): Ekaterina V. Poverennaya, Olga I. Kiseleva, Anastasia Romanova, Mikhail A. Pyatnitskiy
Software Mentions: 10
Published: almost 4 years ago

10.1534/g3.117.300131

CONE: Community Oriented Network Estimation Is a Versatile Framework for Inferring Population Structure in Large-Scale Sequencing Data
Cited by: 12
Author(s): Markku Kuismin, Jon Ahlinder, Mikko Sillanpää
Software Mentions: 10
Published: over 6 years ago

10.1186/s41065-021-00202-z

RNA-Seq based transcriptome analysis in oral lichen planus
Cited by: 5
Author(s): Haoyu Wang, Yiwen Deng, Siqi Peng, Yán Li, Hui Xu, Qingzhong Wang, Zhenhua Shen
Software Mentions: 10
Published: over 2 years ago

10.1016/j.devcel.2018.01.022

Innate Immune Response and Off-Target Mis-splicing Are Common Morpholino-Induced Side Effects in Xenopus
Cited by: 40
Author(s): George E. Gentsch, Thomas Spruce, Rita S. Monteiro, Nick Owens, Stephen R. Martin, James C. Smith
Software Mentions: 10
Published: about 6 years ago

10.7554/eLife.18683

Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development
Cited by: 185
Author(s): Felipe Mora‐Bermúdez, Farhath Badsha, Sabina Kanton, J. Gray Camp, Benjamin Vernot, Kathrin Köhler, Birger Voigt, Keisuke Okita, Tomislav Maričić, Zhisong He, Robert Lachmann, Svante Pääbo, Barbara Treutlein, Wieland B. Huttner
Software Mentions: 10
Published: over 7 years ago

10.1038/s42003-021-02009-0

Pests, diseases, and aridity have shaped the genome of Corymbia citriodora
Cited by: 15
Author(s): Adam Healey, Mervyn Shepherd, Graham J. King, Jakob B. Butler, Jules S. Freeman, David J Lee, Brad M. Potts, Orzenil B. Silva‐Junior, Abdul Baten, Jerry Jenkins, Shengqiang Shu, John T. Lovell, Avinash Sreedasyam, Jane Grimwood, Agnelo Furtado, Dário Grattapaglia, Kerrie Barry, Hope Hundley, Blake A. Simmons, Jeremy Schmutz, René E. Vaillancourt, Robert J. Henry
Software Mentions: 10
Published: about 3 years ago

10.1128/mBio.01105-19

Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant Staphylococcus aureus Lineage from the Indian Subcontinent
Cited by: 42
Author(s): Eike J. Steinig, Sebastián Duchêne, D. Ashley Robinson, Stefan Monecke, Maho Yokoyama, Maisem Laabei, Peter Slickers, Patiyan Andersson, Deborah A. Williamson, Angela Kearns, Richard V. Goering, Elizabeth Dickson, Ralf Ehricht, Margaret Ip, Matthew V. N. O’Sullivan, Geoffrey W. Coombs, Andreas Petersen, Gráinne I. Brennan, Anna C. Shore, David C. Coleman, Annalisa Pantosti, Hermı́nia de Lencastre, Henrik Westh, Nobumichi Kobayashi, Helen Heffernan, Birgit Strommenger, Franziska Layer, Stefan Weber, Hege Vangstein Aamot, Leila Skakni, Sharon J. Peacock, Derek S. Sarovich, Simon R. Harris, Julian Parkhill, Ruth C. Massey, Matthew T. G. Holden, Stephen D. Bentley, Steven Y. C. Tong
Software Mentions: 10
Published: over 4 years ago

10.1371/journal.pbio.2005396

Gut microbiome transition across a lifestyle gradient in Himalaya
Cited by: 109
Author(s): Aashish R. Jha, Emily Davenport, Yoshina Gautam, Dinesh Bhandari, Sarmila Tandukar, Katharine M. Ng, Gabriela K. Fragiadakis, Susan Holmes, Guru Prasad Gautam, Jeff D. Leach, Jeevan Bahadur Sherchand, Carlos D. Bustamante, Justin L. Sonnenburg
Software Mentions: 10
Published: over 5 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: over 8 years ago

