10.1186/s12870-017-1062-y

Relationships between drought, heat and air humidity responses revealed by transcriptome-metabolome co-analysis
Cited by: 46
Author(s): Elisabeth Georgii, Ming Jin, Jin Zhao, Basem Kanawati, Philippe Schmitt‐Kopplin, Andreas Albert, Jana Barbro Winkler, Anton R. Schäffner
Software Mentions: 4
Published: over 9 years ago

10.1186/s12889-018-5588-1

Development and testing of a novel survey to assess Stakeholder-driven Community Diffusion of childhood obesity prevention efforts
Cited by: 26
Author(s): Ariella R. Korn, Erin Hennessy, Ross A. Hammond, Steven Allender, Matthew W. Gillman, Matt Kasman, Jaimie McGlashan, Lynne Millar, Brynle Owen, Mark C. Pachucki, Boyd Swinburn, Alison Tovar, Christina D. Economos
Software Mentions: 4
Published: over 8 years ago

10.1186/s12859-019-2659-y

IMMAN: an R/Bioconductor package for Interolog protein network reconstruction, mapping and mining analysis
Cited by: 2
Author(s): Mohieddin Jafari, Payman Nickchi, Soheil Jahangiri, Abdollah Safari, Mehdi Mirzaie, Mohieddin Jafari
Software Mentions: 4
Published: over 7 years ago

10.1186/1752-0509-5-1

Metabolomic correlation-network modules in Arabidopsis based on a graph-clustering approach
Cited by: 118
Author(s): Atsushi Fukushima, Miyako Kusano, Henning Redestig, Masanori Arita, Kazuki Saito
Software Mentions: 4
Published: almost 16 years ago

10.3389/fneur.2020.00773

Computer Modeling of Clot Retrieval—Circle of Willis
Cited by: 6
Author(s): Thanh G. Phan, Henry Ma, Mayank Goyal, James Hilton, Matthew D. Sinnott, Velandai Srikanth, Richard Beare
Software Mentions: 4
Published: about 6 years ago

10.1186/s12918-017-0412-6

Detection of statistically significant network changes in complex biological networks
Cited by: 27
Author(s): Raghvendra Mall, Luigi Cerulo, Halima Bensmail, Antonio Iavarone, Michele Ceccarelli
Software Mentions: 4
Published: over 9 years ago

10.1186/1752-0509-6-72

Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum
Cited by: 12
Author(s): Daniela Beißer, Markus A. Grohme, Joachim Kopka, Marcus Frohme, Ralph O. Schill, Steffen Hengherr, Thomas Dandekar, Gunnar W. Klau, Marcus Dittrich, Tobias Müller
Software Mentions: 4
Published: over 14 years ago

10.1186/1471-2105-16-S17-S5

A computational method for drug repositioning using publicly available gene expression data
Cited by: 4
Author(s): K M Shabana, K. A. Abdul Nazeer, Meeta Pradhan, Mathew Palakal
Software Mentions: 4
Published: almost 11 years ago

10.1186/1752-0509-5-127

Exploring pathway interactions in insulin resistant mouse liver
Cited by: 16
Author(s): Thomas Kelder, Lars Eijssen, Robert Kleemann, Marjan van Erk, Teake Kooistra, Chris T. Evelo
Software Mentions: 4
Published: almost 16 years ago

10.1186/s12918-016-0313-0

XMRF: an R package to fit Markov Networks to high-throughput genetics data
Cited by: 18
Author(s): Ying-Wooi Wan, Genevera I. Allen, Yulia Baker, Eunho Yang, Pradeep Ravikumar, Matthew L. Anderson, Zhandong Liu
Software Mentions: 4
Published: over 10 years ago

10.1186/s12917-018-1406-3

Dynamic network measures reveal the impact of cattle markets and alpine summering on the risk of epidemic outbreaks in the Swiss cattle population
Cited by: 21
Author(s): Beatriz Vidondo, Bernhard Voelkl
Software Mentions: 4
Published: over 8 years ago

10.3389/fmicb.2020.491425

Stream Microbial Community Structured by Trace Elements, Headwater Dispersal, and Large Reservoirs in Sub-Alpine and Urban Ecosystems
Cited by: 5
Author(s): Erin Jones, Natasha A. Griffin, Julia E. Kelso, Gregory T. Carling, Michelle A. Baker, Zachary T. Aanderud
Software Mentions: 4
Published: almost 6 years ago

10.1186/1471-2105-13-294

Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction
Cited by: 25
Author(s): Antonio M. Mora, Ian Donaldson
Software Mentions: 4
Published: almost 14 years ago

10.3758/s13428-018-1186-5

spreadr: An R package to simulate spreading activation in a network
Cited by: 24
Author(s): Cynthia S. Q. Siew
Software Mentions: 4
Published: over 7 years ago

