cran: ggraph | Projects | Ecosyste.ms: Papers

10.3389/fonc.2020.617890

Comparative Proteome Identifies Complement Component 3-Mediated Immune Response as Key Difference of Colon Adenocarcinoma and Rectal Adenocarcinoma
Cited by: 9
Author(s): Jun-Ze Liang, Xiaoling Liang, Liye Zhong, Chutian Wu, Jing Zhang, Yang Wang
Software Mentions: 30
Published: over 3 years ago

10.1007/s10734-020-00674-4

Lights, camera, active! appreciation of active learning predicts positive attitudes towards lecture capture
Cited by: 6
Author(s): Emily Nordmann, Anne L. Clark, Elliott Spaeth, Jill R D MacKay
Software Mentions: 18
Published: almost 4 years ago

10.1016/j.cell.2020.12.016

Spatiotemporal analysis of human intestinal development at single-cell resolution
Cited by: 215
Author(s): David Fawkner-Corbett, Agne Antanaviciute, Kaushal Parikh, Marta Jagielowicz, Ana Sousa Gerós, Tarun Gupta, Neil Ashley, Doran Khamis, Darren J. Fowler, Edward Morrissey, Christine M. Cunningham, Johnson Prv., Hashem Koohy, Alison Simmons
Software Mentions: 18
Published: almost 4 years ago

10.1186/s40168-019-0725-3

Baseline microbiota composition modulates antibiotic-mediated effects on the gut microbiota and host
Cited by: 43
Author(s): Aonghus Lavelle, Thomas Hoffmann, Hang-Phuong Pham, Philippe Langella, Éric Guédon, Harry Sokol
Software Mentions: 16
Published: over 5 years ago

10.1371/journal.pone.0244876

Predicting drug-metagenome interactions: Variation in the microbial β-glucuronidase level in the human gut metagenomes
Cited by: 12
Author(s): Moamen M. Elmassry, Sunghwan Kim, Ben Busby
Software Mentions: 16
Published: almost 4 years ago

10.3390/biom10081095

Glutenin and Gliadin, a Piece in the Puzzle of their Structural Properties in the Cell Described through Monte Carlo Simulations
Cited by: 26
Author(s): Joel Markgren, Mikael S. Hedenqvist, Faiza Rasheed, Marie Skepö, Eva Johansson
Software Mentions: 15
Published: over 4 years ago

10.3390/biomedicines9020144

Dietary Rice Bran-Modified Human Gut Microbial Consortia Confers Protection against Colon Carcinogenesis Following Fecal Transfaunation
Cited by: 19
Author(s): Kristopher D. Parker, Akhilendra Kumar Maurya, Hend Ibrahim, Sangeeta Rao, Petronella R. Hove, Dileep Kumar, Rama Kant, B. L. Raina, Rajesh Agarwal, Kristine A. Kuhn, Komal Raina, Elizabeth P. Ryan
Software Mentions: 15
Published: almost 4 years ago

10.3390/biom10121606

A Customizable Analysis Flow in Integrative Multi-Omics
Cited by: 14
Author(s): Samuel M. Lancaster, Akshay Sanghi, Si Wu, M Snyder
Software Mentions: 15
Published: almost 4 years ago

10.1371/journal.pone.0248185

Gut microbiota profiles in diarrheic patients with co-occurrence of Clostridioides difficile and Blastocystis
Cited by: 15
Author(s): Laura Vega, Giovanny Herrera, Marina Muñoz, Manuel A. Patarroyo, Jenny G. Maloney, Mónica Santı́n, Juan David Ramírez
Software Mentions: 14
Published: over 3 years ago

10.1186/s13059-019-1783-3

AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design
Cited by: 20
Author(s): Kathleen C. Keough, Svetlana Lyalina, Michael P. Olvera, Sean Whalen, Bruce R. Conklin, Katherine S. Pollard
Software Mentions: 14
Published: about 5 years ago

10.3389/fpubh.2020.00425

Political Consequences of COVID-19 and Media Framing in South Korea
Cited by: 13
Author(s): Wonkwang Jo, Daesung Chang
Software Mentions: 12
Published: about 4 years ago

10.3389/fmed.2021.644724

Exploring the Clinical Characteristics of COVID-19 Clusters Identified Using Factor Analysis of Mixed Data-Based Cluster Analysis
Cited by: 10
Author(s): Han Liang, Pan Shen, Jiahui Yan, Yao Huang, Xin Ba, Wei Chen Lin, Hui Wang, Ying Huang, Kai Qin, Yu Wei, Zhe Chen, Shenghao Tu
Software Mentions: 12
Published: over 3 years ago

