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.

  1. 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
  2. Fengchao Yu, Ning Li and Weichuan Yu
    ECL 2.0: Exhaustively Identifying Cross-Linked Peptides with a Linear Computational Complexity
  3. 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
  4. 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
  5. Robert Brown, Eleazar Eskin and Bogdan Pasaniuc
    Haplotype-based eQTL Mapping Increases Power to Identify eGenes
  6. 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
  7. Serghei Mangul, Igor Mandric, Alex Zelikovsky and Eleazar Eskin
    Profiling adaptive immune repertoires across multiple human tissues by RNA Sequencing
  8. 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
  9. Jennifer Zou, Farhad Hormozdiari, Jason Ernst, Jae-Hoon Sul and Eleazar Eskin
    Leveraging allele-specific expression to improve fine-mapping for eQTL studies
  10. Luca Alessandrì and Raffaele Calogero
    CASC: Classification Analysis of Single Cell Sequencing Data
  11. 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
  12. 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
  13. 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
  14. Andreas Dwi Maryanto Gunawan, Bingxin Lu, Hon Wai Leong and Louxin Zhang
    Computer Program for Verification of Phylogenetic Networks
  15. Vera Kaiser and Colin Semple
    Diversity of mutational loads at CTCF binding sites predicts foci of dysregulated expression
  16. Dong-Jun Lee and Hyeon-So Gi
    Comparative transcriptome analysis of resistant and susceptible Korea rice genotype in response to bakanae disease
  17. Thrasyvoulos Karydis, Aditya Khosla, Manolis Kellis and Joseph M. Jacobson
    Learning hierarchical motif representations for protein analysis, search and design
  18. 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
  19. 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
  20. 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
  21. Luming Meng, Wenjun Xie, Sirui Liu, Ling Zhang and Yiqin Gao
    Chromatin modeling reveals segregation of chromosome characteristics and fuctions in 3D space
  22. Harry Taegyun Yang, Serghei Mangul, Noah Zaitlen, Sagiv Shifman and Eleazar Eskin
    Repeat Elements Profile Across Different Tissues in GTEx Samples
  23. 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
  24. 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
  25. Magdalena Strauss, Lorenz Wernisch and John Reid
    New MCMC methods for pseudo-time estimation using Gaussian processes
  26. 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
  27. Chalida Rangsiwutisak, Treenut Saithong and Saowalak Kalapanulak
    Exploring the landscape of regulatory elements on non-coding regions of cassava genome via motif-based screening
  28. Zhun Miao and Xuegong Zhang
    A new differential expression analysis method for single-cell RNA-Seq data
  29. Robert Schöpflin and Martin Vingron
    Interactive visualization of Hi-C data and epigenetic marks
  30. Sang Chun, Caitlin Rodriguez, Ryan Mills and Peter Todd
    Regulation of Differentiation in SH-SY5Y Neuroblastoma Cells by Translation of Upstream Open Reading Frames
  31. 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
  32. 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
  33. Xin Li, Chong Chu, Jingwen Pei, Ion Mandoiu and Yufeng Wu
    CircMarker: A Fast and Accurate Algorithm for Circular RNA Detection
  34. Lisa Gai, Dat Duong and Eleazar Eskin
    Finding associated variants in genome-wide associations studies on multiple traits
  35. Gongchao Jing, Jian Xu and Xiaoquan Su
    Microbiome Search Engine: Enabling Rapid Microbiome Samples Search In Large-scale Database
  36. Diya Sen, Mathu Malar Chandrababunaidu and Sucheta Tripathy
    An efficient contamination removal tool for improving prokaryotic genome assembly
  37. Dan Huang, Fu Yan Hu and Nelson Tang
