cran: DCA | Projects | Ecosyste.ms: Papers

10.3389/fninf.2019.00057

Comparing Open-Source Toolboxes for Processing and Analysis of Spike and Local Field Potentials Data
Cited by: 14
Author(s): Valentina A. Unakafova, Alexander Gail
Software Mentions: 23
Published: about 5 years ago

10.1186/s13059-020-02136-7

pipeComp, a general framework for the evaluation of computational pipelines, reveals performant single cell RNA-seq preprocessing tools
Cited by: 53
Author(s): Pierre-Luc Germain, Anthony Sonrel, Mark D. Robinson
Software Mentions: 21
Published: about 4 years ago

10.15252/msb.20188746

Current best practices in single‐cell RNA‐seq analysis: a tutorial
Cited by: 1,173
Author(s): Malte D. Luecken, Fabian J. Theis
Software Mentions: 20
Published: over 5 years ago

10.1186/s13059-020-02132-x

A systematic evaluation of single-cell RNA-sequencing imputation methods
Cited by: 156
Author(s): Wenpin Hou, Zhicheng Ji, Hongkai Ji, Stephanie Hicks
Software Mentions: 15
Published: about 4 years ago

10.1186/s13059-019-1898-6

Accuracy, robustness and scalability of dimensionality reduction methods for single-cell RNA-seq analysis
Cited by: 123
Author(s): Shuang Sun, Jiaqiang Zhu, Ying Ma, Xiang Zhou
Software Mentions: 13
Published: almost 5 years ago

10.1186/s13059-020-1926-6

Eleven grand challenges in single-cell data science
Cited by: 646
Author(s): David Laehnemann, Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie Hicks, Mark D. Robinson, Catalina A. Vallejos, Kieran R Campbell, Niko Beerenwinkel, Ahmed Mahfouz, Luca Pinello, Pavel Skums, Alexandros Stamatakis, Camille Stephan‐Otto Attolini, Samuel Aparicio, Jasmijn A. Baaijens, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas E. Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharina Jahn, Thamar Jessurun Lobo, Emma M Keizer, Indu Khatri, Szymon M. Kiełbasa, Jan Korbel, Alexey M Kozlov, Tzu Hao Kuo, Boudewijn P. F. Lelieveldt, Ion Măndoiu, John C. Marioni, Tobias Marschall, Felix Mölder, Amir Niknejad, Łukasz Rączkowski, Marcel J. T. Reinders, Jeroen de Ridder, Antoine Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian J. Theis, Huan Yang, Alexander Zelikovsky, Alice C. McHardy, Benjamin J. Raphael, Sohrab P. Shah, Alexander Schönhuth
Software Mentions: 11
Published: over 4 years ago

10.1186/s13059-020-02083-3

DISC: a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning
Cited by: 23
Author(s): Yong He, Hao Yuan, Changbao Wu, Zhi Xie
Software Mentions: 9
Published: about 4 years ago

10.1186/s13059-020-02096-y

Demystifying “drop-outs” in single-cell UMI data
Cited by: 66
Author(s): Tae Hyun Kim, Xiang Zhou, Mengjie Chen
Software Mentions: 9
Published: about 4 years ago

10.1371/journal.pcbi.1009029

G2S3: A gene graph-based imputation method for single-cell RNA sequencing data
Cited by: 7
Author(s): Weimiao Wu, Yunqing Liu, Qile Dai, Xiting Yan, Zuoheng Wang
Software Mentions: 9
Published: over 3 years ago

10.18632/aging.103508

Radiomics-based prediction of survival in patients with head and neck squamous cell carcinoma based on pre- and post-treatment 18F-PET/CT
Cited by: 26
Author(s): Zheran Liu, Yuan Cao, Wei Diao, Yue Cheng, Zhiyun Jia, Xingchen Peng
Software Mentions: 9
Published: about 4 years ago

10.1093/jmcb/mjaa052

Imputing single-cell RNA-seq data by considering cell heterogeneity and prior expression of dropouts
Cited by: 18
Author(s): Lihua Zhang, Shihua Zhang
Software Mentions: 9
Published: almost 4 years ago

10.3390/genes11050532

Sparsity-Penalized Stacked Denoising Autoencoders for Imputing Single-Cell RNA-seq Data
Cited by: 9
Author(s): Weilai Chi, Minghua Deng
Software Mentions: 9
Published: over 4 years ago