10.3390/jcm10184071

Diagnostic and Prognostic Potential of MiR-379/656 MicroRNA Cluster in Molecular Subtypes of Breast Cancer
Cited by: 2
Author(s): Megha Lal, Asgar Hussain Ansari, Anurag Agrawal, Arijit Mukhopadhyay
Software Mentions: 12
Published: about 3 years ago

10.3390/genes9120569

NeVOmics: An Enrichment Tool for Gene Ontology and Functional Network Analysis and Visualization of Data from OMICs Technologies
Cited by: 13
Author(s): Eduardo Zúñiga-León, Ulises Carrasco-Navarro, Francisco Fierro
Software Mentions: 12
Published: almost 6 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: over 3 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: almost 7 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: almost 4 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: over 6 years ago

10.7717/peerj.11916

The composition, geography, biology and assembly of the coastal flora of the Cape Floristic Region
Cited by: 5
Author(s): B. Adriaan Grobler, Richard M. Cowling
Software Mentions: 8
Published: about 3 years ago

10.1371/journal.pone.0208370

Measuring popularity of ecological topics in a temporal dynamical knowledge network
Cited by: 3
Author(s): Tian-Yuan Huang, Bin Zhao
Software Mentions: 8
Published: almost 6 years ago

10.1038/s41598-021-87837-0

A social network analysis of the spread of COVID-19 in South Korea and policy implications
Cited by: 34
Author(s): Wonkwang Jo, Daesung Chang, Myoungsoon You, Ghi Hoon Ghim
Software Mentions: 8
Published: over 3 years ago

10.3390/biom11050695

Variations in Gut Microbiome are Associated with Prognosis of Hypertriglyceridemia-Associated Acute Pancreatitis
Cited by: 10
Author(s): Xiaomin Hu, Liang Gong, Ronggang Zhou, Ziying Han, Ji Li, Yan Zhang, Shuyang Zhang, Dong Wu
Software Mentions: 8
Published: over 3 years ago

10.1099/mgen.0.000244

Where the plasmids roam: large-scale sequence analysis reveals plasmids with large host ranges
Cited by: 10
Author(s): Lauren Brooks, Mo Kaze, Mark Sistrom
Software Mentions: 7
Published: almost 6 years ago

10.7717/peerj.4718

phylopath: Easy phylogenetic path analysis in R
Cited by: 90
Author(s): Wouter van der Bijl
Software Mentions: 7
Published: over 6 years ago

10.1186/s12864-021-07441-4

A comparative analysis of heart microRNAs in vertebrates brings novel insights into the evolution of genetic regulatory networks
Cited by: 2
Author(s): Pedro Gabriel Nachtigall, Luiz Augusto Bovolenta, James G. Patton, Bastian Fromm, Ney Lemke, Danillo Pinhal
Software Mentions: 7
Published: over 3 years ago

10.3389/fimmu.2020.596514

Intestinal Transcriptome Analysis Reveals Soy Derivative-Linked Changes in Atlantic Salmon
Cited by: 26
Author(s): Viswanath Kiron, Youngjin Park, Prabhugouda Siriyappagouder, Dalia Dahle, Ghana Kalerammana Vasanth, Jorge Dias, Jorge M. O. Fernandes, Mette Sørensen, Viviane Verlhac Trichet
Software Mentions: 7
Published: almost 4 years ago

10.3389/fpls.2019.01521

The Contribution of Functional Traits to the Breeding Progress of Central-European Winter Wheat Under Differing Crop Management Intensities
Cited by: 14
Author(s): Till Rose, Henning Kage
Software Mentions: 7
Published: almost 5 years ago

10.1038/s41598-021-88745-z

A Graph Theory approach to assess nature’s contribution to people at a global scale
Cited by: 13
Author(s): Sílvia de Juan, Andrés Ospina-Álvarez, Sebastián Villasante, Ana Ruiz‐Frau
Software Mentions: 7
Published: over 3 years ago

10.18632/aging.103168

Gut microbiota and metabolite alterations associated with reduced bone mineral density or bone metabolic indexes in postmenopausal osteoporosis
Cited by: 103
Author(s): Jianquan He, Shuaimei Xu, Bangzhou Zhang, Chuanxing Xiao, Zhangran Chen, Fuyou Si, Jifan Fu, Xiaobo Lin, Guohua Zheng, Guangchuang Yu, Jian Chen
Software Mentions: 6
Published: over 4 years ago

