cran: dynamicTreeCut | Projects | Ecosyste.ms: Papers

10.3389/fmolb.2020.570702

Prognostic Prediction Using a Stemness Index-Related Signature in a Cohort of Gastric Cancer
Cited by: 27
Author(s): Xiaowei Chen, Dawei Zhang, Fei Jiang, Yan Shen, Xin Li, Xin Hu, Pingmin Wei, Xiaobing Shen
Software Mentions: 24
Published: over 4 years ago

10.3390/genes11030257

mRNAsi Index: Machine Learning in Mining Lung Adenocarcinoma Stem Cell Biomarkers
Cited by: 61
Author(s): Yitong Zhang, Joseph T. Tseng, I-Chia Lien, Fenglan Li, Wei Wu, Hui Li
Software Mentions: 20
Published: almost 5 years ago

10.1186/s13059-019-1739-7

CellSIUS provides sensitive and specific detection of rare cell populations from complex single-cell RNA-seq data
Cited by: 33
Author(s): Rebekka Wegmann, Marilisa Neri, Sven Schuierer, Bilada Bilican, Huyen Hartkopf, Florian Nigsch, Felipa Mapa, Annick Waldt, Rachel Cuttat, Max R. Salick, Joe Raymond, Ajamete Kaykas, Guglielmo Roma, Caroline Gubser Keller
Software Mentions: 13
Published: over 5 years ago

10.1186/s41065-021-00202-z

RNA-Seq based transcriptome analysis in oral lichen planus
Cited by: 5
Author(s): Haoyu Wang, Yiwen Deng, Siqi Peng, Yán Li, Hui Xu, Qingzhong Wang, Zhenhua Shen
Software Mentions: 10
Published: about 3 years ago

10.1371/journal.ppat.1005996

A Mouse Model of Chronic West Nile Virus Disease
Cited by: 44
Author(s): Jessica B. Graham, Jessica L. Swarts, Courtney Wilkins, Sunil Thomas, Richard Green, Aimee Sekine, Kathleen Voss, Reneé C. Ireton, Michael A. Mooney, Gabrielle Choonoo, Darla R. Miller, Piper M. Treuting, Fernando Pardo Manuel de Villena, Martin T. Ferris, Shannon K. McWeeney, Michael Gale, Jennifer M. Lund
Software Mentions: 10
Published: about 8 years ago

10.1038/s42003-020-0842-3

Loss of the branched-chain amino acid transporter CD98hc alters the development of colonic macrophages in mice
Cited by: 17
Author(s): Philipp Wuggenig, Berna Kaya, Hassan Melhem, C. Korcan Ayata, Swiss Ibd Cohort Investigators, Petr Hrúz, Emre Sayan, Hideki Tsumura, Morihiro Ito, Julien Roux, Jan Hendrik Niess
Software Mentions: 10
Published: almost 5 years ago

10.1093/bioinformatics/btv428

dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering
Cited by: 1,079
Author(s): Tal Galili
Software Mentions: 10
Published: over 9 years ago

10.1371/journal.pone.0240462

The origins of money: Calculation of similarity indexes demonstrates the earliest development of commodity money in prehistoric Central Europe
Cited by: 11
Author(s): Maikel H.G. Kuijpers, Cătălin Nicolae Popa
Software Mentions: 9
Published: almost 4 years ago

10.15252/embj.2020104983

Interactions between lineage‐associated transcription factors govern haematopoietic progenitor states
Cited by: 17
Author(s): Iwo Kuciński, Nicola K. Wilson, Rebecca Hannah, Sarah Kinston, Pierre Cauchy, Aurelie Lenaerts, Rudolf Grosschedl, Berthold Göttgens
Software Mentions: 9
Published: about 4 years ago

