Journal: Quant. Biol.

Volume 6, Issue 4

287 -- 306Jenny Jeong, Qinwei Zhuang, Mark K. Transtrum, Enlu Zhou, Peng Qiu. Experimental design and model reduction in systems biology
307 -- 312Li Li, Huanqian Yan, Yonggang Lu. Selecting near-native protein structures from ab initio models using ensemble clustering
313 -- 320Youfu Su, Can Zhao, Zheng Chen, Bo Tian, Zengyou He. On the statistical significance of protein complex
321 -- 333Hui Wang, Gang Wang, Li-Da Zhu, Xuan Xu, Bo Diao, Hong-Yu Zhang. Subnetwork identification and chemical modulation for neural regeneration: A study combining network guided forest and heat diffusion model
334 -- 343Tanlin Sun, Luhua Lai, Jianfeng Pei. Analysis of protein features and machine learning algorithms for prediction of druggable proteins
344 -- 358Xiaoqi Chai, Qinle Ba, Ge Yang. Characterizing robustness and sensitivity of convolutional neural networks for quantitative analysis of mitochondrial morphology
359 -- 368Sheng Wang 0001, Zhen Li, Yizhou Yu, Xin Gao 0001. WaveNano: a signal-level nanopore base-caller via simultaneous prediction of nucleotide labels and move labels through bi-directional WaveNets

Volume 6, Issue 3

193 -- 194Xinshu Xiao, Chaolin Zhang. Special issue on RNA processing and regulation
195 -- 209Wei Vivian Li, Jingyi Jessica Li. Modeling and analysis of RNA-seq data: a review from a statistical perspective
210 -- 227Nicole M. Martinez, Wendy V. Gilbert. Pre-mRNA modifications and their role in nuclear processing
228 -- 238Molly M. Hannigan, Leah L. Zagore, Donny D. Licatalosi. Mapping transcriptome-wide protein-RNA interactions to elucidate RNA regulatory programs
239 -- 252Jing Gong, Yanyan Ju, Di Shao, Qiangfeng Cliff Zhang. Advances and challenges towards the study of RNA-RNA interactions in a transcriptome-wide scale
253 -- 266Aysegul Guvenek, Bin Tian. Analysis of alternative cleavage and polyadenylation in mature and differentiating neurons using RNA-seq data
267 -- 274Allison J. Taggart, William G. Fairbrother. ShapeShifter: a novel approach for identifying and quantifying stable lariat intronic species in RNAseq data
275 -- 286Minzhe Zhang, Qiwei Li, Yang Xie. A Bayesian hierarchical model for analyzing methylated RNA immunoprecipitation sequencing data

Volume 6, Issue 2

99 -- 112Chaima Aouiche, Xuequn Shang, Bolin Chen. Copy number variation related disease genes
113 -- 128Zhi-Ping Liu. Towards precise reconstruction of gene regulatory networks by data integration
129 -- 141David Skelding, Samuel F. M. Hart, Thejas Vidyasagar, Alexander E. Pozhitkov, Wenying Shou. Developing a low-cost milliliter-scale chemostat array for precise control of cellular growth
142 -- 154Guanghui Li 0003, Jiawei Luo, Zheng Xiao, Cheng Liang. MTMO: an efficient network-centric algorithm for subtree counting and enumeration
155 -- 162Morihiro Hayashida, Noriyuki Okada, Mayumi Kamada, Hitoshi Koyano. Improving conditional random field model for prediction of protein-RNA residue-base contacts
163 -- 174Yongxiao Yang, Wei Wang, Yuan Lou, Jianxin Yin, Xinqi Gong. Geometric and amino acid type determinants for protein-protein interaction interfaces
175 -- 185Shansong Liu, Kui Hua, Sijie Chen, Xuegong Zhang. Comprehensive simulation of metagenomic sequencing data with non-uniform sampling distribution
186 -- 192Bei Wang, Jinyu Chen, Shihua Zhang. BMTK: a toolkit for determining modules in biological bipartite networks

Volume 6, Issue 1

1 -- 14Zhengda Li, Qiong Yang. Systems and synthetic biology approaches in understanding biological oscillators
15 -- 29Zhe Yang, Xiaoxuan Wu, Ning Yang, Feng Liu. Noise transmission during the dynamic pattern formation in fly embryos
30 -- 39Abraham A. Labena, Yi-Zhou Gao, Chuan Dong, Hong-Li Hua, Feng-Biao Guo. Metabolic pathway databases and model repositories
40 -- 55Yu Zhang, Sha Cao, Jing Zhao, Burair Alsaihati, Qin Ma 0003, Chi Zhang. MRHCA: a nonparametric statistics based method for hub and co-expression module identification in large gene co-expression network
56 -- 67Harold Pimentel, Zhiyue Hu, Haiyan Huang. Biclustering by sparse canonical correlation analysis
68 -- 84Adam P. Joyce, James J. Havranek. Deciphering the protein-DNA code of bacterial winged helix-turn-helix transcription factors
85 -- 97Saad M. Khan, Jason E. Denney, Michael X. Wang, Dong Xu. Whole-exome sequencing and microRNA profiling reveal PI3K/AKT pathway's involvement in juvenile myelomonocytic leukemia