cran: CCA | Projects | Ecosyste.ms: Papers

10.1038/s41598-021-81688-5

Fungal diversity and community structure from coastal and barrier island beaches in the United States Gulf of Mexico
Cited by: 14
Author(s): Allison K. Walker, Brent M. Robicheau
Software Mentions: 16
Published: over 3 years ago

10.1002/ece3.7881

Conversion of rainforest into oil palm and rubber plantations affects the functional composition of litter and soil Collembola
Cited by: 4
Author(s): Winda Ika Susanti, Tamara Bartels, Valentyna Krashevska, Rahayu Widyastuti, Louis Deharveng, Stefan Scheu, Anton M. Potapov
Software Mentions: 11
Published: almost 3 years ago

10.1186/s12859-017-1487-1

A systematic comparative evaluation of biclustering techniques
Cited by: 94
Author(s): Victor Alexandre Padilha, Ricardo J. G. B. Campello
Software Mentions: 10
Published: over 7 years ago

10.1172/jci.insight.147535

The relationship between cytokine and neutrophil gene network distinguishes SARS-CoV-2–infected patients by sex and age
Cited by: 12
Author(s): Paula Paccielli Freire, Amélia Pasqual Marques, G. Baiocchi, Lena F. Schimke, Dennyson Leandro M. Fonseca, Ranieri Coelho Salgado, Igor Salerno Filgueiras, Sarah M.S. Napoleao, Desirée Rodrigues Plaça, Karen Tiemi Akashi, Thiago Dominguez Crespo Hirata, Nadia El Khawanky, Lasse Melvær Giil, Gustavo Cabral-Miranda, Robson Francisco Carvalho, Luís Carlos S. Ferreira, Antônio Condino‐Neto, Helder I. Nakaya, Igor Jurišica, Hans D. Ochs, Niels Olsen Saraiva Câmara, Vera Lúcia Garcia Calich, Otávio Cabral-Marques
Software Mentions: 10
Published: almost 3 years ago

10.3390/insects10030065

Multi-Scenario Species Distribution Modeling
Cited by: 12
Author(s): Senait D. Senay, Susan P. Worner
Software Mentions: 10
Published: about 5 years ago

10.1093/bib/bbv108

Dimension reduction techniques for the integrative analysis of multi-omics data
Cited by: 262
Author(s): Chen Meng, Oana A. Zeleznik, Gerhard G. Thallinger, Bernhard Küster, Amin Moghaddas Gholami, Aedín C. Culhane
Software Mentions: 10
Published: about 8 years ago

10.3389/fonc.2020.00973

Impact of Data Preprocessing on Integrative Matrix Factorization of Single Cell Data
Cited by: 8
Author(s): Lauren Hsu, Aedín C. Culhane
Software Mentions: 10
Published: almost 4 years ago

10.1093/bioinformatics/btaa201

Resolving single-cell heterogeneity from hundreds of thousands of cells through sequential hybrid clustering and NMF
Cited by: 37
Author(s): Meenakshi Venkatasubramanian, Kashish Chetal, Daniel Schnell, Gowtham Atluri, Nathan Salomonis
Software Mentions: 10
Published: about 4 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: over 6 years ago

10.3389/fmicb.2019.02736

Habitat Heterogeneity and Connectivity: Effects on the Planktonic Protist Community Structure at Two Adjacent Coastal Sites (the Lagoon and the Gulf of Venice, Northern Adriatic Sea, Italy) Revealed by Metabarcoding
Cited by: 14
Author(s): Simona Armeli Minicante, Roberta Piredda, Grazia Marina Quero, Stefania Finotto, Fabrizio Bernardi Aubry, Mauro Bastianini, Alessandra Pugnetti, Adriana Zingone
Software Mentions: 8
Published: over 4 years ago

10.1007/s00248-018-1209-x

Rapid Microbial Community Changes During Initial Stages of Pine Litter Decomposition
Cited by: 35
Author(s): Marcin Gołębiewski, Agata Tarasek, Marcin Sikora, Edyta Deja-Sikora, Andrzej Tretyn, Maria Niklińska
Software Mentions: 7
Published: almost 6 years ago

10.1186/s13071-017-2140-6

Landscape structure affects distribution of potential disease vectors (Diptera: Culicidae)
Cited by: 41
Author(s): Carina Zittra, Simon Vitecek, Adelheid G. Obwaller, Heidemarie Rossiter, Barbara Eigner, Thomas Zechmeister, Johann Waringer, Hans‐Peter Fuehrer
Software Mentions: 7
Published: about 7 years ago