10.3389/fgene.2020.00295

Single-Cell Transcriptome Data Clustering via Multinomial Modeling and Adaptive Fuzzy K-Means Algorithm
Cited by: 13
Author(s): Liang Chen, Weinan Wang, Yuyao Zhai, Minghua Deng
Software Mentions: 8
Published: over 4 years ago

10.1186/s12859-019-3099-4

DIRECT: RNA contact predictions by integrating structural patterns
Cited by: 14
Author(s): Yiren Jian, Xiaonan Wang, Jaidi Qiu, Huiwen Wang, Zhichao Liu, Yunjie Zhao, Chen Zeng
Software Mentions: 7
Published: almost 5 years ago

10.3389/fgene.2021.722992

A Coagulation-Related Gene-Based Prognostic Model for Invasive Ductal Carcinoma
Cited by: 11
Author(s): Jing Li, Jiang Du, Yanhong Wang, Hong-Ti Jia
Software Mentions: 7
Published: almost 3 years ago

10.3389/fgene.2020.00012

Identification and Validation of an Individualized Prognostic Signature of Bladder Cancer Based on Seven Immune Related Genes
Cited by: 61
Author(s): Huaide Qiu, Xiaorong Hu, Chuan He, Bin Yu, Yongqiang Li, Jianan Li
Software Mentions: 7
Published: over 4 years ago

10.3389/fgene.2020.570255

A Review of Integrative Imputation for Multi-Omics Datasets
Cited by: 48
Author(s): Meng Song, Jonathan Greenbaum, Joseph Luttrell, Weihua Zhou, Chong Wu, Hui Shen, Ping Gong, Chaoyang Zhang, Hong Wen Deng
Software Mentions: 6
Published: almost 4 years ago

10.1002/ece3.2736

Shortcuts in biodiversity research: What determines the performance of higher taxa as surrogates for species?
Cited by: 29
Author(s): Neil Rosser
Software Mentions: 6
Published: over 7 years ago

10.1186/s13059-020-02128-7

Tuning parameters of dimensionality reduction methods for single-cell RNA-seq analysis
Cited by: 15
Author(s): Félix Raimundo, Céline Vallot, Jean-Philippe Vert
Software Mentions: 6
Published: about 4 years ago

10.1186/s13059-019-1837-6

DeepImpute: an accurate, fast, and scalable deep neural network method to impute single-cell RNA-seq data
Cited by: 162
Author(s): Cédric Arisdakessian, Olivier Poirion, Breck Yunits, Xun Zhu, Lana X. Garmire
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pcbi.1009118

SDImpute: A statistical block imputation method based on cell-level and gene-level information for dropouts in single-cell RNA-seq data
Cited by: 6
Author(s): Jing Qi, Yang Zhou, Zhao Zhang, Shuilin Jin
Software Mentions: 6
Published: over 3 years ago

10.3389/fgene.2021.646936

A Comparison for Dimensionality Reduction Methods of Single-Cell RNA-seq Data
Cited by: 44
Author(s): Ruizhi Xiang, Wencan Wang, Lei Yang, Shiyuan Wang, Chaohan Xu, Xiaowen Chen
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pcbi.1006767

The intrinsic dimension of protein sequence evolution
Cited by: 14
Author(s): Elena Facco, Andrea Pagnani, Elena Tea Russo, Alessandro Laio
Software Mentions: 5
Published: over 5 years ago

10.1093/bib/bbab038

Accurate prediction of inter-protein residue–residue contacts for homo-oligomeric protein complexes
Cited by: 39
Author(s): Yumeng Yan, Sheng‐You Huang
Software Mentions: 5
Published: over 3 years ago

10.3389/fonc.2021.729175

Development and Validation of a Simple-to-Use Nomogram to Predict Early Death in Metastatic Pancreatic Adenocarcinoma
Cited by: 10
Author(s): Zhong Zhang, Juan Pu, Haijun Zhang
Software Mentions: 5
Published: about 3 years ago

10.1371/journal.pgen.1002763

Divergence of the Yeast Transcription Factor FZF1 Affects Sulfite Resistance
Cited by: 28
Author(s): Elizabeth K. Engle, Justin C. Fay
Software Mentions: 5
Published: over 12 years ago

