cran: BART | Projects | Ecosyste.ms: Papers

10.3390/ijms21010019

Use of QSAR Global Models and Molecular Docking for Developing New Inhibitors of c-src Tyrosine Kinase
Cited by: 8
Author(s): Robert Ancuceanu, Bogdan Ionel Tamba, C. Stoicescu, Mihaela Dinu
Software Mentions: 13
Published: almost 5 years ago

10.1371/journal.pone.0135784

Comparison of Nine Statistical Model Based Warfarin Pharmacogenetic Dosing Algorithms Using the Racially Diverse International Warfarin Pharmacogenetic Consortium Cohort Database
Cited by: 38
Author(s): Rong Liu, Xi Li, Wei Zhang, Hong‐Hao Zhou
Software Mentions: 13
Published: about 9 years ago

10.1186/s12940-017-0310-9

Construction of environmental risk score beyond standard linear models using machine learning methods: application to metal mixtures, oxidative stress and cardiovascular disease in NHANES
Cited by: 73
Author(s): Sung Kyun Park, Zhangchen Zhao, Bhramar Mukherjee
Software Mentions: 9
Published: about 7 years ago

10.1038/s41598-019-43125-6

Predicting protein-ligand interactions based on bow-pharmacological space and Bayesian additive regression trees
Cited by: 33
Author(s): Li Li, Ching Chiek Koh, Daniel Reker, J.B. Brown, Haishuai Wang, Nicholas Keone Lee, Hien-haw Liow, Hao Dai, H. K. Fan, Luonan Chen, Dong‐Qing Wei
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pcbi.1007800

MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
Cited by: 30
Author(s): Avtar Roopra
Software Mentions: 6
Published: over 4 years ago

10.1038/s41598-021-94805-1

AnnoMiner is a new web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators
Cited by: 4
Author(s): Arno Meiler, Fabio Marchianò, Margaux Haering, Manuela Weitkunat, Frank Schnorrer, Bianca Habermann
Software Mentions: 6
Published: over 3 years ago

10.1186/s12711-016-0219-8

Genome-wide prediction using Bayesian additive regression trees
Cited by: 35
Author(s): Patrik Waldmann
Software Mentions: 6
Published: over 8 years ago

10.1155/2020/8810143

An Efficient and Effective Model to Handle Missing Data in Classification
Cited by: 8
Author(s): Kamran Mehrabani-Zeinabad, Marziyeh Doostfatemeh, Seyyed Mohammad Taghi Ayatollahi
Software Mentions: 6
Published: almost 4 years ago

10.1080/21655979.2020.1862527

The underlying molecular mechanism and identification of transcription factor markers for laryngeal squamous cell carcinoma
Cited by: 8
Author(s): Bin-Yu Mo, Guosheng Li, Su-Hua Huang, Wei-Ying He, Lu Xie, Zhu‐Xin Wei, Ya-Si Su, Liang Yue, Li Yang, Ya Cheng, Wei Dai, Run Lin
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12859-020-03718-9

binomialRF: interpretable combinatoric efficiency of random forests to identify biomarker interactions
Cited by: 2
Author(s): Samir Rachid Zaim, Colleen Kenost, Joanne Berghout, Wesley Chiu, L. Wilson, Hao Helen Zhang, Yves A. Lussier
Software Mentions: 5
Published: about 4 years ago

10.1038/s41598-019-47046-2

SMAC, a computational system to link literature, biomedical and expression data
Cited by: 2
Author(s): S. Pirro, Emanuela Gadaleta, Andrea Galgani, Vittorio Colizzi, Claude Chelala
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0213245

Optimizing predictive performance of criminal recidivism models using registration data with binary and survival outcomes
Cited by: 14
Author(s): Nikolaj Tollenaar, P.G.M. van der Heijden
Software Mentions: 4
Published: over 5 years ago

10.3390/jcm8060865

The Role of Genetic Factors in Characterizing Extra-Intestinal Manifestations in Crohn’s Disease Patients: Are Bayesian Machine Learning Methods Improving Outcome Predictions?
Cited by: 10
Author(s): Daniele Bottigliengo, Paola Berchialla, Corrado Lanera, Danila Azzolina, Giulia Lorenzoni, Matteo Martinato, Daniela Giachino, Ileana Baldi, Darío Gregori
Software Mentions: 4
Published: over 5 years ago