10.3390/plants10091921

UHPLC-Orbitrap-MS Tentative Identification of 51 Oleraceins (Cyclo-Dopa Amides) in Portulaca oleracea L. Cluster Analysis and MS2 Filtering by Mass Difference
Cited by: 2
Author(s): Yulian Voynikov, Paraskev Nedialkov, Reneta Gevrenova, Dimitrina Zheleva‐Dimitrova, Vessela Balabanova, Иван Димитров
Software Mentions: 10
Published: over 2 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: over 3 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: over 7 years ago

10.1186/s12859-015-0613-1

tcR: an R package for T cell receptor repertoire advanced data analysis
Cited by: 199
Author(s): Vadim Nazarov, Mikhail V. Pogorelyy, Ekaterina A. Komech, Ivan V. Zvyagin, Dmitriy A. Bolotin, Mikhail Shugay, Dmitriy M. Chudakov, Yuri B. Lebedev, Ilgar Z. Mamedov
Software Mentions: 10
Published: almost 9 years ago

10.3389/fonc.2018.00659

The Role of COL5A2 in Patients With Muscle-Invasive Bladder Cancer: A Bioinformatics Analysis of Public Datasets Involving 787 Subjects and 29 Cell Lines
Cited by: 28
Author(s): Xiangyu Meng, Mingjun Shi, Zhao-Yi Zeng, Chen Chen, Tong-Zu Liu, Qiuji Wu, Shuo Li
Software Mentions: 10
Published: over 5 years ago

10.3389/fmicb.2021.679671

Measurement of Volatile Compounds for Real-Time Analysis of Soil Microbial Metabolic Response to Simulated Snowmelt
Cited by: 4
Author(s): Junhyeong Kim, A. H. Goldstein, Romy Chakraborty, Kolby Jardine, Robert J. Weber, P. Sørensen, Wang Shi, Boris Faybishenko, Pawel K. Misztal, Eoin L. Brodie
Software Mentions: 10
Published: almost 3 years ago

10.1186/s13062-018-0214-9

Predicting clinical outcome of neuroblastoma patients using an integrative network-based approach
Cited by: 13
Author(s): Léon-Charles Tranchevent, Petr V. Nazarov, Tony Kaoma, Georges Pierre Schmartz, Arnaud Muller, Sang Yoon Kim, Jagath C. Rajapakse, Francisco Azuaje
Software Mentions: 10
Published: over 6 years ago

10.1038/s41598-020-79875-x

Relationship between dental and periodontal health status and the salivary microbiome: bacterial diversity, co-occurrence networks and predictive models
Cited by: 23
Author(s): Marta Relvas, Alba Regueira-Iglesias, Carlos Balsa-Castro, Filomena Salazar, José Júlio Pacheco, Cristina Cabral, Corsina Velazco de Henriques, Inmaculada Tomás
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: almost 5 years ago

10.7717/peerj.10264

MutRank: an R shiny web-application for exploratory targeted mutual rank-based coexpression analyses integrated with user-provided supporting information
Cited by: 6
Author(s): Elly Poretsky, Alisa Huffaker
Software Mentions: 10
Published: over 3 years ago

10.1038/tp.2016.119

Transcriptomic signatures of neuronal differentiation and their association with risk genes for autism spectrum and related neuropsychiatric disorders
Cited by: 23
Author(s): Andreas G. Chiocchetti, Denise Haslinger, Jason L. Stein, Luis de la Torre-Ubieta, Enrico Cocchi, Thomas Rothämel, Silvia Lindlar, Regina Waltes, Simone Fulda, Daniel H. Geschwind, Christine M. Freitag
Software Mentions: 10
Published: almost 8 years ago