10.3389/fmicb.2019.00708

Antimicrobial Resistance Diversity Suggestive of Distinct Salmonella Typhimurium Sources or Selective Pressures in Food-Production Animals
Cited by: 24
Author(s): Kate C. Mellor, Liljana Petrovska, Nicholas R. Thomson, Kate Harris, S. Reid, Alison E. Mather
Software Mentions: 4
Published: over 7 years ago

10.6026/97320630013025

Elucidation of the sequential transcriptional activity in Escherichia coli using time-series RNA-seq data
Cited by: 1
Author(s): Pui Shan Wong, Kosuke Tashiro, Satoru Kuhara, Sachiyo Aburatani
Software Mentions: 4
Published: almost 10 years ago

10.1242/bio.049809

Single cell force profiling of human myofibroblasts reveals a biophysical spectrum of cell states
Cited by: 6
Author(s): T. B. Layton, Lynn M. Williams, Huw Colin‐York, Fiona E. McCann, Marisa Cabrita, Marc Feldmann, Cameron Brown, Weilin Xie, Marco Fritzsche, Dominic Furniss, Jagdeep Nanchahal
Software Mentions: 4
Published: almost 7 years ago

10.1111/acel.13073

Global metabolic profiling to model biological processes of aging in twins
Cited by: 29
Author(s): Bryan Bunning, Kévin Contrepois, Brittany Lee‐McMullen, Gopal Krishna Dhondalay, Wenming Zhang, Dana Tupa, Olivia Raeber, Manisha Desai, Kari Nadeau, M Snyder
Software Mentions: 4
Published: almost 7 years ago

10.3389/fpsyg.2018.02252

Orthographic Networks in the Developing Mental Lexicon. Insights From Graph Theory and Implications for the Study of Language Processing
Cited by: 5
Author(s): Jutta Trautwein, Sascha Schroeder
Software Mentions: 4
Published: almost 8 years ago

10.1155/2015/167249

mmnet: An R Package for Metagenomics Systems Biology Analysis
Cited by: 10
Author(s): Yang Cao, Xiaofei Zheng, Fēi Li, Xiaochen Bo
Software Mentions: 4
Published: almost 12 years ago

10.3390/biom10060850

Can We Assume the Gene Expression Profile as a Proxy for Signaling Network Activity?
Cited by: 8
Author(s): Mehran Piran, Reza Karbalaei, Mehrdad Piran, Jehad Aldahdooh, Mehdi Mirzaie, Naser Ansari-Pour, Jing Tang, Mohieddin Jafari
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2018.01201

Microbial Community Structure and Associations During a Marine Dinoflagellate Bloom
Cited by: 93
Author(s): Jin Zhou, Mindy L. Richlen, Taylor R. Sehein, David M. Kulis, Donald M. Anderson, Zhonghua Cai
Software Mentions: 4
Published: over 8 years ago

10.3389/fmicb.2016.01688

Systems Biomedicine of Rabies Delineates the Affected Signaling Pathways
Cited by: 19
Author(s): Sadegh Azimzadeh Jamalkandi, Sayed‐Hamidreza Mozhgani, Hamid Gholami Pourbadie, Mehdi Mirzaie, Farshid Noorbakhsh, Behrouz Vaziri, Alireza Gholami, Naser Ansari-Pour, Mohieddin Jafari
Software Mentions: 4
Published: almost 10 years ago

10.1186/s12859-017-1762-1

Variable selection for disease progression models: methods for oncogenetic trees and application to cancer and HIV
Cited by: 3
Author(s): Katrin Hainke, Sebastian Szugat, Roland Fried, Jörg Rahnenführer
Software Mentions: 4
Published: over 9 years ago

10.3390/brainsci11010094

Assessing the Relationship between Verbal and Nonverbal Cognitive Abilities Using Resting-State EEG Functional Connectivity
Cited by: 1
Author(s): Inna Feklicheva, Ilya Zakharov, Nadezda Chipeeva, Ekaterina Maslennikova, Svetlana Korobova, Timofey Adamovich, Victoria Ismatullina, Sergey Malykh
Software Mentions: 4
Published: almost 6 years ago

10.1007/s00262-020-02833-z

Early changes in the circulating T cells are associated with clinical outcomes after PD-L1 blockade by durvalumab in advanced NSCLC patients
Cited by: 14
Author(s): Elliot Naidus, Jérôme Bouquet, David Y. Oh, Timothy J. Looney, Hai Yang, Lawrence Fong, Nathan Standifer, Li Zhang
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmicb.2020.579290

