Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: igraph

https://packages.ecosyste.ms/registries/pypi.org/packages/igraph

High performance graph data structures and algorithms
28 versions
Latest release: about 1 year ago
126 dependent packages
1,074,658 downloads last month

Papers Mentioning igraph 1,555

10.3389/fmicb.2020.579427
Environmental and Microbial Interactions Shape Methane-Oxidizing Bacterial Communities in a Stratified Lake
Cited by: 12
Author(s): Carole Guggenheim, Remo Freimann, Magdalena Mayr, Karin Beck, Bernhard Wehrli, Helmut Bürgmann
Software Mentions: 8
Published: about 4 years ago
10.3389/fmicb.2019.02872
Soil Bacterial and Fungal Communities Exhibit Distinct Long-Term Responses to Disturbance in Temperate Forests
Cited by: 33
Author(s): Ernest D. Osburn, Steven G. McBride, Frank O. Aylward, Brian D. Badgley, Brian D. Strahm, Jennifer D. Knoepp, John E. Barrett
Software Mentions: 8
Published: almost 5 years ago
10.3389/fgene.2019.00853
SeqDeχ: A Sequence Deconvolution Tool for Genome Separation of Endosymbionts From Mixed Sequencing Samples
Cited by: 0
Author(s): Alice Chiodi, Francesco Comandatore, Davide Sassera, Giulio Petroni, Claudio Bandi, Matteo Brilli
Software Mentions: 8
Published: about 5 years ago
10.1128/mSystems.00112-21
Metagenomic Analysis of Common Intestinal Diseases Reveals Relationships among Microbial Signatures and Powers Multidisease Diagnostic Models
Cited by: 10
Author(s): Puzi Jiang, Sicheng Wu, Qibin Luo, Xing‐Ming Zhao, Weihua Chen
Software Mentions: 8
Published: over 3 years ago
10.3390/ijms22168742
Inhibition of WHSC1 Allows for Reprogramming of the Immune Compartment in Prostate Cancer
Cited by: 5
Author(s): Muzamil Y. Want, Ellen Karasik, Bryan M. Gillard, AJ Robert McGray, Sebastiano Battaglia
Software Mentions: 8
Published: over 3 years ago
10.1523/JNEUROSCI.2146-20.2020
Unexpected Role of Physiological Estrogen in Acute Stress-Induced Memory Deficits
Cited by: 19
Author(s): Rachael E. Hokenson, Annabel K. Short, Yuncai Chen, Aidan L Pham, Emily T. Adams, Jessica L. Bolton, Vivek Swarup, Christine M. Gall, Tallie Z. Baram
Software Mentions: 8
Published: almost 4 years ago
10.3390/ijms22094696
Metabolic Profiling of VOCs Emitted by Bacteria Isolated from Pressure Ulcers and Treated with Different Concentrations of Bio-AgNPs
Cited by: 3
Author(s): Fernanda Monedeiro, Viorica Railean, Maciej Monedeiro-Milanowski
Software Mentions: 8
Published: over 3 years ago
10.3389/fmicb.2019.02492
Do Organic Substrates Drive Microbial Community Interactions in Arctic Snow?