10.1002/acn3.51441

Gut microbiome is associated with multiple sclerosis activity in children
Cited by: 18
Author(s): Mary Horton, Kathryn McCauley, Douglas Fadrosh, Kei E. Fujimura, Jennifer Graves, Jayne Ness, Yolanda Wheeler, Mark Gorman, Leslie Benson, Bianca Weinstock‐Guttman, Amy Waldman, Moses Rodriguez, Jan‐Mendelt Tillema, Lauren Krupp, Anita Belman, Soe Mar, Mary Rensel, Tanuja Chitnis, T. Charles Casper, John Rose, Janace Hart, Xiaorong Shao, Helen Tremlett, Susan V. Lynch, Lisa F. Barcellos, Emmanuelle Waubant
Software Mentions: 8
Published: over 3 years ago

10.1038/s41598-021-81952-8

Gene co-expression network analysis reveals immune cell infiltration as a favorable prognostic marker in non-uterine leiomyosarcoma
Cited by: 12
Author(s): Mohammad Darzi, Saeid Gorgin, Keivan Majidzadeh‐A, Rezvan Esmaeili
Software Mentions: 7
Published: almost 4 years ago

10.1111/eva.12935

The power and limitations of gene expression pathway analyses toward predicting population response to environmental stressors
Cited by: 9
Author(s): Brenna Callista Moreau Stanford, Danielle Jessica Clake, Matthew R. J. Morris, Sean M. Rogers
Software Mentions: 7
Published: almost 5 years ago

10.15252/emmm.201910606

Novel Alzheimer risk genes determine the microglia response to amyloid‐β but not to TAU pathology
Cited by: 149
Author(s): Annerieke Sierksma, Ashley Lu, Renzo Mancuso, Nicola Fattorelli, Nicola Thrupp, Evgenia Salta, Jesus Zoco, David Blum, Luc Buée, Bart De Strooper, Mark Fiers
Software Mentions: 7
Published: almost 5 years ago

10.1186/s12864-021-07595-1

Dynamics of rumen gene expression, microbiome colonization, and their interplay in goats
Cited by: 15
Author(s): Xiangyu Pan, Zongjun Li, Bibo Li, Chen Zhao, Yu Wang, Yulin Chen, Yu Jiang
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0216793

Patterns of gene expression characterize T1 and T3 clear cell renal cell carcinoma subtypes
Cited by: 4
Author(s): A. Borys, Michał Seweryn, Tomasz Gołąbek, Łukasz Bełch, Agnieszka Klimkowska, Justyna Totoń‐Żurańska, Julita Machlowska, Piotr Chłosta, Krzysztof Okoń, Paweł Wołkow
Software Mentions: 7
Published: over 5 years ago

10.1038/s41598-019-55441-y

Exploring inflammatory signatures in arthritic joint biopsies with Spatial Transcriptomics
Cited by: 50
Author(s): Konstantin Carlberg, Marina Korotkova, Ludvig Larsson, Anca I. Catrina, Patrik L. Ståhl, Vivianne Malmström
Software Mentions: 6
Published: about 5 years ago

10.1016/j.cell.2016.09.007

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

10.3390/jcm10163520

An Integrative Systems Biology Approach Identifies Molecular Signatures Associated with Gallbladder Cancer Pathogenesis
Cited by: 3
Author(s): Nabanita Roy, Mrinmoy Kshattry, Subhrangsu S. Mandal, Mohit Kumar Jolly, Dhruba K. Bhattacharyya, Pankaj Barah
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-019-6003-8

RNAi based transcriptome suggests genes potentially regulated by HSF1 in the Pacific oyster Crassostrea gigas under thermal stress
Cited by: 14
Author(s): Youli Liu, Li Li, Baoyu Huang, Wei Wang, Guofan Zhang
Software Mentions: 5
Published: over 5 years ago

10.1038/s42003-021-01892-x

Transcriptomic analyses of the termite, Cryptotermes secundus, reveal a gene network underlying a long lifespan and high fecundity
Cited by: 15
Author(s): Silu Lin, Jana Werle, Judith Korb
Software Mentions: 5
Published: almost 4 years ago

