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  1. Research Article

    Meta-aligner: long-read alignment based on genome statistics

    Current development of sequencing technologies is towards generating longer and noisier reads. Evidently, accurate alignment of these reads play an important role in any downstream analysis. Similarly, reducin...

    Damoon Nashta-ali, Ali Aliyari, Ahmad Ahmadian Moghadam, Mohammad Amin Edrisi, Seyed Abolfazl Motahari and Babak Hossein Khalaj

    BMC Bioinformatics 2017 18:126

    Published on: 23 February 2017

  2. Software

    stpm: an R package for stochastic process model

    The Stochastic Process Model (SPM) represents a general framework for modeling the joint evolution of repeatedly measured variables and time-to-event outcomes observed in longitudinal studies, i.e., SPM relate...

    Ilya Y. Zhbannikov, Konstantin Arbeev, Igor Akushevich, Eric Stallard and Anatoliy I. Yashin

    BMC Bioinformatics 2017 18:125

    Published on: 23 February 2017

  3. Software

    SEEG assistant: a 3DSlicer extension to support epilepsy surgery

    In the evaluation of Stereo-Electroencephalography (SEEG) signals, the physicist’s workflow involves several operations, including determining the position of individual electrode contacts in terms of both rel...

    Massimo Narizzano, Gabriele Arnulfo, Serena Ricci, Benedetta Toselli, Martin Tisdall, Andrea Canessa, Marco Massimo Fato and Francesco Cardinale

    BMC Bioinformatics 2017 18:124

    Published on: 23 February 2017

  4. Software

    SFREEMAP - A simulation-free tool for stochastic mapping

    Stochastic mapping is frequently used in comparative biology to simulate character evolution, enabling the probabilistic computation of statistics such as number of state transitions along a tree and distribut...

    Diego Pasqualin, Marcos Barbeitos and Fabiano Silva

    BMC Bioinformatics 2017 18:123

    Published on: 22 February 2017

  5. Research article

    Exploring the transcriptome of non-model oleaginous microalga Dunaliella tertiolecta through high-throughput sequencing and high performance computing

    RNA-Seq technology has received a lot of attention in recent years for microalgal global transcriptomic profiling. It is widely used in transcriptome-wide analysis of gene expression., particularly for microal...

    Lina Yao, Kenneth Wei Min Tan, Tin Wee Tan and Yuan Kun Lee

    BMC Bioinformatics 2017 18:122

    Published on: 22 February 2017

  6. Software

    ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data

    In the last years, applications based on massively parallelized RNA sequencing (RNA-seq) have become valuable approaches for studying non-model species, e.g., without a fully sequenced genome. RNA-seq is a use...

    Sergio Gonzalez, Bernardo Clavijo, Máximo Rivarola, Patricio Moreno, Paula Fernandez, Joaquín Dopazo and Norma Paniego

    BMC Bioinformatics 2017 18:121

    Published on: 22 February 2017

  7. Software

    Manananggal - a novel viewer for alternative splicing events

    Alternative splicing is an important cellular mechanism that can be analyzed by RNA sequencing. However, identification of splicing events in an automated fashion is error-prone. Thus, further validation is re...

    Matthias Barann, Ralf Zimmer and Fabian Birzele

    BMC Bioinformatics 2017 18:120

    Published on: 21 February 2017

  8. Methodology article

    Distribution based nearest neighbor imputation for truncated high dimensional data with applications to pre-clinical and clinical metabolomics studies

    High throughput metabolomics makes it possible to measure the relative abundances of numerous metabolites in biological samples, which is useful to many areas of biomedical research. However, missing values (M...

    Jasmit S. Shah, Shesh N. Rai, Andrew P. DeFilippis, Bradford G. Hill, Aruni Bhatnagar and Guy N. Brock

    BMC Bioinformatics 2017 18:114

    Published on: 20 February 2017

  9. Software

    Orthograph: a versatile tool for mapping coding nucleotide sequences to clusters of orthologous genes

    Orthology characterizes genes of different organisms that arose from a single ancestral gene via speciation, in contrast to paralogy, which is assigned to genes that arose via gene duplication. An accurate ort...

