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https://doi.org/10.12688/f1000research.52549.1
Method Article metrics
Supervised topic modeling for predicting molecular substructure from mass spectrometry
[version 1; peer review: 2 approved with reservations]
Gabriel K. Reder, Adamo Young, Jaan Altosaar, Jakub Rajniak, Noémie Elhadad, Michael Fischbach, Susan Holmes
Peer Reviewers Joe Wandy; Hunter N B Moseley
  • Funder
  • National Institutes of Health
PUBLISHED 19 May 2021
https://doi.org/10.12688/f1000research.27384.1
Software Tool Article metrics
Meta-Signer: Metagenomic Signature Identifier based onrank aggregation of features
[version 1; peer review: 1 approved with reservations, 1 not approved]
Derek Reiman, Ahmed Metwally, Jun Sun, Yang Dai
Peer Reviewers Braden T Tierney; Boyang JI
PUBLISHED 09 Mar 2021
https://doi.org/10.12688/f1000research.25877.2
Software Tool Article metrics
Revised
Umpire 2.0: Simulating realistic, mixed-type, clinical data for machine learning
[version 2; peer review: 1 approved, 1 approved with reservations]
Caitlin E. Coombes, Zachary B. Abrams, Samantha Nakayiza, Guy Brock, Kevin R. Coombes
Peer Reviewers Julia Wrobel; Justin Mower and Andrew Zimolzak
  • Funders
  • National Center for Advancing Translational Sciences
  • National Cancer Institute
LATEST VERSION PUBLISHED 05 Mar 2021
https://doi.org/10.12688/f1000research.50798.1
Software Tool Article metrics
Interactive biomedical segmentation tool powered by deep learning and ImJoy
[version 1; peer review: 1 approved, 1 approved with reservations]
Wei Ouyang, Trang Le, Hao Xu, Emma Lundberg
Peer Reviewers Jean-Yves Tinevez and Dmitry Ershov; Jan Funke
  • Funders
  • Knut and Alice Wallenberg Foundation
  • Swedish Research Council
  • LST Platform at KTH Royal Institute of Technology
PUBLISHED 24 Feb 2021
https://doi.org/10.12688/f1000research.26429.2
Software Tool Article metrics
Revised
netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks
[version 2; peer review: 2 approved]
Shraddha Pai, Philipp Weber, Ruth Isserlin, Hussam Kaka, Shirley Hui, Muhammad Ahmad Shah, Luca Giudice, Rosalba Giugno, Anne Krogh Nøhr, Jan Baumbach, Gary D. Bader
Peer Reviewers Kim-Anh Lê Cao; Anais Baudot, Judith Lambert and Laurent Tichit
  • Funders
  • Villum Fonden
  • Horizon 2020
  • National Institutes of Health
LATEST VERSION PUBLISHED 22 Jan 2021
https://doi.org/10.12688/f1000research.28288.1
Research Article metrics
Comparison of different machine learning methods and dimensionality reduction for classification astrocytoma and glioblastoma tissues by mass spectra
[version 1; peer review: 1 approved with reservations, 1 not approved]
Evgeny S. Zhvansky, Anatoly A. Sorokin, Denis S. Zavorotnyuk, Vsevolod A. Shurkhay, Vasiliy A. Eliferov, Denis S. Bormotov, Daniil G. Ivanov, Alexander A. Potapov
Peer Reviewers Sergei A. Moshkovskii; Konstantin Chingin
  • Funder
  • Ministry of Science and Higher Education of the Russian Federation
PUBLISHED 21 Jan 2021
https://doi.org/10.12688/f1000research.26880.2
Software Tool Article metrics
Revised
Recursive Cluster Elimination based Rank Function (SVM-RCE-R) implemented in KNIME
[version 2; peer review: 3 approved]
Malik Yousef, Burcu Bakir-Gungor, Amhar Jabeer, Gokhan Goy, Rehman Qureshi, Louise C. Showe
Peer Reviewers Marco Chierici; Osman Ugur Sezerman; Abhishek Kumar