Spatiotemporal Patterns in Diversity and Assembly Process of Marine Protist Communities of the Changjiang (Yangtze River) Plume and Its Adjacent Waters
Cited by: 8
Author(s): Xin Guo, Lianghuan Wu, Lingfeng Huang
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0230941

Demarcating geographic regions using community detection in commuting networks with significant self-loops
Cited by: 14
Author(s): Mark He, Joseph Glasser, Nathaniel Pritchard, Shankar Bhamidi, Nikhil Kaza
Software Mentions: 4
Published: over 6 years ago

10.3390/metabo10060220

Non-Targeted Metabolite Profiles and Sensory Properties Elucidate Commonalities and Differences of Wines Made with the Same Variety but Different Cultivar Clones
Cited by: 6
Author(s): Álvaro Cuadros-Inostroza, Claudio Verdugo-Alegría, Lothar Willmitzer, Yerko Moreno-Simunovic, José G. Vallarino
Software Mentions: 4
Published: over 6 years ago

10.1007/s00248-021-01719-6

Assessing Biotic and Abiotic Interactions of Microorganisms in Amazonia through Co-Occurrence Networks and DNA Metabarcoding
Cited by: 8
Author(s): Camila Duarte Ritter, Dominik Forster, Josué A. R. Azevedo, Alexandre Antonelli, R. Henrik Nilsson, Martha E. Trujillo, Micah Dunthorn
Software Mentions: 4
Published: over 5 years ago

10.1099/mgen.0.000070

Phylogenetic structure of European Salmonella Enteritidis outbreak correlates with national and international egg distribution network
Cited by: 53
Author(s): Tim Dallman, Thomas Inns, Thibaut Jombart, Philip Ashton, Nicholas J. Loman, Carol Chatt, Ute Messelhaeusser, Wolfgang Rabsch, Sandra Simon, Sergejs Nikisins, Helen Bernard, Simon Le Hello, Nathalie Jourdan da-Silva, Christian Kornschober, Joël Mossong, Peter M. Hawkey, Elizabeth de Pinna, Kathie Grant, Paul Cleary
Software Mentions: 4
Published: about 10 years ago

10.1099/mgen.0.000108

A population genomics approach to exploiting the accessory 'resistome' of Escherichia coli
Cited by: 18
Author(s): Robert Goldstone, David George Emslie Smith
Software Mentions: 4
Published: over 9 years ago

10.3389/fmicb.2020.526898

Seasonal Changes in Pinus tabuliformis Root-Associated Fungal Microbiota Drive N and P Cycling in Terrestrial Ecosystem
Cited by: 12
Author(s): Haihua Wang, Honglong Chu, Qing Dou, Huijin Feng, Ming Tang, Shuoxin Zhang, Chunyan Wang
Software Mentions: 4
Published: almost 6 years ago

10.1002/mbo3.727

Change in the intestinal bacterial community structure associated with environmental microorganisms during the growth of <i>Eriocheir sinensis</i>
Cited by: 25
Author(s): Chenhe Wang, Yanfeng Zhou, Dawei Lv, You Ge, Huan Li, You Yang
Software Mentions: 4
Published: about 8 years ago

10.1002/mbo3.1200

Active microbial ecosystem in glacier basal ice fuelled by iron and silicate comminution‐derived hydrogen
Cited by: 2
Author(s): Mario Toubes-Rodrigo, Sanja Potgieter‐Vermaak, Robin Sen, Edda Sigurdís Oddsdóttir, David R. Elliott, Simon J. Cook
Software Mentions: 4
Published: over 5 years ago

10.1186/s40168-019-0721-7

Longitudinal investigation of the swine gut microbiome from birth to market reveals stage and growth performance associated bacteria
Cited by: 231
Author(s): Xiaofan Wang, Tsung Cheng Tsai, Feilong Deng, Xiaoyuan Wei, Jianmin Chai, J. S. Knapp, J. K. Apple, C. V. Maxwell, Jung Ae Lee, Ying Liu, Jiangchao Zhao
Software Mentions: 4
Published: over 7 years ago

10.1186/s12859-019-2800-y

Integrating data and knowledge to identify functional modules of genes: a multilayer approach
Cited by: 10
Author(s): Lifan Liang, Vicky Chen, Kunju Zhu, Xiao-Nan Fan, Xinghua Lu, Songjian Lu
Software Mentions: 4
Published: over 7 years ago

10.1186/s40168-020-00827-8

Disentangling the mechanisms shaping the surface ocean microbiota
Cited by: 131
Author(s): Ramiro Logares, Ina Maria Deutschmann, Pedro C. Junger, Caterina R. Giner, Anders K. Krabberød, Thomas Sebastian Benedikt Schmidt, Laura Rubinat-Ripoll, Mireia Mestre, Guillem Salazar, Clara Ruiz‐González, Marta Sebastián, Colomban de Vargas, Silvia G. Acinas, Carlos M. Duarte, Josep M. Gasol, Ramón Massana
Software Mentions: 4
Published: over 6 years ago

