Preprints (not yet peer-reviewed)

29 downloads
170 views

The immune system protects a host from foreign pathogens. In rare cases, the immune system can attack the cells of the host organism causing autoimmune diseases. We outline a computational framework that combines bioinformatics and network analysis with an emerging...

["Bioinformatics","Computational Biology","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.3217v3
43 downloads
93 views

The conditional mutual information \(I(X;Y|Z)\) measures the average information that X and Y contain about each other given Z. This is an important primitive in many learning problems including conditional independence testing, graphical model inference, causal...

["Data Mining and Machine Learning","Data Science"]
doi:10.7287/peerj.preprints.3345v1
192 downloads
563 views

Computational models in biology encode molecular and cell biological processes. These models often can be represented as biochemical reaction networks. Studying such networks, one is mostly interested in systems that share similar reactions and mechanisms. Typical...

["Bioinformatics","Computational Biology","Data Mining and Machine Learning","Data Science"]
doi:10.7287/peerj.preprints.1479v3
13 downloads
80 views

Given a dataset \(\mathcal{R}=\{R_1, R_2, \dots, R_r\}\) of \(r\)~records of waitlisted incoming freshman students (WIFS), where for any \(i=1, 2, \dots, r\), \(R_i\) is a \((m+1)\)--tuple \((O_i, P_i^{(1)}, P_i^{(2)}, \dots, P_i^{(m)})\), \(O_i\) is any one in...

["Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.3312v1
33 downloads
75 views

We present GenotypeAnalytics (GA), a RESTFul service that makes it possible to mine association rules from Single Nucleotide Polymorphism (SNP) datasets using standard web browsers. GA can speed up and simplify the analysis of this massive amount of data, highlighting...

["Bioinformatics","Computational Biology","Data Mining and Machine Learning","Data Science","World Wide Web and Web Science"]
doi:10.7287/peerj.preprints.3299v1
41 downloads
109 views

Background. Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease primarily affecting upper and lower motor neurons in the brain and spinal cord. The heterogeneity in the course of ALS clinical progression and ultimately survival, coupled...

["Bioinformatics","Computational Biology","Data Mining and Machine Learning","Scientific Computing and Simulation"]
doi:10.7287/peerj.preprints.3262v1
99 downloads
164 views

Species distribution models (SDMs) have become important and essential tools in conservation and management. However, SDMs built with count data, commonly referred to as species abundance models (SAMs), are still less used so far. SDMs are increasingly used now...

["Biodiversity","Biogeography","Conservation Biology","Ecology","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.3240v1
119 downloads
362 views

Epilepsy is a complex brain disorder characterized by repetitive seizure events. Epilepsy patients often suffer from various and severe physical and psychological comorbidities. While general comorbidity prevalence and incidences can be estimated from epidemiological...

["Bioinformatics","Data Mining and Machine Learning","Data Science"]
doi:10.7287/peerj.preprints.3228v1
389 downloads
997 views

Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed...

["Agricultural Science","Bioinformatics","Computational Biology","Plant Science","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.3225v1
31 downloads
364 views

Epigenetic research focuses on understanding non-inheritable factors influencing gene regulation and covers various cellular mechanisms such as DNA methylation, histone modification, miRNA function and transcription factor binding sites. Recent advances in high-throughput...

["Bioinformatics","Computational Biology","Genetics","Molecular Biology","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.3224v1
149 downloads
219 views

The USA National Center for Biotechnology Information (NCBI) is one of the world’s most important sources of biological information. NCBI databases like PubMed and GenBank contain millions of records describing bibliographic, genetic, genomic, and medical data....

["Bioinformatics","Genetics","Genomics","Molecular Biology","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.3179v2
77 downloads
228 views

The regulatory code that determines whether and how a given genetic variant affects the function of a regulatory element remains poorly understood for most classes of regulatory variation. Indeed the large majority of bioinformatics tools have been developed to...

["Bioinformatics","Computational Biology","Computational Science","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.3185v1
1,176 downloads
3,830 views

The R language has withstood the test of time. Forty years after it was initially developed (in the form of the S language) R is being used by millions of programmers on workflows the inventors of the language could never have imagined. Although base R packages...

["Data Mining and Machine Learning","Data Science"]
doi:10.7287/peerj.preprints.3180v1
35 downloads
173 views

We present in this article a lightweight ontology named PGxO and a set of rules for its instantiation, which we developed as a frame for reconciling and tracing pharmacogenomics (PGx) knowledge. PGx studies how genomic variations impact variations in drug response...

["Bioinformatics","Artificial Intelligence","Data Mining and Machine Learning","Databases","World Wide Web and Web Science"]
doi:10.7287/peerj.preprints.3140v1
162 downloads
398 views

Metabarcoding and metagenomic approaches are becoming routine techniques in biodiversity assessment and ecological studies. The assignment of taxonomic information to sequences is challenging, as many reference libraries are lacking information on certain taxonomic...

["Biodiversity","Bioinformatics","Ecology","Molecular Biology","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.3133v1
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