pypi: igraph | Projects | Ecosyste.ms: Papers

10.1186/s13059-015-0675-4

Extensive rewiring of epithelial-stromal co-expression networks in breast cancer
Cited by: 42
Author(s): Eunsun Oh, Stephen M Christensen, Sindhu Ghanta, Jong Cheol Jeong, Octavian Bucur, Benjamin Glass, Laleh Montaser‐Kouhsari, Nicholas W. Knoblauch, Nicholas Bertos, Sadiq M.I. Saleh, Benjamin Haibe‐Kains, Morag Park, Andrew H. Beck
Software Mentions: 7
Published: over 9 years ago

10.3390/ijms21176028

Developmental Methylome of the Medicinal Plant Catharanthus roseus Unravels the Tissue-Specific Control of the Monoterpene Indole Alkaloid Pathway by DNA Methylation
Cited by: 12
Author(s): Thomas Dugé de Bernonville, Stéphane Maury, Alain Delaunay, Christian Daviaud, Cristian Chaparro, Jörg Tost, Sarah E. O’Connor, Vincent Courdavault
Software Mentions: 7
Published: over 4 years ago

10.1186/1756-0500-5-360

LXtoo: an integrated live Linux distribution for the bioinformatics community
Cited by: 5
Author(s): Guangchuang Yu, Li-Gen Wang, Xiaohong Meng, Qing-Yu He
Software Mentions: 7
Published: over 12 years ago

10.1186/s40462-020-00233-7

Urban specialization reduces habitat connectivity by a highly mobile wading bird
Cited by: 7
Author(s): Claire S. Teitelbaum, Jeffrey Hepinstall‐Cymerman, Anjelika Kidd-Weaver, Sonia M. Hernández, Sonia Altizer, Richard J. Hall
Software Mentions: 7
Published: almost 4 years ago

10.15252/msb.20188497

netDx: interpretable patient classification using integrated patient similarity networks
Cited by: 59
Author(s): Shraddha Pai, Shirley Hui, Ruth Isserlin, Manjool Shah, Hussam Kaka, Gary D. Bader
Software Mentions: 7
Published: over 5 years ago

10.7554/eLife.61138

The biphasic and age-dependent impact of klotho on hallmarks of aging and skeletal muscle function
Cited by: 15
Author(s): Zachary Clemens, Sruthi Sivakumar, Abish Pius, Amrita Sahu, Sunita Shinde, Hikaru Mamiya, Nathaniel Luketich, Jian Cui, Purushottam D. Dixit, Joerg D. Hoeck, Sebastian Kreuz, Michael Franti, Aaron Barchowsky, Fabrisia Ambrosio
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pcbi.1006826

Machine learning analysis of gene expression data reveals novel diagnostic and prognostic biomarkers and identifies therapeutic targets for soft tissue sarcomas
Cited by: 65
Author(s): David G.P. van IJzendoorn, Károly Szuhai, Inge H. Briaire-de Bruijn, Marie Kostine, Marieke L. Kuijjer, Judith V.M.G. Bovée
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pone.0234669

netboxr: Automated discovery of biological process modules by network analysis in R
Cited by: 2
Author(s): Eric Minwei Liu, Augustin Luna, Guanlan Dong, Chris Sander
Software Mentions: 7
Published: about 4 years ago

10.3390/ijerph15122893

Comorbidity of Symptoms of Alcohol and Cannabis Use Disorders among a Population-Based Sample of Simultaneous Users. Insight from a Network Perspective
Cited by: 9
Author(s): Stéphanie Baggio, Marlène Sapin, Yasser Khazaal, Joseph Studer, Hans Wolff, Gerhard Gmel
Software Mentions: 7
Published: almost 6 years ago

10.3389/fvets.2018.00269

The Use of Kernel Density Estimation With a Bio-Physical Model Provides a Method to Quantify Connectivity Among Salmon Farms: Spatial Planning and Management With Epidemiological Relevance
Cited by: 27
Author(s): Danielle L. Cantrell, Erin E. Rees, Raphaël Vanderstichel, Jon E. Grant, Ramón Filgueira, Crawford W. Revie
Software Mentions: 7
Published: about 6 years ago

10.1186/s42523-021-00117-0

Gut microbiome is affected by gut region but robust to host physiological changes in captive active-season ground squirrels
Cited by: 3
Author(s): Kirsten Grond, Courtney C. Kurtz, Jasmine J. Hatton, Michelle M. Sonsalla, Khrystyne N. Duddleston
Software Mentions: 7
Published: over 3 years ago

10.1186/1471-2105-15-132

Investigating perturbed pathway modules from gene expression data via structural equation models
Cited by: 19
Author(s): Daniele Pepe, Mario Grassi
Software Mentions: 7
Published: over 10 years ago

