The 21st Annual International Conference on Research in Computational Molecular Biology
Hong Kong, May 3-7, 2017
(May 3: Registration & Reception, May 4-7: Talks)
Accepted Posters
Guidelines for poster presentation can be found here. Poster abstracts can be downloaded here.
Jiaan Dai, Fengchao Yu, Ning Li and Weichuan Yu Is it feasible to only use tags in database search for PTM-invariant peptide identification? --- A simulation-based study
Fengchao Yu, Ning Li and Weichuan Yu ECL 2.0: Exhaustively Identifying Cross-Linked Peptides with a Linear Computational Complexity
João Herminio Martins Da Silva, Disraeli Vasconcelos, Lia Pinho and Beatriz Chaves De novo Receptor-Based Design of new Integrin Beta 1 Inhibitors and in silico ADMET methods evaluation
Natalie Fox, Emilie Lalonde, Julie Livingstone, Julia Hopkins, Yu-Jia Shiah, Vincent Huang, Takafumi Yamaguchi, Veronica Sabelnykova, Lawrence Heisler, Michael Fraser, Theodorus van der Kwast, Robert Bristow and Paul Boutros Integrated somatic subtypes of localized prostate cancer with prognostic implications
Robert Brown, Eleazar Eskin and Bogdan Pasaniuc Haplotype-based eQTL Mapping Increases Power to Identify eGenes
Thahmina Ali, Baekdoo Kim, Carlos Lijeron and Konstantinos Krampis Xplore-seq: a comprehensive, standardized and scalable method to transcriptomic profiling as a clinically-useful application
Serghei Mangul, Igor Mandric, Alex Zelikovsky and Eleazar Eskin Profiling adaptive immune repertoires across multiple human tissues by RNA Sequencing
Jing Qin, Yaohua Hu, Jen-Chih Yao, Yiming Qin, Ka Hou Chu and Junwen Wang Group Sparse Optimization: An Integrative OMICs Method to Predict Master Transcription Factors for Cell Fate Conversion
Jennifer Zou, Farhad Hormozdiari, Jason Ernst, Jae-Hoon Sul and Eleazar Eskin Leveraging allele-specific expression to improve fine-mapping for eQTL studies
Luca Alessandrì and Raffaele Calogero CASC: Classification Analysis of Single Cell Sequencing Data
Nan Papili Gao, S.M Minhaz Ud-Dean and Rudiyanto Gunawan SINCERITIES: Inferring gene regulatory net-works from time-stamped single cell transcrip-tional expression profiles
Feng Yang, Wei Zeng, Ke Liu, Guangbin Wang, Zhengwen Li, Keli Huang and Nini Rao The Roles of Signal Pathways mediated by AF-VHD-related microRNA combinations in Development from VHD to AF-VHD
Egor Dolzhenko, Joke J.F.A. van Vugt, Subramanian S. Ajay, Ryan Taft, David R. Bentley, Jan H. Veldink and Michael A. Eberle Detection of long repeat expansions from PCR-free whole-genome sequence data
Andreas Dwi Maryanto Gunawan, Bingxin Lu, Hon Wai Leong and Louxin Zhang Computer Program for Verification of Phylogenetic Networks
Vera Kaiser and Colin Semple Diversity of mutational loads at CTCF binding sites predicts foci of dysregulated expression
Dong-Jun Lee and Hyeon-So Gi Comparative transcriptome analysis of resistant and susceptible Korea rice genotype in response to bakanae disease
Thrasyvoulos Karydis, Aditya Khosla, Manolis Kellis and Joseph M. Jacobson Learning hierarchical motif representations for protein analysis, search and design
Jie Ren, Fengzhu Sun, Nathan A Ahlgren, Jed A Fuhrman and Yang Young Lu VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data
Dat Duong, Lisa Gai, Sagi Snir, Eun Yong Kang, Buhm Han, Jae Hoon Sul and Eleazar Eskin Applying meta-analysis to Genotype-Tissue Expression data from multiple tissues to identify eQTLs and increase the number of eGenes
Ruban Durairaj D, Murugesh Easwaran and Shanmughavel P Molecular docking and dynamics simulation studies of Antitubercular compounds with Enoyl-ACP reductase enzyme of MDR-Tuberculosis
