RECOMB 2008
 

LIST OF ACCECPTED POSTERS

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Authors
Title
2
Virendra Gomase, Shruti Gomase, Somnath Tagore, Dayanand Bhiwgade, Vaseem Baig and Karbhari Kale.
Computer aided multi parameter antigen design: Impact of synthetic peptide vaccines
3
Virendra Gomase, Shruti Gomase, Somnath Tagore, Dayanand Bhiwgade, Vaseem Baig and Karbhari Kale.
Prediction of MHC binder for fragment based viral peptide vaccines from cabbage leaf curl virus
4 Madhu Priyadarshi and Manjusha Verma. Plant DNA fingerprint software
5 David Wood, Mhairi Marshall, Shuzhi Cai, Matthew Bryant and Dominique Gorse. Platform for integrated and accessible bioInformatics
6 Susan Tang, Fiona Hyland, Tom Wessel, Jon Sorenson, Heather Peckham and Francisco De La Vega. DiBayes: A SNP detection algorithm for next-generation dibase sequencing
7 Yu Xue, Jian Ren, Longping Wen,
and Xuebiao Yao
GPS 2.0: Prediction of kinase-specific phosphorylation sites in hierarchy
8 Jaya Iyer, Arathi Raghunath
and Jignesh Bhate.
Analyzing the role of CREBBP co-activator in erythroid differentiation --- a literature
mining approach
10 Lesheng Kong and Alan Christoffels. Large-scale gene duplication detection in Ciona savignyi and Ciona intestinalis
11 Thanneer Malai Perumal, Yan Wu and Rudiyanto Gunawan. In silico dynamical analysis of cellular systems: A molecular perturbation approach
12 Marta Szachniuk, Marek Blazewicz,
Mariusz Popenda and Ryszard Adamiak.
On the design of RNA fragments structural database
13 Hongseok Tae and Kiejung Park. ASMPKS: an analysis system for modular polyketide synthases
14 Saurabh Shukla and Alok Shekhar In-silico analysis of HIV-1 p1 sequence and structure prediction.
15 Paul Yoo, Yung Shwen Ho, Bing Zhou and Albert Zomaya. SiteSeek: Protein phosphorylation site predictor using adaptive locality-effective
kernel methods and new profiles
16 Nandita Das, Vaibhav Navaghare, Vidyendra Sadanandan, Jignesh Bhate and Jaya Iyer. Exploring protein-protein interactions at domain level
17 Sangjukta Kashyap, Nandita Das, Usha Mahadevan and Jignesh Bhate. In-silico disease target screening and evaluation with RNAi data
18 Victor Tomilov, Valery Chernukhin, Murat Abdurashitov, Danila Gonchar and Sergei Degtyarev. Cleavage of mammalian chromosomal DNA by restriction enzymes in silico
20 Murat Abdurashitov, Victor Tomilov, Valery Chernukhin, Danila Gonchar and Sergei Degtyarev. Comparative analysis of human chromosomal DNA digestion with restriction endonucleases in vitro and in silico
21 Sebastian Maurer-Stroh, Petra Van Damme, Joost Van Durme, Kim Plasman, Evy Timmerman, Pieter-Jan De Bock, Marc Goethals, Frederic Rousseau, Joost Schymkowitz, Joel Vandekerckhove and Kris Gevaert. Granzyme B cleavage site predictions based on sequence, physical property and structural description of the motif
22 Javed Khan and Shoba Ranganathan. A multi-species comparative structural bioinformatic analysis of inherited mutations in α-D-mannosidase
23 Diane Simarmata, Joo Chuan Tong, Philippe Kourilsky and Lisa F P Ng. Large-scale analysis and screening of Chikungunya virus T-cell epitopes
24 Shunsuke Kamijo, Akihiko Fujii, Kenji Onodera, Kenichi Wakabayashi, Takatsugu Kobayashi and Kensaku Sakamoto. Statistical analysis of KMSKS motif in aminoacyl-tRNA synthetase by building
a library of random sequences
26 Jacek Blazewicz, Marcin Bryja, Marek Figlerowicz, Piotr Gawron, Marta Kasprzak, Darren Platt, Jakub Przybytek, Aleksandra Swiercz and Lukasz Szajkowski. Whole genome assembly from 454 sequencing output
27 Hongseok Tae and Ki Jung Park. ConView: An easy and fast visualization tool for contig assembly
28 Bhakti Bhagwat, Santosh Atanur, Sunitha Manjari Kasibhatla and Rajendra Joshi. Deciphering functional linkages between Mycobacterium tuberculosis H37Rv proteins via Gene Ontology Similarity scores
29 Bruno Schwenk, Joachim Selbig and Matthias Holschneider. Planes in 3-dimensional metabolite triplet data: A robust Bayesian approach
30 Tara Hessa, Nadja M. Meindl-Beinker, Andreas Bernsel, Hyun Kim, Yoko Sato, Mirjam Lerch-Bader, IngMarie Nilsson, Stephen H. White and Gunnar von Heijne Deciphering transmembrane helix recognition by the ER translocon
31 Jens-Uwe Krause, Juergen Kleffe BACOLAP: BAC assembly based on bit-vectors
32