10.1186/s40168-015-0089-2

Linear growth faltering in infants is associated with Acidaminococcus sp. and community-level changes in the gut microbiota
Cited by: 101
Author(s): Ethan Gough, David A. Stephens, Erica E. M. Moodie, Andrew J. Prendergast, Rebecca J. Stoltzfus, Jean H. Humphrey, Amee R. Manges
Software Mentions: 4
Published: over 11 years ago

10.1186/s40168-021-01016-x

Revealing taxon-specific heavy metal-resistance mechanisms in denitrifying phosphorus removal sludge using genome-centric metaproteomics
Cited by: 27
Author(s): Yuan Lin, Liye Wang, Ke Xu, Kan Li, Hongqiang Ren
Software Mentions: 4
Published: over 5 years ago

10.1186/s12859-018-2131-4

On the rank-distance median of 3 permutations
Cited by: 4
Author(s): Leonid Chindelevitch, João Paulo Pereira Zanetti, João Meidânis
Software Mentions: 4
Published: over 8 years ago

10.1186/s40168-020-00799-9

Rhizosphere protists are key determinants of plant health
Cited by: 123
Author(s): Wu Xiong, Yuqi Song, Kun Yang, Yian Gu, Zhong Wei, George A. Kowalchuk, Yangchun Xu, Alexandre Jousset, Qirong Shen, Stefan Geisen
Software Mentions: 4
Published: over 6 years ago

10.3390/microorganisms7120611

Elevation is Associated with Human Skin Microbiomes
Cited by: 16
Author(s): Huan Li, Yijie Wang, Qiaoling Yu, Tianshu Feng, Rui Zhou, Liye Shao, Jiapeng Qu, Nan Li, Tingbei Bo, Huakun Zhou
Software Mentions: 4
Published: almost 7 years ago

10.3390/microorganisms8111631

Rapid Changes in Microbial Community Structures along a Meandering River
Cited by: 11
Author(s): Perrine Cruaud, Adrien Vigneron, Caetano C. Dorea, Manuel J. Rodriguez, Steve J. Charette
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2020.575207

Fungal Communities in Sediments Along a Depth Gradient in the Eastern Tropical Pacific
Cited by: 9
Author(s): Keilor Rojas‐Jimenez, Hans‐Peter Grossart, Erik E. Cordes, Jorge Cortés
Software Mentions: 4
Published: almost 6 years ago

10.3390/microorganisms8020190

Keystone Species and Modularity in Microbial Hydrocarbon Degradation Uncovered by Network Analysis and Association Rule Mining
Cited by: 5
Author(s): Florian Centler, Sarah Günnigmann, Ingo Fetzer, Annelie Wendeberg
Software Mentions: 4
Published: almost 7 years ago

10.3390/microorganisms9030549

Lake Ecosystem Robustness and Resilience Inferred from a Climate-Stressed Protistan Plankton Network
Cited by: 16
Author(s): Dominik Forster, Zhishuai Qu, Gianna Pitsch, Estelle P. Bruni, Barbara Kammerlander, Thomas Pröschold, Bettina Sonntag, Thomas Posch, Thorsten Stoeck
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2020.607396

Distinct Microbial Communities in Adjacent Rock and Soil Substrates on a High Arctic Polar Desert
Cited by: 16
Author(s): Yong‐Hoe Choe, Min‐Cheol Kim, Yoo Kyung Lee
Software Mentions: 4
Published: almost 6 years ago

10.1016/j.mcpro.2021.100061

Protein Phosphorylation in Depolarized Synaptosomes: Dissecting Primary Effects of Calcium from Synaptic Vesicle Cycling
Cited by: 8
Author(s): Ivan Silbern, Kuan‐Ting Pan, Maksims Fiošins, Stefan Bonn, Silvio O. Rizzoli, Eugenio F. Fornasiero, Henning Urlaub, Reinhard Jahn
Software Mentions: 4
Published: almost 6 years ago

10.3390/molecules24142529

High Impact: The Role of Promiscuous Binding Sites in Polypharmacology
Cited by: 8
Author(s): Natacha Cerisier, Michel Petitjean, Leslie Regad, Quentin Bayard, Manon Réau, Anne Badel, Anne-Claude Camproux
Software Mentions: 4
Published: over 7 years ago

10.3390/molecules15085354

Effects of Time Point Measurement on the Reconstruction of Gene Regulatory Networks
Cited by: 10
Author(s): Wenying Yan, Huangqiong Zhu, Yang Yang, Jiajia Chen, Yuanyuan Zhang, Bairong Shen
Software Mentions: 4
Published: over 16 years ago