10.1186/s13059-021-02485-x

Mapping the evolving landscape of super-enhancers during cell differentiation
Cited by: 16
Author(s): Yan Kai, Bin E. Li, Min Zhu, Grace Y Li, Fei Chen, Yingli Han, Hye Young Ji, Stuart H. Orkin, Wenqing Cai, Jialiang Huang, Guo‐Cheng Yuan
Software Mentions: 4
Published: about 3 years ago

10.3390/ijms22115763

Integration of the Microbiome, Metabolome and Transcriptomics Data Identified Novel Metabolic Pathway Regulation in Colorectal Cancer
Cited by: 11
Author(s): Vartika Bisht, Katrina Nash, Yuanwei Xu, Prasoon Agarwal, Sofie Bosch, Georgios V. Gkoutos, Animesh Acharjee
Software Mentions: 3
Published: over 3 years ago

10.1186/s13072-019-0324-3

Nickel-induced transcriptional changes persist post exposure through epigenetic reprogramming
Cited by: 19
Author(s): Cynthia C. Jose, Zhenjia Wang, Vinay Singh Tanwar, Xiaoru Zhang, Chongzhi Zang, Suresh Cuddapah
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41597-020-00667-z

Question-driven summarization of answers to consumer health questions
Cited by: 31
Author(s): Max E. Savery, Asma Ben Abacha, Soumya Gayen, Dina Demner‐Fushman
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-019-55763-x

Minimal Linear Networks for Magnetic Resonance Image Reconstruction
Cited by: 9
Author(s): Gilad Liberman, Benedikt A. Poser
Software Mentions: 2
Published: almost 5 years ago

10.1002/hbm.25010

Quality and denoising in real‐time functional magnetic resonance imaging neurofeedback: A methods review
Cited by: 34
Author(s): Stephan Heunis, Rolf Lamerichs, Svitlana Zinger, César Caballero-Gaudes, Jacobus F. A. Jansen, Bert Aldenkamp, Marcel Breeuwer
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-020-70551-8

CINENet: deep learning-based 3D cardiac CINE MRI reconstruction with multi-coil complex-valued 4D spatio-temporal convolutions
Cited by: 101
Author(s): Thomas Küstner, Niccolò Fuin, Kerstin Hammernik, Aurélien Bustin, Haikun Qi, Reza Hajhosseiny, Pier Giorgio Masci, Radhouène Neji, Daniel Rueckert, René M. Botnar, Claudia Prieto
Software Mentions: 2
Published: over 4 years ago

10.3389/fpsyt.2020.00545

Machine Learning for Differential Diagnosis Between Clinical Conditions With Social Difficulty: Autism Spectrum Disorder, Early Psychosis, and Social Anxiety Disorder
Cited by: 9
Author(s): Eleni Demetriou, Shin H. Park, Nicholas Ho, Karen L. Pepper, Yun Ju Christine Song, Sharon L. Naismith, Emma Thomas, Ian B. Hickie, Adam J. Guastella
Software Mentions: 2
Published: over 4 years ago

10.1007/s10334-020-00859-z

Generalization of three-dimensional golden-angle radial acquisition to reduce eddy current artifacts in bSSFP CMR imaging
Cited by: 6
Author(s): Alexander Fyrdahl, Karen Holst, Kenneth Caidahl, Martin Ugander, Andreas Sigfridsson
Software Mentions: 2
Published: over 4 years ago

10.1186/s12871-020-01036-4

Cannabis use is associated with a small increase in the risk of postoperative nausea and vomiting: a retrospective machine-learning causal analysis
Cited by: 10
Author(s): Wendy Suhre, Vikas N O’Reilly-Shah, Wil Van Cleve
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0207919

The UK Research Excellence Framework and the Matthew effect: Insights from machine learning
Cited by: 3
Author(s): Lloyd Balbuena
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13059-015-0740-z

Predicting chromatin organization using histone marks
Cited by: 100
Author(s): Jialiang Huang, Eugenio Marco, Luca Pinello, Guo Cheng Yuan
Software Mentions: 2
Published: over 9 years ago

10.1186/s13063-017-2179-x

Effects of a liquefied petroleum gas stove intervention on pollutant exposure and adult cardiopulmonary outcomes (CHAP): study protocol for a randomized controlled trial
Cited by: 30
Author(s): Magdalena Fandiño-Del-Río, Dina Goodman, Josiah L. Kephart, Catherine H. Miele, Kendra N. Williams, Mitra Moazzami, Elizabeth Fung, Kirsten Koehler, Víctor G. Dávila‐Román, Kathryn A. Lee, Saachi Nangia, Steven A. Harvey, Kyle Steenland, Gustavo F. Gonzáles, William Checkley
Software Mentions: 2
Published: about 7 years ago