10.1186/s12859-021-04179-4

GWENA: gene co-expression networks analysis and extended modules characterization in a single Bioconductor package
Cited by: 12
Author(s): Gwenaëlle G. Lemoine, Marie‐Pier Scott‐Boyer, Bathilde Ambroise, Olivier Périn, Arnaud Droit
Software Mentions: 10
Published: almost 3 years ago

10.1371/journal.pone.0131656

iCOSSY: An Online Tool for Context-Specific Subnetwork Discovery from Gene Expression Data
Cited by: 1
Author(s): Ashis Saha, Minji Jeon, Aik Choon Tan, Jaewoo Kang
Software Mentions: 10
Published: almost 9 years ago

10.1038/s41598-018-33077-8

Machine-learning based lipid mediator serum concentration patterns allow identification of multiple sclerosis patients with high accuracy
Cited by: 41
Author(s): Jörn Lötsch, Susanne Schiffmann, Katja Schmitz, R. Brunkhorst, F. Javier Lerch, Nerea Ferreirós, Sabine Wicker, Irmgard Tegeder, Gerd Geißlinger, Alfred Ultsch
Software Mentions: 10
Published: over 5 years ago

10.1186/s12920-019-0628-y

A deep neural network approach to predicting clinical outcomes of neuroblastoma patients
Cited by: 14
Author(s): Léon-Charles Tranchevent, Francisco Azuaje, Jagath C. Rajapakse
Software Mentions: 10
Published: over 4 years ago

10.1038/srep42808

Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data
Cited by: 21
Author(s): Fredrick M. Mobegi, Amelieke J. H. Cremers, Marien I. de Jonge, Stephen D. Bentley, Sacha A. F. T. van Hijum, Aldert Zomer
Software Mentions: 10
Published: over 7 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: about 7 years ago

10.1186/s12917-018-1331-5

A large-scale study of a poultry trading network in Bangladesh: implications for control and surveillance of avian influenza viruses
Cited by: 32
Author(s): Natalie Moyen, Graba Ahmed, Suman Das Gupta, Tenzin Tenzin, Rasheda Khan, Tooba Khan, Nitish Debnath, Mat Yamage, Dirk U. Pfeiffer, Guillaume Fournié
Software Mentions: 10
Published: over 6 years ago

10.1186/s42523-019-0007-1

Impaired glucose metabolism and altered gut microbiome despite calorie restriction of ob/ob mice
Cited by: 15
Author(s): Alireza Kashani, Asker Brejnrod, Chunyu Jin, Timo Kern, Andreas Nygaard Madsen, Louise Holm, Georg K. Gerber, Jens-Christian Holm, Torben Hansen, Birgitte Holst, Manimozhiyan Arumugam
Software Mentions: 10
Published: over 4 years ago

10.1126/sciadv.abc3781

Extensive tissue-specific expression variation and novel regulators underlying circadian behavior
Cited by: 21
Author(s): Maria Litovchenko, Antonio C. A. Meireles-Filho, Michael Frochaux, R. Bevers, Alessio Prunotto, Ane Martín Anduaga, Brian Hollis, Vincent Gardeux, Virginie Braman, Julie Russeil, Sebastián Kadener, Matteo Dal Peraro, Bart Deplancke
Software Mentions: 10
Published: over 3 years ago

10.18632/aging.202174

Periodontitis in elderly patients with type 2 diabetes mellitus: impact on gut microbiota and systemic inflammation
Cited by: 18
Author(s): Jinyou Li, Haifeng Lü, Hengchao Wu, Shunmei Huang, Lufang Chen, Qifeng Gui, Wenjing Zhou, Yichen Yang, Yue Wu, Hua Zhang, Qin Zhang, Yunmei Yang
Software Mentions: 10
Published: over 3 years ago

10.1186/s40168-019-0756-9

Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling
Cited by: 174
Author(s): Jennifer E. Schmidt, Angela D. Kent, Vanessa Brisson, Amélie C. M. Gaudin
Software Mentions: 10
Published: over 4 years ago