Cited by: 17
Author(s): Benoît Bergk Pinto, Lorrie Maccario, Aurélien Dommergue, Timothy M. Vogel, Catherine Larose
Software Mentions: 8
Published: about 5 years ago
10.1038/s41396-019-0383-2
Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots
Cited by: 596
Author(s): Samiran Banerjee, Florian Walder, Lucie Büchi, Marion Meyer, Alain Held, Andreas Gattinger, Thomas Keller, Raphaël Charles, Marcel G. A. van der Heijden
Software Mentions: 8
Published: over 5 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: about 4 years ago
10.1128/mSystems.00174-16
Distinct Biogeographic Patterns for Archaea, Bacteria, and Fungi along the Vegetation Gradient at the Continental Scale in Eastern China
Cited by: 89
Author(s): Bin Ma, Zhongmin Dai, Haizhen Wang, Melissa Dsouza, Xingmei Liu, Yan He, Jianjun Wu, Jorge L. Mazza Rodrigues, Jack A. Gilbert, Philip C. Brookes, Jianming Xu
Software Mentions: 8
Published: over 7 years ago
10.1038/s41396-021-00949-3
Social networks strongly predict the gut microbiota of wild mice
Cited by: 51
Author(s): Aura Raulo, Bryony Allen, Tanya Troitsky, Arild Husby, Josh A. Firth, Tim Coulson, Sarah C. L. Knowles
Software Mentions: 8
Published: over 3 years ago
10.1155/2021/7488188
m6A-Related lncRNA to Develop Prognostic Signature and Predict the Immune Landscape in Bladder Cancer
Cited by: 28
Author(s): Zuwei Li, Yuwu Li, Weizhang Zhong, Peiyuan Huang
Software Mentions: 8
Published: over 3 years ago
10.3389/fmicb.2018.03150
The Human Gut Virome in Hypertension
Cited by: 34
Author(s): Maozhen Han, Pengshuo Yang, Chunrong Zhong, Kang Ning
Software Mentions: 8
Published: almost 6 years ago
10.1038/s41396-020-0621-7
Spatiotemporal dynamics of the archaeal community in coastal sediments: assembly process and co-occurrence relationship
Cited by: 120
Author(s): Jiwen Liu, Shangqing Zhu, Xiaoyue Liu, Peng Yao, Tiantian Ge, Xiao‐Hua Zhang
Software Mentions: 8
Published: over 4 years ago
10.1186/s12859-019-3105-x
MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis
Cited by: 190
Author(s): Valerio Licursi, Federica Conte, Giulia Fiscon, Paola Paci
Software Mentions: 8
Published: about 5 years ago
10.1186/s12864-019-5747-5
scNPF: an integrative framework assisted by network propagation and network fusion for preprocessing of single-cell RNA-seq data
Cited by: 10
Author(s): Michael Fraser, Guoli Ji, Pengchao Ye, Yuqi Long, Xuesong Xiao, Shuchao Li, Yangfeng Su, Xiaohui Wu
Software Mentions: 8
Published: over 5 years ago
10.1371/journal.pone.0207359
Chronic lifestyle diseases display seasonal sensitive comorbid trend in human population evidence from Google Trends
Cited by: 14
Author(s): Jai Chand Patel, Pankaj Khurana, Y. K. Sharma, Bhuvnesh Kumar, R. Sugadev
Software Mentions: 8
Published: almost 6 years ago
10.1042/BSR20203676
Identification of pivotal genes associated with the prognosis of gastric carcinoma through integrated analysis
Cited by: 7
Author(s): Zhenchao Ma, Jingyu Xu, Lixin Ru, Weihua Zhu
Software Mentions: 8
Published: over 3 years ago
10.1186/s40169-020-0259-0
Whole‐transcriptome sequencing uncovers core regulatory modules and gene signatures of human fetal growth restriction
Cited by: 13
Author(s): Xing Wang, Jun Yu, Yiwei Yang, Xiaoqin Liu, Xiaobo Zhao, Xudong Guo, Tao Duan, Chenqi Lu