10.1017/S0950268818002996

Parasitic infections in relation to practices and knowledge in a rural village in Northern Thailand with emphasis on fish-borne trematode infection
Cited by: 8
Author(s): Kittipong Chaisiri, Chloé Jollivet, Pauline Della Rossa, Surapol Sanguankiat, Dorn Wattanakulpanich, Claire Lajaunie, Aurélie Binot, Malee Tanita, Sungkhom Rattanapikul, D. Sutdan, Serge Morand, Alexis Ribas
Software Mentions: 7
Published: over 5 years ago

10.1186/s12859-016-0970-4

MetICA: independent component analysis for high-resolution mass-spectrometry based non-targeted metabolomics
Cited by: 22
Author(s): Youzhong Liu, Kirill S. Smirnov, Marianna Lucio, Régis D. Gougeon, Hervé Alexandre, Philippe Schmitt‐Kopplin
Software Mentions: 7
Published: about 8 years ago

10.3389/fimmu.2018.01444

Elucidating T Cell Activation-Dependent Mechanisms for Bifurcation of Regulatory and Effector T Cell Differentiation by Multidimensional and Single-Cell Analysis
Cited by: 10
Author(s): Alla Bradley, Takeji Hashimoto, M. Ono
Software Mentions: 7
Published: almost 6 years ago

10.1186/s12864-017-4429-4

Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains
Cited by: 27
Author(s): Luis A. Amador, Aline Primot, Édouard Cadieu, Alain Roulet, Frédérique Barloy-Hubler
Software Mentions: 7
Published: over 6 years ago

10.3389/fmicb.2018.00651

How Does Salinity Shape Bacterial and Fungal Microbiomes of Alnus glutinosa Roots?
Cited by: 53
Author(s): Dominika Thiem, Marcin Gołębiewski, Piotr Hulisz, Agnieszka Piernik, Katarzyna Hrynkiewicz
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pone.0053544

Visualising the Cross-Level Relationships between Pathological and Physiological Processes and Gene Expression: Analyses of Haematological Diseases
Cited by: 13
Author(s): M. Ono, Reiko Tanaka, Manabu Kano, Toshio Sugiman
Software Mentions: 6
Published: over 11 years ago

10.1186/1471-2164-15-1028

Visualisation of the T cell differentiation programme by Canonical Correspondence Analysis of transcriptomes
Cited by: 17
Author(s): M. Ono, Reiko Tanaka, Manabu Kano
Software Mentions: 6
Published: over 10 years ago

10.3389/fmicb.2021.607601

Temperature Stress Induces Shift From Co-Existence to Competition for Organic Carbon in Microalgae-Bacterial Photobioreactor Community – Enabling Continuous Production of Microalgal Biomass
Cited by: 7
Author(s): Eva Sörenson, Eric Capo, Hanna Farnelid, Elin Lindehoff, Catherine Legrand
Software Mentions: 6
Published: over 3 years ago

10.1038/s41396-021-00931-z

Fine-scale metabolic discontinuity in a stratified prokaryote microbiome of a Red Sea deep halocline
Cited by: 8
Author(s): Grégoire Michoud, David Kamanda Ngugi, Alan Barozzi, Giuseppe Merlino, María Ll. Calleja, António Delgado Huertas, Xosé Anxelu G. Morán, Daniele Daffonchio
Software Mentions: 6
Published: about 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: almost 7 years ago

10.3389/fpls.2021.647709

The Effects of Host Plant Genotype and Environmental Conditions on Fungal Community Composition and Phosphorus Solubilization in Willow Short Rotation Coppice
Cited by: 7
Author(s): Piotr Koczorski, Bliss Ursula Furtado, Marcin Gołębiewski, Piotr Hulisz, Christel Baum, Martin Weih, Katarzyna Hrynkiewicz
Software Mentions: 6
Published: almost 3 years ago

10.1186/s13059-019-1743-y

CONFINED: distinguishing biological from technical sources of variation by leveraging multiple methylation datasets
Cited by: 6
Author(s): Michael Thompson, Zeyuan Johnson Chen, Elior Rahmani, Eran Halperin
Software Mentions: 6
Published: almost 5 years ago

10.1038/s41438-018-0090-6

Genetic characterization of worldwide Prunus domestica (plum) germplasm using sequence-based genotyping
Cited by: 50
Author(s): Tetyana Zhebentyayeva, Vijay Shankar, R. Scorza, Ann M. Callahan, Michel Ravelonandro, Sarah Castro, Theodore M. DeJong, Christopher Saski, Chris Dardick
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0116095

ICan: An Integrated Co-Alteration Network to Identify Ovarian Cancer-Related Genes
Cited by: 9
Author(s): Yuanshuai Zhou, Yongjing Liu, Kening Li, Rui Zhang, Fujun Qiu, Ning Zhao, Yan Xu
Software Mentions: 6
Published: about 9 years ago