10.1371/journal.pone.0179337

The acoustic repertoire and behavioural context of the vocalisations of a nocturnal dasyurid, the eastern quoll (Dasyurus viverrinus)
Cited by: 5
Author(s): Annalie Dorph, Paul G. McDonald
Software Mentions: 9
Published: almost 7 years ago

10.3389/fpls.2015.01172

The Potential of the MAGIC TOM Parental Accessions to Explore the Genetic Variability in Tomato Acclimation to Repeated Cycles of Water Deficit and Recovery
Cited by: 23
Author(s): Julie Ripoll, Laurent Urban, Nadia Bertin
Software Mentions: 9
Published: over 8 years ago

10.1371/journal.pone.0158259

Extensive Transcriptomic and Genomic Analysis Provides New Insights about Luminal Breast Cancers
Cited by: 15
Author(s): Inna Tishchenko, Heloisa Helena Milioli, Carlos Riveros, Pablo Moscato
Software Mentions: 9
Published: almost 8 years ago

10.1371/journal.pone.0084227

Automatic Context-Specific Subnetwork Discovery from Large Interaction Networks
Cited by: 10
Author(s): Ashis Saha, Aik Choon Tan, Jaewoo Kang
Software Mentions: 9
Published: over 10 years ago

10.3390/microorganisms9061313

Influential Insider: Wolbachia, an Intracellular Symbiont, Manipulates Bacterial Diversity in Its Insect Host
Cited by: 5
Author(s): Morgane Ourry, Agathe Crosland, Valérie Lopez, Stéphane A. P. Derocles, Christophe Mougel, Anne‐Marie Cortesero, Denis Poinsot
Software Mentions: 9
Published: almost 3 years ago

10.3389/fonc.2021.624395

Comprehensive Analysis of Expression Regulation for RNA m6A Regulators With Clinical Significance in Human Cancers
Cited by: 12
Author(s): Xiaonan Liu, Pei Wang, Xufei Teng, Zhang Zhang, Shuhui Song
Software Mentions: 9
Published: about 3 years ago

10.3389/fpls.2019.00910

Characterization of the Wood Mycobiome of Vitis vinifera in a Vineyard Affected by Esca. Spatial Distribution of Fungal Communities and Their Putative Relation With Leaf Symptoms
Cited by: 57
Author(s): Giovanni Del Frari, Alex Gobbi, Marie Rønne Aggerbeck, Helena Oliveira, Lars Hestbjerg Hansen, Ricardo B. Ferreira
Software Mentions: 9
Published: almost 5 years ago

10.1186/s12859-018-2254-7

Netpredictor: R and Shiny package to perform drug-target network analysis and prediction of missing links
Cited by: 12
Author(s): Abhik Seal, David Wild
Software Mentions: 9
Published: almost 6 years ago

10.1016/j.anbehav.2017.04.001

Male great tits assort by personality during the breeding season
Cited by: 29
Author(s): Katerina V.‐A. Johnson, Lucy M. Aplin, Ella F. Cole, Damien R. Farine, Josh A. Firth, Samantha C. Patrick, Ben C. Sheldon
Software Mentions: 9
Published: almost 7 years ago

10.3390/ani11092708

Patterns of Exposure and Infection with Microparasites in Iberian Wild Carnivores: A Review and Meta-Analysis
Cited by: 0
Author(s): Javier Millán, Daniel J. Becker
Software Mentions: 9
Published: over 2 years ago

10.1371/journal.pone.0165881

High Interannual Variability in Connectivity and Genetic Pool of a Temperate Clingfish Matches Oceanographic Transport Predictions
Cited by: 14
Author(s): Maria Klein, Sara Teixeira, Jorge Assis, Ester A. Serrão, Emanuel João Gonçalves, Rita Alexandra Borges
Software Mentions: 9
Published: over 7 years ago

10.1371/journal.pone.0067048

Complete Mitochondrial DNA Sequences of the Threadfin Cichlid (Petrochromis trewavasae) and the Blunthead Cichlid (Tropheus moorii) and Patterns of Mitochondrial Genome Evolution in Cichlid Fishes
Cited by: 40
Author(s): Christoph Fischer, Stephan Koblmüller, Christian Gülly, Christian Schlötterer, Christian Sturmbauer, Gerhard G. Thallinger
Software Mentions: 9
Published: almost 11 years ago