Software Mentions: 8
Published: almost 5 years ago
10.3389/fvets.2018.00071
Effective Network Size Predicted From Simulations of Pathogen Outbreaks Through Social Networks Provides a Novel Measure of Structure-Standardized Group Size
Cited by: 12
Author(s): Collin M. McCabe, Charles L. Nunn
Software Mentions: 8
Published: over 6 years ago
10.1534/g3.118.200892
Isolation by Distance, Source-Sink Population Dynamics and Dispersal Facilitation by Trade Routes: Impact on Population Genetic Structure of a Stored Grain Pest
Cited by: 14
Author(s): Erick M. G. Cordeiro, James F. Campbell, Thomas W. Phillips, Eduard Akhunov
Software Mentions: 8
Published: over 5 years ago
10.1371/journal.pone.0240523
Whole transcriptomic network analysis using Co-expression Differential Network Analysis (CoDiNA)
Cited by: 12
Author(s): Deisy Morselli Gysi, Tiago de Miranda Fragoso, Fatemeh Zebardast, Wesley Bertoli, Volker Busskamp, Eivind Almaas, Katja Nowick
Software Mentions: 8
Published: about 4 years ago
10.1186/s13029-015-0043-5
CyNetworkBMA: a Cytoscape app for inferring gene regulatory networks
Cited by: 5
Author(s): Maciej Fronczuk, Adrian E. Raftery, Ka Yee Yeung
Software Mentions: 8
Published: about 9 years ago
10.3389/fvets.2018.00173
The Distribution of Bovine Tuberculosis in Cattle Farms Is Linked to Cattle Trade and Badger-Mediated Contact Networks in South-Western France, 2007–2015
Cited by: 18
Author(s): Malika Bouchez-Zacria, Aurélie Courcoul, Benoı̂t Durand
Software Mentions: 8
Published: over 6 years ago
10.1038/s41598-021-89065-y
Exposure to airborne bacteria depends upon vertical stratification and vegetation complexity
Cited by: 24
Author(s): Jake M. Robinson, Christian Cando‐Dumancela, Rachael E. Antwis, Ross Cameron, Craig Liddicoat, Ravin Poudel, Philip Weinstein, Martin F. Breed
Software Mentions: 8
Published: over 3 years ago
10.3390/microorganisms9091943
Fungi in Permafrost-Affected Soils of the Canadian Arctic: Horizon- and Site-Specific Keystone Taxa Revealed by Co-Occurrence Network
Cited by: 6
Author(s): Milan Varsadiya, Tim Urich, Gustaf Hugelius, Jiří Bárta
Software Mentions: 8
Published: about 3 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
10.1371/journal.pone.0122070
Using Lidar Data to Analyse Sinkhole Characteristics Relevant for Understory Vegetation under Forest Cover—Case Study of a High Karst Area in the Dinaric Mountains
Cited by: 74
Author(s): Milan Kobal, Irena Bertoncelj, Jinhu Wang, Igor Dak̇skobler, Lado Kutnar
Software Mentions: 8
Published: over 9 years ago
10.1007/s11571-020-09645-y
Construction of embedded fMRI resting-state functional connectivity networks using manifold learning
Cited by: 12
Author(s): Ioannis Gallos, Evangelos Galaris, Constantinos Siettos
Software Mentions: 8
Published: about 4 years ago
10.3390/microorganisms9061326
Root-Associated Bacterial Community Shifts in Hydroponic Lettuce Cultured with Urine-Derived Fertilizer
Cited by: 5
Author(s): Thijs Van Gerrewey, Christophe El‐Nakhel, Stefania De Pascale, Jolien De Paepe, Peter Clauwaert, Frederiek‐Maarten Kerckhof, Nico Boon, Danny Geelen
Software Mentions: 8
Published: over 3 years ago
10.1371/journal.pone.0125000
From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data
