cran: Clustering | Projects | Ecosyste.ms: Papers

10.3390/vaccines8010138

From Bivariate to Multivariate Analysis of Cytometric Data: Overview of Computational Methods and Their Application in Vaccination Studies
Cited by: 12
Author(s): Simone Lucchesi, Simone Furini, Donata Medaglini, Annalisa Ciabattini
Software Mentions: 9
Published: over 4 years ago

10.3389/fmicb.2021.649517

Decentralized Investigation of Bacterial Outbreaks Based on Hashed cgMLST
Cited by: 15
Author(s): Carlus Deneke, Laura Uelze, Holger Brendebach, Simon H. Tausch, Burkhard Malorny
Software Mentions: 9
Published: over 3 years ago

10.1371/journal.pone.0217050

Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples
Cited by: 61
Author(s): Lucas Czech, Alexandros Stamatakis
Software Mentions: 6
Published: over 5 years ago

10.1186/s12862-019-1479-z

Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa (Rosaceae)
Cited by: 16
Author(s): Kévin Debray, Jordan Marie‐Magdelaine, Tom Ruttink, Jérémy Clotault, Fabrice Foucher, Valéry Malécot
Software Mentions: 5
Published: over 5 years ago

10.1155/2019/6151587

Direct Extracellular Electron Transfer of the Geobacter sulfurreducens Pili Relevant to Interaromatic Distances
Cited by: 6
Author(s): Chuanjun Shu, Qunzhi Zhu, Ke Xiao, Yanbing Hou, Haibo Ma, Jing Ma, Xiao Sun
Software Mentions: 5
Published: about 5 years ago

10.3390/cancers11101566

PD-1-Associated Gene Expression Signature of Neoadjuvant Trastuzumab-Treated Tumors Correlates with Patient Survival in HER2-Positive Breast Cancer
Cited by: 6
Author(s): William P.D. Hendricks, Natalia Briones, Rebecca F. Halperin, Salvatore Facista, Paul R. Heaton, Daruka Mahadevan, Suwon Kim
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-019-6294-9

Refining modules to determine functionally significant clusters in molecular networks
Cited by: 2
Author(s): Rama Kaalia, Jagath C. Rajapakse
Software Mentions: 4
Published: almost 5 years ago

10.1083/jcb.202004010

mTORC1 activity is supported by spatial association with focal adhesions
Cited by: 35
Author(s): Yoana Rabanal‐Ruiz, Adam Byron, Alexander Wirth, Ralitsa R. Madsen, Lucia Sedlackova, Graeme Hewitt, Glyn Nelson, Julian Stingele, Jimi Wills, Tong Zhang, André Zeug, Reinhard Fässler, Bart Vanhaesebroeck, Oliver D.K. Maddocks, Evgeni Ponimaskin, Bernadette Carroll, Viktor I. Korolchuk
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-017-04070-4

A GPU-accelerated algorithm for biclustering analysis and detection of condition-dependent coexpression network modules
Cited by: 21
Author(s): Anindya Bhattacharya, Yan Cui
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.ppat.1007601

RNAi-based small molecule repositioning reveals clinically approved urea-based kinase inhibitors as broadly active antivirals
Cited by: 25
Author(s): Markus Lesch, Madlen Luckner, Michaël Meyer, Friderike Weege, Isabella Gravenstein, Martin Raftery, Christian Sieben, Laura Martin-Sancho, Aki Imai-Matsushima, Robert-William Welke, Rebecca Frise, William Barclay, Günther Schönrich, Andreas Herrmann, Thomas Meyer, Alexander Karlas
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2164-15-754

Transcriptome profiling of natural dichromatism in the annual fishes Nothobranchius furzeri and Nothobranchius kadleci
Cited by: 21
Author(s): Enoch Ng’oma, Marco Groth, Roberto Ripa, Matthias Platzer, Alessandro Cellerino
Software Mentions: 3
Published: about 10 years ago

10.1007/s00248-015-0568-9

Microbial Consortium Associated with the Antarctic Marine Ciliate Euplotes focardii: An Investigation from Genomic Sequences
Cited by: 37
Author(s): Sandra Pucciarelli, Raghul Rajan Devaraj, Alessio Mancini, Patrizia Ballarini, Michele Castelli, Martina Schrallhammer, Giulio Petroni, Cristina Miceli
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0157069

A Method for Quantifying, Visualising, and Analysing Gastropod Shell Form
Cited by: 14
Author(s): Thor‐Seng Liew, Menno Schilthuizen
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0108277

SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation
Cited by: 1,102
Author(s): Brejnev Muhire, Arvind Varsani
Software Mentions: 3
Published: about 10 years ago