  • Funder
  • National Cancer Institute
LATEST VERSION PUBLISHED 05 Jan 2021
https://doi.org/10.12688/f1000research.26459.1
Software Tool Article metrics PEER REVIEW DISCONTINUED
Uncovering host-microbiome interactions in global systems with collaborative programming: a novel approach integrating social and data sciences
[version 1; peer review: 1 approved with reservations]
Jenna Oberstaller, Swamy Rakesh Adapa, Guy W. Dayhoff II, Justin Gibbons, Thomas E. Keller, Chang Li, Jean Lim, Minh Pham, Anujit Sarkar, Ravi Sharma, Agaz H. Wani, Andrea Vianello, Linh M. Duong, Chenggi Wang, Celine Grace F. Atkinson, Madeleine Barrow, Nathan W. Van Bibber, Jan Dahrendorff, David A. E. Dean, Omkar Dokur, Gloria C. Ferreira, Mitchell Hastings, Gregory S. Herbert, Khandaker Tasnim Huq, Youngchul Kim, Xiangyun Liao, XiaoMing Liu, Fahad Mansuri, Lynn B. Martin, Elizabeth M. Miller, Ojas Natarajan, Jinyong Pang, Francesca Prieto, Peter W. Radulovic, Vyoma Sheth, Matthew Sumpter, Desirae Sutherland, Nisha Vijayakumar, Rays H. Y. Jiang
Peer Reviewers Sucheta Tripathy
  • Funder
  • University of South Florida
PUBLISHED 17 Dec 2020
https://doi.org/10.12688/f1000research.15666.3
Research Article metrics
Revised
A systematic performance evaluation of clustering methods for single-cell RNA-seq data
[version 3; peer review: 2 approved]
Angelo Duò, Mark D. Robinson, Charlotte Soneson
Peer Reviewers Jean Fan; Saskia Freytag
  • Funders
  • Swiss National Science Foundation
  • Chan Zuckerberg Initiative
LATEST VERSION PUBLISHED 16 Nov 2020
https://doi.org/10.12688/f1000research.25501.1
Software Tool Article metrics
MSclassifier: median-supplement model-based classification tool for automated knowledge discovery
[version 1; peer review: 2 approved]
Emmanuel S. Adabor, George K. Acquaah-Mensah, Gaston K. Mazandu
Peer Reviewers Gregory Hart; Alper Uzun
  • Funders
  • Ghana Institute of Management and Public Administration
  • National Institutes of Health
  • African Institute for Mathematical Sciences
  • Massachusetts College of Pharmacy and Health Sciences
PUBLISHED 10 Sep 2020
https://doi.org/10.12688/f1000research.22090.2
Research Article metrics
Revised
Machine learning meets pKa
[version 2; peer review: 2 approved]
Marcel Baltruschat, Paul Czodrowski
Peer Reviewers Ruth Brenk; Johannes Kirchmair
LATEST VERSION PUBLISHED 27 Apr 2020
https://doi.org/10.12688/f1000research.22823.1
Method Article metrics
PRESa2i: incremental decision trees for prediction of Adenosine to Inosine RNA editing sites
[version 1; peer review: 1 approved with reservations, 2 not approved]
Alif Choyon, Ashiqur Rahman, Md. Hasanuzzaman, Dewan Md Farid, Swakkhar Shatabda
Peer Reviewers Avdesh Mishra; Shizuka Uchida; Xiaoyong Pan
PUBLISHED 16 Apr 2020
https://doi.org/10.12688/f1000research.20277.2
Research Article metrics
Revised
EEG anticipation of random high and low arousal faces and sounds
[version 2; peer review: 1 approved, 1 not approved]
Gian Marco Duma, Giovanni Mento, Luca Semenzato, Patrizio E. Tressoldi
Peer Reviewers J. Bruno Debruille; Xifu Zheng and Jingchu Hu
  • Funder
  • Università degli Studi di Padova
LATEST VERSION PUBLISHED 12 Dec 2019
https://doi.org/10.12688/f1000research.21016.1
Study Protocol metrics