Cited by: 6
Author(s): Jilong Li, Jie Hou, Sun Liang, Jordan Wilkins, Yuan Lu, Chad E. Niederhuth, Benjamin Ryan Merideth, Thomas P. Mawhinney, Valeri V. Mossine, C. Michael Greenlief, John C. Walker, William R. Folk, Mark Hannink, Dennis B. Lubahn, James A. Birchler, Jianlin Cheng
Software Mentions: 8
Published: over 9 years ago
10.3389/fgene.2021.665843
RFCell: A Gene Selection Approach for scRNA-seq Clustering Based on Permutation and Random Forest
Cited by: 3
Author(s): Yuan Zhao, Zhao-Yu Fang, Cui-Xiang Lin, Chao Deng, Yunpei Xu, Hongdong Li
Software Mentions: 8
Published: over 3 years ago
10.3389/fgene.2021.683037
De novo Transcriptome Sequencing Coupled With Co-expression Analysis Reveal the Transcriptional Regulation of Key Genes Involved in the Formation of Active Ingredients in Peucedanum praeruptorum Dunn Under Bolting Period
Cited by: 7
Author(s): Cheng Song, Xiaoli Li, Bin Jia, Li Liu, Jinmei Ou, Bangxing Han
Software Mentions: 8
Published: over 3 years ago
10.1371/journal.pone.0221167
Reconstructing systematic persistent impacts of promotional marketing with empirical nonlinear dynamics
Cited by: 6
Author(s): Ray Huffaker, Andrew Fearne
Software Mentions: 8
Published: about 5 years ago
10.3389/fgene.2021.664654
Integrative Ranking of Enhancer Networks Facilitates the Discovery of Epigenetic Markers in Cancer
Cited by: 0
Author(s): Qi Wang, Yonghe Wu, Tim Vorberg, Roland Eils, Carl Herrmann
Software Mentions: 8
Published: over 3 years ago
10.1038/s41598-019-53342-8
Mixed-Cropping Between Field Pea Varieties Alters Root Bacterial and Fungal Communities
Cited by: 12
Author(s): Anthony A. Horner, Samuel S. Browett, Rachael E. Antwis
Software Mentions: 8
Published: about 5 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/s41598-019-48746-5
Gene Expression Predicts Histological Severity and Reveals Distinct Molecular Profiles of Nonalcoholic Fatty Liver Disease
Cited by: 93
Author(s): Stephen A. Hoang, Abdul M. Oseini, Ryan E. Feaver, Banumathi K. Cole, Amon Asgharpour, Robert Vincent, Mohammad Shadab Siddiqui, Mark Lawson, Nathan Day, Justin M. Taylor, Brian R. Wamhoff, Faridoddin Mirshahi, Melissa J. Contos, Michael O. Idowu, Arun J. Sanyal
Software Mentions: 8
Published: about 5 years ago
10.1186/s12889-021-11772-y
Firearm laws and the network of firearm movement among US states
Cited by: 4
Author(s): Sae Takada, Kristen R. Choi, Shaw Natsui, Altaf Saadi, Liza Buchbinder, Molly C. Easterlin, Frederick J. Zimmerman
Software Mentions: 8
Published: about 3 years ago
10.1038/s41598-018-24733-0
Insular threat associations within taxa worldwide
Cited by: 39
Author(s): Camille Leclerc, Franck Courchamp, Céline Bellard
Software Mentions: 8
Published: over 6 years ago
10.7717/peerj.12063
Dongsha Atoll is an important stepping-stone that promotes regional genetic connectivity in the South China Sea
Cited by: 3
Author(s): Shang-Yin Vanson Liu, Jacob Green, Dana Briggs, Ruth Hastings, Ylva Jondelius, Skylar Kensinger, Hannah Leever, Sophia Santos, Trevor Throne, Chi Cheng, Hawis Madduppa, Robert J. Toonen, Michelle R. Gaither, Eric D. Crandall
Software Mentions: 8
Published: about 3 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: over 3 years ago