10.1371/journal.pone.0187142

Spatial-temporal dynamics of neotropical velvet ant (Hymenoptera: Mutillidae) communities along a forest-savanna gradient
Cited by: 2
Author(s): Júlio Miguel Alvarenga, Cecília Rodrigues Vieira, Leandro Braga Godinho, Pedro Henrique Campelo, James P. Pitts, Guarino Rinaldi Colli
Software Mentions: 6
Published: over 6 years ago

10.7717/peerj.3098

Metagenomic analysis exploring taxonomic and functional diversity of soil microbial communities in Chilean vineyards and surrounding native forests
Cited by: 107
Author(s): Luis E. Castañeda, Olga Barbosa
Software Mentions: 5
Published: about 7 years ago

10.7554/eLife.68967

Spatially patterned excitatory neuron subtypes and projections of the claustrum
Cited by: 17
Author(s): Sarah R. Erwin, Brianna N. Bristow, Kaitlin E Sullivan, Rennie M Kendrick, Brian A. Marriott, Lihua Wang, Jody Clements, Andrew L. Lemire, Jesse Jackson, Mark S. Cembrowski
Software Mentions: 5
Published: almost 3 years ago

10.1186/s12874-018-0653-0

Multiple imputation methods for handling missing values in a longitudinal categorical variable with restrictions on transitions over time: a simulation study
Cited by: 24
Author(s): Anurika De Silva, Margarita Moreno‐Betancur, Alysha M De Livera, Katherine Jane Lee, Julie A. Simpson
Software Mentions: 5
Published: over 5 years ago

10.18632/oncotarget.16417

Interaction of Epstein-Barr virus genes with human gastric carcinoma transcriptome
Cited by: 10
Author(s): Ruiyuan Zhang, Michael J. Strong, Melody Baddoo, Zhen Lin, Yuping Wang, Erik K. Flemington, Yaozhong Liu
Software Mentions: 5
Published: about 7 years ago

10.1186/s12859-019-3289-0

Identifying gene-specific subgroups: an alternative to biclustering
Cited by: 3
Author(s): Vincent Branders, Pierre Schaus, Pierre Dupont
Software Mentions: 5
Published: over 4 years ago

10.1186/s13059-021-02313-2

Schema: metric learning enables interpretable synthesis of heterogeneous single-cell modalities
Cited by: 19
Author(s): Rohit Singh, Brian Hie, Ashwin Narayan, Bonnie Berger
Software Mentions: 5
Published: about 3 years ago

10.1371/journal.pone.0236165

Diversity and structure of soil microbiota of the Jinsha earthen relic
Cited by: 4
Author(s): Sheng Yang, Linfeng Wu, Bin Wu, Yizheng Zhang, Haiyan Wang, Xuemei Tan
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12864-020-07300-8

Rapid single cell evaluation of human disease and disorder targets using REVEAL: SingleCell™
Cited by: 2
Author(s): Namit Kumar, Ryan Golhar, Kriti Sen Sharma, James L. Holloway, Srikant Sarangi, Isaac M. Neuhaus, Alice M. Walsh, Zachary W. Pitluk
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2019.03153

Diversity of Bacterial Community in the Oxygen Minimum Zones of Arabian Sea and Bay of Bengal as Deduced by Illumina Sequencing
Cited by: 33
Author(s): Genevieve L. Fernandes, Belle Damodara Shenoy, Samir Damare
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pcbi.1009021

MiMeNet: Exploring microbiome-metabolome relationships using neural networks
Cited by: 33
Author(s): Derek Reiman, Brian T. Layden, Yang Dai
Software Mentions: 5
Published: about 3 years ago

10.1186/1756-0381-5-19

Visualising associations between paired ‘omics’ data sets
Cited by: 211
Author(s): Ignacio González, Kim‐Anh Lê Cao, Melissa J. Davis, Sébastien Déjean
Software Mentions: 5
Published: over 11 years ago

10.1002/ece3.3797

Sea ice meiofauna distribution on local to pan‐Arctic scales
Cited by: 24
Author(s): Bodil A. Bluhm, Haakon Hop, Mikko Vihtakari, Rolf Gradinger, Katrin Iken, I. A. Melnikov, Janne E. Søreide
Software Mentions: 4
Published: over 6 years ago

10.1128/AEM.00305-19

Bacterial and Fungal Endophytic Microbiomes of Salicornia europaea
Cited by: 46
Author(s): Bliss Ursula Furtado, Marcin Gołębiewski, Monika Skorupa, Piotr Hulisz, Katarzyna Hrynkiewicz
Software Mentions: 4
Published: almost 5 years ago