Luming Meng, Wenjun Xie, Sirui Liu, Ling Zhang and Yiqin Gao Chromatin modeling reveals segregation of chromosome characteristics and fuctions in 3D space
Harry Taegyun Yang, Serghei Mangul, Noah Zaitlen, Sagiv Shifman and Eleazar Eskin Repeat Elements Profile Across Different Tissues in GTEx Samples
Ung-Han Yoon, Jaecheol Jeong, Jang-Ho Hahn, Jung-Wook Yang, Tae-Ho Kim, Hyeong-Un Lee, Young-Ju Seol, Sang-Sik Nam, Sang-Soo Kwak and Tae-Ho Lee Structural and evolutionary analysis of sweetpotato chloroplast genomes
Roven Rommel Fuentes, Dmytro Chebotarov, Sean Smith, Jorge Duitama, Marghoob Mohiyuddin, Ramil Mauleon, Andrey Grigoriev, Rod Wing and Nickolai Alexandrov Discovery of Structural Variants in 3,024 Rice Genomes
Magdalena Strauss, Lorenz Wernisch and John Reid New MCMC methods for pseudo-time estimation using Gaussian processes
Yali Xiao, Ssu-Min Fang, Yun-Hsin Tsou, Cheng-Fang Tsai and Pei-Chun Chang The Potential Inhibitors in Chinese Traditional Medicine for Bcr-AblT315I Mutation of Chronic Myelogenous Leukemia
Chalida Rangsiwutisak, Treenut Saithong and Saowalak Kalapanulak Exploring the landscape of regulatory elements on non-coding regions of cassava genome via motif-based screening
Zhun Miao and Xuegong Zhang A new differential expression analysis method for single-cell RNA-Seq data
Robert Schöpflin and Martin Vingron Interactive visualization of Hi-C data and epigenetic marks
Sang Chun, Caitlin Rodriguez, Ryan Mills and Peter Todd Regulation of Differentiation in SH-SY5Y Neuroblastoma Cells by Translation of Upstream Open Reading Frames
Jian-Ying Chiu, Tse-Ching Ho, Syun-Wun Liang and Yen-Hua Huang Quality assessment of genome assembly generated by the third-generation sequencing platform PacBio and an online editor for continuous update of genome annotation
Michael Altenbuchinger, Philipp Schwarzfischer, Thorsten Rehberg, Jörg Reinders, Christian W. Kohler, Wolfram Gronwald, Julia Richter, Monika Szczepanowski, Neus Masqué-Soler, Wolfram Klapper, Pete J. Oefner and Rainer Spang Molecular signatures that can be transferred
across different omics platforms
Xin Li, Chong Chu, Jingwen Pei, Ion Mandoiu and Yufeng Wu CircMarker: A Fast and Accurate Algorithm for Circular RNA Detection
Lisa Gai, Dat Duong and Eleazar Eskin Finding associated variants in genome-wide associations studies on multiple traits
Gongchao Jing, Jian Xu and Xiaoquan Su Microbiome Search Engine: Enabling Rapid Microbiome Samples Search In Large-scale Database
Diya Sen, Mathu Malar Chandrababunaidu and Sucheta Tripathy An efficient contamination removal tool for improving prokaryotic genome assembly
Dan Huang, Fu Yan Hu and Nelson Tang Splicing aberration of TP53 transcripts in cancers: mechanisms and effects
Alexey Morgunov, Alexander Gunnarsson, Norbert Fehér and Madan Babu Investigating residue coevolution in proteins from a structural perspective
Gregory Smith, Alan Stern and Marc Birtwistle Inferring Dynamic Network Architecture from Time Series Perturbation Data
Daniel Hogan, Bharathi Vellalore, Ronald Geyer and Anthony Kusalik SeqMiner: A Weka package for mining phage display sequence data
Chao Sima, Shanaz Ghandhi, Sally A. Amundson, David J. Brenner and Michael Bittner Feature reduction for practical radiation biodosimetry using combined approach of gene co-expression network and pathway knowledge
Kimberly Mackay, Christopher Eskiw and Anthony Kusalik 3D Yeast Genome Prediction with Constraint Logic Programming
Jae Hyeon Oh, Tae Ho Lee, Chang Kug Kim, Lee Dong-Jun and Dowan Kim Transcripsome and metabolism studies to identify alkaloid biosynthesis genes in poppies
Wendao Liu, Zhun Miao and Xuegong Zhang Assessing mRNA integrity of single-cell RNA-Seq data using mRIN
