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https://doi.org/10.12688/f1000research.15090.3
Brief Report metrics
Revised
Analysis of the complete genome of hepatitis B virus subgenotype C2 isolate NHB17965 from a HBV infected patient
[version 3; peer review: 2 approved, 1 approved with reservations]
Modhusudon Shaha, Palash Kumar Sarker, Md. Saddam Hossain, Keshob Chandra Das, Munira Jahan, Shuvra Kanti Dey, Shahina Tabassum, Abu Hashem, Md. Salimullah
Peer Reviewers Mohammad Ariful Islam; Paul Klapper; Ashesh Kumar Chowdhury
  • Funder
  • Ministry of Science and Technology, Government of the People’s Republic of Bangladesh
LATEST VERSION PUBLISHED 10 Sep 2018
https://doi.org/10.12688/f1000research.16047.1
Software Tool Article metrics
methyvim: Targeted, robust, and model-free differential methylation analysis in R
[version 1; peer review: 1 approved with reservations, 2 not approved]
Nima S. Hejazi, Rachael V. Phillips, Alan E. Hubbard, Mark J. van der Laan
Peer Reviewers Peter F.  Hickey; Jimmy Breen and Nader Aryamanesh; Nandita Mitra and Ted Westling
  • Funders
  • National Institute of Environmental Health Sciences
  • U.S. National Library of Medicine
PUBLISHED 07 Sep 2018
https://doi.org/10.12688/f1000research.15704.1
Software Tool Article metrics
ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis
[version 1; peer review: 2 approved]
Adam R. Rivers, Kyle C. Weber, Terrence G. Gardner, Shuang Liu, Shalamar D. Armstrong
Peer Reviewers J. Gregory Caporaso; Johanna B. Holm
  • Funder
  • USDA Agricultural Research Service
PUBLISHED 06 Sep 2018
https://doi.org/10.12688/f1000research.14840.2
Research Article metrics
Revised
Absence of toll-like receptor 9 Pro99Leu polymorphism in cervical cancer
[version 2; peer review: 2 approved, 1 not approved]
Alex Chauhan, Nilesh Pandey, Nitin Raithatha, Purvi Patel, Ajesh Desai, Neeraj Jain
Peer Reviewers Gopeshwar Narayan; Balraj Mittal; Bhudev C. Das
  • Funder
  • Charotar University of Science and Technology
LATEST VERSION PUBLISHED 30 Aug 2018
https://doi.org/10.12688/f1000research.15653.1
Data Note metrics
Complete plastome sequences of two Psidium species from the Galápagos Islands
[version 1; peer review: 2 approved]
Bryan Reatini, Maria de Lourdes Torres, Hugo Valdebenito, Todd Vision
Peer Reviewers Michael O. Dillon; Carolyn Proença
  • Funder
  • University of North Carolina at Chapel Hill
PUBLISHED 30 Aug 2018
https://doi.org/10.12688/f1000research.15408.1
Review metrics
Recent advances in understanding DNA replication: cell type–specific adaptation of the DNA replication program
[version 1; peer review: 2 approved]
Antoine Aze, Domenico Maiorano
Peer Reviewers Christian Speck; David M. MacAlpine and Rachel Hoffman
  • Funders
  • INSERM
  • La ligue contre le Cancer
  • MSD AVenir
  • Fondation ARC pour la Recherche sur le cancer
PUBLISHED 29 Aug 2018
https://doi.org/10.12688/f1000research.14795.1
Research Article metrics
Using Lamin B1 mRNA for the early diagnosis of hepatocellular carcinoma: a cross-sectional diagnostic accuracy study
[version 1; peer review: 2 approved]
Amani M. Abdelghany, Nasser Sadek Rezk, Mona Mostafa Osman, Amira I. Hamid, Ashraf Mohammad Al-Breedy, Hoda A. Abdelsattar
Peer Reviewers Dina Fekry; Sherief Abd-Elsalam
PUBLISHED 24 Aug 2018
https://doi.org/10.12688/f1000research.15606.1
Review metrics
Milestones achieved in response to drought stress through reverse genetic approaches
[version 1; peer review: 2 approved]
Baljeet Singh, Sarvjeet Kukreja, Umesh Goutam
Peer Reviewers Elangovan Mani; Pardeep Kumar Bhardwaj
PUBLISHED 17 Aug 2018
https://doi.org/10.12688/f1000research.15845.1
Method Article metrics
Recursive module extraction using Louvain and PageRank
[version 1; peer review: 2 approved]
Dimitri Perrin, Guido Zuccon
Peer Reviewers Raghvendra Mall; Alina Sîrbu
PUBLISHED 14 Aug 2018
https://doi.org/10.12688/f1000research.15391.1
Review metrics
Establishing sharp and homogeneous segments in the hindbrain
[version 1; peer review: 3 approved]
David G. Wilkinson
Peer Reviewers Robb Krumlauf; Kyo Yamasu; Dalit Sela-Donenfeld
  • Funders
  • UK Medical Research Council
  • Wellcome Trust
  • Cancer Research UK
PUBLISHED 13 Aug 2018
https://doi.org/10.12688/f1000research.15579.1
Research Article metrics
Formation of 53BP1 foci and ATM activation under oxidative stress is facilitated by RNA:DNA hybrids and loss of ATM-53BP1 expression promotes photoreceptor cell survival in mice