10.3389/fmicb.2021.705712

Dual Transcriptomic Analyses Unveil Host–Pathogen Interactions Between Salmonella enterica Serovar Enteritidis and Laying Ducks (Anas platyrhynchos)
Cited by: 1
Author(s): Yu Zhang, Lina Song, Li-e Hou, Zhen Cao, Wanwipa Vongsangnak, Guoqiang Zhu, Qi Xu, Guohong Chen
Software Mentions: 5
Published: over 3 years ago

10.1038/srep05193

Quantitative scoring of differential drug sensitivity for individually optimized anticancer therapies
Cited by: 230
Author(s): Bhagwan Yadav, Tea Pemovska, Agnieszka Szwajda, Evgeny Kulesskiy, Mika Kontro, Reijo Karjalainen, Muntasir Mamun Majumder, Disha Malani, Astrid Murumägi, Jonathan Knowles, Kimmo Porkka, Caroline A. Heckman, Olli Kallioniemi, Krister Wennerberg, Tero Aittokallio
Software Mentions: 5
Published: over 10 years ago

10.1038/s41598-020-77318-1

Improving existing analysis pipeline to identify and analyze cancer driver genes using multi-omics data
Cited by: 9
Author(s): Quang-Huy Nguyen, Duc-Hau Le
Software Mentions: 5
Published: about 4 years ago

10.1038/s41598-020-77284-8

Lung squamous cell carcinoma and lung adenocarcinoma differential gene expression regulation through pathways of Notch, Hedgehog, Wnt, and ErbB signalling
Cited by: 34
Author(s): Dorota Anusewicz, Magdalena Orzechowska, Andrzej K. Bednarek
Software Mentions: 5
Published: about 4 years ago

10.1186/s12974-021-02154-7

Identification of aberrant innate and adaptive immunity based on changes in global gene expression in the blood of adults with autism spectrum disorder
Cited by: 11
Author(s): Fumie Horiuchi, Yuta Yoshino, Hiroshi Kumon, Rie Hosokawa, Kiwamu Nakachi, Kentaro Kawabe, Jun‐ichi Iga, Shu‐ichi Ueno
Software Mentions: 5
Published: over 3 years ago

10.1186/1471-2164-11-674

Apoplast proteome reveals that extracellular matrix contributes to multistress response in poplar
Cited by: 69
Author(s): Oľga Pecháňová, Chuan-Yu Hsu, J. F. Adams, Tibor Pechan, Lindsay Vandervelde, Jenny Drnevich, Sara Jawdy, Ardeshir Adeli, Jeffrey C. Suttle, Andrew D. Lawrence, Timothy J. Tschaplinski, Armand Séguin, Çetin Yüceer
Software Mentions: 4
Published: about 14 years ago

10.3389/fmicb.2020.01931

Insights Into Subspecies Discrimination Potentiality From Bacteria MALDI-TOF Mass Spectra by Using Data Mining and Diversity Studies
Cited by: 10
Author(s): Audrey Giraud-Gatineau, Gaétan Texier, Éric Garnotel, Didier Raoult, Hervé Chaudet
Software Mentions: 4
Published: over 4 years ago

10.3389/fgene.2020.597803

A Novel Transcriptome Integrated Network Approach Identifies the Key Driver lncRNA Involved in Cell Cycle With Chromium (VI)-Treated BEAS-2B Cells
Cited by: 0
Author(s): Pai Zheng, Yulin Kang, Shuo Han, Huimin Feng, Feizai Ha, Changmao Long, Di Zhou, Guiping Hu, Zhangjian Chen, Zengmiao Wang, Tiancheng Wang, Guang Jia
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-021-91907-8

Y disruption, autosomal hypomethylation and poor male lung cancer survival
Cited by: 13
Author(s): Saffron A.G. Willis‐Owen, C. Domingo-Sabugo, E. Starren, Liming Liang, Maxim B. Freidin, Madeleine Arseneault, Youming Zhang, Shir Kiong Lu, Sanjay Popat, Eric Lim, Andrew G. Nicholson, Yasser Riazalhosseini, Mark Lathrop, William Cookson, Miriam F. Moffatt
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-017-03871-x