10.3390/microorganisms9020227

Use of Network Analysis and Spread Models to Target Control Actions for Bovine Tuberculosis in a State from Brazil
Cited by: 4
Author(s): Nicolás Céspedes Cárdenas, Pilar Pozo, Francisco Paulo Nunes Lopes, José Henrique Hildebrand Grisi-Filho, Julio Álvarez
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pone.0127653

Anatomical Network Analysis Shows Decoupling of Modular Lability and Complexity in the Evolution of the Primate Skull
Cited by: 32
Author(s): Borja Esteve‐Altava, Julia C. Boughner, Rui Diogo, Brian Villmoare, Diego Rasskin‐Gutman
Software Mentions: 7
Published: over 9 years ago

10.1186/1471-2105-12-492

Structural Measures for Network Biology Using QuACN
Cited by: 18
Author(s): Laurin A. J. Mueller, Karl G. Kugler, Armin Graber, Frank Emmert‐Streib, Matthias Dehmer
Software Mentions: 7
Published: almost 13 years ago

10.1128/mSystems.01381-20

Biogeography, Assembly Patterns, Driving Factors, and Interactions of Archaeal Community in Mangrove Sediments
Cited by: 24
Author(s): Zhifeng Zhang, Jie Pan, Yue-Ping Pan, Meng Li
Software Mentions: 7
Published: over 3 years ago

10.1038/s41396-018-0159-0

Distinct patterns and processes of abundant and rare eukaryotic plankton communities following a reservoir cyanobacterial bloom
Cited by: 346
Author(s): Yuanyuan Xue, Huihuang Chen, Jun Yang, Min Liu, Bangqin Huang, Jun Yang
Software Mentions: 7
Published: over 6 years ago

10.1016/j.erss.2020.101704

Grounded reality meets machine learning: A deep-narrative analysis framework for energy policy research
Cited by: 20
Author(s): Ramit Debnath, Sarah Darby, Ronita Bardhan, Kamiar Mohaddes, Minna Sunikka-Blank
Software Mentions: 7
Published: about 4 years ago

10.3389/fphys.2020.612598

Physiological Network From Anthropometric and Blood Test Biomarkers
Cited by: 7
Author(s): Antonio Barajas-Martínez, Elizabeth Ibarra-Coronado, Martha Patricia Sierra-Vargas, Ivette Cruz-Bautista, Paloma Almeda‐Valdés, Carlos A. Aguilar-Salinas, Rubén Fossión, Christopher R. Stephens, Claudia Vargas-Domínguez, Octavio Gamaliel Atzatzi-Aguilar, Yazmín Debray-García, Rogelio García-Torrentera, Karen Bobadilla, María Augusta Naranjo Meneses, Dulce Abril Mena Orozco, Cesar Lam, Vania Jocelyn Martínez-Garcés, Octavio A. Lecona, Arlex Marín-García, A. Frank, Ana Leonor Rivera
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pone.0227804

Exponential random graph model parameter estimation for very large directed networks
Cited by: 26
Author(s): Alex Stivala, Garry Robins, Alessandro Lomi
Software Mentions: 7
Published: almost 5 years ago

10.1002/ece3.6479

Generation and application of river network analogues for use in ecology and evolution
Cited by: 38
Author(s): Luca Carraro, Enrico Bertuzzo, Emanuel A. Fronhofer, Reinhard Furrer, Isabelle Gounand, Andrea Rinaldo, Florian Altermatt
Software Mentions: 7
Published: over 4 years ago

10.7150/thno.44306

Single-cell Transcriptome Profiling reveals Dermal and Epithelial cell fate decisions during Embryonic Hair Follicle Development
Cited by: 39
Author(s): Wei Ge, Shao-Jing Tan, Shan-He Wang, Lan Li, Xiaowen Sun, Wei Shen, Xin Wang
Software Mentions: 7
Published: almost 5 years ago

10.1186/s40168-016-0154-5

Recovering complete and draft population genomes from metagenome datasets
Cited by: 195
Author(s): Naseer Sangwan, Fangfang Xia, Jack A. Gilbert
Software Mentions: 7
Published: over 8 years ago

10.1017/S2045796019000222

Item and domain network structures of the Resilience Scale for Adults in 675 university students
Cited by: 18
Author(s): Giovanni Briganti, Paul Linkowski
Software Mentions: 7
Published: over 5 years ago

10.4056/sigs.3377516

Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron.
Cited by: 8
Author(s): Kristen M. DeAngelis, Patrik D’haeseleer, Dylan Chivian, Blake A. Simmons, Adam P. Arkin, Konstantinos Mavromatis, Stephanie Malfatti, Susannah G. Tringe, Terry C. Hazen
Software Mentions: 7
Published: almost 12 years ago