10.7554/eLife.29880

Inferring joint sequence-structural determinants of protein functional specificity
Cited by: 13
Author(s): Andrew F. Neuwald, L. Aravind, Stephen F. Altschul
Software Mentions: 4
Published: over 6 years ago

10.1186/1755-8794-7-S1-S5

Derivative component analysis for mass spectral serum proteomic profiles
Cited by: 13
Author(s): Henry Han
Software Mentions: 4
Published: over 10 years ago

10.3389/fgene.2021.733906

SCDRHA: A scRNA-Seq Data Dimensionality Reduction Algorithm Based on Hierarchical Autoencoder
Cited by: 8
Author(s): Jianping Zhao, Na Wang, Haiyun Wang, Chun-Hou Zheng, Yansen Su
Software Mentions: 4
Published: about 3 years ago

10.1093/gigascience/giaa122

DrivAER: Identification of driving transcriptional programs in single-cell RNA sequencing data
Cited by: 9
Author(s): Lukas M. Simon, Fangfang Yan, Zhongming Zhao
Software Mentions: 4
Published: almost 4 years ago

10.1038/sdata.2014.38

DNA methylation temporal profiling following peripheral versus central nervous system axotomy
Cited by: 14
Author(s): Ricco Lindner, Radhika Puttagunta, Tuan Nguyen, Simone Di Giovanni
Software Mentions: 4
Published: almost 10 years ago

10.1155/2019/3726721

Identifying Protein Complexes from Dynamic Temporal Interval Protein-Protein Interaction Networks
Cited by: 1
Author(s): Jinxiong Zhang, Cheng Zhong, Hai Lin, Mian Wang
Software Mentions: 4
Published: about 5 years ago

10.1186/s12859-018-2583-6

hoDCA: higher order direct-coupling analysis
Cited by: 4
Author(s): Michael Schmidt, Kay Hamacher
Software Mentions: 4
Published: almost 6 years ago

10.1002/cam4.3838

A machine learning‐based survival prediction model of high grade glioma by integration of clinical and dose‐volume histogram parameters
Cited by: 8
Author(s): Haiyan Chen, Chao Li, Lin Zheng, Wei Lu, Yanlin Liu, Qichun Wei
Software Mentions: 4
Published: over 3 years ago

10.1186/s12859-018-2150-1

Identification of residue pairing in interacting β-strands from a predicted residue contact map
Cited by: 4
Author(s): Wenzhi Mao, Tong Wang, Wenxuan Zhang, H. Gong
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0221350

Prediction of significant prostate cancer in biopsy-naïve men: Validation of a novel risk model combining MRI and clinical parameters and comparison to an ERSPC risk calculator and PI-RADS
Cited by: 12
Author(s): Jan Philipp Radtke, Francesco Giganti, Manuel Wiesenfarth, Armando Stabile, José Luis Marenco, Clément Orczyk, Veeru Kasivisvanathan, Joanne Nyarangi‐Dix, Viktoria Schütz, Svenja Dieffenbacher, Magdalena Görtz, Albrecht Stenzinger, Wilfried Roth, Alex Freeman, Shonit Punwani, David Bonekamp, Heinz Peter Schlemmer, Markus Hohenfellner, Mark Emberton, Caroline M. Moore
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0092721

Fast and Accurate Multivariate Gaussian Modeling of Protein Families: Predicting Residue Contacts and Protein-Interaction Partners
Cited by: 134
Author(s): Carlo Baldassi, Marco Zamparo, Christoph Feinauer, Andrea Procaccini, Riccardo Zecchina, Martin Weigt, Andrea Pagnani
Software Mentions: 4
Published: over 10 years ago

10.1038/srep13652

Dimeric interactions and complex formation using direct coevolutionary couplings
Cited by: 72
Author(s): Ricardo Nascimento dos Santos, Faruck Morcos, Biman Jana, Adriano D. Andricopulo, José N. Onuchic
Software Mentions: 3
Published: about 9 years ago

10.1186/s12859-016-0975-z

CoeViz: a web-based tool for coevolution analysis of protein residues
Cited by: 39
Author(s): Frazier N. Baker, Aleksey Porollo
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pcbi.1009027