10.1186/s12859-020-03818-6

Calculating the most likely intron splicing orders in S. pombe, fruit fly, Arabidopsis thaliana, and humans
Cited by: 2
Author(s): Meng Li
Software Mentions: 6
Published: about 4 years ago

10.3390/metabo11040194

Plasma Metabolomic Profiling in 1391 Subjects with Overweight and Obesity from the SPHERE Study
Cited by: 12
Author(s): G. Frigerio, Chiara Favero, Diego Savino, Rosa Mercadante, Benedetta Albetti, Laura Dioni, Luisella Vigna, Valentina Bollati, Angela Cecilia Pesatori, Silvia Fustinoni
Software Mentions: 6
Published: over 3 years ago

10.3390/microorganisms8091367

Lifestyle, Lineage, and Geographical Origin Influence Temperature-Dependent Phenotypic Variation across Yeast Strains during Wine Fermentation
Cited by: 4
Author(s): Rebecca C. Deed, Lisa I. Pilkington
Software Mentions: 6
Published: about 4 years ago

10.1007/s00421-021-04676-7

Individual cardiovascular responsiveness to work-matched exercise within the moderate- and severe-intensity domains
Cited by: 17
Author(s): Felipe Mattioni Maturana, Philipp Schellhorn, Gunnar Erz, Christof Burgstahler, Manuel Widmann, Barbara Munz, Rogério N. Soares, Juan M. Murias, Ansgar Thiel, Andreas M. Nieß
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-018-37512-8

Sheathless CE-MS based metabolic profiling of kidney tissue section samples from a mouse model of Polycystic Kidney Disease
Cited by: 22
Author(s): Elena Sánchez-López, Guinevere S. M. Kammeijer, Antonio L. Crego, Marı́a Luisa Marina, Rawi Ramautar, Dorien J.M. Peters, Oleg A. Mayboroda
Software Mentions: 6
Published: almost 6 years ago

10.1038/s41598-021-86032-5

A hierarchical regulatory network analysis of the vitamin D induced transcriptome reveals novel regulators and complete VDR dependency in monocytes
Cited by: 18
Author(s): Timothy Warwick, Marcel H. Schulz, Stefan Günther, Ralf Gilsbach, Antonio Neme, Carsten Carlberg, Ralf P. Brandes, Sabine Seuter
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-021-97805-3

Differences and similarities in the conceptualization of COVID-19 and other diseases in the first Italian lockdown
Cited by: 6
Author(s): Claudia María, Ilenia Falcinelli, Arthur-Henri Michalland, Luca Tummolini, Anna M. Borghi
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.pone.0242955

Lessons from movement ecology for the return to work: Modeling contacts and the spread of COVID-19
Cited by: 4
Author(s): Allison K. Shaw, Lauren A. White, Matthew Michalska‐Smith, Elizabeth T. Borer, Meggan E. Craft, Eric W. Seabloom, Emilie C. Snell‐Rood, Michael Travisano
Software Mentions: 5
Published: almost 4 years ago

10.3389/fgene.2021.706854

Crosslink: An R Package for Network Visualization of Grouped Nodes
Cited by: 1
Author(s): Di Liu, Zhijie Bai, Bing Liu, Zongcheng Li
Software Mentions: 5
Published: over 3 years ago

10.3390/ani11051229

A Preliminary Investigation of Social Network Analysis Applied to Dairy Cow Behavior in Automatic Milking System Environments
Cited by: 2
Author(s): Liliana Fadul-Pacheco, Michael Liou, Douglas J. Reinemann, Víctor E. Cabrera
Software Mentions: 5
Published: over 3 years ago

10.1093/hmg/ddaa140

Motor neuron translatome reveals deregulation of SYNGR4 and PLEKHB1 in mutant TDP-43 amyotrophic lateral sclerosis models
Cited by: 13
Author(s): Rita F Marques, Jan Broder Engler, Katrin Küchler, Ross A. Jones, Thomas Lingner, Gabriela Salinas, Thomas H. Gillingwater, Manuel A. Friese, Kent E. Duncan
Software Mentions: 5
Published: over 4 years ago

10.3389/fgene.2020.00680

Identification of a Six-Immune-Related Long Non-coding RNA Signature for Predicting Survival and Immune Infiltrating Status in Breast Cancer
Cited by: 24
Author(s): Zheng Li, Yaming Li, Xiaolong Wang
Software Mentions: 5
Published: over 4 years ago