10.1002/mgg3.214

Computational assessment of feature combinations for pathogenic variant prediction
Cited by: 12
Author(s): Eva König, Johannes Michael Rainer, Francisco S. Domingues
Software Mentions: 4
Published: over 10 years ago

10.3389/fmicb.2019.01407

Predominance of Cand. Patescibacteria in Groundwater Is Caused by Their Preferential Mobilization From Soils and Flourishing Under Oligotrophic Conditions
Cited by: 143
Author(s): Martina Herrmann, Carl‐Eric Wegner, Martin Taubert, Patricia Geesink, Katharina Lehmann, Lijuan Yan, Robert Lehmann, Kai Uwe Totsche, Kirsten Küsel
Software Mentions: 4
Published: over 7 years ago

10.1016/j.jvacx.2019.100019

Mapping the Dutch vaccination debate on Twitter: Identifying communities, narratives, and interactions
Cited by: 18
Author(s): Roel Lutkenhaus, Jeroen Jansz, Martine Bouman
Software Mentions: 4
Published: over 7 years ago

10.3389/fmicb.2017.00991

Multigenerational Influences of the Fut2 Gene on the Dynamics of the Gut Microbiota in Mice
Cited by: 16
Author(s): Philipp Rausch, Sven Künzel, Abdulhadi Suwandi, Guntram A. Grassl, Philip Rosenstiel, John F. Baines
Software Mentions: 4
Published: over 9 years ago

10.14202/vetworld.2018.1203-1209

An innovative approach to predict immune-associated genes mutually targeted by cow and human milk microRNAs expression profiles
Cited by: 6
Author(s): Kaj Chokeshaiusaha, Thanida Sananmuang, Denis Puthier, Catherine Nguyen
Software Mentions: 4
Published: about 8 years ago

10.3390/v12090931

Tracking Community Timing: Pattern and Determinants of Seasonality in Culicoides (Diptera: Ceratopogonidae) in Northern Florida
Cited by: 8
Author(s): Agustín Quaglia, Erik M. Blosser, Bethany L. McGregor, Alfred E. Runkel, Kristin E. Sloyer, Dinesh Erram, Samantha M. Wisely, Nathan D. Burkett‐Cadena
Software Mentions: 4
Published: about 6 years ago

10.3390/v13010063

Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts
Cited by: 45
Author(s): Lakshminarayan M. Iyer, Vivek Anantharaman, Arunkumar Krishnan, A. Maxwell Burroughs, L. Aravind
Software Mentions: 4
Published: almost 6 years ago

10.3389/fpsyg.2020.00742

All Happy Emotions Are Alike but Every Unhappy Emotion Is Unhappy in Its Own Way: A Network Perspective to Academic Emotions.
Cited by: 3
Author(s): Markus Mattsson, Telle Hailikari, Anna Parpala
Software Mentions: 4
Published: almost 7 years ago

10.3390/pathogens9110903

Quantitative Risk Assessment for the Introduction of Bovine Leukemia Virus-Infected Cattle Using a Cattle Movement Network Analysis
Cited by: 6
Author(s): Kosuke Notsu, Anuwat Wiratsudakul, Shuya Mitoma, Hala El Daous, Chiho Kaneko, Heba M. El-Khaiat, Junzo Norimine, Satoshi Sekiguchi
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2020.576661

Distinct Distribution of Archaea From Soil to Freshwater to Estuary: Implications of Archaeal Composition and Function in Different Environments
Cited by: 14
Author(s): Hualong Wang, Raven L. Bier, Laura Zgleszewski, Marc Peipoch, Emmanuel C. Omondi, Atanu Mukherjee, Feng Chen, Chuanlun Zhang, Jinjun Kan
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2016.00434

Restructuring of Epibacterial Communities on Fucus vesiculosus forma mytili in Response to Elevated pCO2 and Increased Temperature Levels
Cited by: 26
Author(s): Birte Mensch, Sven C. Neulinger, Angelika Graiff, Andreas Pansch, Sven Künzel, Martin Fischer, Ruth A. Schmitz
Software Mentions: 4
Published: over 10 years ago

10.7717/peerj.6994

RITAN: rapid integration of term annotation and network resources
Cited by: 15
Author(s): Michael T. Zimmermann, Brian Kabat, Diane E. Grill, Richard B. Kennedy, Gregory A. Poland
Software Mentions: 4
Published: over 7 years ago

10.3389/fpsyg.2019.02448

The Differential Role of Central and Bridge Symptoms in Deactivating Psychopathological Networks
Cited by: 37
Author(s): Daniel Castro, Filipa Ferreira, Inês de Castro, Ana Rita Rodrigues, Marta Correia, Josefina Ribeiro, Tiago Ferreira
Software Mentions: 4
Published: about 7 years ago