10.1186/s40168-019-0736-0

Differential dynamics of microbial community networks help identify microorganisms interacting with residue-borne pathogens: the case of Zymoseptoria tritici in wheat
Cited by: 39
Author(s): Lydie Kerdraon, Matthieu Barret, Valérie Laval, Frédéric Suffert
Software Mentions: 7
Published: about 5 years ago

10.1186/s40168-017-0387-y

In-depth resistome analysis by targeted metagenomics
Cited by: 103
Author(s): Val F. Lanza, Fernando Baquero, José Luis Martínez, Ricardo Ramos-Ruíz, Bruno González‐Zorn, Antoine Andremont, Antonio Sánchez-Valenzuela, S. Dusko Ehrlich, Sean Kennedy, Étienne Ruppé, Willem van Schaik, Rob J. L. Willems, Fernando de la Cruz, Teresa M. Coque
Software Mentions: 7
Published: almost 7 years ago

10.1038/s41598-021-88662-1

A network analysis of crab metamorphosis and the hypothesis of development as a process of unfolding of an intensive complexity
Cited by: 2
Author(s): Agustín Ostachuk
Software Mentions: 7
Published: over 3 years ago

10.1038/s41598-021-93645-3

Tree-aggregated predictive modeling of microbiome data
Cited by: 14
Author(s): Jacob Bien, Xiaohan Yan, Léo Simpson, Christian L. Müller
Software Mentions: 7
Published: over 3 years ago

10.1186/s40168-019-0677-7

Maize synthesized benzoxazinoids affect the host associated microbiome
Cited by: 160
Author(s): Enoch Narh Kudjordjie, Rumakanta Sapkota, Stine K. Steffensen, Inge S. Fomsgaard, Mogens Nicolaisen
Software Mentions: 7
Published: over 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

10.1038/s41598-021-94608-4

Non-random associations in group housed rats (Rattus norvegicus)
Cited by: 5
Author(s): Leanne Proops, Camille A. Troisi, Tanja K. Kleinhappel, Teresa Romero
Software Mentions: 7
Published: over 3 years ago

10.1038/s41598-021-81451-w

Network analysis of Down syndrome and SARS-CoV-2 identifies risk and protective factors for COVID-19
Cited by: 33
Author(s): Ilario De Toma, Mara Dierssen
Software Mentions: 7
Published: almost 4 years ago

10.1186/s12859-016-1088-4

RevEcoR: an R package for the reverse ecology analysis of microbiomes
Cited by: 22
Author(s): Yang Cao, Yuanyuan Wang, Xiaofei Zheng, Fēi Li, Xiaochen Bo
Software Mentions: 7
Published: over 8 years ago

10.3389/fpsyg.2021.679016

The Setting Questionnaire for the Ayahuasca Experience: Questionnaire Development and Internal Structure
Cited by: 7
Author(s): Alexandre Augusto de Deus Pontual, Luís Fernando Tófoli, Carlos Fernando Collares, Johannes G. Ramaekers, Clarissa Mendonça Corradi-Webster
Software Mentions: 7
Published: over 3 years ago

10.7717/peerj.11018

Integrated analysis of immune-related long noncoding RNAs as diagnostic biomarkers in psoriasis
Cited by: 13
Author(s): Feixiang Fan, Zhen Huang, Yongfeng Chen
Software Mentions: 7
Published: over 3 years ago

10.1186/1471-2105-10-S11-S14

NATbox: a network analysis toolbox in R
Cited by: 10
Author(s): Shweta S. Chavan, Michael Bauer, Marco Scutari, Radhakrishnan Nagarajan
Software Mentions: 7
Published: about 15 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

10.1007/s00248-019-01426-3

Fusarium Head Blight Modifies Fungal Endophytic Communities During Infection of Wheat Spikes
Cited by: 45
Author(s): Edward C. Rojas, Rumakanta Sapkota, Birgit Jensen, Henning Jørgensen, Tina Henriksson, Lise Nistrup Jørgensen, Mogens Nicolaisen, David B. Collinge
Software Mentions: 7
Published: about 5 years ago

10.1186/s12859-021-04012-y

CeNet Omnibus: an R/Shiny application to the construction and analysis of competing endogenous RNA network
Cited by: 4
Author(s): Wen Xiao, Lin Gao, Tuo Song, Chaoqun Jiang
Software Mentions: 7
Published: almost 4 years ago

10.1111/1751-7915.13640

Synthetic community with six Pseudomonas strains screened from garlic rhizosphere microbiome promotes plant growth
Cited by: 55
Author(s): Lubo Zhuang, Yán Li, Zhenshuo Wang, Yue Yu, Nan Zhang, Chang Yeol Yang, Qingchao Zeng, Qi Wang
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0178904

Modeling the live-pig trade network in Georgia: Implications for disease prevention and control
Cited by: 28
Author(s): Esther A. Kukielka, Beatriz Martínez‐López, Daniel Beltrán‐Alcrudo
Software Mentions: 7
Published: over 7 years ago