Evaluation of residue-residue contact prediction methods: From retrospective to prospective
Cited by: 14
Author(s): Huiling Zhang, Zhendong Bei, Wenhui Xi, Min Hao, Zhen Ju, Konda Mani Saravanan, Haiping Zhang, Ning Guo, Yanjie Wei
Software Mentions: 3
Published: over 3 years ago

10.1186/s12870-019-1854-3

Arabidopsis thaliana organelles mimic the T7 phage DNA replisome with specific interactions between Twinkle protein and DNA polymerases Pol1A and Pol1B
Cited by: 15
Author(s): Stewart A. Morley, Antolín Peralta-Castro, Luis G. Brieba, Justin Miller, Kai Li Ong, Perry G. Ridge, Amanda E. Oliphant, Stephen Aldous, Brent L. Nielsen
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-018-34508-2

“Infostery” analysis of short molecular dynamics simulations identifies highly sensitive residues and predicts deleterious mutations
Cited by: 16
Author(s): Yasaman Karami, Tristan Bitard‐Feildel, Élodie Laine, Alessandra Carbone
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pcbi.1007630

Direct coupling analysis of epistasis in allosteric materials
Cited by: 13
Author(s): Barbara Bravi, Riccardo Ravasio, Carolina Brito, Matthieu Wyart
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0246718

The role of clustering algorithm-based big data processing in information economy development
Cited by: 2
Author(s): Hongyan Ma
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1006508

Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis
Cited by: 88
Author(s): Marcin J. Skwark, Nicholas J. Croucher, Santeri Puranen, Claire Chewapreecha, Maiju Pesonen, Yingying Xu, Paul Turner, Simon R. Harris, Stephen B. Beres, James M. Musser, Julian Parkhill, Stephen D. Bentley, Erik Aurell, Jukka Corander
Software Mentions: 3
Published: over 7 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: about 8 years ago

10.1099/mgen.0.000184

SuperDCA for genome-wide epistasis analysis
Cited by: 21
Author(s): Santeri Puranen, Maiju Pesonen, Johan Pensar, Ying Xu, John A. Lees, Stephen D. Bentley, Nicholas J. Croucher, Jukka Corander
Software Mentions: 3
Published: over 6 years ago

10.3390/s19133022

Location Privacy Protection in Distributed IoT Environments Based on Dynamic Sensor Node Clustering
Cited by: 3
Author(s): Konstantinos Dimitriou, Ioanna Roussaki
Software Mentions: 3
Published: about 5 years ago

10.1186/s12859-021-04330-1

Velo-Predictor: an ensemble learning pipeline for RNA velocity prediction
Cited by: 4
Author(s): Xin Wang, Jie Zheng
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0167978

Using the Amino Acid Network to Modulate the Hydrolytic Activity of β-Glycosidases
Cited by: 12
Author(s): Fábio K. Tamaki, Diorge P. Souza, Valquiria P. Souza, Cecília M. Ikegami, Chuck S. Farah, Sandro R. Marana
Software Mentions: 3
Published: almost 8 years ago

10.1128/mSystems.00310-20

Coevolutionary Analysis Reveals a Conserved Dual Binding Interface between Extracytoplasmic Function σ Factors and Class I Anti-σ Factors
Cited by: 2
Author(s): Delia Casas-Pastor, Angelika Diehl, Georg Fritz
Software Mentions: 3
Published: about 4 years ago

10.3389/fgene.2020.00786

NeuralEE: A GPU-Accelerated Elastic Embedding Dimensionality Reduction Method for Visualizing Large-Scale scRNA-Seq Data
Cited by: 2
Author(s): Jiankang Xiong, Fuzhou Gong, Lin Wan, Liang Ma
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12920-015-0116-y

Diagnostic biases in translational bioinformatics
Cited by: 14
Author(s): Henry Han
Software Mentions: 3
Published: about 9 years ago

10.7554/eLife.23471

Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and coevolutionary sequence analysis
Cited by: 46
Author(s): Duccio Malinverni, Alfredo Jost López, Paolo De Los Rios, Gerhard Hummer, Alessandro Barducci
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0199585

Contact prediction is hardest for the most informative contacts, but improves with the incorporation of contact potentials
Cited by: 6
Author(s): John E. Holland, Qinxin Pan, Gevorg Grigoryan
Software Mentions: 3
Published: about 6 years ago