10.7717/peerj.9691

Delimiting the boundaries of sesamoid identities under the network theory framework
Cited by: 4
Author(s): Gabriela Fontanarrosa, Jéssica Fratani, Miriam Corina Vera
Software Mentions: 4
Published: about 6 years ago

10.7717/peerj.9395

Doing nothing and what it looks like: inactivity in fattening cattle
Cited by: 8
Author(s): Sara Hintze, Freija Maulbetsch, Lucy Asher, Christoph Winckler
Software Mentions: 4
Published: over 6 years ago

10.7717/peerj.10594

Identification of hub genes and biological pathways in hepatocellular carcinoma by integrated bioinformatics analysis
Cited by: 6
Author(s): Qian Zhao, Yan Zhang, Shichun Shao, Yeqing Sun, Zhengkui Lin
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmicb.2019.01015

Leaf and Root Endospheres Harbor Lower Fungal Diversity and Less Complex Fungal Co-occurrence Patterns Than Rhizosphere
Cited by: 48
Author(s): Xin Qian, Hanzhou Li, Yong-Long Wang, Bian Wu, Mingsong Wu, Liang Chen, Xingchun Li, Ying Zhang, Xiangping Wang, Miaomiao Shi, Yong Zheng, Liang‐Dong Guo, Dianxiang Zhang
Software Mentions: 4
Published: over 7 years ago

10.3389/fpls.2020.00574

Decoding Gene Networks Modules That Explain the Recovery of Hymenoglossum cruentum Cav. After Extreme Desiccation
Cited by: 6
Author(s): Enrique Ostria‐Gallardo, Giovanni Larama, Graciela Berríos, Ana Fallard, Ana Gutiérrez-Moraga, Ingo Ensminger, Patrício Manque, Luisa Bascuñán‐Godoy, León A. Bravo
Software Mentions: 4
Published: over 6 years ago

10.7717/peerj.10057

Brain hothubs and dark functional networks: correlation analysis between amplitude and connectivity for Broca’s aphasia
Cited by: 1
Author(s): Feng Lin, Sheue-yann Cheng, Dongqing Qi, Yu-Er Jiang, Qian-Qian Lyu, Lijuan Zhong, Zhongli Jiang
Software Mentions: 4
Published: about 6 years ago

10.3390/ph14060553

Equine Mesenchymal Stem/Stromal Cells Freeze-Dried Secretome (Lyosecretome) for the Treatment of Musculoskeletal Diseases: Production Process Validation and Batch Release Test for Clinical Use
Cited by: 8
Author(s): Michela Mocchi, Stefano Grolli, Silvia Dotti, Dario Di Silvestre, Riccardo Villa, Priscilla Berni, Virna Conti, Giulia Passignani, Francesca Brambilla, Maurizio Del Bue, Laura Catenacci, Milena Sorrenti, Lorena Segale, Elia Bari, Pierluigi Mauri, Maria Luisa Torre, Sara Perteghella
Software Mentions: 4
Published: over 5 years ago

10.1098/rstb.2016.0095

Uncertain links in host–parasite networks: lessons for parasite transmission in a multi-host system
Cited by: 28
Author(s): Josephine G. Walker, Michaela Plein, Eric R. Morgan, Peter A. Vesk
Software Mentions: 4
Published: over 9 years ago

10.3389/fmicb.2018.02922

Occurrence and Fate of Ultramicrobacteria in a Full-Scale Drinking Water Treatment Plant
Cited by: 8
Author(s): Jie Liu, Renxin Zhao, Jiayu Zhang, Guijuan Zhang, Ke Yu, Xiaoyan Li, Bing Li
Software Mentions: 4
Published: almost 8 years ago

10.3389/fmicb.2021.726923

Genome-Resolved Metagenomics of the Chicken Gut Microbiome
Cited by: 25
Author(s): Maia Segura-Wang, Nikolaus Grabner, Andreas Koestelbauer, Viviana Klose, Mahdi Ghanbari
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2021.657471

Comparative Genomics and Environmental Distribution of Large dsDNA Viruses in the Family Asfarviridae
Cited by: 15
Author(s): Sangita Karki, Mohammad Moniruzzaman, Frank O. Aylward
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1002223

Transcriptomic Coordination in the Human Metabolic Network Reveals Links between n-3 Fat Intake, Adipose Tissue Gene Expression and Metabolic Health
Cited by: 35
Author(s): Melissa J. Morine, Audrey C. Tierney, Ben van Ommen, Hannelore Daniel, Sinéad Toomey, Ingrid M.F. Gjelstad, Isobel Claire Gormley, Pablo Pérez-Martı́nez, Christian A. Drevon, José López‐Miranda, Helen M. Roche
Software Mentions: 4
Published: about 15 years ago