10.3389/fgene.2019.00936

Enhancer LncRNAs Influence Chromatin Interactions in Different Ways
Cited by: 32
Author(s): Yue Hou, Rong Xin Zhang, Xiao Sun
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-020-77766-9

SkipGNN: predicting molecular interactions with skip-graph networks
Cited by: 43
Author(s): Kexin Huang, Cao Xiao, Lucas M. Glass, Marinka Žitnik, Jimeng Sun
Software Mentions: 3
Published: almost 4 years ago

10.1007/s00122-019-03276-6

Training population selection and use of fixed effects to optimize genomic predictions in a historical USA winter wheat panel
Cited by: 70
Author(s): Jose Martin Sarinelli, J. Paul Murphy, Priyanka Tyagi, James B. Holland, J. W. Johnson, Maryati Mohamed, Richard E. Mason, Ali Babar, Stephen A. Harrison, Russell Sutton, Carl A. Griffey, Gina Brown-Guedira
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0082411

The Combined Expression Patterns of Ikaros Isoforms Characterize Different Hematological Tumor Subtypes
Cited by: 7
Author(s): Carlos Orozco, Andrés Acevedo, Lázaro Cortina, Gina Cuéllar, Mónica Duarte, Liliana Martín, Néstor M. Mesa, Javier Muñoz, Carlos Andrés Portilla, Sandra Quijano, Guillermo Quintero, Martín González Rodríguez, Carlos Saavedra, Helena Groot, María Mercedes Torres, Valeriano López-Segura
Software Mentions: 2
Published: almost 11 years ago

10.1155/2012/467531

A Study of the Wound Healing Mechanism of a Traditional Chinese Medicine,Angelica sinensis, Using a Proteomic Approach
Cited by: 36
Author(s): Chia Yen Hsiao, Ching Yi Hung, Tung Hu Tsai, Kin‐Fu Chak
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pcbi.1005072

Determining Physical Mechanisms of Gene Expression Regulation from Single Cell Gene Expression Data
Cited by: 17
Author(s): Daphne Ezer, Victoria Moignard, Berthold Göttgens, Boris Adryan
Software Mentions: 2
Published: about 8 years ago

10.1186/s12864-017-4131-6

An uncertain model-based approach for identifying dynamic protein complexes in uncertain protein-protein interaction networks
Cited by: 8
Author(s): Yijia Zhang, Hongfei Lin, Zhihao Yang, Jian Wang, Yiwei Liu
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-017-09285-z

Genome-wide Target Enrichment-aided Chip Design: a 66 K SNP Chip for Cashmere Goat
Cited by: 11
Author(s): Xuguang Qiao, Rui Su, Yan Wang, Ruijun Wang, Ting Yang, Xiaokai Li, Wei Chen, Shiyang He, Yu Jiang, Qiwu Xu, Wenting Wan, Yaolei Zhang, Wenguang Zhang, Chen Jiang, Bin Liu, Xin Liu, Yixing Fan, Duoyuan Chen, Jiang Huai-zhi, Dongming Fang, Zhihong Liu, Xiaowen Wang, Yanjun Zhang, Danqing Mao, Zhiying Wang, Ran Di, Qianjun Zhao, Tao Zhong, Huanming Yang, Jian Wang, Wen Wang, Yang Dong, Xiaoli Chen, Xun Xu, Jinquan Li
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-55063-4

Land use change effects on diversity of soil bacterial, Acidobacterial and fungal communities in wetlands of the Sanjiang Plain, northeastern China
Cited by: 57
Author(s): Xin Sui, Rongtao Zhang, Beat Frey, Libin Yang, Mai‐He Li, Hongwei Ni
Software Mentions: 2
Published: almost 5 years ago

10.3389/fmicb.2014.00666

Multitasking SecB chaperones in bacteria
Cited by: 63
Author(s): Ambre Sala, Patricia Bordes, Pierre Genevaux
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0138993

Exploring Genetic Divergence in a Species-Rich Insect Genus Using 2790 DNA Barcodes
Cited by: 73
Author(s): Lin X, Elisabeth Stur, Torbjørn Ekrem
Software Mentions: 2
Published: about 9 years ago

10.3389/fnins.2019.00221

Graph Theoretical Characteristics of EEG-Based Functional Brain Networks in Patients With Epilepsy: The Effect of Reference Choice and Volume Conduction
Cited by: 17
Author(s): Maria Anastasiadou, Manolis Christodoulakis, Eleftherios S. Papathanasiou, Savvas Papacostas, Avgis Hadjipapas, Georgios D. Mitsis
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2164-11-523