10.1038/s41598-019-52865-4

Niche partitioning of microbial communities in riverine floodplains
Cited by: 7
Author(s): Marc Peipoch, Scott R. Miller, Tiago Antão, H. Maurice Valett
Software Mentions: 7
Published: about 5 years ago

10.1038/s41598-020-69265-8

A multilevel statistical toolkit to study animal social networks: the Animal Network Toolkit Software (ANTs) R package
Cited by: 18
Author(s): Sebastián Sosa, Ivan Puga-Gonzalez, Fenghe Hu, Jérôme Pansanel, Xiaohua Xie, Cédric Sueur
Software Mentions: 7
Published: over 4 years ago

10.1007/s00406-019-01078-x

The network structure of schizotypy in the general population
Cited by: 12
Author(s): Bertalan Polner, Eliana Faiola, María Fernanda Urquijo, Inga Meyhöfer, Maria Steffens, Levente Rónai, Nikolaos Koutsouleris, Ulrich Ettinger
Software Mentions: 7
Published: about 5 years ago

10.1038/s41598-018-34138-8

A network analysis of female sexual function: comparing symptom networks in women with decreased, increased, and stable sexual desire
Cited by: 8
Author(s): Annika Gunst, Marlene Werner, Lourens J. Waldorp, Ellen Laan, Marianne Källström, Patrick Jern
Software Mentions: 7
Published: about 6 years ago

10.1590/0074-02760190105

Gene regulatory network inference and analysis of multidrug-resistant Pseudomonas aeruginosa
Cited by: 5
Author(s): Fernando Medeiros Filho, Ana Paula Barbosa do Nascimento, M. Tadeu dos Santos, Ana Paula D’Alincourt Carvalho-Assef, Fabrício Silva
Software Mentions: 7
Published: almost 6 years ago

10.1016/j.celrep.2020.107694

A Landscape of Murine Long Non-Coding RNAs Reveals the Leading Transcriptome Alterations in Adipose Tissue during Aging
Cited by: 24
Author(s): Qi Zhou, Qianfen Wan, Yuxi Jiang, Jin Liu, Qiang Li, Li Sun
Software Mentions: 7
Published: over 4 years ago

10.1038/s41598-017-16050-9

Computational derivation of a molecular framework for hair follicle biology from disease genes
Cited by: 4
Author(s): Rachel K. Severin, Xinwei Li, Kun Qian, Andreas Mueller, Lynn Petukhova
Software Mentions: 7
Published: almost 7 years ago

10.3389/fpsyg.2019.02783

The Network Structure of Adolescent Well-Being Traits: Results From a Large-Scale Chinese Sample
Cited by: 8
Author(s): Guang Zeng, Kaiping Peng, Hu Chuan-Peng
Software Mentions: 7
Published: almost 5 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

10.7717/peerj.281

Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction
Cited by: 1,961
Author(s): Zhian N. Kamvar, Javier F. Tabima, Niklaus J. Grünwald
Software Mentions: 7
Published: over 10 years ago

10.3389/fnins.2021.600462

Dysregulation of MicroRNAs and PIWI-Interacting RNAs in a Caenorhabditis elegans Parkinson’s Disease Model Overexpressing Human α-Synuclein and Influence of tdp-1
Cited by: 10
Author(s): Linjing Shen, Changliang Wang, Liang Chen, Garry Wong
Software Mentions: 7
Published: over 3 years ago

10.1038/s41598-019-43829-9

Tissue-specific genes as an underutilized resource in drug discovery
Cited by: 29
Author(s): Maria Ryaboshapkina, Mårten Hammar
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0047508

Early Social Networks Predict Survival in Wild Bottlenose Dolphins
Cited by: 177
Author(s): Margaret A. Stanton, Janet Mann
Software Mentions: 6
Published: about 12 years ago

10.1371/journal.pone.0128854

ONION: Functional Approach for Integration of Lipidomics and Transcriptomics Data
Cited by: 5
Author(s): Monika Piwowar, Wiktor Jurkowski
Software Mentions: 6
Published: over 9 years ago

10.3389/fmicb.2021.614957

Genomic Metrics Applied to Rhizobiales (Hyphomicrobiales): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains
Cited by: 34
Author(s): Camila Gazolla Volpiano, Fernando Hayashi Sant’Anna, Adriana Ambrosini, Jackson Freitas Brilhante de São José, Anelise Beneduzi, William B. Whitman, Emanuel Maltempi de Souza, Bruno Brito Lisboa, Luciano Kayser Vargas, Luciane Maria Pereira Passaglia
Software Mentions: 6
Published: over 3 years ago

