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: dynamicTreeCut
https://packages.ecosyste.ms/registries/pypi.org/packages/dynamicTreeCut
Dynamic Tree Cut
2 versions
Latest release: about 3 years ago
9,606 downloads last month
Papers Mentioning dynamicTreeCut 49
10.3389/fmolb.2020.570702
Prognostic Prediction Using a Stemness Index-Related Signature in a Cohort of Gastric CancerCited by: 27
Author(s): Xiaowei Chen, Dawei Zhang, Fei Jiang, Yan Shen, Xin Li, Xin Hu, Pingmin Wei, Xiaobing Shen
Software Mentions: 24
Published: about 4 years ago
10.3390/genes11030257
mRNAsi Index: Machine Learning in Mining Lung Adenocarcinoma Stem Cell BiomarkersCited by: 61
Author(s): Yitong Zhang, Joseph T. Tseng, I-Chia Lien, Fenglan Li, Wei Wu, Hui Li
Software Mentions: 20
Published: over 4 years ago
10.1186/s13059-019-1739-7
CellSIUS provides sensitive and specific detection of rare cell populations from complex single-cell RNA-seq dataCited 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 planusCited 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 DiseaseCited 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 miceCited 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: over 4 years ago
10.1093/bioinformatics/btv428
dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clusteringCited 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 EuropeCited 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 statesCited 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 childrenCited 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: about 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 leiomyosarcomaCited 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 stressorsCited by: 9
Author(s): Brenna Callista Moreau Stanford, Danielle Jessica Clake, Matthew R. J. Morris, Sean M. Rogers
Software Mentions: 7
Published: over 4 years ago
10.15252/emmm.201910606
Novel Alzheimer risk genes determine the microglia response to amyloid‐β but not to TAU pathologyCited 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 goatsCited 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 subtypesCited 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 TranscriptomicsCited by: 50
Author(s): Konstantin Carlberg, Marina Korotkova, Ludvig Larsson, Anca I. Catrina, Patrik L. Ståhl, Vivianne Malmström
Software Mentions: 6
Published: almost 5 years ago
10.1016/j.cell.2016.09.007
Functional Metabolomics Describes the Yeast Biosynthetic RegulomeCited 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 PathogenesisCited by: 3
Author(s): Nabanita Roy, Mrinmoy Kshattry, Subhrangsu S. Mandal, Mohit Kumar Jolly, Dhruba K. Bhattacharyya, Pankaj Barah
Software Mentions: 5
Published: about 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 stressCited by: 14
Author(s): Youli Liu, Li Li, Baoyu Huang, Wei Wang, Guofan Zhang
Software Mentions: 5
Published: about 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 fecundityCited by: 15
Author(s): Silu Lin, Jana Werle, Judith Korb
Software Mentions: 5
Published: over 3 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 therapiesCited 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 dataCited by: 9
Author(s): Quang-Huy Nguyen, Duc-Hau Le
Software Mentions: 5
Published: almost 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 signallingCited by: 34
Author(s): Dorota Anusewicz, Magdalena Orzechowska, Andrzej K. Bednarek
Software Mentions: 5
Published: almost 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 disorderCited 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 poplarCited 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: almost 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 StudiesCited by: 10
Author(s): Audrey Giraud-Gatineau, Gaétan Texier, Éric Garnotel, Didier Raoult, Hervé Chaudet
Software Mentions: 4
Published: about 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 CellsCited 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 survivalCited 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. pallidaCited 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 patternsCited 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 samplesCited 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 MicrobiomeCited 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: over 6 years ago
10.1186/s12957-021-02248-9
Potential role of chimeric genes in pathway-related gene co-expression modulesCited 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 CancerCited by: 19
Author(s): Alexander E. Ivliev, Peter A.C. ’t Hoen, Dmitrii Borisevich, Yuri Nikolsky, Marina G. Sergeeva
Software Mentions: 4
Published: almost 8 years ago
10.1371/journal.pcbi.1006089
Propagating annotations of molecular networks using in silico fragmentationCited 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 AssessmentCited 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 CorrelationsCited 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 modulesCited 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 fastingCited 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 communicationCited 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 backgroundCited 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 modulesCited 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 EmbryosCited 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: over 8 years ago
10.1016/j.jspi.2018.03.004
A group analysis using the Multiregression Dynamic Models for fMRI networked time seriesCited 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 ProfilesCited by: 11
Author(s): Daniel A. Llano, Lina K Issa, Priya Devanarayan, Viswanath Devanarayan, Alzheimer's Disease Neuroimaging Initiative ADNI
Software Mentions: 2
Published: almost 4 years ago
10.3390/genes12091452
Novel Approach Combining Transcriptional and Evolutionary Signatures to Identify New Multiciliation GenesCited by: 3
Author(s): Audrey Defosset, Dorine Merlat, Laetitia Poidevin, Yannis Nevers, Arnaud Kress, Olivier Poch, Odile Lecompte
Software Mentions: 2
Published: about 3 years ago
10.1371/journal.pone.0107230
Characterization of Chemically Induced Liver Injuries Using Gene Co-Expression ModulesCited 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: about 10 years ago
10.1186/1752-0509-4-S2-S11
Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer's disease brainsCited by: 77
Author(s): Zhiping Liu, Yong Wang, Yu Xia, Luonan Chen
Software Mentions: 2
Published: about 14 years ago