10.1186/s12885-020-06774-9

Sepsis-associated pathways segregate cancer groups
Cited by: 5
Author(s): Himanshu Tripathi, Samanwoy Mukhopadhyay, Saroj Kant Mohapatra
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2020.580363

Compositions and Co-occurrence Patterns of Bacterial Communities Associated With Polymer- and ASP-Flooded Petroleum Reservoir Blocks
Cited by: 6
Author(s): Guoling Ren, Jinlong Wang, Lei Qu, Wei Li, Min Hu, Lihong Bian, Yiting Zhang, Jing Liu, Xumou Dou, Xinhong Chen, Lulu Bai, Yue Li
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pcbi.1008018

Visual perception of liquids: Insights from deep neural networks
Cited by: 11
Author(s): Jan Jaap R. van Assen, Shin’ya Nishida, Roland W. Fleming
Software Mentions: 4
Published: about 6 years ago

10.1186/s12862-020-01690-9

Genotypic similarities among the parthenogenetic Darevskia rock lizards with different hybrid origins
Cited by: 9
Author(s): David Tarkhnishvili, Alexey Yanchukov, Mehmet Kürşat Şahin, Mariam Gabelaia, Marine Murtskhvaladze, Kamίl Candan, Eduard Galoyan, Marine Arakelyan, Giorgi Iankoshvili, Yusuf Kumlutaş, Çetίn Ilgaz, Ferhat Matur, Faruk Çolak, Meriç Erdolu, Sofiko Kurdadze, Natia Barateli, Cort L. Anderson
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pcbi.1003808

SANTA: Quantifying the Functional Content of Molecular Networks
Cited by: 56
Author(s): Alex J. Cornish, Florian Markowetz
Software Mentions: 4
Published: about 12 years ago

10.3389/fmicb.2020.00158

Distinct Assembly Mechanisms Underlie Similar Biogeographic Patterns of Rare and Abundant Bacterioplankton in Cascade Reservoirs of a Large River
Cited by: 31
Author(s): Carlos Juan, Peifang Wang, Chao Wang, Xun Wang, Lingzhan Miao, Sheng Liu, Qiusheng Yuan, Shenghao Sun
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2017.02559

Patterns and Drivers of Vertical Distribution of the Ciliate Community from the Surface to the Abyssopelagic Zone in the Western Pacific Ocean
Cited by: 32
Author(s): Feng Zhao, Sabine Filker, Kuidong Xu, Pingping Huang, Shan Zheng
Software Mentions: 4
Published: almost 9 years ago

10.3389/fmicb.2020.618287

Niche Differentiation of Comammox Nitrospira in the Mudflat and Reclaimed Agricultural Soils Along the North Branch of Yangtze River Estuary
Cited by: 22
Author(s): Xinxin Wang, Lu Lu, Xue Zhou, Xiufeng Tang, Lu Kuang, Junhui Chen, Jun Shan, Huijie Lü, Hua Qin, Jonathan M. Adams, Baozhan Wang
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pcbi.1002603

An Integrated Regulatory Network Reveals Pervasive Cross-Regulation among Transcription and Splicing Factors
Cited by: 15
Author(s): Idit Kosti, Predrag Radivojac, Yael Mandel-Gutfreund
Software Mentions: 4
Published: over 14 years ago

10.1186/s12862-015-0298-0

A Boolean gene regulatory model of heterosis and speciation
Cited by: 8
Author(s): Peter M. F. Emmrich, Hannah Roberts, Véra Pancaldi
Software Mentions: 4
Published: over 11 years ago

10.3389/fpls.2019.01593

Cultivated Olive Diversification at Local and Regional Scales: Evidence From the Genetic Characterization of French Genetic Resources
Cited by: 17
Author(s): Bouchaïb Khadari, Ahmed El Bakkali, Laila Essalouh, Christine Tollon, Christian Pinatel, Guillaume Besnard
Software Mentions: 4
Published: almost 7 years ago

10.3389/fmed.2021.685124

Network Analysis of Outpatients to Identify Predictive Symptoms and Combinations of Symptoms Associated With Positive/Negative SARS-CoV-2 Nasopharyngeal Swabs
Cited by: 4
Author(s): Hervé Spechbach, Frédérique Jacquerioz, Virginie Prendki, Laurent Kaiser, Mikaëla Smit, Alexandra Calmy, François Chappuis, Idris Guessous, Julien Salamun, Stéphanie Baggio
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2020.00852