Study of inter- and intra-individual variations in the salivary microbiota
Cited by: 197
Author(s): Vladimir Lazarević, Katrine Whiteson, David Hernández, Patrice François, Jacques Schrenzel
Software Mentions: 2
Published: almost 15 years ago

10.3390/s18051593

SOBER-MCS: Sociability-Oriented and Battery Efficient Recruitment for Mobile Crowd-Sensing
Cited by: 17
Author(s): Fazel Anjomshoa, Burak Kantarcı
Software Mentions: 2
Published: over 6 years ago

10.1093/database/bau041

PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins
Cited by: 45
Author(s): Pierrick Craveur, Joseph Rebehmed, Alexandre G. de Brevern
Software Mentions: 2
Published: over 10 years ago

10.1093/gbe/evt184

Reduction and Expansion in Microsporidian Genome Evolution: New Insights from Comparative Genomics
Cited by: 103
Author(s): Sirintra Nakjang, Tom A. Williams, Eva Heinz, Andrew K. Watson, Peter G. Foster, Kacper Sendra, Sarah E. Heaps, Robert P. Hirt, T. Martin Embley
Software Mentions: 2
Published: about 11 years ago

10.1093/gbe/evy263

Genome and Transcriptome Sequencing of the Astaxanthin-Producing Green Microalga,Haematococcus pluvialis
Cited by: 52
Author(s): Qiulan Luo, Chao Bian, Ming Tao, Yu Huang, Ye Zheng, Yunyun Lv, Jia Li, Chaogang Wang, Xinxin You, Bin Jia, Junmin Xu, Jiancheng Li, Ze Li, Qiong Shi, Zhangli Hu
Software Mentions: 2
Published: almost 6 years ago

10.1093/molbev/msz053

Phylogenetic Clustering by Linear Integer Programming (PhyCLIP)
Cited by: 46
Author(s): Alvin X. Han, Edyth Parker, Frits Scholer, Sebastian Maurer‐Stroh, Colin A. Russell
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-015-1953-y

Genome-wide identification of long noncoding RNA genes and their potential association with fecundity and virulence in rice brown planthopper, Nilaparvata lugens
Cited by: 57
Author(s): Huamei Xiao, Zhuting Yuan, Dan Guo, Bofeng Hou, Chuanlin Yin, Wenqing Zhang, Fēi Li
Software Mentions: 2
Published: about 9 years ago

10.7717/peerj.4374

MIA-Clustering: a novel method for segmentation of paleontological material
Cited by: 27
Author(s): Christopher J. Dunmore, Gert Wollny, Matthew M. Skinner
Software Mentions: 2
Published: over 6 years ago

10.3389/fphar.2018.00036

Calycosin Orchestrates Osteogenesis of Danggui Buxue Tang in Cultured Osteoblasts: Evaluating the Mechanism of Action by Omics and Chemical Knock-out Methodologies
Cited by: 15
Author(s): Amy G. W. Gong, Ran Duan, Huaiyou Wang, Ting Dong, Karl Wah Keung Tsim
Software Mentions: 1
Published: almost 7 years ago

10.1007/s00705-014-2197-x

Improvements to pairwise sequence comparison (PASC): a genome-based web tool for virus classification
Cited by: 136
Author(s): Yīmíng Bào, Vyacheslav Chetvernin, Tatiana Tatusova
Software Mentions: 1
Published: over 10 years ago

10.1038/srep12894

Progeny Clustering: A Method to Identify Biological Phenotypes
Cited by: 32
Author(s): Chenyue W. Hu, Steven M. Kornblau, John H. Slater, Amina A. Qutub
Software Mentions: 1
Published: over 9 years ago

10.1038/srep36372

Scanning of selection signature provides a glimpse into important economic traits in goats (Capra hircus)
Cited by: 45
Author(s): Dailu Guan, Nanjian Luo, Xiaoshan Tan, Zhongquan Zhao, Yongfu Huang, Risu Na, Jiahua Zhang, Yongju Zhao
Software Mentions: 1
Published: about 8 years ago

10.1186/s12885-017-3568-y

Distinct molecular subtypes of uterine leiomyosarcoma respond differently to chemotherapy treatment
Cited by: 18
Author(s): Yang An, Shuzhen Wang, Songlin Li, Lulu Zhang, Dayong Wang, Haojie Wang, Shibai Zhu, Wan Zhu, Yongqiang Li, Wenwu Chen, Shaoping Ji, Xiangqian Guo
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-020-57904-z

Characterization of the woody biomass feedstock potential resulting from California’s drought
Cited by: 9
Author(s): Carmen L. Tubbesing, José Daniel Lara, John J. Battles, Peter Tittmann, Daniel M. Kammen
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-020-73623-x

