Proceedings of the 13th Annual MCBIOS conference

Proceedings of the 2016 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference

Authors: Jonathan D. Wren, Inimary Toby, Huxiao Hong, Bindu Nanduri, Rakesh Kaundal, Mikhail G. Dozmorov and Shraddha Thakkar

VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements

The genes that produce antibodies and the immune receptors expressed on lymphocytes are not germline encoded; rather, they are somatically generated in each developing lymphocyte by a process called V(D)J reco...

Authors: Inimary T. Toby, Mikhail K. Levin, Edward A. Salinas, Scott Christley, Sanchita Bhattacharya, Felix Breden, Adam Buntzman, Brian Corrie, John Fonner, Namita T. Gupta, Uri Hershberg, Nishanth Marthandan, Aaron Rosenfeld, William Rounds, Florian Rubelt, Walter Scarborough…

Effective comparative analysis of protein-protein interaction networks by measuring the steady-state network flow using a Markov model

Comparative analysis of protein-protein interaction (PPI) networks provides an effective means of detecting conserved functional network modules across different species. Such modules typically consist of orth...

Authors: Hyundoo Jeong, Xiaoning Qian and Byung-Jun Yoon

Analysis of optimal alignments unfolds aligners’ bias in existing variant profiles

Efforts such as International HapMap Project and 1000 Genomes Project resulted in a catalog of millions of single nucleotides and insertion/deletion (INDEL) variants of the human population. Viewed as a refere...

Authors: Quang Tran, Shanshan Gao and Vinhthuy Phan

CC-PROMISE effectively integrates two forms of molecular data with multiple biologically related endpoints

As new technologies allow investigators to collect multiple forms of molecular data (genomic, epigenomic, transcriptomic, etc) and multiple endpoints on a clinical trial cohort, it will become necessary to eff...

Authors: Xueyuan Cao, Kristine R. Crews, James Downing, Jatinder Lamba and Stanley B. Pounds

Successful classification of cocaine dependence using brain imaging: a generalizable machine learning approach

Neuroimaging studies have yielded significant advances in the understanding of neural processes relevant to the development and persistence of addiction. However, these advances have not explored extensively f...

Authors: Mutlu Mete, Unal Sakoglu, Jeffrey S. Spence, Michael D. Devous Sr., Thomas S. Harris and Bryon Adinoff

Dissecting the biological relationship between TCGA miRNA and mRNA sequencing data using MMiRNA-Viewer

MicroRNAs (miRNA) are short nucleotides that interact with their target genes through 3′ untranslated regions (UTRs). The Cancer Genome Atlas (TCGA) harbors an increasing amount of cancer genome data for both ...

Authors: Yongsheng Bai, Lizhong Ding, Steve Baker, Jenny M. Bai, Ethan Rath, Feng Jiang, Jianghong Wu, Hui Jiang and Gary Stuart

Leveraging graph topology and semantic context for pharmacovigilance through twitter-streams

Adverse drug events (ADEs) constitute one of the leading causes of post-therapeutic death and their identification constitutes an important challenge of modern precision medicine. Unfortunately, the onset and ...

Authors: Ryan Eshleman and Rahul Singh

Abrupt skin lesion border cutoff measurement for malignancy detection in dermoscopy images

Automated skin lesion border examination and analysis techniques have become an important field of research for distinguishing malignant pigmented lesions from benign lesions. An abrupt pigment pattern cutoff ...

Authors: Sertan Kaya, Mustafa Bayraktar, Sinan Kockara, Mutlu Mete, Tansel Halic, Halle E. Field and Henry K. Wong

Phylogenetic tree construction using trinucleotide usage profile (TUP)

It has been a challenging task to build a genome-wide phylogenetic tree for a large group of species containing a large number of genes with long nucleotides sequences. The most popular method, called feature ...

Authors: Si Chen, Lih-Yuan Deng, Dale Bowman, Jyh-Jen Horng Shiau, Tit-Yee Wong, Behrouz Madahian and Henry Horng-Shing Lu

Prioritization, clustering and functional annotation of MicroRNAs using latent semantic indexing of MEDLINE abstracts

The amount of scientific information about MicroRNAs (miRNAs) is growing exponentially, making it difficult for researchers to interpret experimental results. In this study, we present an automated text mining...

Authors: Sujoy Roy, Brandon C. Curry, Behrouz Madahian and Ramin Homayouni

Incorporating topological information for predicting robust cancer subnetwork markers in human protein-protein interaction network

Discovering robust markers for cancer prognosis based on gene expression data is an important yet challenging problem in translational bioinformatics. By integrating additional information in biological pathwa...

Authors: Navadon Khunlertgit and Byung-Jun Yoon

Application of dynamic topic models to toxicogenomics data

All biological processes are inherently dynamic. Biological systems evolve transiently or sustainably according to sequential time points after perturbation by environment insults, drugs and chemicals. Investi...

Authors: Mikyung Lee, Zhichao Liu, Ruili Huang and Weida Tong

Improving sensitivity of linear regression-based cell type-specific differential expression deconvolution with per-gene vs. global significance threshold

The goal of many human disease-oriented studies is to detect molecular mechanisms different between healthy controls and patients. Yet, commonly used gene expression measurements from blood samples suffer from...

Authors: Edmund R. Glass and Mikhail G. Dozmorov

PGen: large-scale genomic variations analysis workflow and browser in SoyKB

With the advances in next-generation sequencing (NGS) technology and significant reductions in sequencing costs, it is now possible to sequence large collections of germplasm in crops for detecting genome-scal...

Authors: Yang Liu, Saad M. Khan, Juexin Wang, Mats Rynge, Yuanxun Zhang, Shuai Zeng, Shiyuan Chen, Joao V. Maldonado dos Santos, Babu Valliyodan, Prasad P. Calyam, Nirav Merchant, Henry T. Nguyen, Dong Xu and Trupti Joshi