Lnc-ITSN1-2, Derived From RNA Sequencing, Correlates With Increased Disease Risk, Activity and Promotes CD4+ T Cell Activation, Proliferation and Th1/Th17 Cell Differentiation by Serving as a ceRNA for IL-23R via Sponging miR-125a in Inflammatory Bowel Disease
Cited by: 36
Author(s): Jiayan Nie, Qiu Zhao
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-017-4242-0

Unraveling the evolution and coevolution of small regulatory RNAs and coding genes in Listeria
Cited by: 16
Author(s): Franck Cerutti, Ludovic Mallet, Anaïs Painset, Claire Hoede, Annick Moisan, Christophe Bécavin, Manuel Duval, Olivier Dussurget, Pascale Cossart, Christine Gaspin, Hélène Chiapello
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pone.0070551

The Discrimination Power of Structural SuperIndices
Cited by: 3
Author(s): Matthias Dehmer, Abbe Mowshowitz
Software Mentions: 4
Published: over 13 years ago

10.1371/journal.pone.0057780

Functional and Structural Neural Network Characterization of Serotonin Transporter Knockout Rats
Cited by: 15
Author(s): Kajo van der Marel, Judith R. Homberg, Willem M. Otte, Rick M. Dijkhuizen
Software Mentions: 4
Published: over 13 years ago

10.1371/journal.pone.0202063

Cross-species alcohol dependence-associated gene networks: Co-analysis of mouse brain gene expression and human genome-wide association data
Cited by: 11
Author(s): Kristin M. Mignogna, Silviu‐Alin Bacanu, Brien P. Riley, Aaron R. Wolen, Michael F. Miles
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-020-07148-y

Analysing the meta-interaction between pathways by gene set topological impact analysis
Cited by: 2
Author(s): Yan Shu, Xu Chi, Xiao Chang, Mengliang Tian
Software Mentions: 4
Published: about 6 years ago

10.3389/fnhum.2015.00440

Genetic network properties of the human cortex based on regional thickness and surface area measures
Cited by: 12
Author(s): Anna R. Docherty, Chelsea Sawyers, Matthew S. Panizzon, Michael C. Neale, Lisa T. Eyler, Christine Fennema-Notestine, Carol E. Franz, Chi‐Hua Chen, Linda K. McEvoy, Brad Verhulst, Ming T. Tsuang, William S. Kremen
Software Mentions: 4
Published: about 11 years ago

10.1371/journal.pone.0165987

Networks Depicting the Fine-Scale Co-Occurrences of Fungi in Soil Horizons
Cited by: 67
Author(s): Hirokazu Toju, Osamu Kishida, Noboru Katayama, Kentaro Takagi
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pone.0123082

Genomic Heterogeneity of Osteosarcoma - Shift from Single Candidates to Functional Modules
Cited by: 27
Author(s): Kathrin Poos, Jan Smida, Doris Maugg, Gertrud Eckstein, Daniel Baumhoer, Michaela Nathrath, Eberhard Korsching
Software Mentions: 4
Published: over 11 years ago

10.3389/fnhum.2020.00255

Aerobic Exercise Induces Functional and Structural Reorganization of CNS Networks in Multiple Sclerosis: A Randomized Controlled Trial
Cited by: 9
Author(s): Jan‐Patrick Stellmann, Adil Maarouf, Schulz Kh, Lisa Baquet, Jana Pöttgen, Stefan Patra, Iris Katharina Penner, Susanne Gellißen, Gesche Ketels, Pierre Besson, Jean Philippe Ranjeva, Maxime Guye, Guido Nolte, Andreas K. Engel, Bertrand Audoin, Christoph Heesen, Stefan M. Gold
Software Mentions: 4
Published: over 6 years ago

10.3389/fpls.2017.01725

Combined Effects of Irrigation Regime, Genotype, and Harvest Stage Determine Tomato Fruit Quality and Aptitude for Processing into Puree
Cited by: 20
Author(s): Alexandre Arbex de Castro Vilas Boas, David L. Page, Robert Giovinazzo, Nadia Bertin, Anne-Laure Fanciullino
Software Mentions: 4
Published: about 9 years ago

10.3389/fphys.2021.678507

Sex Differences in the Physiological Network of Healthy Young Subjects
Cited by: 6
Author(s): Antonio Barajas-Martínez, Elizabeth Ibarra-Coronado, Rubén Fossión, J. C. Toledo-Roy, Vania Jocelyn Martínez-Garcés, Juan Antonio López-Rivera, Geraldine Tello-Santoyo, Rusland D Lavin, José Luis Díaz Gómez, Christopher R. Stephens, Carlos A. Aguilar-Salinas, Bruno Estañol, Nimbe Torres, Armando R. Tovar, Osbaldo Reséndis-Antonio, Marcia Hiriart, A. Frank, Ana Leonor Rivera
Software Mentions: 4
Published: over 5 years ago