Analysis of survival and hatching transcriptomes from potato cyst nematodes, Globodera rostochiensis and G. pallida
Cited by: 21
Author(s): Marc‐Olivier Duceppe, Joël Lafond-Lapalme, Juan E. Palomares-Rius, Michaël Sabeh, Vivian C. Blok, Peter Moffett, Benjamin Mimee
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-018-34162-8

Remotely-sensed productivity clusters capture global biodiversity patterns
Cited by: 16
Author(s): Nicholas C. Coops, Sean P. Kearney, Douglas K. Bolton, Volker C. Radeloff
Software Mentions: 4
Published: about 6 years ago

10.1186/s12859-021-04153-0

DR2S: an integrated algorithm providing reference-grade haplotype sequences from heterozygous samples
Cited by: 3
Author(s): Steffen Klasberg, Alexander H. Schmidt, Vinzenz Lange, Gerhard Schöfl
Software Mentions: 4
Published: over 3 years ago

10.1128/mSystems.00070-17

Abiotic Stresses Shift Belowground <i>Populus</i> -Associated Bacteria Toward a Core Stress Microbiome
Cited by: 75
Author(s): Collin M. Timm, Kelsey Carter, Alyssa A. Carrell, Se‐Ran Jun, Sara Jawdy, Jessica M. Vélez, Lee E. Gunter, Zamin K. Yang, Intawat Nookaew, Nancy L. Engle, Tse-Yuan S. Lu, Christopher W. Schadt, Timothy J. Tschaplinski, Mitchel J. Doktycz, Gerald A. Tuskan, Dale A. Pelletier, David J. Weston
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12957-021-02248-9

Potential role of chimeric genes in pathway-related gene co-expression modules
Cited by: 7
Author(s): Piaopiao Li, Yingxia Li, Lei Ma
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0165059

Drug Repositioning through Systematic Mining of Gene Coexpression Networks in Cancer
Cited by: 19
Author(s): Alexander E. Ivliev, Peter A.C. ’t Hoen, Dmitrii Borisevich, Yuri Nikolsky, Marina G. Sergeeva
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pcbi.1006089

Propagating annotations of molecular networks using in silico fragmentation
Cited by: 216
Author(s): Ricardo R. da Silva, Mingxun Wang, Louis Félix Nothias, Justin J. J. van der Hooft, Andrés Mauricio Caraballo‐Rodríguez, Evan Fox, Marcy J. Balunas, Jonathan L. Klassen, Norberto Peporine Lopes, Pieter C. Dorrestein
Software Mentions: 3
Published: over 6 years ago

10.3390/v11070607

Combining Viral Genetics and Statistical Modeling to Improve HIV-1 Time-of-Infection Estimation towards Enhanced Vaccine Efficacy Assessment
Cited by: 11
Author(s): Raabya Rossenkhan, Morgane Rolland, Jan Phillipus Lourens Labuschagne, Roux-Cil Ferreira, Craig A. Magaret, Lindsay N. Carpp, F. A. Matsen, Yunda Huang, Erika Rudnicki, Yuanyuan Zhang, Nonkululeko Ndabambi, Murray Logan, Ted Holzman, Melissa-Rose Abrahams, Colin Anthony, Sodsai Tovanabutra, Christopher Warth, G. Botha, David Matten, Sorachai Nitayaphan, Hannah Kibuuka, Fred Sawe, Denis Chopera, Leigh Anne Eller, Simon Travers, Merlin L. Robb, Carolyn Williamson, Peter B. Gilbert, Paul T. Edlefsen
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2021.680560