Alden King-Yung Leung, Nana Jin, Kevin Y. Yip and Ting-Fung Chan OMView: a comprehensive visualization suite for interpreting optical mapping data
Heng Xiong, Dongbing Liu and Leo Lee RED-ML: a novel, effective RNA editing detection method based on machine learning
Dawn Chen and Ming-Jing Hwang Reducing Runtime in CONTRAlign by Feature Reduction
Yu-Chieh Liao and Hsin-Hung Lin drVM: detect and reconstruct known viral genomes from metagenomes
Kuei-Ling Sun, Onkar Singh and Emily Chia-Yu Su Predicting Allergens and Identifying Interpretable Allergenic Biological Features using Machine Learning Algorithms
Xiang-Tian Yu, Jin-Song Zhang, Shao-Yan Sun, Tao Zeng and Luonan Chen Individual-specific edge network analysis for disease prediction
Juan Zhao, Yiwei Zhou, Xiujun Zhang and Luonan Chen Part mutual information for quantifying direct associations in networks
Dowan Kim, Jae-Hyeon Oh, Dong-Jun Lee, Chang-Kug Kim and Tae-Ho Lee Transcriptome analysis in some varieties of Papaver rhoeas
Hojin Gwak and Mina Rho ABCProfiler: a program for Alignment Based Clustering and taxonomy Profiling
Jehyun Jeon and Mina Rho Modular typeⅠPKS cluster in sediment microbiomes
Julian Zaugg, Yosephine Gumulya and Mikael Bodén Learning From Sequence-Activity Data - Predicting Enantioselectivity of an Epoxide Hydrolase
Julian Zaugg, Yosephine Gumulya, Mikael Bodén and Alpeshkumar Malde Using Theory to Reconcile Experiments: Understanding the Origin of Enantioselectivity of Epoxide Hydrolase
Ingoo Lee and Hojung Nam Identification of drug-target interactions using weighted interactome network
Kavya Vaddadi, Naveen Sivadasan, Kshitij Tayal and Rajgopal Srinivasan Sequence Alignment on Directed Graphs
Naveen Sivadasan, Rajgopal Srinivasan and Kshama Goyal Kmerlight: fast and accurate k-mer abundance estimation
Kang Ning, Shaojun Yu and Maozhen Han Species-species network analysis for microbial communities
Przemyslaw Szalaj, Zhonghui Tang, Yijun Ruan and Dariusz Plewczynski Three-dimensional genome modeling based on ChIA-PET data
Mika Gustafsson LASSIM - a network inference toolbox for genome-wide mechanistic modeling
Saad Mneimneh and Syed Ali Ahmed Combinatorial and Probabilistic Aspects of the Multiple RNA Interaction Problem
Bingxin Lu and Hon Wai Leong GI-Cluster: detecting genomic islands in newly sequenced microbial genomes via consensus clustering on multiple features
Wanatsanan Siriwat, Saowalak Kalapanulak and Treenut Saithong Investigation of canonical metabolic network of plants through topology-based analysis
Shah Md. Shahik, Md. Saiful Islam, Md Sohel and Mohd.Omar Faruk Sikder Mining the Proteome of Fusobacterium nucleatum subsp. nucleatum ATCC 25586 for Potential Therapeutics Discovery: An In Silico Approach
Abhishek Das, Subhadeep Das, Samrat Ghosh and Sucheta Tripathy Classification of promoter and enhancer pairs based on expression patterns for building a predictive model
Alexander Shlemov, Alexey Gurevich, Alla Mikheenko, Anastasiia Abramova, Anton Korobeynikov, Hosein Mohimani and Pavel Pevzner Identification of novel peptidic antibiotics by searching large-scale mass spectra against natural products databases
Heeju Noh, Ziyi Hua and Rudiyanto Gunawan Identifying molecular targets of drugs from gene transcriptional profiles
Kui Hua and Xuegong Zhang Modeling genome coverage and estimating genome length in metagenomics
Jongsoo Keum and Hojung Nam Constructing prediction of drug-target interaction model using deep neural network approach
Sajad Mirzaei and Yufeng Wu RENT+: An Improved Method for Inferring Local Genealogical Trees from Haplotypes with Recombination