    Splicing aberration of TP53 transcripts in cancers: mechanisms and effects
  38. Alexey Morgunov, Alexander Gunnarsson, Norbert Fehér and Madan Babu
    Investigating residue coevolution in proteins from a structural perspective
  39. Gregory Smith, Alan Stern and Marc Birtwistle
    Inferring Dynamic Network Architecture from Time Series Perturbation Data
  40. Daniel Hogan, Bharathi Vellalore, Ronald Geyer and Anthony Kusalik
    SeqMiner: A Weka package for mining phage display sequence data
  41. 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
  42. Kimberly Mackay, Christopher Eskiw and Anthony Kusalik
    3D Yeast Genome Prediction with Constraint Logic Programming
  43. 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
  44. Wendao Liu, Zhun Miao and Xuegong Zhang
    Assessing mRNA integrity of single-cell RNA-Seq data using mRIN
  45. Alden King-Yung Leung, Nana Jin, Kevin Y. Yip and Ting-Fung Chan
    OMView: a comprehensive visualization suite for interpreting optical mapping data
  46. Heng Xiong, Dongbing Liu and Leo Lee
    RED-ML: a novel, effective RNA editing detection method based on machine learning
  47. Dawn Chen and Ming-Jing Hwang
    Reducing Runtime in CONTRAlign by Feature Reduction
  48. Yu-Chieh Liao and Hsin-Hung Lin
    drVM: detect and reconstruct known viral genomes from metagenomes
  49. Kuei-Ling Sun, Onkar Singh and Emily Chia-Yu Su
    Predicting Allergens and Identifying Interpretable Allergenic Biological Features using Machine Learning Algorithms
  50. Xiang-Tian Yu, Jin-Song Zhang, Shao-Yan Sun, Tao Zeng and Luonan Chen
    Individual-specific edge network analysis for disease prediction
  51. Juan Zhao, Yiwei Zhou, Xiujun Zhang and Luonan Chen
    Part mutual information for quantifying direct associations in networks
  52. Dowan Kim, Jae-Hyeon Oh, Dong-Jun Lee, Chang-Kug Kim and Tae-Ho Lee
    Transcriptome analysis in some varieties of Papaver rhoeas
  53. Hojin Gwak and Mina Rho
    ABCProfiler: a program for Alignment Based Clustering and taxonomy Profiling
  54. Jehyun Jeon and Mina Rho
    Modular typeⅠPKS cluster in sediment microbiomes
  55. Julian Zaugg, Yosephine Gumulya and Mikael Bodén
    Learning From Sequence-Activity Data - Predicting Enantioselectivity of an Epoxide Hydrolase
  56. Julian Zaugg, Yosephine Gumulya, Mikael Bodén and Alpeshkumar Malde
    Using Theory to Reconcile Experiments: Understanding the Origin of Enantioselectivity of Epoxide Hydrolase
  57. Ingoo Lee and Hojung Nam
    Identification of drug-target interactions using weighted interactome network
  58. Kavya Vaddadi, Naveen Sivadasan, Kshitij Tayal and Rajgopal Srinivasan
    Sequence Alignment on Directed Graphs
  59. Naveen Sivadasan, Rajgopal Srinivasan and Kshama Goyal
    Kmerlight: fast and accurate k-mer abundance estimation
  60. Kang Ning, Shaojun Yu and Maozhen Han
    Species-species network analysis for microbial communities
  61. Przemyslaw Szalaj, Zhonghui Tang, Yijun Ruan and Dariusz Plewczynski
    Three-dimensional genome modeling based on ChIA-PET data
  62. Mika Gustafsson
    LASSIM - a network inference toolbox for genome-wide mechanistic modeling
  63. Saad Mneimneh and Syed Ali Ahmed
    Combinatorial and Probabilistic Aspects of the Multiple RNA Interaction Problem
  64. Bingxin Lu and Hon Wai Leong
    GI-Cluster: detecting genomic islands in newly sequenced microbial genomes via consensus clustering on multiple features
  65. Wanatsanan Siriwat, Saowalak Kalapanulak and Treenut Saithong
    Investigation of canonical metabolic network of plants through topology-based analysis
  66. 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
  67. Abhishek Das, Subhadeep Das, Samrat Ghosh and Sucheta Tripathy
    Classification of promoter and enhancer pairs based on expression patterns for building a predictive model
  68. 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