10.3389/fmicb.2017.01452

Watershed Urbanization Linked to Differences in Stream Bacterial Community Composition
Cited by: 88
Author(s): Jacob D. Hosen, Catherine M. Febria, Byron C. Crump, Margaret A. Palmer
Software Mentions: 6
Published: over 7 years ago

10.3389/fmicb.2017.01563

Role of Age-Related Shifts in Rumen Bacteria and Methanogens in Methane Production in Cattle
Cited by: 28
Author(s): Chong Liu, Qinghui Meng, Yongxing Chen, Mengsi Xu, Min Shen, Rui Gao, Shangquan Gan
Software Mentions: 6
Published: over 7 years ago

10.1186/s13068-021-01948-4

Differential expression of starch and sucrose metabolic genes linked to varying biomass yield in Miscanthus hybrids
Cited by: 6
Author(s): Jose J De Vega, Ned Peel, Sarah Purdy, Sarah Hawkins, Iain S. Donnison, Sarah Dyer, Kerrie Farrar
Software Mentions: 6
Published: over 3 years ago

10.1093/biosci/biw175

Using Social Network Measures in Wildlife Disease Ecology, Epidemiology, and Management
Cited by: 101
Author(s): Matthew J. Silk, Darren P. Croft, Richard J. Delahay, David J. Hodgson, Mike Boots, Nicola Weber, Robbie A. McDonald
Software Mentions: 6
Published: almost 8 years ago

10.1371/journal.pone.0150495

Network Analysis of Metabolite GWAS Hits: Implication of CPS1 and the Urea Cycle in Weight Maintenance
Cited by: 11
Author(s): Alice Matone, Marie Pier Scott-Boyer, Jérôme Carayol, Parastoo Fazelzadeh, Grégory Lefebvre, Armand Valsesia, Céline Charon, Jacques Vervoort, Arne Astrup, Wim H. M. Saris, Melissa J. Morine, Jörg Hager
Software Mentions: 6
Published: over 8 years ago

10.1038/srep33555

The Tara Oceans voyage reveals global diversity and distribution patterns of marine planktonic ciliates
Cited by: 65
Author(s): Anna Gimmler, Ralf Korn, Colomban de Vargas, Stéphane Audic, Thorsten Stoeck
Software Mentions: 6
Published: about 8 years ago

10.1016/j.cell.2020.08.013

Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution
Cited by: 302
Author(s): Cameron Cowan, Magdalena Renner, Martina De Gennaro, Brigitte Gross-Scherf, David Goldblum, Yanyan Hou, Martin Munz, Tiago M. Rodrigues, Jacek Król, Tamás Szikra, Rachel Cuttat, Annick Waldt, Panagiotis Papasaikas, Roland Diggelmann, Claudia P. Patino-Alvarez, Patricia Galliker, Stefan Erich Spirig, Dinko Pavlinic, Nadine Gerber-Hollbach, Sven Schuierer, Aldin Srdanovic, Márton Balogh, Riccardo Panero, Ákos Kusnyerik, Arnold Szabó, Michael Stadler, Selim Orgül, Simone Picelli, Pascal W. Hasler, Andreas Hierlemann, Hendrik P. N. Scholl, Guglielmo Roma, Florian Nigsch, Botond Roska
Software Mentions: 6
Published: about 4 years ago

10.3389/fmicb.2020.01036

Niche Differentiation in the Composition, Predicted Function, and Co-occurrence Networks in Bacterial Communities Associated With Antarctic Vascular Plants
Cited by: 29
Author(s): Qian Zhang, Jacquelinne J. Acuña, Nitza G. Inostroza, Paola Durán, Marı́a de la Luz Mora, Michael J. Sadowsky, Milko A. Jorquera
Software Mentions: 6
Published: over 4 years ago

10.1186/s42523-020-00032-w

Oyster hemolymph is a complex and dynamic ecosystem hosting bacteria, protists and viruses
Cited by: 18
Author(s): Samuel Dupont, Ana Lokmer, Erwan Corre, Jean‐Christophe Auguet, Bruno Petton, Ève Toulza, Caroline Montagnani, Gwenn Tanguy, David Pecqueur, Christophe Salmeron, Laure Guillou, Christelle Desnues, Bernard La Scola, Jacques Bou Khalil, Julien de Lorgeril, Guillaume Mitta, Yannick Gueguen, Jean-Michel Escoubas
Software Mentions: 6
Published: over 4 years ago

10.3390/biom10060938

CoRNeA: A Pipeline to Decrypt the Inter-Protein Interfaces from Amino Acid Sequence Information
Cited by: 5
Author(s): Kriti Chopra, Bhawna Burdak, Kaushal Sharma, Ajit Kembhavi, Shekhar C. Mande, Radha Chauhan
Software Mentions: 6
Published: over 4 years ago