10.7554/eLife.08932

Codon-level information improves predictions of inter-residue contacts in proteins by correlated mutation analysis
Cited by: 7
Author(s): Etai Jacob, Ron Unger, Amnon Horovitz
Software Mentions: 3
Published: about 9 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: almost 13 years ago

10.1371/journal.pcbi.1008957

On the effect of phylogenetic correlations in coevolution-based contact prediction in proteins
Cited by: 15
Author(s): Edwin Rodríguez Horta, Martin Weigt
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0143245

Coevolution Analysis of HIV-1 Envelope Glycoprotein Complex
Cited by: 9
Author(s): Reda Rawi, Khalid Kunji, Abdelali Haoudi, Halima Bensmail
Software Mentions: 3
Published: almost 9 years ago

10.7717/peerj.9837

Rediscovery of Cyperus flavescens (Cyperaceae) on the northeast periphery of its range in Europe
Cited by: 1
Author(s): P. Marciniuk, Jolanta Marciniuk, Andrzej Łysko, Łukasz Krajewski, J. Chudecka, J. Skrzyczyńska, Agnieszka Popiela
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pcbi.1007621

FilterDCA: Interpretable supervised contact prediction using inter-domain coevolution
Cited by: 9
Author(s): Maureen Muscat, Giancarlo Croce, Edoardo Sarti, Martin Weigt
Software Mentions: 3
Published: almost 4 years ago

10.3389/fpsyg.2019.02197

A Scientometric Review of Rasch Measurement: The Rise and Progress of a Specialty
Cited by: 53
Author(s): Vahid Aryadoust, Hannah Ann Hui Tan, Li Ying Ng
Software Mentions: 3
Published: almost 5 years ago

10.3389/fphar.2021.623070

Insular Pharmacopoeias: Ethnobotanical Characteristics of Medicinal Plants Used on the Adriatic Islands
Cited by: 14
Author(s): Łukasz Łuczaj, Marija Jug-Dujaković, Katija Dolina, Mirjana Jeričević, Ivana Vitasović‐Kosić
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pcbi.1006188

Polymorphic sites preferentially avoid co-evolving residues in MHC class I proteins
Cited by: 6
Author(s): Linda Dib, Nicolas Salamin, David Gfeller
Software Mentions: 3
Published: over 6 years ago

10.1002/acm2.12450

A hybrid planning strategy for stereotactic body radiation therapy of early stage non-small-cell lung cancer
Cited by: 2
Author(s): Han Liu, B Sintay, Keith Pearman, Qingyang Shang, Lane Hayes, J Mäurer, Caroline Vanderstraeten, D Wiant
Software Mentions: 3
Published: almost 6 years ago

10.1093/bioinformatics/btz082

Incorporating alignment uncertainty into Felsenstein’s phylogenetic bootstrap to improve its reliability
Cited by: 7
Author(s): Jia‐Ming Chang, Evan Floden, Javier Herrero, Olivier Gascuel, Paolo Di Tommaso, Cédric Notredame
Software Mentions: 3
Published: over 5 years ago

10.1089/cmb.2019.0337

Semisupervised Generative Autoencoder for Single-Cell Data
Cited by: 12
Author(s): Trung Ngô Trọng, Juha Mehtonen, Gerardo González, Roger Kramer, Ville Hautamäki, Merja Heinäniemi
Software Mentions: 3
Published: about 4 years ago

10.1073/pnas.2012331117

Global analysis of more than 50,000 SARS-CoV-2 genomes reveals epistasis between eight viral genes
Cited by: 50
Author(s): Hong Zeng, Vito Dichio, Edwin Rodríguez Horta, Kaisa Thorell, Erik Aurell
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pcbi.1005294

Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations
Cited by: 8
Author(s): Andrew F. Neuwald, Stephen F. Altschul
Software Mentions: 3
Published: over 7 years ago

10.3390/nu10111701

Phloridzin, an Apple Polyphenol, Exerted Unfavorable Effects on Bone and Muscle in an Experimental Model of Type 2 Diabetes in Rats
Cited by: 34
Author(s): Piotr Londzin, Szymon Siudak, Urszula Cegieła, Maria Pytlik, Aleksandra Janas, A Waligóra, Joanna Folwarczna
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2105-11-142

MISHIMA - a new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data
Cited by: 16
Author(s): Kirill Kryukov, Naruya Saitou
Software Mentions: 2
Published: over 14 years ago