10.7554/eLife.61646

Neural encoding of actual and imagined touch within human posterior parietal cortex
Cited by: 16
Author(s): Srinivas Chivukula, Carey Y. Zhang, Tyson Aflalo, Matiar Jafari, Kelsie Pejsa, Nader Pouratian, Richard A. Andersen
Software Mentions: 4
Published: about 3 years ago

10.1186/1756-0381-6-17

Using random walks to identify cancer-associated modules in expression data
Cited by: 32
Author(s): Deanna Petrochilos, Ali Shojaie, John H. Gennari, Neil F. Abernethy
Software Mentions: 4
Published: over 10 years ago

10.1038/s42003-021-02674-1

Genomic characterization of rare molecular subclasses of hepatocellular carcinoma
Cited by: 4
Author(s): Jeffrey S. Damrauer, Markia A. Smith, Vonn Walter, Aatish Thennavan, Lisle E. Mose, Sara R. Selitsky, Katherine A. Hoadley
Software Mentions: 4
Published: over 2 years ago

10.1038/s41598-021-97516-9

Phytoplankton communities in temporary ponds under different climate scenarios
Cited by: 6
Author(s): Sofia Celewicz-Gołdyn, Bartłomiej Gołdyn
Software Mentions: 4
Published: over 2 years ago

10.1002/ece3.4944

Conservation of genetic diversity hotspots of the high‐valued relic yellowhorn ( Xanthoceras sorbifolium ) considering climate change predictions
Cited by: 1
Author(s): Renbin Zhu, Qing Wang, Wei Guan, Yanjia Mao, Bin Tian, Jimin Cheng, Yousry A. El‐Kassaby
Software Mentions: 4
Published: about 5 years ago

10.1083/jcb.201711048

A timer for analyzing temporally dynamic changes in transcription during differentiation in vivo
Cited by: 54
Author(s): David Bending, Paz Prieto Martín, Alina Paduraru, Catherine Ducker, Erik Marzaganov, Marie Laviron, Satsuki Kitano, Hitoshi Miyachi, Tessa Crompton, M. Ono
Software Mentions: 4
Published: almost 6 years ago

10.1098/rsos.201797

Seasonal shifts in the competitive ability of macroalgae influence the outcomes of coral–algal competition
Cited by: 6
Author(s): Kristen T. Brown, Dorothea Bender-Champ, Ove Hoegh‐Guldberg, Sophie Dove
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0224214

Early succession on slag compared to urban soil: A slower recovery
Cited by: 4
Author(s): Heng-Xing Zou, Alison E. Anastasio, Catherine A. Pfister
Software Mentions: 4
Published: over 4 years ago

10.1186/gb-2011-12-3-r27

A genome-wide view of mutation rate co-variation using multivariate analyses
Cited by: 38
Author(s): Guruprasad Ananda, Francesca Chiaromonte, Kateryna D. Makova
Software Mentions: 4
Published: over 13 years ago

10.1371/journal.pone.0144702

Archaeal and Bacterial Communities Associated with the Surface Mucus of Caribbean Corals Differ in Their Degree of Host Specificity and Community Turnover Over Reefs
Cited by: 23
Author(s): Pedro R. Frade, Katharina Roll, Kristin Bergauer, Gerhard J. Herndl
Software Mentions: 4
Published: over 8 years ago

10.3389/fvets.2020.00635

The Iconic Atlantic Goliath Grouper (Epinephelus itajara): A Comprehensive Assessment of Health Indices in the Southeastern United States Population
Cited by: 6
Author(s): Christopher R. Malinowski, Justin R. Perrault, Felicia C. Coleman, Christopher C. Koenig, Justin M. Stilwell, Carolyn Cray, Nicole I. Stacy
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0050267

Multivariate Approach for Studying Interactions between Environmental Variables and Microbial Communities
Cited by: 21
Author(s): Xinhui Wang, Marinus J.C. Eijkemans, Jacco Wallinga, Giske Biesbroek, Krzysztof Trzciński, Elisabeth A. M. Sanders, Debby Bogaert
Software Mentions: 4
Published: over 11 years ago

10.1093/gigascience/giz047

Single-cell transcriptomic landscape of nucleated cells in umbilical cord blood
Cited by: 24
Author(s): Yi Zhao, Xiao Li, Weihua Zhao, Jingwan Wang, Jun Yu, Ziyun Wan, Kai Gao, Gang Ye, Wang Xie, Bingbing Fan, Qinkai Wu, Bangwei Chen, Feng Xie, Jinghua Wu, Wei Zhang, Fang Chen, Huanming Yang, Jian Wang, Xun Xu, Bin Li, Shiping Liu, Yong Hou, Xiao Liu
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pcbi.1001034