10.3389/fpls.2014.00078

Plasma membrane lipidâ€“protein interactions affect signaling processes in sterol-biosynthesis mutants in Arabidopsis thaliana
Cited by: 24
Author(s): Henrik Zauber, Asdrúbal Burgos, Prashanth Garapati, Waltraud X. Schulze
Software Mentions: 9
Published: about 10 years ago

10.1007/s11192-016-1885-6

Scientific workflows for bibliometrics
Cited by: 103
Author(s): Arzu Güler, Cathelijn J. F. Waaijer, Magnus Palmblad
Software Mentions: 9
Published: over 8 years ago

10.1038/s41598-021-93699-3

Analysing omics data sets with weighted nodes networks (WNNets)
Cited by: 1
Author(s): Gabriele Tosadori, Dario Di Silvestre, Fausto Spoto, Pierluigi Mauri, Carlo Laudanna, Giovanni Scardoni
Software Mentions: 9
Published: almost 3 years ago

10.3389/fmicb.2021.616956

Assembly Processes and Co-occurrence Patterns of Abundant and Rare Bacterial Community in the Eastern Indian Ocean
Cited by: 9
Author(s): Liuyang Li, Laxman Pujari, Chao Wu, Dongyang Huang, Yuqiu Wei, Congcong Guo, Guicheng Zhang, Wenzhe Xu, Haijiao Liu, Xingzhou Wang, Min Wang, Jun Sun
Software Mentions: 9
Published: almost 3 years ago

10.3389/fmicb.2021.649981

Differential Impacts of Water Table and Temperature on Bacterial Communities in Pore Water From a Subalpine Peatland, Central China
Cited by: 7
Author(s): Wen Tian, Xiang Xiao, Hongmei Wang
Software Mentions: 9
Published: almost 3 years ago

10.3389/fmicb.2021.641643

Temporal Bacterial Community Diversity in the Nicotiana tabacum Rhizosphere Over Years of Continuous Monocropping
Cited by: 10
Author(s): Yan Ling, Wenyou Zhang, Wangjun Duan, Yizheng Zhang, Wen Zheng, Xianjun Lai
Software Mentions: 9
Published: almost 3 years ago

10.1186/s12885-020-06882-6

Inferring the role of the microbiome on survival in patients treated with immune checkpoint inhibitors: causal modeling, timing, and classes of concomitant medications
Cited by: 39
Author(s): Daniel Spakowicz, Rebecca Hoyd, Mitchell Muniak, Marium Husain, James S. Bassett, Lei Wang, Gabriel Tinoco, Sandip Patel, Jarred Burkart, Abdul Miah, Mingjia Li, Andrew Johns, Madison Grogan, David P. Carbone, Claire F. Verschraegen, Kari Kendra, Gregory A. Otterson, Lang Li, Carolyn J. Presley, Dwight H. Owen
Software Mentions: 9
Published: about 4 years ago

10.7150/thno.53092

Network- and systems-based re-engineering of dendritic cells with non-coding RNAs for cancer immunotherapy
Cited by: 7
Author(s): Xin Lai, Florian S. Dreyer, Martina Cantone, Martin Eberhardt, Kerstin F. Gerer, Tanushree Jaitly, Steffen Uebe, Christopher Lischer, Arif B. Ekici, Jürgen Wittmann, Hans‐Martin Jäck, Niels Schaft, Jan Dörrie, Julio Vera
Software Mentions: 9
Published: over 3 years ago

10.1186/s12889-020-08923-y

Temporal and textual analysis of social media on collective discourses during the Zika virus pandemic
Cited by: 8
Author(s): May O. Lwin, Jiahui Lu, Anita Sheldenkar, Ysa Marie Cayabyab, Andrew Yee, Helen Smith
Software Mentions: 9
Published: almost 4 years ago