10.1186/s12942-020-00225-1

A multimethod approach for county-scale geospatial analysis of emerging infectious diseases: a cross-sectional case study of COVID-19 incidence in Germany
Cited by: 62
Author(s): Christopher Scarpone, Sebastian T. Brinkmann, Tim Große, Daniel Sonnenwald, M Fuchs, Blake Byron Walker
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-018-36207-4

Optimised LAMP allows single copy detection of 35Sp and NOSt in transgenic maize using Bioluminescent Assay in Real Time (BART)
Cited by: 28
Author(s): Patrick Hardinge, Guy Kiddle, Laurence Tisi, James A. H. Murray
Software Mentions: 2
Published: almost 6 years ago

10.3389/fnins.2020.00900

Pyneal: Open Source Real-Time fMRI Software
Cited by: 5
Author(s): Jeff MacInnes, R. Alison Adcock, Andrea Stocco, Chantel S. Prat, Rajesh P. N. Rao, Kathryn C. Dickerson
Software Mentions: 2
Published: about 4 years ago

10.1186/s12859-018-2308-x

BART: bioinformatics array research tool
Cited by: 27
Author(s): Maria Luisa Amaral, Galina Erikson, Maxim N. Shokhirev
Software Mentions: 2
Published: over 6 years ago

10.3390/diagnostics11010061

PIC-GAN: A Parallel Imaging Coupled Generative Adversarial Network for Accelerated Multi-Channel MRI Reconstruction
Cited by: 31
Author(s): Jun Lyu, Chengyan Wang, Guang Yang
Software Mentions: 2
Published: almost 4 years ago

10.1186/s13059-020-1934-6

Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data
Cited by: 138
Author(s): Qian Qin, Jingyu Fan, Rongbin Zheng, Changxin Wan, Shenglin Mei, Qiu Liang Wu, Hanfei Sun, Myles Brown, Jing Zhang, Clifford A. Meyer, X. Shirley Liu
Software Mentions: 1
Published: almost 5 years ago

10.1186/1472-6750-12-15

GMO detection using a bioluminescent real time reporter (BART) of loop mediated isothermal amplification (LAMP) suitable for field use
Cited by: 108
Author(s): Guy Kiddle, Patrick Hardinge, Neil Buttigieg, Olga Gandelman, Clint Pereira, Cathal J. McElgunn, Manuela Rizzoli, Rebecca Jackson, Nigel Appleton, Cathy Moore, Laurence Tisi, James A. H. Murray
Software Mentions: 1
Published: over 12 years ago

10.1186/s12968-018-0499-y

Regional assessment of carotid artery pulse wave velocity using compressed sensing accelerated high temporal resolution 2D CINE phase contrast cardiovascular magnetic resonance
Cited by: 16
Author(s): Eva S. Peper, Gustav J. Strijkers, Katja Gazzola, Wouter V. Potters, Abdallah G. Motaal, Ilse K. Luirink, Barbara A. Hutten, Albert Wiegman, Pim van Ooij, Bert‐Jan H. van den Born, Aart J. Nederveen, Bram F. Coolen
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12859-020-03822-w

Correction to: binomialRF: interpretable combinatoric efficiency of random forests to identify biomarker interactions
Cited by: 2
Author(s): Samir Rachid Zaim, Colleen Kenost, Joanne Berghout, Wesley Chiu, L. Wilson, Hao Helen Zhang, Yves A. Lussier
Software Mentions: 1
Published: about 4 years ago

10.3390/atmos11111233

Application of Bayesian Additive Regression Trees for Estimating Daily Concentrations of PM2.5 Components
Cited by: 9
Author(s): Tianyu Zhang, Guannan Geng, Yang Liu, Howard H. Chang
Software Mentions: 1
Published: about 4 years ago

10.1038/srep41669

The PRC2-binding long non-coding RNAs in human and mouse genomes are associated with predictive sequence features
Cited by: 12
Author(s): Shiqi Tu, Guo‐Cheng Yuan, Zongshu Shao
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-019-39888-7

ENLIVE: An Efficient Nonlinear Method for Calibrationless and Robust Parallel Imaging
Cited by: 23
Author(s): H. Christian M. Holme, Sebastian Rosenzweig, Frank Ong, Robin N. Wilke, Michael Lustig, Martin Uecker
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2105-10-345

BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors
Cited by: 16
Author(s): Junbai Wang, Morigen Morigen
Software Mentions: 1
Published: about 15 years ago

10.1038/s41598-020-66202-7

3D Magnetic Resonance Spirometry
Cited by: 8
Author(s): Tanguy Boucneau, Brice Fernandez, Peder E. Z. Larson, Luc Darrasse, Xavier Maı̂tre
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-020-80102-w

Tissue-specific endothelial cell heterogeneity contributes to unequal inflammatory responses
Cited by: 29
Author(s): Hasitha Gunawardana, Tahmineh Romero, Ning Yao, Sebastiaan Heidt, Arend Mulder, David Elashoff, Nicole M. Valenzuela
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-021-94692-6

Reducing SAR in 7T brain fMRI by circumventing fat suppression while removing the lipid signal through a parallel acquisition approach
Cited by: 4
Author(s): Amir Seginer, Edna Furman‐Haran, Ilan Goldberg, Rita Schmidt
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-021-97685-7

Validation metrics of homogenization techniques on artificially inhomogenized monthly temperature networks in Sweden and Slovenia (1950–2005)
Cited by: 3
Author(s): Roberto Coscarelli, Giulio Nils Caroletti, Magnus Joelsson, Erik Engström, Tommaso Caloiero
Software Mentions: 1
Published: about 3 years ago

10.1177/0962280220920669

Optimal individualized decision rules from a multi-arm trial: A comparison of methods and an application to tailoring inter-donation intervals among blood donors in the UK
Cited by: 3
Author(s): Yuejia Xu, Angela Wood, Michael Sweeting, David Roberts, Brian D. M. Tom
Software Mentions: 1
Published: over 4 years ago

10.1007/s00414-019-02231-w

The four-minute approach revisited: accelerating MRI-based multi-factorial age estimation
Cited by: 8
Author(s): Bernhard Neumayer, Andreas Lesch, Franz Thaler, Thomas Widek, Sebastian Tschauner, Jannick De Tobel, Thomas Ehammer, Barbara Kirnbauer, Julian Boldt, Mayonne van Wijk, Rudolf Stollberger, Martin Urschler
Software Mentions: 1
Published: almost 5 years ago

10.2196/12590

Biofeedback-Assisted Resilience Training for Traumatic and Operational Stress: Preliminary Analysis of a Self-Delivered Digital Health Methodology
Cited by: 15
Author(s): Paul Kizakevich, Randall Eckhoff, Gregory F. Lewis, Maria I. Davila, Laurel L. Hourani, Rebecca L Watkins, Belinda Weimer, Tracy Wills, Jessica Kelley Morgan, Tim Morgan, Sreelatha Meleth, Amanda M. Lewis, Michelle Krzyzanowski, Derek Ramirez, Matthew Boyce, Stephen Litavecz, Marian E. Lane, Laura Strange
Software Mentions: 1
Published: about 5 years ago

10.1002/mrm.27694

High‐dimensionality undersampled patch‐based reconstruction (HD‐PROST) for accelerated multi‐contrast MRI
Cited by: 75
Author(s): Aurélien Bustin, Gastão Cruz, Olivier Jaubert, Karina López, René M. Botnar, Claudia Prieto
Software Mentions: 1
Published: over 5 years ago

10.1002/mrm.28063

Navigator‐based reacquisition and estimation of motion‐corrupted data: Application to multi‐echo spin echo for carotid wall MRI
Cited by: 6
Author(s): Robert Frost, Luca Biasiolli, Linqing Li, Katherine Hurst, Mohammad Alkhalil, Robin P. Choudhury, Matthew D Robson, Aaron T. Hess, Peter Jezzard
Software Mentions: 1
Published: about 5 years ago

10.1002/mrm.27354

Five‐minute whole‐heart coronary MRA with sub‐millimeter isotropic resolution, 100% respiratory scan efficiency, and 3D‐PROST reconstruction
Cited by: 69
Author(s): Aurélien Bustin, Giulia Ginami, Gastão Cruz, Teresa Correia, Tevfik F Ismail, Imran Rashid, Radhouène Neji, René M. Botnar, Claudia Prieto
Software Mentions: 1
Published: over 6 years ago