10.3389/fmicb.2021.689855

Wheat Rhizosphere Metagenome Reveals Newfound Potential Soil Zn-Mobilizing Bacteria Contributing to Cultivars’ Variation in Grain Zn Concentration
Cited by: 5
Author(s): Sen Wang, Zikang Guo, Li Wang, Yan Zhang, Fan Jiang, Xingshu Wang, Lei Yin, Bo Liu, Hangwei Liu, Hengchao Wang, Anqi Wang, Yingxue Ren, Conghui Liu, Wei Fan, Zhaohui Wang
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0143748

Curriculum Mapping with Academic Analytics in Medical and Healthcare Education
Cited by: 38
Author(s): Martin Komenda, Martin Víta, Christos Vaitsis, Daniel Schwarz, Andrea Pokorná, Nabil Zary, Ladislav Dušek
Software Mentions: 6
Published: almost 9 years ago

10.3389/fmicb.2014.00358

Demonstrating microbial co-occurrence pattern analyses within and between ecosystems
Cited by: 239
Author(s): Ryan J. Williams, Adina Howe, Kirsten Hofmockel
Software Mentions: 6
Published: over 10 years ago

10.1371/journal.pmed.1001944

Evidence for Community Transmission of Community-Associated but Not Health-Care-Associated Methicillin-Resistant Staphylococcus Aureus Strains Linked to Social and Material Deprivation: Spatial Analysis of Cross-sectional Data
Cited by: 60
Author(s): Olga Tosas Auguet, Jason R. Betley, Richard A. Stabler, Amita Patel, Avgousta Ioannou, Helene Marbach, Pasco Hearn, Anna Aryee, Simon Goldenberg, Jonathan A. Otter, Nergish Desai, Tacim Karadag, Chris Grundy, Michael W. Gaunt, Ben S. Cooper, Jonathan D Edgeworth, Theodore Kypraios
Software Mentions: 6
Published: almost 9 years ago

10.1186/s12859-017-1482-6

GSAR: Bioconductor package for Gene Set analysis in R
Cited by: 34
Author(s): Yasir Rahmatallah, Boris Zybailov, Frank Emmert‐Streib, Galina Glazko
Software Mentions: 6
Published: almost 8 years ago

10.1186/s12864-016-2718-y

Ribosome quality control is a central protection mechanism for yeast exposed to deoxynivalenol and trichothecin
Cited by: 11
Author(s): Karl G. Kugler, Zeljkica Jandric, Reinhard Beyer, Eva Klopf, Walter Glaser, Marc Lemmens, Mehrdad Shams, Klaus Mayer, Gerhard Adam, Christoph Schüller
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pone.0187091

DiffSLC: A graph centrality method to detect essential proteins of a protein-protein interaction network
Cited by: 43
Author(s): Divya Mistry, Roger P. Wise, Julie A. Dickerson
Software Mentions: 6
Published: about 7 years ago

10.1186/1471-2105-12-455

iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database
Cited by: 62
Author(s): Antonio M. Mora, Ian Donaldson
Software Mentions: 6
Published: almost 13 years ago

10.1371/journal.pntd.0005246

The Biomphalaria glabrata DNA methylation machinery displays spatial tissue expression, is differentially active in distinct snail populations and is modulated by interactions with Schistosoma mansoni
Cited by: 39
Author(s): Kathrin K. Geyer, Umar Niazi, David Timothy Duval, Céline Cosseau, Chad Tomlinson, Iain W. Chalmers, Martin Swain, David Cutress, Utibe Bickham-Wright, Sabrina E. Munshi, Christoph Grunau, Timothy P. Yoshino, Karl F. Hoffmann
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.pone.0174035

Exploratory graph analysis: A new approach for estimating the number of dimensions in psychological research
Cited by: 342
Author(s): Hudson Golino, Sacha Epskamp
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.pgen.1008198

Bayesian network analysis incorporating genetic anchors complements conventional Mendelian randomization approaches for exploratory analysis of causal relationships in complex data
Cited by: 33
Author(s): Richard Howey, So–Youn Shin, Caroline L Relton, George Davey Smith, Heather J. Cordell
Software Mentions: 6
Published: over 4 years ago

10.1186/s12284-021-00522-8

Strategies and Structure Feature of the Aboveground and Belowground Microbial Community Respond to Drought in Wild Rice (Oryza longistaminata)
Cited by: 11
Author(s): Jian Xie, Xiaoqing Wang, Jiawang Xu, Haizhu Xie, Yaohui Cai, Yizheng Liu, Xia Ding
Software Mentions: 6
Published: about 3 years ago

10.3389/fmicb.2019.02887

Soil Microbial Networks Shift Across a High-Elevation Successional Gradient
Cited by: 13
Author(s): Emily C. Farrer, Dorota L. Porazinska, Marko J. Spasojevic, Andrew J. King, Clifton P. Bueno de Mesquita, Samuel A. Sartwell, J. A. Smith, C. T. White, Steven K. Schmidt, Katharine N. Suding
Software Mentions: 6
Published: almost 5 years ago