Mohammadhossein Moeinzadeh, Jun Yang and Martin Vingron De novo assembly and haplotyping of Sweet Potato (Ipomoea Batatas [L
Jingwen Pei and Yufeng Wu STELLS2: Fast and Accurate Coalescent-based Maximum Likelihood Inference of Species Trees from Gene Tree Topologies
Xintong Chen, David Chiang, M. Cecilia Berlin and Bojan Losic Single cell RNA-seq immunodynamics in peanut allergy
Chirag Jain, Luis M. Rodriguez, Alexander Dilthey, Adam Phillippy, Kostas Konstantinidis and Srinivas Aluru Breaking the Scalability Barrier for Core-genome Identity Computation
Chong Chu, Jingwen Pei and Yufeng Wu An improved approach for reconstructing consensus repeats from short sequence reads
Chong Chu, Xin Li and Yufeng Wu GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads
Chen Yang, Readman Chiu, Daniel MacMillan, Zhuyi Xue, Rene Warren and Inanc Birol Differential Expression Analysis of Alternatively Polyadenylated 3’UTR using RNA-Seq
Cenk Sahinalp The Cancer Genome Collaboratory
Alexander Shlemov, Sergey Bankevich, Andrey Bzikadze and Yana Safonova Antibody repertoire construction for organisms with unknown germline V/J genes
Sergey Bankevich, Alexander Shlemov, Andrey Bzikadze and Yana Safonova Antibody repertoire construction from short HiSeq Rep-Seq reads
Sergey Bankevich, Alexander Shlemov, Andrey Bzikadze and Yana Safonova Antibody repertoire construction from Ion Torrent Rep-seq reads
Andrey Bzikadze, Sergey Bankevich, Alexander Shlemov and Yana Safonova AntEvolo: a novel approach for clonal analysis of antibody repertoires
Yue Wu, Eleazar Eskin and Sriram Sankararaman Improving imputation by maximizing power
Rayan Chikhi, Charles Deltel, Guillaume Rizk, Claire Lemaitre, Pierre Peterlongo, Kristoffer Sahlin, Lars Arvestad, Paul Medvedev and Dominique Lavenier High-quality, fast, and memory-efficient assembly of metagenomes and large genomes using Minia-pipeline
Luiz Carlos Irber Junior, C. Titus Brown and Tim Head Decentralized indexes for public genomic data
Andrzej Kloczkowski, Girik Malik and Anirban Banerji Deciphering general characteristics of residues constituting allosteric communication paths
Sheida Hayati and Antonina Mitrofanova Computational approaches to identify alternative splice variants as biomarkers of disease progression and drug resistance in Acute Myeloid Leukemia
Praveen Kumar, Murugesh Easwaran, Nilavamuthan Chandrasekaran and Shanmughavel Piramanayagam Molecular Insights of Peptide Folding Propensities for Cancer Drug Target Improvisation and Anti Microbial Peptide Library
R. Gonzalo Parra, Nikolaos Papadopoulos, Laura Ahumada-Arranz and Johannes Soeding scTree: reconstructing complex cellular lineage trees from single-cell RNA-seq data
Eric Ho IDICAP2: An Improved Tool for Integrating Drug Intervention Based on Cancer Panel
Pravin Dudhagara, Anjana Ghelani and Rajesh Patel Comparative extreme microbiomes exploration using bioinformatics methodologies
Weronika Wronowska, Krzysztof Gogolewski, Bogdan Lesyng and Anna Gambin PARP inhibition cytotoxicity or cytoprotection - inferring molecular pathways heterogeneity from transcriptional data
Nazar Zaki and Chandana Tennakoon BioCarian: A Search Engine for Performing Exploratory Searches of Biological Databases
Sunhye Park, Young Chan Park, Kiejung Park and In-Song Koh A comprehensive variation analysis based on whole-genome of 62 Koreans and constructing Korean variome database called as HYKVB
Camille Scott and C. Titus Brown Characterizing RNA-seq assembly graphs: when is enough, enough?
Retracted
Jong Wha J. Joo, Farhad Hormozdiari, Jeahoon Sul, and Eleazar Eskin Model-based multiple variants test considering causal status