Complex societies and the growth of the law
Cited by: 18
Author(s): Daniel Katz, Corinna Coupette, Janis Beckedorf, Dirk Hartung
Software Mentions: 1
Published: about 4 years ago

10.3390/ijms160715009

Identification and Characterization of 40 Isolated Rehmannia glutinosa MYB Family Genes and Their Expression Profiles in Response to Shading and Continuous Cropping
Cited by: 19
Author(s): Fengqing Wang, Yanfei Suo, Wei He, Mingjie Li, Chaotian Xie, Lina Wang, Xinjian Chen, Zhongyi Zhang
Software Mentions: 1
Published: over 9 years ago

10.3390/s140406584

Uncertain Data Clustering-Based Distance Estimation in Wireless Sensor Networks
Cited by: 25
Author(s): Qinghua Luo, Peng Yu, Xiyuan Peng, Abdulmotaleb El Saddik
Software Mentions: 1
Published: over 10 years ago

10.3390/biology10020166

Establishing a Percutaneous Infection Model Using Zebrafish and a Salmon Pathogen
Cited by: 3
Author(s): Hajime Nakatani, Katsutoshi Hori
Software Mentions: 1
Published: over 3 years ago

10.1186/scrt398

Towards an advanced therapy medicinal product based on mesenchymal stromal cells isolated from the umbilical cord tissue: quality and safety data
Cited by: 51
Author(s): José Paulo Martins, Jorge M. Santos, Joana M. Almeida, Mariana Filipe, Mariana Vargas Teixeira de Almeida, Sílvia Cristina Cristina Almeida, Ana Água-Doce, Alexandre Varela, Mari Gilljam, Birgitta Stellan, Susanne Pohl, Kurt E.J. Dittmar, Werner Lindenmaier, Evren Alici, Luís Graça, Pedro Cruz, Hélder Cruz, Rita N. Bárcia
Software Mentions: 1
Published: almost 11 years ago

10.3390/mi9050249

Motion Constraints and Vanishing Point Aided Land Vehicle Navigation
Cited by: 14
Author(s): Zhenbo Liu, Naser El‐Sheimy, Chunyang Yu, Qin Yong-yuan
Software Mentions: 1
Published: over 6 years ago

10.1186/1476-4598-10-54

The structural impact of cancer-associated missense mutations in oncogenes and tumor suppressors
Cited by: 58
Author(s): Henning Stehr, Seon-Hi J Jang, José M. Duarte, Christoph Wierling, Hans Lehrach, Michael Lappé, Bodo Lange
Software Mentions: 1
Published: over 13 years ago

10.1186/s12864-018-5165-0

Distinct esophageal adenocarcinoma molecular subtype has subtype-specific gene expression and mutation patterns
Cited by: 8
Author(s): Xiangqian Guo, Yaxun Tang, Wan Zhu
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pbio.3000314

Detecting T cell receptors involved in immune responses from single repertoire snapshots
Cited by: 99
Author(s): Mikhail V. Pogorelyy, Anastasia A. Minervina, Mikhail Shugay, Dmitriy M. Chudakov, Yuri B. Lebedev, Thierry Mora, Aleksandra M. Walczak
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1005505

XBP1-Independent UPR Pathways Suppress C/EBP-β Mediated Chondrocyte Differentiation in ER-Stress Related Skeletal Disease
Cited by: 28
Author(s): Trevor L. Cameron, Katrina M. Bell, Irma Gresshoff, Lisa Sampurno, Lorna Mullan, Joerg Ermann, Laurie H. Glimcher, Raymond P. Boot-Handford, John F. Bateman
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0094556

Proliferation Potential of Müller Glia after Retinal Damage Varies between Mouse Strains
Cited by: 36
Author(s): Akiko Suga, Kazuyo Sadamoto, Momo Fujii, Michiko Mandai, Masayo Takahashi
Software Mentions: 1
Published: over 10 years ago

10.18632/oncotarget.26057

The core sequence of PIF competes for insulin/amyloid β in insulin degrading enzyme: potential treatment for Alzheimer's disease
Cited by: 7
Author(s): Soren Hayrabedyan, Krassimira Todorova, Marialuigia Spinelli, Eytan R. Barnea, Martin Mueller
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0197624

Genomic variants in an inbred mouse model predict mania-like behaviors
Cited by: 1
Author(s): Michael C. Saul, Sharon A. Stevenson, Changjiu Zhao, Terri M. Driessen, Brian E. Eisinger, Stephen C. Gammie
Software Mentions: 1
Published: over 6 years ago