  69. Heeju Noh, Ziyi Hua and Rudiyanto Gunawan
    Identifying molecular targets of drugs from gene transcriptional profiles
  70. Kui Hua and Xuegong Zhang
    Modeling genome coverage and estimating genome length in metagenomics
  71. Jongsoo Keum and Hojung Nam
    Constructing prediction of drug-target interaction model using deep neural network approach
  72. Sajad Mirzaei and Yufeng Wu
    RENT+: An Improved Method for Inferring Local Genealogical Trees from Haplotypes with Recombination
  73. Mohammadhossein Moeinzadeh, Jun Yang and Martin Vingron
    De novo assembly and haplotyping of Sweet Potato (Ipomoea Batatas [L
  74. Jingwen Pei and Yufeng Wu
    STELLS2: Fast and Accurate Coalescent-based Maximum Likelihood Inference of Species Trees from Gene Tree Topologies
  75. Xintong Chen, David Chiang, M. Cecilia Berlin and Bojan Losic
    Single cell RNA-seq immunodynamics in peanut allergy
  76. Chirag Jain, Luis M. Rodriguez, Alexander Dilthey, Adam Phillippy, Kostas Konstantinidis and Srinivas Aluru
    Breaking the Scalability Barrier for Core-genome Identity Computation
  77. Chong Chu, Jingwen Pei and Yufeng Wu
    An improved approach for reconstructing consensus repeats from short sequence reads
  78. Chong Chu, Xin Li and Yufeng Wu
    GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads
  79. Chen Yang, Readman Chiu, Daniel MacMillan, Zhuyi Xue, Rene Warren and Inanc Birol
    Differential Expression Analysis of Alternatively Polyadenylated 3’UTR using RNA-Seq
  80. Cenk Sahinalp
    The Cancer Genome Collaboratory
  81. Alexander Shlemov, Sergey Bankevich, Andrey Bzikadze and Yana Safonova
    Antibody repertoire construction for organisms with unknown germline V/J genes
  82. Sergey Bankevich, Alexander Shlemov, Andrey Bzikadze and Yana Safonova
    Antibody repertoire construction from short HiSeq Rep-Seq reads
  83. Sergey Bankevich, Alexander Shlemov, Andrey Bzikadze and Yana Safonova
    Antibody repertoire construction from Ion Torrent Rep-seq reads
  84. Andrey Bzikadze, Sergey Bankevich, Alexander Shlemov and Yana Safonova
    AntEvolo: a novel approach for clonal analysis of antibody repertoires
  85. Yue Wu, Eleazar Eskin and Sriram Sankararaman
    Improving imputation by maximizing power
  86. 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
  87. Luiz Carlos Irber Junior, C. Titus Brown and Tim Head
    Decentralized indexes for public genomic data
  88. Andrzej Kloczkowski, Girik Malik and Anirban Banerji
    Deciphering general characteristics of residues constituting allosteric communication paths
  89. Sheida Hayati and Antonina Mitrofanova
    Computational approaches to identify alternative splice variants as biomarkers of disease progression and drug resistance in Acute Myeloid Leukemia
  90. 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
  91. R. Gonzalo Parra, Nikolaos Papadopoulos, Laura Ahumada-Arranz and Johannes Soeding
    scTree: reconstructing complex cellular lineage trees from single-cell RNA-seq data
  92. Eric Ho
    IDICAP2: An Improved Tool for Integrating Drug Intervention Based on Cancer Panel
  93. Pravin Dudhagara, Anjana Ghelani and Rajesh Patel
    Comparative extreme microbiomes exploration using bioinformatics methodologies
  94. Weronika Wronowska, Krzysztof Gogolewski, Bogdan Lesyng and Anna Gambin
    PARP inhibition cytotoxicity or cytoprotection - inferring molecular pathways heterogeneity from transcriptional data
  95. Nazar Zaki and Chandana Tennakoon
    BioCarian: A Search Engine for Performing Exploratory Searches of Biological Databases
  96. 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
  97. Camille Scott and C. Titus Brown
    Characterizing RNA-seq assembly graphs: when is enough, enough?
  98. Retracted
  99. Jong Wha J. Joo, Farhad Hormozdiari, Jeahoon Sul, and Eleazar Eskin
    Model-based multiple variants test considering causal status