Mapping Dynamic Histone Acetylation Patterns to Gene Expression in Nanog-Depleted Murine Embryonic Stem Cells
Cited by: 21
Author(s): Florian Markowetz, Klaas W. Mulder, Edoardo M. Airoldi, Ihor R. Lemischka, Olga G. Troyanskaya
Software Mentions: 4
Published: over 13 years ago

10.3389/fmicb.2018.00869

Taxon-Function Decoupling as an Adaptive Signature of Lake Microbial Metacommunities Under a Chronic Polymetallic Pollution Gradient
Cited by: 20
Author(s): Bachar Cheaib, Malo Le Boulch, Pierre-Luc Mercier, Nicolas Derôme
Software Mentions: 4
Published: about 6 years ago

10.1038/s42003-021-01820-z

The gut mycobiome of healthy mice is shaped by the environment and correlates with metabolic outcomes in response to diet
Cited by: 50
Author(s): Tahliyah S. Mims, Qusai Al Abdallah, James Monroe Stewart, Sydney Watts, Catrina T. White, Thomas Rousselle, Ankush Gosain, Amandeep Bajwa, Joan C. Han, Kent A. Willis, Joseph F. Pierre
Software Mentions: 4
Published: about 3 years ago

10.1126/sciadv.abg1512

Dopaminergic organization of striatum is linked to cortical activity and brain expression of genes associated with psychiatric illness
Cited by: 9
Author(s): Robert McCutcheon, Kirsten Brown, Matthew M. Nour, Stephen M. Smith, Mattia Veronese, Fernando Zelaya, Martin Osugo, Sameer Jauhar, William A. Hallett, Mitul Mehta, Oliver Howes
Software Mentions: 4
Published: almost 3 years ago

10.3390/ijerph13090855

The Relationship between Phytoplankton Evenness and Copepod Abundance in Lake Nansihu, China
Cited by: 6
Author(s): Tian Wu, Huayong Zhang, Lei Zhao, Xiang Xu, Huang Hai
Software Mentions: 3
Published: over 7 years ago

10.1186/s12859-021-04150-3

Analysis of single-cell RNA sequencing data based on autoencoders
Cited by: 12
Author(s): Andrea Tangherloni, Federico Ricciuti, Daniela Besozzi, Píetro Lió, Ana Cvejic
Software Mentions: 3
Published: almost 3 years ago

10.7554/eLife.64875

Single-cell and single-nucleus RNA-seq uncovers shared and distinct axes of variation in dorsal LGN neurons in mice, non-human primates, and humans
Cited by: 30
Author(s): Trygve E. Bakken, Cindy Tj van Velthoven, Vilas Menon, Rebecca D. Hodge, Zizhen Yao, Thuc Nghi Nguyen, Lucas T. Graybuck, Gregory D. Horwitz, Darren Bertagnolli, Jeff Goldy, Anna Marie Yanny, Emma Garren, Sheana Parry, Tamara Casper, Soraya I. Shehata, Eliza Barkan, Aaron Szafer, Boaz P. Levi, Nick Dee, Kimberly A. Smith, Susan M. Sunkin, Amy Bernard, John W. Phillips, Michael Hawrylycz, Christof Koch, Gabe J. Murphy, Ed Lein, Hongkui Zeng, Bosiljka Tasic
Software Mentions: 3
Published: over 2 years ago

10.1002/ece3.2262

Biogeography of dinoflagellate cysts in northwest Atlantic estuaries
Cited by: 22
Author(s): Andrea Price, Vera Pospelova, Michael R.S. Coffin, James S. Latimer, Gail L. Chmura
Software Mentions: 3
Published: almost 8 years ago

10.3390/s21072321

CCA: Cost-Capacity-Aware Caching for In-Memory Data Analytics Frameworks
Cited by: 1
Author(s): Seongsoo Park, Minseop Jeong, Hwansoo Han
Software Mentions: 3
Published: about 3 years ago

10.1038/s41598-017-05454-2

Microbiota composition of the koala (Phascolarctos cinereus) ocular and urogenital sites, and their association with Chlamydia infection and disease
Cited by: 13
Author(s): Miranda E. Vidgen, Jon Hanger, Peter Timms
Software Mentions: 3
Published: almost 7 years ago

10.1038/srep12179

Resilience and receptivity worked in tandem to sustain a geothermal mat community amidst erratic environmental conditions
Cited by: 18
Author(s): Wriddhiman Ghosh, Chayan Roy, Ranjit Roy, Pravin Nilawe, Amartya Mukherjee, Prabir Kumar Haldar, Neeraj Chauhan, Sabyasachi Bhattacharya, Atima Agarwal, Ashish George, Prosenjit Pyne, Sanjay K. Mandal, Moidu Jameela Rameez, Goutam Bala
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-019-40872-4