10.1264/jsme2.ME18109

Impact of Introduction of Arbuscular Mycorrhizal Fungi on the Root Microbial Community in Agricultural Fields
Cited by: 33
Author(s): Turgut Yiğit Akyol, Rieko Niwa, Hideki Hirakawa, Hayato Maruyama, Takumi Sato, Takae Suzuki, Ayako Fukunaga, Takashi Sato, Shigenobu Yoshida, Keitaro Tawaraya, Masanori Saitô, Tatsuhiro Ezawa, Shusei Sato
Software Mentions: 9
Published: over 5 years ago

10.1186/s12870-019-1679-0

Inferring the regulatory network of the miRNA-mediated response to biotic and abiotic stress in melon
Cited by: 34
Author(s): Alejandro Sanz-Carbonell, Maria Carmen Marqués, Alexander Bustamante, Mario A. Fares, Guillermo Rodrigo, Gustavo Gómez
Software Mentions: 9
Published: about 5 years ago

10.3389/fnhum.2013.00520

Decreased small-world functional network connectivity and clustering across resting state networks in schizophrenia: an fMRI classification tutorial
Cited by: 74
Author(s): Ariana Anderson, Mark S. Cohen
Software Mentions: 9
Published: over 11 years ago

10.1038/s41598-019-56288-z

Interactions with humans are jointly influenced by life history stage and social network factors and reduce group cohesion in moor macaques (Macaca maura)
Cited by: 26
Author(s): Kristen S. Morrow, Hunter Glanz, Putu Oka Ngakan, Erin P. Riley
Software Mentions: 9
Published: over 4 years ago

10.18632/aging.203390

Comprehensive analysis of new prognostic signature based on ferroptosis-related genes in clear cell renal cell carcinoma
Cited by: 8
Author(s): Bin Zheng, Zhihong Niu, Shubin Si, Guiting Zhao, Jianwei Wang, Zhongshun Yao, Fajuan Cheng
Software Mentions: 9
Published: almost 3 years ago

10.1038/s41598-017-15525-z

Single-cell Co-expression Subnetwork Analysis
Cited by: 20
Author(s): Thomas E. Bartlett, Sören Müller, Aaron A. Diaz
Software Mentions: 9
Published: over 6 years ago

10.1002/mbo3.780

Biases in the metabarcoding of plant pathogens using rust fungi as a model system
Cited by: 13
Author(s): Andreas Makiola, Ian A. Dickie, Robert J. Holdaway, Jamie R. Wood, Kate H. Orwin, Charles K. Lee, Travis R. Glare
Software Mentions: 9
Published: over 5 years ago

10.1038/s41598-017-10753-9

Evidence for rangewide panmixia despite multiple barriers to dispersal in a marine mussel
Cited by: 20
Author(s): Carla R. Lourenço, Katy R. Nicastro, Christopher D. McQuaid, Rosa M. Chefaoui, Jorge Assis, M. Taleb, Gerardo I. Zardi
Software Mentions: 9
Published: over 6 years ago

10.3389/fmicb.2020.575707

Evaluating the Potential Antibiotic Resistance Status in Environment Based on the Trait of Microbial Community
Cited by: 9
Author(s): Zhiguo Su, Bei Huang, Quanquan Mu, Donghui Wen
Software Mentions: 9
Published: over 3 years ago

10.1007/s00265-021-03041-0

Neophobia in 10 ungulate species—a comparative approach
Cited by: 14
Author(s): Alina Schaffer, Álvaro López Caicoya, Montserrat Colell, Ruben Holland, Lorenzo von Fersen, Anja Widdig, Federica Amici
Software Mentions: 9
Published: almost 3 years ago

10.1186/s12859-021-04020-y

MeltingPlot, a user-friendly online tool for epidemiological investigation using High Resolution Melting data
Cited by: 4
Author(s): Matteo Perini, Gherard Batisti Biffignandi, Domenico Di Carlo, Ajay Ratan Pasala, Aurora Piazza, Simona Panelli, Gian Vincenzo Zuccotti, Francesco Comandatore
Software Mentions: 9
Published: about 3 years ago