Protocol for the Effectiveness of an Anesthesiology Control Tower System in Improving Perioperative Quality Metrics and Clinical Outcomes: the TECTONICS randomized, pragmatic trial
[version 1; peer review: 2 approved]
Christopher R. King, Joanna Abraham, Thomas G. Kannampallil, Bradley A. Fritz, Arbi Ben Abdallah, Yixin Chen, Bernadette Henrichs, Mary Politi, Brian A. Torres, Angela Mickle, Thaddeus P. Budelier, Sherry McKinnon, Stephen Gregory, Sachin Kheterpal, Troy Wildes, Michael S. Avidan, TECTONICS Research Group
Peer Reviewers Ben Gibbison; Leon du Toit, Ross Hofmeyr and Maretha Smit
  • Funders
  • Agency for Healthcare Research and Quality
  • National Institute of Nursing Research
  • Washington University in St. Louis
  • National Science Foundation
PUBLISHED 29 Nov 2019
https://doi.org/10.12688/f1000research.20498.2
Systematic Review metrics
Revised
Evidence-based Clinical Decision Support Systems for the prediction and detection of three disease states in critical care: A systematic literature review
[version 2; peer review: 2 approved]
Goran Medic, Melodi Kosaner Kließ, Louis Atallah, Jochen Weichert, Saswat Panda, Maarten Postma, Amer EL-Kerdi
Peer Reviewers Stavros Nikolakopoulos; Milena Kovacevic
  • Funder
  • Philips
LATEST VERSION PUBLISHED 27 Nov 2019
https://doi.org/10.12688/f1000research.19029.2
Software Tool Article metrics
Revised
Network-based Observability and Controllability Analysis of Dynamical Systems: the NOCAD toolbox
[version 2; peer review: 2 approved]
Dániel Leitold, Ágnes Vathy-Fogarassy, János Abonyi
Peer Reviewers Gilles Didier; Arthur Montanari, Ercílio Moreira and Luis A. Aguirre
  • Funders
  • Emberi Eroforrások Minisztériuma
  • Országos Tudományos Kutatási Alapprogramok
LATEST VERSION PUBLISHED 18 Sep 2019
https://doi.org/10.12688/f1000research.19721.1
Review metrics
Cardiac magnetic resonance imaging: the future is bright
[version 1; peer review: 2 approved]
Karthik Seetharam, Stamatios Lerakis
Peer Reviewers Jeroen J. Bax; Lauren A Baldassarre
PUBLISHED 13 Sep 2019
https://doi.org/10.12688/f1000research.16200.2
Research Article metrics
Revised
Predicting transcription factor binding using ensemble random forest models
[version 2; peer review: 2 approved]
Fatemeh Behjati Ardakani, Florian Schmidt, Marcel H. Schulz
Peer Reviewers Jan Grau; Gary D Stormo
  • Funder
  • Cluster of Excellence on Multimodal Computing and Interaction (DFG)
LATEST VERSION PUBLISHED 02 Sep 2019
https://doi.org/10.12688/f1000research.18926.1
Review metrics
Evolving principles underlying neural lineage conversion and their relevance for biomedical translation
[version 1; peer review: 4 approved]
Lea Jessica Flitsch, Oliver Brüstle
Peer Reviewers Andrew Yoo; Kristin Baldwin; Jerome Mertens; Agnete Kirkeby
  • Funders
  • ERA-Net Neuron program
  • Bundesministerium für Bildung und Forschung
  • European Union
  • National Institutes of Health
PUBLISHED 30 Aug 2019
https://doi.org/10.12688/f1000research.14613.2
Software Tool Article metrics
Revised
CyTargetLinker app update: A flexible solution for network extension in Cytoscape
[version 2; peer review: 2 approved]
Martina Kutmon, Friederike Ehrhart, Egon L. Willighagen, Chris T. Evelo, Susan L. Coort
Peer Reviewers Alex Gutteridge; John H. Morris
  • Funders
  • ELIXIR
  • Dutch Province of Limburg
LATEST VERSION PUBLISHED 13 Aug 2019
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