10.1186/s40168-021-01018-9

Diet and gut microbiome interactions of relevance for symptoms in irritable bowel syndrome
Cited by: 24
Author(s): Julien Tap, Stine Störsrud, Boris Le Nevé, Aurélie Cotillard, Nicolas Pons, Joël Doré, Lena Öhman, Hans Törnblom, Muriel Derrien, Magnus Simrén
Software Mentions: 5
Published: over 3 years ago

10.3389/fmolb.2020.605623

Long Non-coding RNA BTG3-7:1 and JUND Co-regulate C21ORF91 to Promote Triple-Negative Breast Cancer Progress
Cited by: 0
Author(s): Dan Zheng, Xiujing He, Ting Luo, Xiaorong Zhong, Hong Zheng, Jiqiao Yang, Yanchu Li, Jing Jing
Software Mentions: 4
Published: almost 4 years ago

10.1099/mgen.0.000569

Genomic and temporal analyses of Mycobacterium bovis in southern Brazil
Cited by: 7
Author(s): Rudielle de Arruda Rodrigues, Flábio R. Araújo, Alberto M. R. Dávila, Rodrigo Nestor Etges, Julian Parkhill, Andries J. van Tonder
Software Mentions: 4
Published: over 3 years ago

10.1186/s12874-021-01352-4

Symptom clusters among cancer survivors: what can machine learning techniques tell us?
Cited by: 6
Author(s): Koen Ilja Neijenhuijs, Carel F.W. Peeters, Henk van Weert, Pim Cuijpers, I. Verdonck-de Leeuw
Software Mentions: 4
Published: about 3 years ago

10.1038/s41438-021-00502-5

Strawberry sweetness and consumer preference are enhanced by specific volatile compounds
Cited by: 41
Author(s): Zhen Fan, Tomas Hasing, Timothy S. Johnson, Drake M. Garner, Michael L. Schwieterman, Christopher R. Barbey, Thomas A. Colquhoun, Charles A. Sims, M. D. V. de Resende, Vance M. Whitaker
Software Mentions: 4
Published: over 3 years ago

10.3389/fpsyt.2021.628397

Facial and Vocal Expressions During Clinical Interviews Suggest an Emotional Modulation Paradox in Borderline Personality Disorder: An Explorative Study
Cited by: 1
Author(s): Javier Villanueva-Valle, José-Luis Dı́az, Said Jiménez, Andrés Rodríguez-Delgado, Iván Arango de Montis, Areli León-Bernal, Edgar Miranda-Terrés, Jairo Muñóz-Delgado
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0232512

Microbial biofilm community structure and composition on the lithic substrates of Herculaneum Suburban Baths
Cited by: 5
Author(s): Antonino De Natale, Bruno Hay Mele, Paola Cennamo, Angelo Del Mondo, Mariagioia Petraretti, Antonino Pollio
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1006817

Pervasive antagonistic interactions among hybrid incompatibility loci
Cited by: 45
Author(s): Rafael F. Guerrero, Christopher D. Muir, Sarah Josway, Leonie C. Moyle
Software Mentions: 3
Published: over 7 years ago

10.1126/sciadv.abd7225

Global political responsibility for the conservation of albatrosses and large petrels
Cited by: 32
Author(s): Martin Beal, Maria P. Dias, Richard A. Phillips, Steffen Oppel, Carolina Hazin, Elizabeth J. Pearmain, Josh Adams, David J. Anderson, Michelle Antolos, Javier Arata, José Manuel Arcos, John P. Y. Arnould, Jill A. Awkerman, Elizabeth A. Bell, Mike Bell, Mark J. Carey, Ryan D. Carle, Thomas A. Clay, Jaimie Cleeland, Valentina Colodro, Melinda G. Conners, Marta Cruz‐Flores, Richard Cuthbert, Karine Delord, Lorna Deppe, Ben J. Dilley, Herculano Dinis, Graeme Elliott, Fernanda De Felipe, Jonathan J. Felis, Manuela G. Forero, Amanda N. D. Freeman, Akira Fukuda, Jacob González‐Solís, José Pedro Granadeiro, April Hedd, Peter Hodum, José Manuel Igual, A. Jaeger, Todd J. Landers, Matthieu Le Corre, Azwianewi B. Makhado, Benjamin Metzger, Teresa Militão, William A. Montevecchi, Virginia Morera‐Pujol, Leia Navarro-Herrero, Deon Nel, David G. Nicholls, Daniel Oró, Ridha Ouni, Kiyoaki Ozaki, Flavio Quintana, Raül Ramos, Tim Reid, José Manuel Reyes‐González, Christopher T. Robertson, Graham Robertson, Mohamed Salah Romdhane, Peter G. Ryan, Paul M. Sagar, Fumio Sato, Stefan Schoombie, R. Paul Scofield, Scott A. Shaffer, Nirmal Shah, Kim L. Stevens, C. Surman, Robert M. Suryan, Akinori Takahashi, Vikash Tatayah, Graeme A. Taylor, David R. Thompson, Leigh G. Torres, Kath Walker, Ross M. Wanless, Susan M. Waugh, Henri Weimerskirch, Takashi Yamamoto, Zuzana Zajková, Laura Zango, Paulo Catry
Software Mentions: 3
Published: over 3 years ago