10.1002/1878-0261.12471

The long noncoding <scp>RNA</scp> <i> <scp>HORAS</scp> 5 </i> mediates castration‐resistant prostate cancer survival by activating the androgen receptor transcriptional program
Cited by: 25
Author(s): Abhijit Parolia, Erik Venalainen, Hui Xue, Rebecca Mather, Dong Lin, Rebecca Wu, Perla Pucci, Jason C. Rogalski, Joseph R. Evans, Felix Y. Feng, Colin C. Collins, Yuzhuo Wang, Francesco Crea
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0014155

Novel Bioluminescent Quantitative Detection of Nucleic Acid Amplification in Real-Time
Cited by: 73
Author(s): Olga Gandelman, Vicki Church, Cathy Moore, Guy Kiddle, Christopher Carne, Surendra Parmar, Hamid Jalal, Laurence Tisi, James A. H. Murray
Software Mentions: 1
Published: almost 14 years ago

10.1186/s12866-016-0730-7

Rapid detection of Salmonella in food and feed by coupling loop-mediated isothermal amplification with bioluminescent assay in real-time
Cited by: 39
Author(s): Qianru Yang, Kelly J. Domesle, Fei Wang, Beilei Ge
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0118890

Flexible Adaptive Paradigms for fMRI Using a Novel Software Package ‘Brain Analysis in Real-Time’ (BART)
Cited by: 12
Author(s): Lydia Hellrung, Maurice Hollmann, Oliver Zscheyge, Torsten Schlumm, Christian Kalberlah, Elisabeth Roggenhofer, Hadas Okon‐Singer, Arno Villringer, Annette Horstmann
Software Mentions: 1
Published: over 9 years ago

10.1186/s12874-021-01383-x

Minimizing bias in massive multi-arm observational studies with BCAUS: balancing covariates automatically using supervision
Cited by: 4
Author(s): Chinmay Belthangady, Will Stedden, Beau Norgeot
Software Mentions: 1
Published: about 3 years ago

10.1371/journal.pone.0221801

EUSKOR: End-to-end coreference resolution system for Basque
Cited by: 0
Author(s): Ander Soraluze, Olatz Arregi, Xabier Arregi, Arantza Díaz de Ilarraza
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0208937

The influence of maternal agency on severe child undernutrition in conflict-ridden Nigeria: Modeling heterogeneous treatment effects with machine learning
Cited by: 10
Author(s): Nadine Kraamwinkel, Hans Ekbrand, Stefania Davia, Adel Daoud
Software Mentions: 1
Published: almost 6 years ago

10.1155/2019/9079840

Minimalistic Approach to Coreference Resolution in Lithuanian Medical Records
Cited by: 8
Author(s): Voldemaras Žitkus, Rita Butkienė, Rimantas Butleris, Rytis Maskeliūnas, Robertas Damaševičius, Marcin Woźniak
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2156-12-63

A strategy analysis for genetic association studies with known inbreeding
Cited by: 9
Author(s): Stefano Cabras, María Eugenia Castellanos, Ginevra Biino, Ivana Persico, Alessandro Sassu, Laura Casula, Stefano Del Giacco, Francesco Bertolino, Mario Pirastu, Nicola Pirastu
Software Mentions: 1
Published: almost 14 years ago

10.1186/1471-2253-14-47

Brachial artery reactivity and vascular reactive hyperemia for preoperative anaesthesia risk assessment – an observational study
Cited by: 2
Author(s): Robert Schier, Volker Schick, Ashley Amsbaugh, Jorge Luis Vázquez Aguilar, Mike Hernandez, Reza J. Mehran, Bernhard Riedel, Jochen Hinkelbein
Software Mentions: 1
Published: over 10 years ago

10.3389/fpls.2020.570862

Molecular Approaches for Low-Cost Point-of-Care Pathogen Detection in Agriculture and Forestry
Cited by: 33
Author(s): Paolo Baldi, Nicola La Porta
Software Mentions: 1
Published: about 4 years ago

10.3389/fpsyg.2019.02461

Predictive Feature Generation and Selection Using Process Data From PISA Interactive Problem-Solving Items: An Application of Random Forests
Cited by: 27
Author(s): Zhuangzhuang Han, Qiwei He, Matthias von Davier
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-2296-14-181

Patient reported barriers and facilitators to using a self-management booklet for hip and knee osteoarthritis in primary care: results of a qualitative interview study
Cited by: 22
Author(s): Nienke Cuperus, A. Smink, Sita M A Bierma-Zeinstra, Joost Dekker, Henk Schers, Fijgje de Boer, C.H. van den Ende, Thea Vliet Vlieland
Software Mentions: 1
Published: almost 11 years ago

Projects: cran: BART

Papers Mentioning BART 63