A Compendium of Age-Related PheWAS and GWAS Traits for Human Genetic Association Studies, Their Networks and Genetic Correlations
Cited by: 2
Author(s): Seung Soo Kim, Adam D. Hudgins, Brenda González, Sofiya Milman, Nir Barzilai, Jan Vijg, Zhidong Tu, Yousin Suh
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2105-11-497

DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules
Cited by: 190
Author(s): Bruno Tesson, Rainer Breitling, Ritsert C. Jansen
Software Mentions: 3
Published: about 14 years ago

10.1016/j.molmet.2020.101038

Differential regulation of the immune system in a brain-liver-fats organ network during short-term fasting
Cited by: 6
Author(s): Shengshu Huang, Mélanie Makhlouf, Eman H. AbouMoussa, Mayra L. Ruiz Tejada Segura, Lisa S. Mathew, Kun Wang, Man C. Leung, Damien Chaussabel, Darren W. Logan, Antonio Scialdone, Mathieu Garand, Luís R. Saraiva
Software Mentions: 3
Published: about 4 years ago

10.1093/bioinformatics/btaa482

COMUNET: a tool to explore and visualize intercellular communication
Cited by: 17
Author(s): Maria Solovey, Antonio Scialdone
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2164-11-20

Gene expression profiling in C57BL/6J and A/J mouse inbred strains reveals gene networks specific for brain regions independent of genetic background
Cited by: 17
Author(s): Simone de Jong, Tova Fuller, Esther Janson, Eric Strengman, Steve Horvath, Martien Kas, Roel A. Ophoff
Software Mentions: 3
Published: almost 15 years ago

10.1186/s12864-016-3143-y

Mining kidney toxicogenomic data by using gene co-expression modules
Cited by: 21
Author(s): Mohamed Diwan M. AbdulHameed, Danielle L. Ippolito, Jonathan D. Stallings, Anders Wallqvist
Software Mentions: 3
Published: about 8 years ago

10.1016/j.cell.2016.01.047

Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos
Cited by: 346
Author(s): Mubeen Goolam, Antonio Scialdone, Sarah J. L. Graham, Iain C. Macaulay, Agnieszka Jędrusik, Anna Hupalowska, Thierry Voet, John C. Marioni, Magdalena Zernicka‐Goetz
Software Mentions: 3
Published: almost 9 years ago

10.1016/j.jspi.2018.03.004

A group analysis using the Multiregression Dynamic Models for fMRI networked time series
Cited by: 5
Author(s): Lino João da Costa, Jean A. Smith, Thomas E. Nichols
Software Mentions: 3
Published: almost 6 years ago

10.3390/cells9122556

Hearing Loss in Alzheimer’s Disease Is Associated with Altered Serum Lipidomic Biomarker Profiles
Cited by: 11
Author(s): Daniel A. Llano, Lina K Issa, Priya Devanarayan, Viswanath Devanarayan, Alzheimer's Disease Neuroimaging Initiative ADNI
Software Mentions: 2
Published: about 4 years ago

10.3390/genes12091452

Novel Approach Combining Transcriptional and Evolutionary Signatures to Identify New Multiciliation Genes
Cited by: 3
Author(s): Audrey Defosset, Dorine Merlat, Laetitia Poidevin, Yannis Nevers, Arnaud Kress, Olivier Poch, Odile Lecompte
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0107230

Characterization of Chemically Induced Liver Injuries Using Gene Co-Expression Modules
Cited by: 29
Author(s): Gregory J. Tawa, Mohamed Diwan M. AbdulHameed, Xueping Yu, Kamal Kumar, Danielle L. Ippolito, John A. Lewis, Jonathan D. Stallings, Anders Wallqvist
Software Mentions: 2
Published: over 10 years ago

10.1186/1752-0509-4-S2-S11

Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer's disease brains
Cited by: 77
Author(s): Zhiping Liu, Yong Wang, Yu Xia, Luonan Chen
Software Mentions: 2
Published: over 14 years ago

Projects: cran: dynamicTreeCut

Papers Mentioning dynamicTreeCut 49