10.1186/1471-2105-7-498

4SALE – A tool for synchronous RNA sequence and secondary structure alignment and editing
Cited by: 318
Author(s): Philipp N. Seibel, Tobias Müller, Thomas Dandekar, Jörg Schultz, Matthias Wolf
Software Mentions: 2
Published: almost 18 years ago

10.1186/1471-2105-15-118

H2rs: Deducing evolutionary and functionally important residue positions by means of an entropy and similarity based analysis of multiple sequence alignments
Cited by: 9
Author(s): Jan-Oliver Janda, Ajmal Popal, Jochen Bauer, Markus Busch, Michael Klocke, Wolfgang Spitzer, Jörg Keller, Rainer Merkl
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2105-7-490

XML schemas for common bioinformatic data types and their application in workflow systems
Cited by: 33
Author(s): Philipp N. Seibel, Jan Walters Kruger, Sven Hartmeier, Knut Schwarzer, Kai Löwenthal, Henning Mersch, Thomas Dandekar, Robert Giegerich
Software Mentions: 2
Published: almost 18 years ago

10.1186/1471-2105-9-S4-S13

GeneFisher-P: variations of GeneFisher as processes in Bio-jETI
Cited by: 34
Author(s): Anna-Lena Lamprecht, Tiziana Margaria, Bernhard Steffen, Alexander Sczyrba, Sven Hartmeier, Robert Giegerich
Software Mentions: 2
Published: over 16 years ago

10.1186/1471-2105-9-383

caBIG™ VISDA: Modeling, visualization, and discovery for cluster analysis of genomic data
Cited by: 14
Author(s): Yangyong Zhu, Huai Li, David J. Miller, Zuyi Wang, Jianhua Xuan, Robert Clarke, Eric P. Hoffman, Yue Joseph Wang
Software Mentions: 2
Published: almost 16 years ago

10.1186/s12872-016-0456-3

Atherosclerotic and thrombotic genetic and environmental determinants in Egyptian coronary artery disease patients: a pilot study
Cited by: 21
Author(s): Manal S. Fawzy, Eman A. Toraih, Nagwa M. Aly, Abeer Fakhr-Eldeen, Dahlia I. Badran, Mohammad Hussein
Software Mentions: 2
Published: over 7 years ago

10.1186/1472-6823-13-41

Non-invasive detection of microvascular changes in a paediatric and adolescent population with type 1 diabetes: a pilot cross-sectional study
Cited by: 32
Author(s): Sarah P. M Hosking, Rani Bhatia, Patricia Crock, Ian Wright, Marline L. Squance, Glenn Reeves
Software Mentions: 2
Published: almost 11 years ago

10.1093/bioinformatics/btu791

MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins
Cited by: 315
Author(s): David T. Jones, Tanya Singh, Tomasz Kościółek, Stuart J. Tetchner
Software Mentions: 2
Published: almost 10 years ago

10.1155/2020/7584968

Protein Contact Map Prediction Based on ResNet and DenseNet
Cited by: 20
Author(s): Li Zhong, Yuele Lin, Arne Elofsson, Yao Yao
Software Mentions: 2
Published: over 4 years ago

10.1186/s40644-019-0249-x

Radiomics models for diagnosing microvascular invasion in hepatocellular carcinoma: which model is the best model?
Cited by: 45
Author(s): Ming Ni, Xiaoming Zhou, Qian Lv, Zhiming Li, Yong Gao, Yongqi Tan, Jihua Liu, Fang Liu, Haiyang Yu, Linlin Jiao, Gang Wang
Software Mentions: 2
Published: about 5 years ago

10.1093/molbev/msz256

Protein Structural Information and Evolutionary Landscape by In Vitro Evolution
Cited by: 19
Author(s): Marco Fantini, Simonetta Lisi, Paolo De Los Rios, Antonino Cattaneo, Annalisa Pastore
Software Mentions: 2
Published: almost 5 years ago