10.1186/1742-4682-9-1

Neural network assessment of herbal protection against chemotherapeutic-induced reproductive toxicity
Cited by: 16
Author(s): Amr Amin, Doaa Mahmoud‐Ghoneim, Muhammed I. Syam, Sayel Daoud
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0142305

Enhancer of Acetyltransferase Chameau (EAChm) Is a Novel Transcriptional Co-Activator
Cited by: 2
Author(s): Takeya Nakagawa, Tsuyoshi Ikehara, Masamichi Doiguchi, Yuko Imamura, Miki Higashi, Mitsuhiro Yoneda, Takashi Ito
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0117921

Malassezia Intra-Specific Diversity and Potentially New Species in the Skin Microbiota from Brazilian Healthy Subjects and Seborrheic Dermatitis Patients
Cited by: 32
Author(s): Renan Cardoso Soares, Marcelo B. Zani, Ana Carolina Belini Bazán Arruda, Lúcia Valéria Ramos de Arruda, Luciana Campos Paulino
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0022715

Differential Effects of Prenatal Stress in 5-Htt Deficient Mice: Towards Molecular Mechanisms of Gene × Environment Interactions
Cited by: 67
Author(s): Daniël L.A. van den Hove, Sissi Brigitte Jakob, Karla‐Gerlinde Schraut, Günter Kenis, Angelika Schmitt, Susanne Kneitz, Claus‐Jürgen Scholz, Valentina Wiescholleck, Guillermo J. Ortega, Jos Prickaerts, Harry W.M. Steinbusch, Klaus–Peter Lesch
Software Mentions: 1
Published: over 13 years ago

10.3390/cancers12092640

Genome-Wide Comparison of the Target Genes of the Reactive Oxygen Species and Non-Reactive Oxygen Species Constituents of Cold Atmospheric Plasma in Cancer Cells
Cited by: 11
Author(s): Hwee Won Ji, Hee Joo Kim, Hyeon Woo Kim, Sung Hwan Yun, Jae Eun Park, Eun Ha Choi, Sun Jung Kim
Software Mentions: 1
Published: about 4 years ago

10.3390/cancers11122011

Cold Atmospheric Plasma Restores Paclitaxel Sensitivity to Paclitaxel-Resistant Breast Cancer Cells by Reversing Expression of Resistance-Related Genes
Cited by: 27
Author(s): Sung-Bin Park, Heejoo Kim, Hwee Won Ji, Hyeon Woo Kim, Sung Hwan Yun, Eun Ha Choi, Sun Jung Kim
Software Mentions: 1
Published: almost 5 years ago

10.3390/e20110830

A Nonparametric Model for Multi-Manifold Clustering with Mixture of Gaussians and Graph Consistency
Cited by: 5
Author(s): Xulun Ye, Jieyu Zhao, Yu Chen
Software Mentions: 1
Published: about 6 years ago

10.1128/mSphere.00472-18

Mycobacterium ulcerans Population Genomics To Inform on the Spread of Buruli Ulcer across Central Africa
Cited by: 13
Author(s): Koen Vandelannoote, Delphin Mavinga Phanzu, Kapay Kibadi, Miriam Eddyani, Conor J. Meehan, Kurt Jordaens, Herwig Leirs, Françoise Portaels, Timothy P. Stinear, Simon R. Harris, Bouke C. de Jong
Software Mentions: 1
Published: over 5 years ago

10.3389/fimmu.2018.00033

Immune Repertoire Sequencing Using Molecular Identifiers Enables Accurate Clonality Discovery and Clone Size Quantification
Cited by: 42
Author(s): Yanxiong Ke, Chenfeng He, Ben S. Wendel, Chad M. Williams, Jun Xiao, Hui Yang, Ning Jiang
Software Mentions: 1
Published: almost 7 years ago

10.1186/1471-2164-13-164

GeSICA: Genome segmentation from intra-chromosomal associations
Cited by: 6
Author(s): Lin Liu, Yiqian Zhang, Jianxing Feng, Ning Zheng, Jun-Feng Yin, Yong Zhang
Software Mentions: 1
Published: over 12 years ago

10.3389/fphar.2018.01312

ABCC10 Plays a Significant Role in the Transport of Gefitinib and Contributes to Acquired Resistance to Gefitinib in NSCLC
Cited by: 27
Author(s): Hongbo Zhao, Yutang Huang, Jingjing Shi, Yi Dai, Long‐Fei Wu, Hong‐Hao Zhou
Software Mentions: 1
Published: about 6 years ago

Projects: cran: Clustering

Papers Mentioning Clustering 65