Composition and Dynamics of the Activated Sludge Microbiome during Seasonal Nitrification Failure
Cited by: 56
Author(s): Juliet Johnston, Timothy M. LaPara, Sebastian Behrens
Software Mentions: 3
Published: about 5 years ago

10.1002/ece3.650

Combining molecular evolution and environmental genomics to unravel adaptive processes of MHC class IIB diversity in European minnows (Phoxinus phoxinus)
Cited by: 13
Author(s): Hélène Collin, Reto Burri, Fabien Comtesse, Luca Fumagalli
Software Mentions: 3
Published: almost 11 years ago

10.18632/aging.103345

Discovering correlates of age-related decline in a healthy late-midlife male birth cohort
Cited by: 1
Author(s): Kiyana Zarnani, Stephen M. Smith, Fidel Alfaro-Almagro, Birgitte Fagerlund, Martin Lauritzen, Egill Rostrup, Thomas E. Nichols
Software Mentions: 3
Published: over 3 years ago

10.1016/j.csbj.2021.01.029

Integrative approaches for analysis of mRNA and microRNA high-throughput data
Cited by: 18
Author(s): Petr V. Nazarov, Stephanie Kreis
Software Mentions: 3
Published: over 3 years ago

10.3390/e22020208

Nonlinear Canonical Correlation Analysis:A Compressed Representation Approach
Cited by: 1
Author(s): Amichai Painsky, Meir Feder, Naftali Tishby
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-020-68785-7

Effects of vegetation restoration and environmental factors on understory vascular plants in a typical karst ecosystem in southern China
Cited by: 17
Author(s): Ou Zhiyang, Pang Shilong, He Qinfei, Yungui Peng, Huang Xiao-rong, Wenhui Shen
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0034527

Not All Kinds of Revegetation Are Created Equal: Revegetation Type Influences Bird Assemblages in Threatened Australian Woodland Ecosystems
Cited by: 57
Author(s): David B. Lindenmayer, Amanda R. Northrop-Mackie, Rebecca Montague‐Drake, Mason Crane, Damian Michael, Sachiko Okada, Philip Gibbons
Software Mentions: 3
Published: about 12 years ago

10.1186/1471-2105-11-499

Bi-directional gene set enrichment and canonical correlation analysis identify key diet-sensitive pathways and biomarkers of metabolic syndrome
Cited by: 21
Author(s): Melissa J. Morine, Jolene McMonagle, Sinéad Toomey, Clare M. Reynolds, A.P. Moloney, Isobel Claire Gormley, Peadar Ó Gaora, Helen M. Roche
Software Mentions: 3
Published: over 13 years ago

10.1186/s13059-018-1455-8

Tensorial blind source separation for improved analysis of multi-omic data
Cited by: 20
Author(s): Andrew E. Teschendorff, Junqiang Han, Dirk S. Paul, Joni Virta, Klaus Nordhausen
Software Mentions: 3
Published: almost 6 years ago

10.1098/rsos.160296

Age-related environmental gradients influence invertebrate distribution in the Prince Charles Mountains, East Antarctica
Cited by: 9
Author(s): Paul Czechowski, Duanne White, Laurence J. Clarke, Alan McKay, Alan Cooper, Mark I. Stevens
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0108924

Fecal Bacterial Community Changes Associated with Isoflavone Metabolites in Postmenopausal Women after Soy Bar Consumption
Cited by: 82
Author(s): Cindy H. Nakatsu, Arthur Armstrong, Andrea Clavijo, Berdine R. Martin, Stephen Barnes, Connie M. Weaver
Software Mentions: 3
Published: over 9 years ago

10.3389/fonc.2019.00649

Construction and Investigation of a lncRNA-Associated ceRNA Regulatory Network in Cholangiocarcinoma
Cited by: 32
Author(s): Junyu Long, Jianping Xiong, Yi Bai, Jianshan Mao, Jianzhen Lin, Weiyu Xu, Hui Zhang, Shuguang Chen, Hong Zhao
Software Mentions: 3
Published: almost 5 years ago

10.1264/jsme2.ME17163

Diarrhea-Associated Intestinal Microbiota in Captive Sichuan Golden Snub-Nosed Monkeys (Rhinopithecus roxellana)
Cited by: 13
Author(s): Hongxiang Zhu, Dong Zeng, Qiang Wang, Ning Wang, Bo Zeng, Lili Niu, Xueqin Ni
Software Mentions: 3
Published: over 6 years ago