Rohit Reja, Venkata Krishnan AJ, Sandeep Kumar Yelakanti, Vishal Kumar Nangla, Umesh Roy, Rajib Bandopadhyay, Prashanth Suravajhala.

Host Pathogenesis and Lateral Gene Transfer Revisited: Challenges to Evolution

33 Duangdao Wichadakul, Supawadee Ingsriswang, Eakasit Pacharawongsakda, Boonyarat Phadermrod and Sunai Yokwai. ATGC-Dom: Alignment, tree, and graph for comparative proteomes by domain architecture
34 Guimei Liu, Jinyan Li, Suryani Lukman and Limsoon Wong. Predicting protein interactions using interacting motif pairs
36 Jacek Blazewicz, Edmund Burke, Marta Kasprzak, Alexandr Kovalev and Mikhail Y. Kovalyov. Dynamic programming and approximation algorithms for the Simplified Partial Digest Problem
37 Yew Chung Tang, Gregory Stephanopoulos and Heng-Phon Too. Information-theoretic analysis for exploring cell death-survival signaling networks
38 Marta Szachniuk, Mariusz Popenda,
Lukasz Popenda and Jacek Blazewicz.
Constructing transfer pathways in multidimensional NMR spectra of RNAs
39 Bo Kim, Bruce Tidor and Jacob White. Robust optimization for biological network calibration
40 Pablo Carbonell and Antonio del Sol Mesa. Specificity and affinity in protein-protein interactions: From a systems biology to a
molecular point of view
41 Difeng Dong and Limsoon Wong. Using gene expression analysis for drug pathway identification: An example on
nasopharyngeal carcinoma (NPC)
42 Geoffrey Koh, David Hsu and PS Thiagarajan. Composition of signaling pathway models and its application to parameter estimation
43 Kazuo Iida, Takako Takai-Igarashi,
Daiya Takai and Hiroshi Tanaka.
Knowledge-based pathway optimization strategy for gene expression profiling analysis
44 Yulia Medvedeva, Marina Fridman, Nina Oparina, Dmitri Malko, Ekaterina Ermakova, Ivan Kulakovsky and Vsevolod Makeev. Reduced CpG mutation rate suggests functional role of intragenic and 3’ CpG islands in human genes
45 Saboura Ashkevarian, Armin Madadkar Sobhani and Bahram Goliaei. Structural modeling of MaSp1 and MaSp2 proteins of dragline silk in Latrodectus hesperus
46 Tal Shay, Wanyu L. Lambiv , Anastasia Murat , Eugenia Migliavacca , Roger Stupp, Monika E. Hegi and Eytan Domany . More is not always more – when does DNA amplification affect gene expression?
47 Kyungsook Kim, Mira Oh, Jangsun Baek and Young Sook Son. Missing Values Estimation for DNA Microarray Gene Expression Data: SPLS
48 Vladimir Kuznetsov and Leonard Lipovich. Analysis of the human cis-antisense transcription: primate-specific exonic sequences, structure-dependent sense-antisense co-expression, and functionally restricted noncoding-RNA transcription
49 Rajeev Kumar, Manmath Routray and Febin Dass. HIV-1 Protease inhibitor comparative docking studies of synthetic and natural compounds