10.1186/s12885-019-6235-7

lionessR: single sample network inference in R
Cited by: 22
Author(s): Marieke L. Kuijjer, Ping-Han Hsieh, John Quackenbush, Kimberly Glass
Software Mentions: 9
Published: over 4 years ago

10.1016/j.molcel.2020.04.008

Single-Cell Analyses Reveal Megakaryocyte-Biased Hematopoiesis in Myelofibrosis and Identify Mutant Clone-Specific Targets
Cited by: 101
Author(s): Bethan Psaila, Guanlin Wang, Alba Rodríguez-Meira, Rong Li, Elisabeth F. Heuston, Lauren C. Murphy, Daniel Yee, Ian S. Hitchcock, Nikolaos Sousos, Jennifer O’Sullivan, Stacie M. Anderson, Yotis A. Senis, Olga K. Weinberg, Monica L. Calicchio, Deena Iskander, Daniel Royston, Dragana Milojković, Irene Roberts, David M. Bodine, Supat Thongjuea, Adam J. Mead
Software Mentions: 9
Published: about 4 years ago

10.7717/peerj.6746

Deterministic processes dominate soil microbial community assembly in subalpine coniferous forests on the Loess Plateau
Cited by: 19
Author(s): Pengyu Zhao, Jiabing Bao, Xue Wang, Yi Liu, Cui Li, Bo Chai
Software Mentions: 9
Published: about 5 years ago

10.3389/fpsyg.2019.02174

Expanding the Map of Intrinsic and Extrinsic Aspirations Using Network Analysis and Multidimensional Scaling: Examining Four New Aspirations
Cited by: 24
Author(s): Frank Martela, Emma L. Bradshaw, Richard M. Ryan
Software Mentions: 9
Published: over 4 years ago

10.1371/journal.pcbi.1007276

Benchmarking network propagation methods for disease gene identification
Cited by: 29
Author(s): Sergio Picart‐Armada, Steven J. Barrett, David Willé, Alexandre Perera-Lluna, Alex Gutteridge, Benoît H. Dessailly
Software Mentions: 9
Published: over 4 years ago

10.1038/s41598-018-33733-z

Human gut microbe co-cultures have greater potential than monocultures for food waste remediation to commodity chemicals
Cited by: 14
Author(s): Matthew Perisin, Christian Sund
Software Mentions: 9
Published: over 5 years ago

10.3390/ijms161226230

MicroRNA-Target Network Inference and Local Network Enrichment Analysis Identify Two microRNA Clusters with Distinct Functions in Head and Neck Squamous Cell Carcinoma
Cited by: 12
Author(s): Steffen Sass, Adriana Pitea, Kristian Unger, Julia Heß, Nikola S. Mueller, Fabian J. Theis
Software Mentions: 9
Published: over 8 years ago

10.1093/gigascience/giy083

Clustering trees: a visualization for evaluating clusterings at multiple resolutions
Cited by: 353
Author(s): Luke Zappia, Alicia Oshlack
Software Mentions: 9
Published: almost 6 years ago

10.1155/2021/7408893

Identification of a Four-lncRNA Prognostic Signature for Colon Cancer Based on Genome Instability
Cited by: 2
Author(s): Duo Yun, Zhimin Yang
Software Mentions: 9
Published: over 2 years ago

10.1038/s41437-018-0059-0

Unexpected mixed-mode transmission and moderate genetic regulation of Symbiodinium communities in a brooding coral
Cited by: 46
Author(s): Kate M. Quigley, Patricia A. Warner, Line K. Bay, Bette L. Willis
Software Mentions: 9
Published: over 6 years ago