10.3389/fnins.2015.00418

Effects of thresholding on correlation-based image similarity metrics
Cited by: 3
Author(s): Vanessa Sochat, Krzysztof J. Gorgolewski, Oluwasanmi Koyejo, Joke Durnez, Russell A. Poldrack
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0053656

Methyl Fluoride Affects Methanogenesis Rather than Community Composition of Methanogenic Archaea in a Rice Field Soil
Cited by: 16
Author(s): Anne Daebeler, Martina Gansen, Peter Frenzel
Software Mentions: 3
Published: over 11 years ago

10.3389/fnins.2019.01037

Clustering the Brain With “CluB”: A New Toolbox for Quantitative Meta-Analysis of Neuroimaging Data
Cited by: 6
Author(s): Manuela Berlingeri, Francantonio Devoto, Francesca Gasparini, Aurora Saibene, Silvia Corchs, Lucia Clemente, L Danelli, Marcello Gallucci, Riccardo Borgoni, N. Alberto Borghese, Eraldo Paulesu
Software Mentions: 3
Published: over 4 years ago

10.1007/s11306-018-1420-2

Characterization of missing values in untargeted MS-based metabolomics data and evaluation of missing data handling strategies
Cited by: 126
Author(s): Kieu Trinh, Simone Wahl, Johannes Raffler, Sophie Molnos, Michael Laimighofer, Jerzy Adamski, Karsten Suhre, Konstantin Strauch, Annette Peters, Christian Gieger, Claudia Langenberg, Isobel D. Stewart, Fabian J. Theis, Harald Grallert, Gabi Kastenmüller, Jan Krumsiek
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0043866

Functional Biogeography of Ocean Microbes Revealed through Non-Negative Matrix Factorization
Cited by: 41
Author(s): Xingpeng Jiang, Morgan G. I. Langille, Russell Y. Neches, Marie A. Elliot, Simon A. Levin, Jonathan A. Eisen, Joshua S. Weitz, Jonathan Dushoff
Software Mentions: 3
Published: over 11 years ago

10.3389/fninf.2016.00049

Pyrcca: Regularized Kernel Canonical Correlation Analysis in Python and Its Applications to Neuroimaging
Cited by: 54
Author(s): Natalia Y. Bilenko, Jack L. Gallant
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2017.00715

Relative Abundance and Diversity of Bacterial Methanotrophs at the Oxic–Anoxic Interface of the Congo Deep-Sea Fan
Cited by: 11
Author(s): Sandrine Bessette, Yann Moalic, Sébastien Gautey, Françoise Lesongeur, Anne Godfroy, Laurent Toffin
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0025604

Metagenomic Profile of the Bacterial Communities Associated with Ixodes ricinus Ticks
Cited by: 238
Author(s): Giovanna Carpi, Francesca Cagnacci, Nicola E. Wittekindt, Fangqing Zhao, Ji Qi, Lynn P. Tomsho, Daniela I. Drautz, Annapaola Rizzoli, Stephan C. Schuster
Software Mentions: 3
Published: over 12 years ago

10.3389/fneur.2021.622719

Artifact Reduction in Simultaneous EEG-fMRI: A Systematic Review of Methods and Contemporary Usage
Cited by: 29
Author(s): Madeleine Bullock, Graeme D. Jackson, David F. Abbott
Software Mentions: 3
Published: about 3 years ago

10.3389/fmicb.2017.02144

Relationship between Gingival Crevicular Fluid Microbiota and Cytokine Profile in Periodontal Host Homeostasis
Cited by: 26
Author(s): Jianye Zhou, Yiqing Yao, Kangli Jiao, Jumei Zhang, Xin Zheng, Fang Wu, Xiao-Pan Hu, Junping Li, Zhenhai Yu, Gaosen Zhang, Nan Jiang, Zhiqiang Liu
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0214389

Free-view gait recognition
Cited by: 12
Author(s): Yonghong Tian, Wei Lan, Shijian Lu, Tiejun Huang
Software Mentions: 3
Published: about 5 years ago

10.3389/fmicb.2018.00578

Benthic Algal Community Structures and Their Response to Geographic Distance and Environmental Variables in the Qinghai-Tibetan Lakes With Different Salinity
Cited by: 23
Author(s): Jian Yang, Hongchen Jiang, Wen Liu, Beichen Wang
Software Mentions: 3
Published: about 6 years ago

10.3389/fmicb.2021.593023

Rhizodegradation of Pyrene by a Non-pathogenic Klebsiella pneumoniae Isolate Applied With Tagetes erecta L. and Changes in the Rhizobacterial Community
Cited by: 11
Author(s): Jina Rajkumari, Yashmin Choudhury, Kasturi Bhattacharjee, Piyush Pandey
Software Mentions: 3
Published: about 3 years ago