10.1128/mSphere.00239-19

Effects of Dairy Manure-Based Amendments and Soil Texture on Lettuce- and Radish-Associated Microbiota and Resistomes
Cited by: 30
Author(s): Giselle Kristi Guron, Gustavo Arango-Argoty, Liqing Zhang, Amy Pruden, Monica A. Ponder
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-89126-2

HNF1A regulates colorectal cancer progression and drug resistance as a downstream of POU5F1
Cited by: 7
Author(s): Shiki Fujino, Norikatsu Miyoshi, Aya Ito, Masayoshi Yasui, Chu Matsuda, Masayuki Ohue, Mamoru Uemura, Tsunekazu Mizushima, Yuichiro Doki, Hidetoshi Eguchi
Software Mentions: 3
Published: over 3 years ago

10.3389/fpls.2017.01524

Identification of Biomarkers for Defense Response to Plasmopara viticola in a Resistant Grape Variety
Cited by: 53
Author(s): Giulia Chitarrini, Evelyn Soini, Samantha Riccadonna, Pietro Franceschi, L. Zulini, Domenico Masuero, A. Vecchione, M. Stefanini, Gabriele Di Gaspero, Fulvio Mattivi, Urška Vrhovšek
Software Mentions: 2
Published: about 7 years ago

10.1186/s13223-021-00569-8

Pre-existing asthma as a comorbidity does not modify cytokine responses and severity of COVID-19
Cited by: 2
Author(s): Jian Luo, Yi‐Ling Chen, Wentao Chen, David A. Duncan, Alexander J. Mentzer, Julian C. Knight, Graham S. Ogg, Paul Klenerman, Ian Pavord, Luzheng Xue
Software Mentions: 2
Published: over 3 years ago

10.3390/ijms221810144

Differential Regulation of Interferon Signaling Pathways in CD4+ T Cells of the Low Type-2 Obesity-Associated Asthma Phenotype
Cited by: 10
Author(s): Fahd Alhamdan, Leigh M. Marsh, Frauke Pedersen, Bilal Alashkar Alhamwe, Clemens Thölken, Petra Ina Pfefferle, Thomas Bahmer, Timm Greulich, Daniel P. Potaczek, Holger Garn
Software Mentions: 1
Published: about 3 years ago

10.1007/s00508-020-01723-9

Emergence of coronavirus disease 2019 (COVID-19) in Austria
Cited by: 46
Author(s): Peter Kreidl, Daniela Schmid, Sabine Maritschnik, Lukas Richter, Wegene Borena, Jakob-Wendelin Genger, Alexandra Popa, Thomas Penz, Christoph Bock, Andréas Bergthaler, Franz Allerberger
Software Mentions: 1
Published: about 4 years ago

10.3389/fpsyg.2021.682838

The Building Blocks of Child Bilingual Code-Mixing: A Cross-Corpus Traceback Approach
Cited by: 6
Author(s): Antje Endesfelder Quick, Stefan Hartmann
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-020-69051-6

Two-omics data revealed commonalities and differences between Rpv12- and Rpv3-mediated resistance in grapevine
Cited by: 22
Author(s): Giulia Chitarrini, Samantha Riccadonna, L. Zulini, A. Vecchione, M. Stefanini, Simone Larger, Massimo Pindo, Alessandro Cestaro, Pietro Franceschi, Gabriele Magris, Serena Foria, Michèle Morgante, Gabriele Di Gaspero, Urška Vrhovšek
Software Mentions: 1
Published: over 4 years ago

Projects: cran: ggraph

Papers Mentioning ggraph 58