10.1038/s41598-018-34921-7
Terminal restriction fragment length polymorphism is an “old school” reliable technique for swift microbial community screening in anaerobic digestion
Cited by: 37
Author(s): Jo De Vrieze, Umer Zeeshan Ijaz, Aaron Marc Saunders, Susanne Theuerl
Software Mentions: 8
Published: about 6 years ago
10.1186/s12870-019-2182-3
A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference
Cited by: 9
Author(s): Enrique Ostria‐Gallardo, Giovanni Larama, Graciela Berríos, Ana Fallard, Ana Gutiérrez-Moraga, Ingo Ensminger, León A. Bravo
Software Mentions: 8
Published: almost 5 years ago
10.1186/s12887-019-1818-7
Transdiagnostic associations across communication, cognitive, and behavioural problems in a developmentally at-risk population: a network approach
Cited by: 16
Author(s): Silvana Mareva, Joni Holmes
Software Mentions: 8
Published: about 5 years ago
10.1186/s40168-018-0593-2
Gut microbiome composition is associated with spatial structuring and social interactions in semi-feral Welsh Mountain ponies
Cited by: 61
Author(s): Rachael E. Antwis, Jessica M. D. Lea, Bryony Unwin, Susanne Shultz
Software Mentions: 8
Published: almost 6 years ago
10.12688/f1000research.6767.1
CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API
Cited by: 77
Author(s): Keiichiro Ono, Tanja Muetze, Georgi Kolishovski, Paul Shannon, Barry Demchak
Software Mentions: 8
Published: over 9 years ago
10.1038/srep44736
Vector Integration Sites Identification for Gene-Trap Screening in Mammalian Haploid Cells
Cited by: 5
Author(s): Jian Yu, Constance Ciaudo
Software Mentions: 8
Published: over 7 years ago
10.1186/s12920-019-0562-z
Clustering analysis of microRNA and mRNA expression data from TCGA using maximum edge-weighted matching algorithms
Cited by: 9
Author(s): Lizhong Ding, Zheyun Feng, Yongsheng Bai
Software Mentions: 8
Published: over 5 years ago
10.18632/aging.103475
Constructing a global transcriptional regulatory landscape for early non-small cell lung cancer to identify hub genes and key pathways
Cited by: 6
Author(s): Jianlong Bu, Pinyi Zhang, Kaibin Zhu, Yubo Yan, Bowen Shi, Junfeng Wang, Shidong Xu
Software Mentions: 8
Published: about 4 years ago
10.1186/s12920-021-01079-7
Lung disease network reveals impact of comorbidity on SARS-CoV-2 infection and opportunities of drug repurposing
Cited by: 4
Author(s): Asim Bikas Das
Software Mentions: 8
Published: about 3 years ago
10.1186/1471-2105-14-179
Modelling and visualizing fine-scale linkage disequilibrium structure
Cited by: 3
Author(s): D.J. Edwards
Software Mentions: 8
Published: over 11 years ago
10.1038/s41598-017-06929-y
A systems approach to a spatio-temporal understanding of the drought stress response in maize
Cited by: 64
Author(s): Zhenyan Miao, Zhaoxue Han, Ting Zhang, Siyuan Chen, Chuang Ma
Software Mentions: 8
Published: over 7 years ago
10.3233/JAD-170011
Analytical Strategy to Prioritize Alzheimer’s Disease Candidate Genes in Gene Regulatory Networks Using Public Expression Data
Cited by: 17
Author(s): Shweta Bagewadi Kawalia, Tamara Raschka, Mufassra Naz, Ricardo de Matos Simoes, Philipp Senger, Martin Hofmann-Apitius
Software Mentions: 8
Published: over 7 years ago
10.1007/s11306-017-1284-x
Metabolomic analysis of tomato seed germination