10.34133/2020/1969142

Hierarchical Canonical Correlation Analysis Reveals Phenotype, Genotype, and Geoclimate Associations in Plants
Cited by: 1
Author(s): Raphael Petegrosso, Tianci Song, Rui Kuang
Software Mentions: 3
Published: over 4 years ago

10.3389/fnhum.2016.00093

Is There Neural Evidence for an Evidence Accumulation Process in Memory Decisions?
Cited by: 7
Author(s): Marieke K. van Vugt, Marijke A. Beulen, Niels Taatgen
Software Mentions: 3
Published: about 8 years ago

10.1107/S2059798316007695

Ab initiophasing by molecular averaging in real space with new criteria: application to structure determination of a betanodavirus
Cited by: 3
Author(s): Masato Yoshimura, Nai Chi Chen, Hongbing Guan, Phimonphan Chuankhayan, Chi‐Chang Lin, Atsushi Nakagawa, Chun‐Jung Chen
Software Mentions: 3
Published: almost 8 years ago

10.3389/fnins.2021.691244

MRI Radiomic Signature of White Matter Hyperintensities Is Associated With Clinical Phenotypes
Cited by: 9
Author(s): Martin Bretzner, Anna K. Bonkhoff, Markus D. Schirmer, Sungmin Hong, Adrian V. Dalca, Kathleen Donahue, Anne‐Katrin Giese, Mark R. Etherton, Pamela M. Rist, Marco Nardin, Rǎzvan V. Marinescu, Clinton Wang, Robert W Regenhardt, Xavier Leclerc, Renaud Lopes, Oscar Benavente, John W. Cole, Amanda Donatti, Christoph J. Griessenauer, Laura Heitsch, Lukas Holmegaard, Katarina Jood, Jordi Jiménez‐Conde, Steven J. Kittner, Robin Lemmens, Christopher Levi, Patrick F. McArdle, Caitrin W. McDonough, James F. Meschia, Chia‐Ling Phuah, Arndt Rolfs, Stefan Ropele, Jonathan Rosand, Jaume Roquer, Tatjana Rundek, Ralph L. Sacco, Reinhold Schmidt, Pankaj Sharma, Agnieszka Słowik, Alessandro Sousa, Tara M. Stanne, Daniel Strbian, Turgut Tatlısumak, Vincent Thijs, Achala Vagal, Johan Wassélius, Daniel Woo, Ona Wu, Ramin Zand, Bradford B. Worrall, Jane Maguire, Arne Lindgren, Christina Jern, Polina Golland, Grégory Kuchcinski, Natalia S. Rost
Software Mentions: 3
Published: almost 3 years ago

10.3389/fcimb.2017.00405

Host Distribution Does Not Limit the Range of the Tick Ixodes ricinus but Impacts the Circulation of Transmitted Pathogens
Cited by: 22
Author(s): Agustı́n Estrada-Peña, José de la Fuente
Software Mentions: 2
Published: over 6 years ago

10.18632/aging.102151

Discovering markers of healthy aging: a prospective study in a Danish male birth cohort
Cited by: 8
Author(s): Kiyana Zarnani, Thomas E. Nichols, Fidel Alfaro-Almagro, Birgitte Fagerlund, Martin Lauritzen, Egill Rostrup, Stephen M. Smith
Software Mentions: 2
Published: over 4 years ago

10.3389/fcimb.2021.692883

A Single Dose of Nitrate Increases Resilience Against Acidification Derived From Sugar Fermentation by the Oral Microbiome
Cited by: 11
Author(s): Bob T. Rosier, Carlos Palazón, Sandra García‐Esteban, Alejandro Artacho, Antonio Galiana, Álex Mira
Software Mentions: 2
Published: almost 3 years ago

10.3389/fcell.2019.00175

Cross-Species Analysis of Single-Cell Transcriptomic Data
Cited by: 66
Author(s): Maxwell E.R. Shafer
Software Mentions: 2
Published: over 4 years ago

10.3389/fncom.2020.00055

Neurons as Canonical Correlation Analyzers
Cited by: 7
Author(s): Cengiz Pehlevan, Xinyuan Zhao, Anirvan M. Sengupta, Dmitri B. Chklovskii
Software Mentions: 2
Published: almost 4 years ago

10.3390/biology10070587

Combined Effect of Laboratory-Simulated Fire and Chromium Pollution on Microbial Communities in an Agricultural Soil
Cited by: 5
Author(s): Ida Rascio, Maddalena Curci, Concetta Eliana Gattullo, Anna Lavecchia, Mohammad Yaghoubi Khanghahi, Roberto Terzano, Carmine Crecchio
Software Mentions: 2
Published: almost 3 years ago

Projects: cran: CCA

Papers Mentioning CCA 449