10.1016/j.omtm.2020.07.001

Lentiviral Hematopoietic Stem Cell Gene Therapy Rescues Clinical Phenotypes in a Murine Model of Pompe Disease
Cited by: 10
Author(s): Giuseppa Piras, Claudia Montiel-Equihua, Yee-Ka Agnes Chan, Slawomir Wantuch, Daniel J. Stuckey, Derek Burke, Helen Prunty, Rahul Phadke, D. Chambers, Armando Partida-Gaytán, Diego León-Rico, Nilam Panchal, Kathryn Victoria Whitmore, Miguel Calero, Sara Benedetti, Giorgia Santilli, Adrian J. Thrasher, H. Bobby Gaspar
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pcbi.1006391

A new dynamic correlation algorithm reveals novel functional aspects in single cell and bulk RNA-seq data
Cited by: 13
Author(s): Tianwei Yu
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pcbi.1006891

A multi-scale coevolutionary approach to predict interactions between protein domains
Cited by: 25
Author(s): Giancarlo Croce, Thomas Gueudré, Maria Virginia Ruiz Cuevas, Victoria Keidel, Matteo Figliuzzi, Hendrik Szurmant, Martin Weigt
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pcbi.1004262

Large-Scale Conformational Transitions and Dimerization Are Encoded in the Amino-Acid Sequences of Hsp70 Chaperones
Cited by: 61
Author(s): Duccio Malinverni, Simone Marsili, Alessandro Barducci, Paolo De Los Rios
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pcbi.1004817

Evolution-Based Functional Decomposition of Proteins
Cited by: 108
Author(s): Olivier Rivoire, Kimberly A. Reynolds, Rama Ranganathan
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pcbi.1004777

The Maximum Entropy Fallacy Redux?
Cited by: 18
Author(s): Erik Aurell
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pcbi.1007179

Phylogenetic correlations can suffice to infer protein partners from sequences
Cited by: 24
Author(s): Guillaume Marmier, Martin Weigt, Anne-Florence Bitbol
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pcbi.1006401

Inferring interaction partners from protein sequences using mutual information
Cited by: 46
Author(s): Anne-Florence Bitbol
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pcbi.1006864

Identification of pathways associated with chemosensitivity through network embedding
Cited by: 12
Author(s): Sheng Wang, Edward Huang, Junmei Cairns, Jian Peng, Liewei Wang, Saurabh Sinha
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.0010039

Comparative Gene Expression Analysis by a Differential Clustering Approach: Application to the Candida albicans Transcription Program
Cited by: 129
Author(s): Jan Ihmels, Sven Bergmann, Judith Berman, Naama Barkai
Software Mentions: 2
Published: almost 19 years ago

10.1371/journal.pgen.1006558

Epistasis Analysis Goes Genome-Wide
Cited by: 6
Author(s): Jianzhi Zhang
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0203085

Widespread evolutionary crosstalk among protein domains in the context of multi-domain proteins
Cited by: 0
Author(s): Dávid Jakubec, Miroslav Kratochvíl, Jiří Vymětal, Jiřı́ Vondrášek
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0133863

Did α-Synuclein and Glucocerebrosidase Coevolve? Implications for Parkinson’s Disease
Cited by: 6
Author(s): James M. Gruschus
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0198645

Amino acid impact factor
Cited by: 5
Author(s): C. K. Sruthi, Meher K. Prakash
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0149166

Inter-Protein Sequence Co-Evolution Predicts Known Physical Interactions in Bacterial Ribosomes and the Trp Operon
Cited by: 55
Author(s): Christoph Feinauer, Hendrik Szurmant, Martin Weigt, Andrea Pagnani
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0047108

Accurate Simulation and Detection of Coevolution Signals in Multiple Sequence Alignments
Cited by: 14
Author(s): Sharon H. Ackerman, Elisabeth R. M. Tillier, Domenico L. Gatti
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0104672

Are There Consistent Grazing Indicators in Drylands? Testing Plant Functional Types of Various Complexity in South Africa’s Grassland and Savanna Biomes
Cited by: 37
Author(s): Anja Linstädter, J. Schellberg, Katharina Brüser, Cristian A. Moreno García, Roelof Oomen, C. C. du Preez, Jan C. Ruppert, Frank Ewert
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0186134

Identifying protein complex by integrating characteristic of core-attachment into dynamic PPI network
Cited by: 9
Author(s): Xin Shen, Yang Li, Xingpeng Jiang, Tingting He, Jincai Yang, Wei Xie, Po Hu, Xiaohua Hu
Software Mentions: 2
Published: almost 7 years ago

Projects: cran: DCA

Papers Mentioning DCA 128