Proceedings of the 14th Annual MCBIOS conference

Proceedings of the 2017 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference

Authors: Jonathan D. Wren, Mikhail G. Dozmorov, Inimary Toby, Bindu Nanduri, Ramin Homayouni, Prashanti Manda and Shraddha Thakkar

ALE: automated label extraction from GEO metadata

NCBI’s Gene Expression Omnibus (GEO) is a rich community resource containing millions of gene expression experiments from human, mouse, rat, and other model organisms. However, information about each experimen...

Authors: Cory B. Giles, Chase A. Brown, Michael Ripperger, Zane Dennis, Xiavan Roopnarinesingh, Hunter Porter, Aleksandra Perz and Jonathan D. Wren

Repositioning drugs by targeting network modules: a Parkinson’s disease case study

Much effort has been devoted to the discovery of specific mechanisms between drugs and single targets to date. However, as biological systems maintain homeostasis at the level of functional networks robustly c...

Authors: Zongliang Yue, Itika Arora, Eric Y. Zhang, Vincent Laufer, S. Louis Bridges and Jake Y. Chen

Identification and characterization of conserved lncRNAs in human and rat brain

Long noncoding RNAs (lncRNAs) are involved in diverse biological processes and play an essential role in various human diseases. The number of lncRNAs identified has increased rapidly in recent years owing to ...

Authors: Dan Li and Mary Qu Yang

Mutation status coupled with RNA-sequencing data can efficiently identify important non-significantly mutated genes serving as diagnostic biomarkers of endometrial cancer

Endometrial cancers (ECs) are one of the most common types of malignant tumor in females. Substantial efforts had been made to identify significantly mutated genes (SMGs) in ECs and use them as biomarkers for ...

Authors: Keqin Liu, Li He, Zhichao Liu, Junmei Xu, Yuan Liu, Qifan Kuang, Zhining Wen and Menglong Li

Texture based skin lesion abruptness quantification to detect malignancy

Abruptness of pigment patterns at the periphery of a skin lesion is one of the most important dermoscopic features for detection of malignancy. In current clinical setting, abrupt cutoff of a skin lesion deter...

Authors: Recep Erol, Mustafa Bayraktar, Sinan Kockara, Sertan Kaya and Tansel Halic

Incorporating biological prior knowledge for Bayesian learning via maximal knowledge-driven information priors

Phenotypic classification is problematic because small samples are ubiquitous; and, for these, use of prior knowledge is critical. If knowledge concerning the feature-label distribution – for instance, genetic...

Authors: Shahin Boluki, Mohammad Shahrokh Esfahani, Xiaoning Qian and Edward R Dougherty

Suggested mechanisms for Zika virus causing microcephaly: what do the genomes tell us?

Zika virus (ZIKV) is an emerging human pathogen. Since its arrival in the Western hemisphere, from Africa via Asia, it has become a serious threat to pregnant women, causing microcephaly and other neuropathies...

Authors: Se-Ran Jun, Trudy M. Wassenaar, Visanu Wanchai, Preecha Patumcharoenpol, Intawat Nookaew and David W. Ussery

Development of models for predicting Torsade de Pointes cardiac arrhythmias using perceptron neural networks

Blockage of some ion channels and in particular, the hERG (human Ether-a’-go-go-Related Gene) cardiac potassium channel delays cardiac repolarization and can induce arrhythmia. In some cases it leads to a pote...

Authors: Mohsen Sharifi, Dan Buzatu, Stephen Harris and Jon Wilkes

Effective computational detection of piRNAs using n-gram models and support vector machine

Piwi-interacting RNAs (piRNAs) are a new class of small non-coding RNAs that are known to be associated with RNA silencing. The piRNAs play an important role in protecting the genome from invasive transposons ...

Authors: Chun-Chi Chen, Xiaoning Qian and Byung-Jun Yoon

Identification of streptococcal small RNAs that are putative targets of RNase III through bioinformatics analysis of RNA sequencing data

Small noncoding regulatory RNAs (sRNAs) are post-transcriptional regulators, regulating mRNAs, proteins, and DNA in bacteria. One class of sRNAs, trans-acting sRNAs, are the most abundant sRNAs transcribed from t...

Authors: Ethan C. Rath, Stephanie Pitman, Kyu Hong Cho and Yongsheng Bai

Deep learning architectures for multi-label classification of intelligent health risk prediction

Multi-label classification of data remains to be a challenging problem. Because of the complexity of the data, it is sometimes difficult to infer information about classes that are not mutually exclusive. For ...

Authors: Andrew Maxwell, Runzhi Li, Bei Yang, Heng Weng, Aihua Ou, Huixiao Hong, Zhaoxian Zhou, Ping Gong and Chaoyang Zhang

CUFID-query: accurate network querying through random walk based network flow estimation

Functional modules in biological networks consist of numerous biomolecules and their complicated interactions. Recent studies have shown that biomolecules in a functional module tend to have similar interactio...

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

dBBQs: dataBase of Bacterial Quality scores

It is well-known that genome sequencing technologies are becoming significantly cheaper and faster. As a result of this, the exponential growth in sequencing data in public databases allows us to explore ever ...

Authors: Visanu Wanchai, Preecha Patumcharoenpol, Intawat Nookaew and David Ussery

Using 16S rRNA gene as marker to detect unknown bacteria in microbial communities

Quantification and identification of microbial genomes based on next-generation sequencing data is a challenging problem in metagenomics. Although current methods have mostly focused on analyzing bacteria whos...

Authors: Quang Tran, Diem-Trang Pham and Vinhthuy Phan

Scaling bioinformatics applications on HPC

Recent breakthroughs in molecular biology and next generation sequencing technologies have led to the expenential growh of the sequence databases. Researchrs use BLAST for processing these sequences. However t...

Authors: Mike Mikailov, Fu-Jyh Luo, Stuart Barkley, Lohit Valleru, Stephen Whitney, Zhichao Liu, Shraddha Thakkar, Weida Tong and Nicholas Petrick