    Malte Petersen, Karen Meusemann, Alexander Donath, Daniel Dowling, Shanlin Liu, Ralph S. Peters, Lars Podsiadlowski, Alexandros Vasilikopoulos, Xin Zhou, Bernhard Misof and Oliver Niehuis

    BMC Bioinformatics 2017 18:111

    Published on: 16 February 2017

  10. Software

    MARV: a tool for genome-wide multi-phenotype analysis of rare variants

    Genome-wide association studies have enabled identification of thousands of loci for hundreds of traits. Yet, for most human traits a substantial part of the estimated heritability is unexplained. This and rec...

    Marika Kaakinen, Reedik Mägi, Krista Fischer, Jani Heikkinen, Marjo-Riitta Järvelin, Andrew P. Morris and Inga Prokopenko

    BMC Bioinformatics 2017 18:110

    Published on: 16 February 2017

  11. Methodology

    Unboxing cluster heatmaps

    Cluster heatmaps are commonly used in biology and related fields to reveal hierarchical clusters in data matrices. This visualization technique has high data density and reveal clusters better than unordered h...

    Sophie Engle, Sean Whalen, Alark Joshi and Katherine S. Pollard

    BMC Bioinformatics 2017 18(Suppl 2):63

    Published on: 15 February 2017

    This article is part of a Supplement: Volume 18 Supplement 2

  12. Research

    Generalized box-plot for root growth ensembles

    In the field of root biology there has been a remarkable progress in root phenotyping, which is the efficient acquisition and quantitative description of root morphology. What is currently missing are means to ef...

    Viktor Vad, Douglas Cedrim, Wolfgang Busch, Peter Filzmoser and Ivan Viola

    BMC Bioinformatics 2017 18(Suppl 2):65

    Published on: 15 February 2017

    This article is part of a Supplement: Volume 18 Supplement 2

  13. Research

    Interactive exploration of ligand transportation through protein tunnels

    Protein structures and their interaction with ligands have been in the focus of biochemistry and structural biology research for decades. The transportation of ligand into the protein active site is often comp...

    Katarína Furmanová, Miroslava Jarešová, Jan Byška, Adam Jurčík, Július Parulek, Helwig Hauser and Barbora Kozlíková

    BMC Bioinformatics 2017 18(Suppl 2):22

    Published on: 15 February 2017

    This article is part of a Supplement: Volume 18 Supplement 2

  14. Research

    Bio-physically plausible visualization of highly scattering fluorescent neocortical models for in silico experimentation

    We present a visualization pipeline capable of accurate rendering of highly scattering fluorescent neocortical neuronal models. The pipeline is mainly developed to serve the computational neurobiology communit...

    Marwan Abdellah, Ahmet Bilgili, Stefan Eilemann, Julian Shillcock, Henry Markram and Felix Schürmann

    BMC Bioinformatics 2017 18(Suppl 2):62

    Published on: 15 February 2017

    This article is part of a Supplement: Volume 18 Supplement 2

  15. Research

    Comparative visualization of protein secondary structures

    Protein function is determined by many factors, namely by its constitution, spatial arrangement, and dynamic behavior. Studying these factors helps the biochemists and biologists to better understand the prote...

    Lucia Kocincová, Miroslava Jarešová, Jan Byška, Július Parulek, Helwig Hauser and Barbora Kozlíková

    BMC Bioinformatics 2017 18(Suppl 2):23

    Published on: 15 February 2017

    This article is part of a Supplement: Volume 18 Supplement 2

  16. Research

    PRODIGEN: visualizing the probability landscape of stochastic gene regulatory networks in state and time space

    Visualizing the complex probability landscape of stochastic gene regulatory networks can further biologists’ understanding of phenotypic behavior associated with specific genes.

    Chihua Ma, Timothy Luciani, Anna Terebus, Jie Liang and G. Elisabeta Marai

    BMC Bioinformatics 2017 18(Suppl 2):24

    Published on: 15 February 2017

    This article is part of a Supplement: Volume 18 Supplement 2

  17. Software

    VacSol: a high throughput in silico pipeline to predict potential therapeutic targets in prokaryotic pathogens using subtractive reverse vaccinology

    With advances in reverse vaccinology approaches, a progressive improvement has been observed in the prediction of putative vaccine candidates. Reverse vaccinology has changed the way of discovery and provides ...

    Muhammad Rizwan, Anam Naz, Jamil Ahmad, Kanwal Naz, Ayesha Obaid, Tamsila Parveen, Muhammad Ahsan and Amjad Ali

    BMC Bioinformatics 2017 18:106

    Published on: 13 February 2017

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