Cited by: 31
Author(s): Rashid H. Kazmi, Leo A.J. Willems, Ronny V.L. Joosen, Naveed Ahmad Khan, Wilco Ligterink, Henk W. M. Hilhorst
Software Mentions: 8
Published: about 7 years ago
10.1186/s40168-019-0630-9
Environmental filtering drives distinct continental atlases of soil archaea between dryland and wetland agricultural ecosystems
Cited by: 103
Author(s): Shuo Jiao, Ye Xu, Jie Zhang, Yahai Lu
Software Mentions: 8
Published: almost 6 years ago
10.1371/journal.pone.0253847
TeamTree analysis: A new approach to evaluate scientific production
Cited by: 2
Author(s): Frank W. Pfrieger
Software Mentions: 8
Published: over 3 years ago
10.1093/gigascience/giz004
The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches
Cited by: 103
Author(s): Darshan B. Dhakan, Abhijit Maji, Ashok Sharma, Rituja Saxena, Joby Pulikkan, Tony Grace, Andrés Gómez, Joy Scaria, Katherine R. Amato, Vineet K. Sharma
Software Mentions: 8
Published: almost 6 years ago
10.3390/metabo10050202
Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources
Cited by: 59
Author(s): Tara Eicher, Garrett Kinnebrew, Andrew Patt, Kyle Spencer, Kevin L. Ying, Qin Ma, Raghu Machiraju, Ewy A. Mathé
Software Mentions: 8
Published: over 4 years ago
10.1371/journal.pone.0116356
Effects of Hierarchical Roost Removal on Northern Long-Eared Bat (Myotis septentrionalis) Maternity Colonies
Cited by: 26
Author(s): Alexander Silvis, W. Mark Ford, Eric R. Britzke
Software Mentions: 8
Published: almost 10 years ago
10.1038/s41598-017-09154-9
Analysis of spatial genetic variation reveals genetic divergence among populations of Primula veris associated to contrasting habitats
Cited by: 3
Author(s): Pablo Deschepper, Rein Brys, Miguel A. Fortuna, Hans Jacquemyn
Software Mentions: 8
Published: over 7 years ago
10.1038/s41598-020-57622-6
Mainland and island populations of Mussaenda kwangtungensis differ in their phyllosphere fungal community composition and network structure
Cited by: 16
Author(s): Xin Qian, Shengchun Li, Bian Wu, Yong-Long Wang, Niu‐Niu Ji, Hui Yao, Hongyue Cai, Miaomiao Shi, Dianxiang Zhang
Software Mentions: 8
Published: almost 5 years ago
10.7717/peerj.9056
Transcriptional profiling to identify the key genes and pathways of pterygium
Cited by: 11
Author(s): Yihui Chen, Haoyu Wang, Yaping Jiang, Xiaoyan Zhang, Qingzhong Wang
Software Mentions: 8
Published: over 4 years ago
10.3390/vetsci7030138
Cattle Manure Trade Network Analysis and the Relevant Spatial Pathways in an Endemic Area of Foot and Mouth Disease in Northern Thailand
Cited by: 0
Author(s): Chalutwan Sansamur, Anuwat Wiratsudakul, Arisara Charoenpanyanet, Veerasak Punyapornwithaya
Software Mentions: 7
Published: about 4 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
10.1186/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/biom11081245
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review
Cited by: 16
Author(s): Fotis A. Baltoumas, Sofia Zafeiropoulou, Evangelos Karatzas, Mikaela Koutrouli, Foteini Thanati, Kleanthi Voutsadaki, Maria Gkonta, Joana Hotova, Ioannis Kasionis, Pantelis Hatzis, Georgios A. Pavlopoulos
Software Mentions: 7
Published: over 3 years ago
10.1186/gb-2012-13-4-r29
RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations.
