Preprints (not yet peer-reviewed)

15 downloads
26 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
32 downloads
46 views

Causality testing methods are being widely used in various disciplines of science. Model-free methods for causality estimation are very useful as the underlying model generating the data is often unknown. However, existing model-free measures assume separability...

["Adaptive and Self-Organizing Systems","Data Science","Scientific Computing and Simulation"]
doi:10.7287/peerj.preprints.27416v1
112 downloads
228 views

Increasingly, big data, coding, and quantitative methods contribute to contemporary ecological and evolutionary endeavours. This is not in opposition to effective ideation nor does it play to the false dichotomy of theory versus data. Computational expeditions...

["Computational Biology","Computer Education","Data Science"]
doi:10.7287/peerj.preprints.27408v1
2,548 downloads
4,401 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
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
70 downloads
139 views

We develop an efficient software package to test for the primality of p2^n+1, p prime and p>2^n. This aids in the determination of large, non-Sierpinski numbers p, for prime p, and in cryptography. It furthermore uniquely allows for the computation of the smallest...

["Cryptography","Data Science","Theory and Formal Methods"]
doi:10.7287/peerj.preprints.27396v1
40 downloads
69 views

Playlist recommendation involves producing a set of songs that a user might enjoy. We investigate this problem in three cold-start scenarios: (i) cold playlists, where we recommend songs to form new personalised playlists for an existing user; (ii) cold users,...

["Data Mining and Machine Learning","Data Science"]
doi:10.7287/peerj.preprints.27383v2
3,415 downloads
5,411 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
29 downloads
59 views

Next-generation sequencing (NGS) technologies are greatly facilitating the sequencing of whole genomes leading to the production of different gene annotations, released often from both reference resources (such as NCBI or Ensembl) and specific consortia. All these...

["Computational Biology","Data Science","Databases"]
doi:10.7287/peerj.preprints.27347v1
1,041 downloads
1,396 views

In this paper, we discuss an extension to two popular approaches to modelling complex structures in ecological data: the generalized additive model (GAM) and the hierarchical model (HGLM). The hierarchical GAM (HGAM), allows modelling of nonlinear functional relationships...

["Ecology","Statistics","Data Science"]
doi:10.7287/peerj.preprints.27320v1
71 downloads
102 views

There are many methods available for each phase of the RNA-Seq analysis and each of them uses different algorithms. It is therefore useful to identify a pipeline that combines the best tools in terms of time and results. For this purpose, we compared five different...

["Bioinformatics","Computational Biology","Data Science"]
doi:10.7287/peerj.preprints.27317v2
3,407 downloads
7,996 views

Statistical inference often fails to replicate. One reason is that many results may be selected for drawing inference because some threshold of a statistic like the P-value was crossed, leading to biased reported effect sizes. Nonetheless, considerable non-replication...

["Science and Medical Education","Science Policy","Statistics","Data Science"]
doi:10.7287/peerj.preprints.26857v4
39 downloads
77 views

Machine learning is a field of study that uses computational and statistical techniques to enable computers to learn. When machine learning is applied, it functions as an instrument that can solve problems or expand knowledge about the surrounding world. Increasingly,...

["Artificial Intelligence","Computer Vision","Data Mining and Machine Learning","Data Science","Multimedia"]
doi:10.7287/peerj.preprints.27280v1
37 downloads
79 views

In this article we consider a certain sub class of Integer Equal Flow problem, which are known NP hard. Currently there exist no direct solutions for the same. It is a common problem in various inventory management systems. Here we discuss a local minima solution...

["Data Science","Optimization Theory and Computation","Theory and Formal Methods"]
doi:10.7287/peerj.preprints.27264v1
52 downloads
103 views

According to predictions bases on a climate-driven large-scale model the areas surrounding Lake Léman and, to some extent, the Swiss Plateau are suitable for the spread of Ae. albopictus North of the Alps, while other areas in Switzerland (e.g., the city of Zürich)...

["Computer Networks and Communications","Data Science","Spatial and Geographic Information Systems"]
doi:10.7287/peerj.preprints.27251v1
What is a PeerJ Preprint?

A PeerJ Preprint is a draft of an article, abstract, or poster that has not yet been peer-reviewed for formal publication. Submit a draft, incomplete, or final version of your work for free.

Submissions today can be approved by Editorial Staff and online in 24 hours.

Establish precedent. Solicit feedback. Publish updates.

Refine by manuscript type

Top subject areas - Preprints

Top subject areas - People

View all subject areas