Preprints (not yet peer-reviewed)

12 downloads
20 views

An empirical understanding of how DNA read features affect read mapping and alignment quality could be useful in designing better read mapping and alignment software, read trimmers, and sequence masks. Many programs appear to use arbitrarily chosen features that...

["Bioinformatics","Data Science"]
doi:10.7287/peerj.preprints.27428v1
16 downloads
69 views

Background. A number of recent high-profile cases have focused attention on scientific misconduct and other problematic issues with the peer review process. The retraction of journal publications is an important part of the scientific publishing process that serves...

["Bioinformatics","Oncology","Ethical Issues","Science Policy"]
doi:10.7287/peerj.preprints.27427v1
83 downloads
215 views

Bioinformatics algorithms are now crucial for processing high throughput “-omics” data and deriving meaningful interpretations in most biomedical and life science research domains. Bioinformatics-related training and research mostly take place in nations with higher...

["Bioinformatics","Computational Biology","Genomics","Science and Medical Education"]
doi:10.7287/peerj.preprints.27415v1
32 downloads
103 views

Superoxide dismutases (SODs) are a key antioxidant enzyme family, which plays a critical function in plant growth and development. Previously, this gene family has been investigated in Arabidopsis and rice. In the present study, it was the first time for us to...

["Agricultural Science","Bioinformatics","Genomics"]
doi:10.7287/peerj.preprints.27402v1
2,537 downloads
4,388 views
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, II, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight, J Gregory Caporaso

We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the microbiome research ecosystem, from scientists and engineers to clinicians and policy makers. QIIME 2 provides new features that will drive the next generation...

["Bioinformatics","Ecology","Microbiology","Data Science"]
doi:10.7287/peerj.preprints.27295v2
47 downloads
82 views

Many Zika virus (ZIKV) pathogenesis-related studies have focused primarily on virus-driven pathology and neurotoxicity, instead of considering the possibility of pathogenesis as an (unintended) consequence of host innate immunity: specifically, as the side-effect...

["Bioinformatics","Neuroscience","Virology","Global Health","Infectious Diseases"]
doi:10.7287/peerj.preprints.27401v1
17 downloads
67 views

Clinical bioinformatics, translational bioinformatics and personalised medicine are connected by the common task of analysing and integrating clinical data and results, in order to find important biomarkers related to pathologies and facilitate their prediction,...

["Bioinformatics","Computational Biology","Pathology","Statistics","Data Science"]
doi:10.7287/peerj.preprints.27398v1
59 downloads
164 views

Background. Metagenomics studies have reported on the complexity of microbiomes associated with seagrass and can provide critical insights into the sustainable use and conservation of seagrasses. Recent conservation activities in Kenya focused mainly on coral reefs...

["Bioinformatics","Ecosystem Science","Genomics","Marine Biology","Natural Resource Management"]
doi:10.7287/peerj.preprints.27387v1
26 downloads
51 views

Clinical studies/trials are experiments or observations on human subjects considered by the scientific community the most appropriate instrument to answer specific research questions on interventions on health outcomes. The time-line of the observations might be...

["Bioinformatics","Clinical Trials","Epidemiology","Statistics","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.27385v1
3,409 downloads
5,397 views

Gene expression is the fundamental level at which the result of various genetic and regulatory programs are observable. The measurement of transcriptome-wide gene expression has convincingly switched from microarrays to sequencing in a matter of years. RNA sequencing...

["Bioinformatics","Computational Biology","Genomics","Data Science"]
doi:10.7287/peerj.preprints.27283v2
229 downloads
359 views

The rapid decrease in DNA sequencing cost is revolutionizing medicine and science. In medicine, genome sequencing has revealed millions of missense variants that change protein sequences, yet we only understand the molecular and phenotypic consequences of a small...

["Bioinformatics","Biophysics","Computational Biology","Genomics","Medical Genetics"]
doi:10.7287/peerj.preprints.27379v1
86 downloads
195 views

The Lung Imaging Data Consortium and Image Database Resource Initiative (LIDC) conducted a multi-site reader study that produced a comprehensive database of Computed Tomography (CT) scans for over 1000 subjects annotated by multiple expert readers. The result is...

["Bioinformatics","Oncology","Radiology and Medical Imaging"]
doi:10.7287/peerj.preprints.27378v1
25 downloads
101 views

Introduction. Whole-metagenome sequencing can be a rich source of information about the structure and function of entire metagenomic communities, but getting accurate and reliable results from these datasets can be challenging. Analysis of these datasets is founded...

["Bioinformatics","Ecology","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.27376v1
32 downloads
85 views

In recent years, several computational methods have been developed to predict protein-protein interactions (PPIs) at a genome-wide level. Between them phylogenetic profiling is routinely used to infer PPIs occurring within an organism. Recent improvements of the...

["Bioinformatics","Parasitology","Infectious Diseases","Computational Science"]
doi:10.7287/peerj.preprints.27373v1
54 downloads
204 views

Photoperiodic flowering aligns plant reproduction to favourable seasons of the year to maximise successful production of seeds and grains. However understanding of this process in the temperate legumes of the Fabaceae family, which are important both agriculturally...

["Bioinformatics","Genomics","Molecular Biology","Plant Science"]
doi:10.7287/peerj.preprints.27366v1
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