Genomics in 2012: challenges and opportunities in the next generation sequencing era

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.

[1]  Judy H. Cho,et al.  Finding the missing heritability of complex diseases , 2009, Nature.

[2]  Trey Ideker,et al.  Boosting Signal-to-Noise in Complex Biology: Prior Knowledge Is Power , 2011, Cell.

[3]  Han Liang,et al.  BM-Map: an efficient software package for accurately allocating multireads of RNA-sequencing data , 2012, BMC Genomics.

[4]  Bing Zhang,et al.  GLAD4U: deriving and prioritizing gene lists from PubMed literature , 2012, BMC Genomics.

[5]  Leng Han,et al.  Investigating the relationship of DNA methylation with mutation rate and allele frequency in the human genome , 2012, BMC Genomics.

[6]  J. Long,et al.  Steps to ensure accuracy in genotype and SNP calling from Illumina sequencing data , 2012, BMC Genomics.

[7]  Shuigeng Zhou,et al.  Automatically clustering large-scale miRNA sequences: methods and experiments , 2012, BMC Genomics.

[8]  Chaochun Wei,et al.  CTF: a CRF-based transcription factor binding sites finding system , 2012, BMC Genomics.

[9]  Tao Huang,et al.  Differential combinatorial regulatory network analysis related to venous metastasis of hepatocellular carcinoma , 2012, BMC Genomics.

[10]  Yu Shyr,et al.  Analysis of high-throughput RNAi screening data in identifying genes mediating sensitivity to chemotherapeutic drugs: statistical approaches and perspectives , 2012, BMC Genomics.

[11]  Ramin Homayouni,et al.  Literature aided determination of data quality and statistical significance threshold for gene expression studies , 2012, BMC Genomics.

[12]  Peilin Jia,et al.  Gene set analysis of genome-wide association studies: methodological issues and perspectives. , 2011, Genomics.

[13]  Elaine R. Mardis,et al.  A decade’s perspective on DNA sequencing technology , 2011, Nature.

[14]  Yixue Li,et al.  Detecting the borders between coding and non-coding DNA regions in prokaryotes based on recursive segmentation and nucleotide doublets statistics , 2012, BMC Genomics.

[15]  Yunlong Liu,et al.  Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data , 2012, BMC Genomics.

[16]  Jie Zhang,et al.  Redistribution of H3K4me2 on neural tissue specific genes during mouse brain development , 2012, BMC Genomics.

[17]  Peilin Jia,et al.  Multi-species data integration and gene ranking enrich significant results in an alcoholism genome-wide association study , 2012, BMC Genomics.

[18]  Kun Huang,et al.  DFI: gene feature discovery in RNA-seq experiments from multiple sources , 2012, BMC Genomics.

[19]  Pearlly Yan,et al.  Enrichment-based DNA methylation analysis using next-generation sequencing: sample exclusion, estimating changes in global methylation, and the contribution of replicate lanes , 2012, BMC Genomics.

[20]  Mikael Henaff,et al.  New methods for separating causes from effects in genomics data , 2012, BMC Genomics.

[21]  Jennifer M. Fettweis,et al.  Species-level classification of the vaginal microbiome , 2012, BMC Genomics.

[22]  Christina Schweikert,et al.  Combining multiple ChIP-seq peak detection systems using combinatorial fusion , 2012, BMC Genomics.

[23]  Jennifer M. Fettweis,et al.  Genomic sequence analysis and characterization of Sneathia amnii sp. nov , 2012, BMC Genomics.

[24]  Zhongming Zhao,et al.  RNA-Seq analysis implicates dysregulation of the immune system in schizophrenia , 2012, BMC Genomics.

[25]  Yufei Huang,et al.  A Bayesian decision fusion approach for microRNA target prediction , 2010, BCB '10.

[26]  Buzhou Tang,et al.  Identifying the status of genetic lesions in cancer clinical trial documents using machine learning , 2012, BMC Genomics.