Cited by: 84
Author(s): Mauro A. A. Castro, Xin Wang, Michael Fletcher, Kerstin B. Meyer, Florian Markowetz
Software Mentions: 7
Published: almost 13 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
10.7150/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
10.1371/journal.pntd.0009607
One hundred years of zoonoses research in the Horn of Africa: A scoping review
Cited by: 17
Author(s): Lisa Cavalerie, Maya Wardeh, Ophélie Lebrasseur, Mark Nanyingi, K. Marie McIntyre, Mirgissa Kaba, Daniel Asrat, Robert M. Christley, Gina Pinchbeck, Matthew Baylis, Siobhan M. Mor
Software Mentions: 7
Published: over 3 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
10.1186/s12864-017-4304-3
Transcriptome profiling of aging Drosophila photoreceptors reveals gene expression trends that correlate with visual senescence
Cited by: 71
Author(s): Hana Hall, Patrick S Medina, Daphne A. Cooper, Spencer E. Escobedo, Jeremiah Rounds, Kaelan J. Brennan, Christopher Vincent, Pedro Miura, R. W. Doerge, Vikki M. Weake
Software Mentions: 7
Published: about 7 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
10.1038/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
10.1371/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.0152578
Role of Cattle Movements in Bovine Tuberculosis Spread in France between 2005 and 2014
Cited by: 44
Author(s): Aurore Palisson, Aurélie Courcoul, Benoı̂t Durand
Software Mentions: 7
Published: over 8 years ago
10.1186/s12859-019-3016-x
NPA: an R package for computing network perturbation amplitudes using gene expression data and two-layer networks
Cited by: 6
Author(s): Florian Martin, Sylvain Gubian, Marja Talikka, Julia Hoeng, Manuel C. Peitsch
Software Mentions: 7
Published: about 5 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
10.3389/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
10.1038/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/s41598-021-81451-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/s12918-018-0598-2
A systematic survey of centrality measures for protein-protein interaction networks
Cited by: 122
Author(s): Mohieddin Jafari, Ali Salehzadeh‐Yazdi, Zahra Razaghi-Moghadam, Holger Hennig, Olaf Wolkenhauer, Mehdi Mirzaie, Mohieddin Jafari
Software Mentions: 7
Published: over 6 years ago
10.1371/journal.pone.0230218
Identification of a master transcription factor and a regulatory mechanism for desiccation tolerance in the anhydrobiotic cell line Pv11
Cited by: 10
Author(s): Takahiro Yamada, Yusuke Hiki, Noriko Hiroi, Elena Shagimardanova, Oleg Gusev, Richard Cornette, Takahiro Kikawada, Akira Funahashi
Software Mentions: 7
Published: over 4 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
10.1371/journal.pcbi.1004765
A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers
Cited by: 29
Author(s): Yasin Şenbabaoğlu, S. Onur Sumer, Francisco Sánchez-Vega, Debra L. Bemis, Giovanni Ciriello, Nikolaus Schultz, Chris Sander
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
10.1371/journal.pcbi.1004575
SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis
Cited by: 292
Author(s): Minzhe Guo, Hui Wang, S. Steven Potter, Jeffrey A. Whitsett, Yan Xu
Software Mentions: 7
Published: almost 9 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
10.4056/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
10.3389/fendo.2021.672319
Adrenocortical Carcinoma Steroid Profiles: In Silico Pan-Cancer Analysis of TCGA Data Uncovers Immunotherapy Targets for Potential Improved Outcomes
Cited by: 6
Author(s): João C. D. Muzzi, Jessica Maria Magno, Milena A. Cardoso, Juliana de Moura, Mauro A. A. Castro, Bonald C. Figueiredo
Software Mentions: 7
Published: over 3 years ago
10.3389/fgene.2019.00516
Microbial Networks in SPRING - Semi-parametric Rank-Based Correlation and Partial Correlation Estimation for Quantitative Microbiome Data
Cited by: 67
Author(s): Grace Yoon, Irina Gaynanova, Christian L. Müller
Software Mentions: 7
Published: over 5 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.0242943
Essential gene prediction using limited gene essentiality information–An integrative semi-supervised machine learning strategy
Cited by: 7
Author(s): Sutanu Nandi, Piyali Ganguli, Ram Rup Sarkar
Software Mentions: 7
Published: almost 4 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
10.3389/fgene.2021.722981
Landscape of the Dark Transcriptome Revealed Through Re-mining Massive RNA-Seq Data
Cited by: 6
Author(s): Jing Li, Urminder Singh, Zebulun Arendsee, Eve Syrkin Wurtele
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.0079729
DCGL v2.0: An R Package for Unveiling Differential Regulation from Differential Co-expression
Cited by: 76
Author(s): Jing Yang, Hui Yu, Baohong Liu, Zhongming Zhao, Lei Liu, Liangxiao Ma, Yixue Li, Yuanyuan Li
Software Mentions: 7
Published: about 11 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