10.1093/beheco/ary012

Social interactions predict genetic diversification: an experimental manipulation in shorebirds
Cited by: 4
Author(s): Charles Cunningham, Jorge Parra, Lucy Coals, Lucila Marcela Beltrán-Tolosa, Sama Zefania, Tamás Székely
Software Mentions: 6
Published: almost 7 years ago

10.1098/rspb.2017.1313

Mortality risk and social network position in resident killer whales: sex differences and the importance of resource abundance
Cited by: 68
Author(s): Stephen Ellis, Daniel W. Franks, Stuart Nattrass, Michael A. Cant, Michael N. Weiss, D. K. Giles, Kenneth C. Balcomb, Darren P. Croft
Software Mentions: 6
Published: about 7 years ago

10.1186/s12917-014-0282-8

Successional changes in the chicken cecal microbiome during 42 days of growth are independent of organic acid feed additives
Cited by: 115
Author(s): Brian B. Oakley, R. J. Buhr, Casey W. Ritz, Brian H. Kiepper, M. E. Berrang, Bruce S. Seal, N. A. Cox
Software Mentions: 6
Published: almost 10 years ago

10.1126/sciadv.abj1132

Plasma lipids and growth faltering: A longitudinal cohort study in rural Gambian children
Cited by: 2
Author(s): Gerard Bryan Gonzales, Daniëlla Brals, Bakary Sonko, Fatou Sosseh, Andrew M. Prentice, Sophie E. Moore, Albert Koulman
Software Mentions: 6
Published: about 3 years ago

10.3389/fimmu.2018.00224

Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires
Cited by: 146
Author(s): Enkelejda Miho, Alexander Yermanos, Cédric R. Weber, Christoph T. Berger, Sai T. Reddy, Victor Greiff
Software Mentions: 6
Published: over 6 years ago

10.1186/1752-0509-6-56

Centrality-based pathway enrichment: a systematic approach for finding significant pathways dominated by key genes
Cited by: 62
Author(s): Zuguang Gu, Jialin Liu, Kun-Ming Cao, Junfeng Zhang, Jin Wang
Software Mentions: 6
Published: over 12 years ago

10.7717/peerj.8844

Dynamics of ammonia oxidizers and denitrifiers in response to compost addition in black soil, Northeast China
Cited by: 8
Author(s): Zhihui Yang, Yupeng Guan, Ayodeji Bello, Yanxiang Wu, Jiayi Ding, Leiqi Wang, Yuqing Ren, Guangxin Chen, Wei Yang
Software Mentions: 6
Published: over 4 years ago

10.3389/fmicb.2018.01401

Stoichiometric Shifts in Soil C:N:P Promote Bacterial Taxa Dominance, Maintain Biodiversity, and Deconstruct Community Assemblages
Cited by: 50
Author(s): Zachary T. Aanderud, Sabrina Saurey, Becky A. Ball, Diana H. Wall, John E. Barrett, Mario E. Muscarella, Natasha A. Griffin, Ross A. Virginia, Albert Barberán, Byron J. Adams
Software Mentions: 6
Published: over 6 years ago

10.1172/jci.insight.130090

Cytomegalovirus infection is a risk factor for tuberculosis disease in infants
Cited by: 38
Author(s): Julius Müller, Rachel Tanner, Magali Matsumiya, Margaret Ann Snowden, Bernard Landry, Iman Satti, Stephanie A. Harris, Matthew K. O’Shea, Lisa Stockdale, Leanne Marsay, Agnieszka Chomka, Rachel Harrington-Kandt, Zita‐Rose Manjaly Thomas, Vivek Naranbhai, Elena Stylianou, Stanley Kimbung Mbandi, Mark Hatherill, Gregory Hussey, Hassan Mahomed, Michèle Tameris, J. Bruce McClain, Thomas G. Evans, Willem A. Hanekom, Thomas J. Scriba, Helen McShane, Helen A. Fletcher
Software Mentions: 6
Published: almost 5 years ago

10.7717/peerj.6674

Epizootic ulcerative syndrome causes cutaneous dysbacteriosis in hybrid snakehead (Channa maculata♀ × Channa argus♂)
Cited by: 6
Author(s): Zhifei Li, Guangjun Wang, Kai Zhang, Wangbao Gong, Ermeng Yu, Jingjing Tian, Jun Xie, Deguang Yu
Software Mentions: 6
Published: over 5 years ago

10.1016/j.cell.2016.09.007

Functional Metabolomics Describes the Yeast Biosynthetic Regulome
Cited by: 129
Author(s): Michael Mülleder, Enrica Calvani, Mohammad Tauqeer Alam, Richard Kangda Wang, Florian Eckerstorfer, Aleksej Zelezniak, Markus Ralser
Software Mentions: 6
Published: about 8 years ago

