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1.  The emerging genomics and systems biology research lead to systems genomics studies 
BMC Genomics  2014;15(Suppl 11):I1.
Synergistically integrating multi-layer genomic data at systems level not only can lead to deeper insights into the molecular mechanisms related to disease initiation and progression, but also can guide pathway-based biomarker and drug target identification. With the advent of high-throughput next-generation sequencing technologies, sequencing both DNA and RNA has generated multi-layer genomic data that can provide DNA polymorphism, non-coding RNA, messenger RNA, gene expression, isoform and alternative splicing information. Systems biology on the other hand studies complex biological systems, particularly systematic study of complex molecular interactions within specific cells or organisms. Genomics and molecular systems biology can be merged into the study of genomic profiles and implicated biological functions at cellular or organism level. The prospectively emerging field can be referred to as systems genomics or genomic systems biology.
The Mid-South Bioinformatics Centre (MBC) and Joint Bioinformatics Ph.D. Program of University of Arkansas at Little Rock and University of Arkansas for Medical Sciences are particularly interested in promoting education and research advancement in this prospectively emerging field. Based on past investigations and research outcomes, MBC is further utilizing differential gene and isoform/exon expression from RNA-seq and co-regulation from the ChiP-seq specific for different phenotypes in combination with protein-protein interactions, and protein-DNA interactions to construct high-level gene networks for an integrative genome-phoneme investigation at systems biology level.
PMCID: PMC4304174  PMID: 25558922
2.  [No title available] 
PMCID: PMC4290585  PMID: 25521539
3.  Proceedings of The Twelfth Annual RECOMB Comparative Genomics Conference 
BMC Genomics  2014;15(Suppl 6):I1.
PMCID: PMC4240505  PMID: 25572111
4.  SNP-SIG 2013: from coding to non-coding - new approaches for genomic variant interpretation 
BMC Genomics  2014;15(Suppl 4):S1.
PMCID: PMC4083406  PMID: 25056427
5.  Summary of talks and papers at ISCB-Asia/SCCG 2012 
BMC Genomics  2013;14(Suppl 2):I1.
The second ISCB-Asia conference of the International Society for Computational Biology took place December 17-19, 2012, in Shenzhen, China. The conference was co-hosted by BGI as the first Shenzhen Conference on Computational Genomics (SCCG).
45 talks were presented at ISCB-Asia/SCCG 2012. The topics covered included software tools, reproducible computing, next-generation sequencing data analysis, transcription and mRNA regulation, protein structure and function, cancer genomics and personalized medicine. Nine of the proceedings track talks are included as full papers in this supplement.
In this report we first give a short overview of the conference by listing some statistics and visualizing the talk abstracts as word clouds. Then we group the talks by topic and briefly summarize each one, providing references to related publications whenever possible. Finally, we close with a few comments on the success of this conference.
PMCID: PMC3639071
6.  CTF: a CRF-based transcription factor binding sites finding system 
BMC Genomics  2012;13(Suppl 8):S18.
Identifying the location of transcription factor bindings is crucial to understand transcriptional regulation. Currently, Chromatin Immunoprecipitation followed with high-throughput Sequencing (ChIP-seq) is able to locate the transcription factor binding sites (TFBSs) accurately in high throughput and it has become the gold-standard method for TFBS finding experimentally. However, due to its high cost, it is impractical to apply the method in a very large scale. Considering the large number of transcription factors, numerous cell types and various conditions, computational methods are still very valuable to accurate TFBS identification.
In this paper, we proposed a novel integrated TFBS prediction system, CTF, based on Conditional Random Fields (CRFs). Integrating information from different sources, CTF was able to capture patterns of TFBSs contained in different features (sequence, chromatin and etc) and predicted the TFBS locations with a high accuracy. We compared CTF with several existing tools as well as the PWM baseline method on a dataset generated by ChIP-seq experiments (TFBSs of 13 transcription factors in mouse genome). Results showed that CTF performed significantly better than existing methods tested.
CTF is a powerful tool to predict TFBSs by integrating high throughput data and different features. It can be a useful complement to ChIP-seq and other experimental methods for TFBS identification and thus improve our ability to investigate functional elements in post-genomic era.
Availability: CTF is freely available to academic users at:
PMCID: PMC3535700  PMID: 23282203
7.  Genomics in 2012: challenges and opportunities in the next generation sequencing era 
BMC Genomics  2012;13(Suppl 8):S1.
We present a report of the 2012 International Conference on Intelligent Biology and Medicine (ICIBM 2012) and the editorial report of the supplement to BMC Genomics that includes 22 research papers selected from ICIBM 2012, which was held on April 22-24, 2012 in Nashville, Tennessee, USA. The conference covered a variety of research areas, including bioinformatics, systems biology, and intelligent computing. It included six sessions, a tutorial - Introduction to Proteome Informatics, a workshop - Next Generation Sequencing, and a poster session. The selected papers in this Supplement issue represent the genomic focus in ICIBM 2012.
PMCID: PMC3535713  PMID: 23281891
8.  Advances in translational bioinformatics and population genomics in the Asia-Pacific 
BMC Genomics  2012;13(Suppl 7):S1.
The theme of the 2012 International Conference on Bioinformatics (InCoB) in Bangkok, Thailand was "From Biological Data to Knowledge to Technological Breakthroughs." Besides providing a forum for life scientists and bioinformatics researchers in the Asia-Pacific region to meet and interact, the conference also hosted thematic sessions on the Pan-Asian Pacific Genome Initiative and immunoinformatics. Over the seven years of conference papers published in BMC Bioinformatics and four years in BMC Genomics, we note that there is increasing interest in the applications of -omics technologies to the understanding of diseases, as a forerunner to personalized genomic medicine.
PMCID: PMC3521394  PMID: 23282089

Results 1-9 (9)