10.1371/journal.pone.0056024

Novel Pancreatic Endocrine Maturation Pathways Identified by Genomic Profiling and Causal Reasoning
Cited by: 14
Author(s): Alex Gutteridge, J. Michael Rukstalis, Daniel Ziemek, Mark Tié, Lin Ji, Rebeca Ramos-Zayas, Nancy A. Nardone, Lisa D. Norquay, Martin Brenner, Kim San Tang, John D. McNeish, Rebecca K. Rowntree
Software Mentions: 9
Published: over 11 years ago

10.1089/cmb.2019.0210

bAIcis: A Novel Bayesian Network Structural Learning Algorithm and Its Comprehensive Performance Evaluation Against Open-Source Software
Cited by: 10
Author(s): Lixia Zhang, Leonardo O. Rodrigues, Niven R. Narain, Viatcheslav R. Akmaev
Software Mentions: 9
Published: about 4 years ago

10.1155/2021/5633514

Roles of the Immune/Methylation/Autophagy Landscape on Single-Cell Genotypes and Stroke Risk in Breast Cancer Microenvironment
Cited by: 22
Author(s): Junyi Wu, Jun Qin, Lei Li, Kun-Dong Zhang, Yisheng Chen, Yang Li, Tao Jin, Jianrong Xu
Software Mentions: 9
Published: almost 3 years ago

10.1186/s13059-019-1662-y

EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data
Cited by: 518
Author(s): Aaron T. L. Lun, Samantha J. Riesenfeld, Tallulah Andrews, Tomás Gomes, John C. Marioni
Software Mentions: 9
Published: about 5 years ago

10.1016/j.celrep.2021.109698

Transitions in lineage specification and gene regulatory networks in hematopoietic stem/progenitor cells over human development
Cited by: 33
Author(s): Anindita Roy, Guanlin Wang, Deena Iskander, Sorcha O’Byrne, Natalina E. Elliott, Jennifer O’Sullivan, Gemma Buck, Elisabeth F. Heuston, Wei Wen, Alba Rodríguez-Meira, Peng Hua, Anastasios Karadimitris, Adam J. Mead, David M. Bodine, Irene Roberts, Bethan Psaila, Supat Thongjuea
Software Mentions: 9
Published: over 2 years ago

10.3390/ijms22116160

Spatially Enriched Paralog Rearrangements Argue Functionally Diverse Ribosomes Arise during Cold Acclimation in Arabidopsis
Cited by: 10
Author(s): Federico Martinez‐Seidel, Olga Beine-Golovchuk, Yin-Chen Hsieh, Kheloud El Eshraky, Michał Górka, Bo-Eng Cheong, Erika Vanessa Jiménez-Posada, Dirk Walther, Aleksandra Skirycz, Ute Roessner, Joachim Kopka, Alexandre Augusto Pereira Firmino
Software Mentions: 9
Published: almost 3 years ago

10.1007/s13238-020-00724-8

A practical guide to amplicon and metagenomic analysis of microbiome data
Cited by: 311
Author(s): Yong‐Xin Liu, Yuan Qin, Tong Chen, Meiping Lu, Xubo Qian, Xiaoxuan Guo, Yang Bai
Software Mentions: 9
Published: about 4 years ago

10.1186/s13073-021-00930-x

DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data
Cited by: 72
Author(s): Olivier Poirion, Jiangbin Zheng, Kumardeep Chaudhary, Sijia Huang, Lana X. Garmire
Software Mentions: 9
Published: almost 3 years ago

10.1186/s12950-020-00260-6

Anatabine ameliorates intestinal inflammation and reduces the production of pro-inflammatory factors in a dextran sulfate sodium mouse model of colitis
Cited by: 11
Author(s): Pedro A. Ruiz-Castro, Ulrike Kogel, Giuseppe Lo Sasso, Blaine Phillips, Alain Sewer, Bjoern Titz, Llenalia Garcia, Athanasios Kondylis, Emmanuel Guedj, Dariusz Peric, David Bornand, Rémi Dulize, Céline Merg, Maica Corciulo, Nikolai V. Ivanov, Manuel C. Peitsch, Julia Hoeng
Software Mentions: 8
Published: over 3 years ago

Projects: cran: igraph

Papers Mentioning igraph 1,555