10.1186/s40104-019-0412-z

Co-expression network analysis predicts a key role of microRNAs in the adaptation of the porcine skeletal muscle to nutrient supply
Cited by: 13
Author(s): Emilio Mármol-Sánchez, Yuliaxis Ramayo-Caldas, Raquel Quintanilla, Tainã Figueiredo Cardoso, Rayner González-Prendes, J. Tibau, Marcel Amills
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pone.0185797

A novel network analysis approach reveals DNA damage, oxidative stress and calcium/cAMP homeostasis-associated biomarkers in frontotemporal dementia
Cited by: 21
Author(s): Fernando Palluzzi, Raffaele Ferrari, Francesca Graziano, Valeria Novelli, Giacomina Rossi, Daniela Galimberti, Innocenzo Rainero, Luisa Benussi, Benedetta Nacmias, Amalia C. Bruni, Daniele Cusi, Erika Salvi, Barbara Borroni, Mario Grassi
Software Mentions: 6
Published: about 7 years ago

10.1186/1752-0509-8-17

Identification of core T cell network based on immunome interactome
Cited by: 4
Author(s): Gabriel Teku, Csaba Ortutay, Mauno Vihinen
Software Mentions: 6
Published: almost 11 years ago

10.1371/journal.pcbi.1007162

Cross-species functional modules link proteostasis to human normal aging
Cited by: 10
Author(s): Andrea Komljenović, Hao Li, Vincenzo Sorrentino, Zoltán Kutalik, Johan Auwerx, Marc Robinson‐Rechavi
Software Mentions: 6
Published: over 5 years ago

10.1098/rspb.2016.2872

Stable producer–scrounger dynamics in wild birds: sociability and learning speed covary with scrounging behaviour
Cited by: 28
Author(s): Lucy M. Aplin, Julie Morand‐Ferron
Software Mentions: 6
Published: over 7 years ago

10.1038/sdata.2017.44

Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.
Cited by: 119
Author(s): Sebastian Beier, Axel Himmelbach, Christian Colmsee, Xiao Qi Zhang, Roberto A. Barrero, Qisen Zhang, Lin Li, Micha Bayer, Dan Bolser, Stefan Taudien, Marco Groth, Marius Felder, Alex Hastie, Hana Šimková, Helena Staňková, Jan Vrána, Saki Chan, María Muñoz‐Amatriaín, Rachid Ounit, Steve Wanamaker, Thomas Schmutzer, Lala Aliyeva-Schnorr, Stefano Grasso, Jaakko Tanskanen, Dharanya Sampath, Darren Heavens, Sujie Cao, Brett Chapman, Fei Dai, Yong Han, Hua Li, Xuan Li, Chongyun Lin, John K. McCooke, Cong Tan, Songbo Wang, Shuya Yin, Gaofeng Zhou, Jesse Poland, M. Bellgard, Andreas Houben, Jaroslav Doležel, Sarah Ayling, Stefano Lonardi, Peter Langridge, Gary J. Muehlbauer, Paul J. Kersey, Matthew D. Clark, Mario Cáccamo, Alan H. Schulman, Matthias Platzer, Timothy J. Close, Mats Hansson, Guoping Zhang, Ilka Braumann, Chengdao Li, Robbie Waugh, Uwe Scholz, Nils Stein, Martin Mascher
Software Mentions: 6
Published: over 7 years ago

10.3390/pathogens10030258

Q Fever: Seroprevalence, Risk Factors in Slaughter Livestock and Genotypes of Coxiella burnetii in South Africa
Cited by: 11
Author(s): Maruping L. Mangena, Nomakorinte Gcebe, Rian Pierneef, Peter N. Thompson, Abiodun A. Adesiyun
Software Mentions: 6
Published: over 3 years ago

10.3390/pathogens10040396

Nanopore-Sequencing Characterization of the Gut Microbiota of Melolontha melolontha Larvae: Contribution to Protection against Entomopathogenic Nematodes?
Cited by: 4
Author(s): Ewa Sajnaga, Marcin Skowronek, Agnieszka Kalwasińska, Waldemar Kazimierczak, Karolina Ferenc, Magdalena Lis, Adrian Wiater
Software Mentions: 6
Published: over 3 years ago

10.3389/fgene.2021.698040

Identification of a Ferroptosis Gene Set That Mediates the Prognosis of Squamous Cell Carcinoma of the Head and Neck
Cited by: 1
Author(s): Chunyan Li, Xuemin Wang, Rujia Qin, Zhaoming Zhong, Chuanzheng Sun
Software Mentions: 6
Published: about 3 years ago

Projects: pypi: igraph

Papers Mentioning igraph 1,555