[version 1; peer review: 1 approved, 3 approved with reservations]
Vaibhav Bhatia, Lourdes Valdés-Sánchez, Daniel Rodriguez-Martinez, Shom Shankar Bhattacharya
Peer Reviewers Travis H. Stracker; Hemant Khanna; Florian Frohns; Maria Tresini
  • Funders
  • Juan de la cierva grant from Ministry of Economy, Industry and Competitiveness, Government of Spain
  • Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía
PUBLISHED 10 Aug 2018
https://doi.org/10.12688/f1000research.15146.2
Software Tool Article metrics
Revised
aMatReader: Importing adjacency matrices via Cytoscape Automation
[version 2; peer review: 2 approved]
Brett Settle, David Otasek, John H Morris, Barry Demchak
Peer Reviewers Hideo Matsuda; Kimberly Glass
  • Funders
  • National Resource for Network Biology
  • National Institute of General Medical Sciences
LATEST VERSION PUBLISHED 10 Aug 2018
https://doi.org/10.12688/f1000research.15144.2
Software Tool Article metrics
Revised
Copycat Layout: Network layout alignment via Cytoscape Automation
[version 2; peer review: 2 approved]
Brett Settle, David Otasek, John H Morris, Barry Demchak
Peer Reviewers Bernhard Mlecnik; Katja Luck
  • Funders
  • National Resource for Network Biology
  • National Institute of General Medical Sciences
LATEST VERSION PUBLISHED 10 Aug 2018
https://doi.org/10.12688/f1000research.13441.2
Brief Report metrics
Revised
DNA sequence features in the establishing of H3K27ac
[version 2; peer review: 2 approved]
Anatoliy Zubritskiy, Yulia A. Medvedeva
Peer Reviewers Vasily N Aushev; Oleg Gusev
  • Funder
  • Russian Science Foundation
LATEST VERSION PUBLISHED 09 Aug 2018
https://doi.org/10.12688/f1000research.9973.2
Software Tool Article metrics
Revised
BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests
[version 2; peer review: 2 approved, 1 approved with reservations]
Andrea Komljenovic, Julien Roux, Julien Wollbrett, Marc Robinson-Rechavi, Frederic B. Bastian
Peer Reviewers Virag Sharma; Daniel S. Himmelstein; Leonardo Collado-Torres
  • Funder
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
LATEST VERSION PUBLISHED 07 Aug 2018
https://doi.org/10.12688/f1000research.14807.2
Software Tool Article metrics
Revised
Identifier Mapping in Cytoscape
[version 2; peer review: 3 approved]
Adam Treister, Alexander R. Pico
Peer Reviewers Ruth Isserlin; Augustin Luna; Nadezhda Doncheva
  • Funder
  • National Institute of General Medical Sciences
LATEST VERSION PUBLISHED 06 Aug 2018
https://doi.org/10.12688/f1000research.11146.2
Research Article metrics
Revised
De novo whole-genome assembly of a wild type yeast isolate using nanopore sequencing
[version 2; peer review: 2 approved, 2 approved with reservations]
Michael Liem, Hans J. Jansen, Ron P. Dirks, Christiaan V. Henkel, G. Paul H. van Heusden, Richard J.L.F. Lemmers, Trifa Omer, Shuai Shao, Peter J. Punt, Herman P. Spaink
Peer Reviewers Mile Šikić; Jean-Marc Aury and Istace Benjamin; Christina A. Cuomo; Hayan Lee
LATEST VERSION PUBLISHED 03 Aug 2018
https://doi.org/10.12688/f1000research.15604.1
Research Article metrics
Androgen-dependent alternative mRNA isoform expression in prostate cancer cells
[version 1; peer review: 3 approved]
Jennifer Munkley, Teresa M. Maia, Nekane Ibarluzea, Karen E. Livermore, Daniel Vodak, Ingrid Ehrmann, Katherine James, Prabhakar Rajan, Nuno L. Barbosa-Morais, David J. Elliott
Peer Reviewers Sebastian Oltean; Cyril F. Bourgeois; Jennifer Byrne
  • Funder
  • Prostate Cancer UK
PUBLISHED 03 Aug 2018
https://doi.org/10.12688/f1000research.14499.1
Review metrics
Recent advances in prostate cancer research: large-scale genomic analyses reveal novel driver mutations and DNA repair defects
[version 1; peer review: 2 approved]
Sander Frank, Peter Nelson, Valeri Vasioukhin
Peer Reviewers Emmanuel S Antonarakis; Christopher E Barbieri
  • Funder
  • National Institutes of Health
PUBLISHED 02 Aug 2018
https://doi.org/10.12688/f1000research.15357.1
Method Article metrics
To select relevant features for longitudinal gene expression data by extending a pathway analysis method
[version 1; peer review: 2 approved, 1 approved with reservations]
Suyan Tian, Chi Wang, Howard H. Chang
Peer Reviewers Hulin Wu; Shengping Yang; Irina Dinu
  • Funder
  • National Natural Science Foundation of China
PUBLISHED 31 Jul 2018
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