50 Andrea Sackmann, Piotr Formanowicz
and Jacek Blazewicz.
A DNA based algorithm for calculating the maxflow in networks
51 Mira Oh, Kyungsook Kim and Young Sook Son. Neural network imputation for missing values in time-course gene expression data
52 Serban Nacu. Gene expression network analysis
53 Chao Xie and Martti Tammi. Discovery of DNA copy number variation using shotgun sequencing data
54 Juntao li, Lei Zhu, Majid Eshaghi,
Jianhua Liu and Radha Krishna Murthy
Karuturi.
Genome-wide high-density chip-chip tiling array data analysis in fission yeast
55 Chee Hong Wong, Hong Sain Ooi and Georg Schneider. The ANNOTATOR software environment: A flexible sequence analysis platform
56 Sumantra Chatterjee, Guillaume Bourque and Thomas Lufkin. A bioinformatic and transgenic approach for elucidating tissue specific regulatory elements.
57 Rosaura Palma and Jorge Luis Rosas. Cellular automata and simulation of biological processes
58 Rory Johnson, Galih Kunarso, Christina Teh, Kee Yew Wong, Kandhadayar G Srinivasan, Sarah S L Chan, R Krishna Murthy Karuturi, Leonard Lipovich, Noel J Buckley and Lawrence W Stanton. Genomic analysis of transcriptional regulation by the factor REST in embryonic stem cells
59 Mohammed A. Khidhir , Kampalli Praveen Kumar, Maraw Al-Aseer Genetic characterization and population structure of Arabian Tahr (Hemitragus jayakari) based on microsatellites analysis
60 Menaka Rajapakse and Feng Lin. Guided discovery of motifs for peptide binding prediction
61 Xiaoli Li and See-Kiong Ng. Mining for domain dependency sets from protein interactions
62 Stephen Rumble and Michael Brudno. SHRiMP -- The SHort Read Mapping Package
63 SeungHeui Ryu, Hwan-Gue Cho, DoHoon Lee COCAW:Comparative Observer for Conserved Areas
65 Ran Elkon, Rita Vesterman, Nira Amit, Igor Ulitsky, Gilad Mass, Idan Zohar, Dorit Sagir, Jackie Assa, Yosef Shiloh and Ron Shamir. SPIKE - Signaling Pathways Integrated Knowledge Engine
66 S.A. Arul Shalom, Manoranjan Dash, Minh Tue GPU-based fast k-means clustering of gene expression profiles
67 Vanishree Srinivas, Lokanath Khamari, Ruby K. Mathew, Jignesh Bhate and Jaya Iyer. Potential cardiovascular disease markers –  CliProTM based analysis
68 Marvin N. Steijaert, Huub M. M. ten Eikelder, Anthony M. L. Liekens, Dragan Bosnacki and Peter A. J. Hilbers. Stochastic switching behavior of a bistable auto-phosphorylation network
69 Bharath Bhat, Ashwin Ram B, Arathi Raghunath, Lokanath Khamari, Vidyendra Sadanandan, Jignesh Bhate and Usha Mahadevan. Ubiquitin-proteasome pathway genes and prostate cancer
70 Meelis Kull and Jaak Vilo. Fast approximate hierarchical clustering using similarity heuristics and adaptation to time constraints
71 Gongjin Dong, Yantao Qiao, Yu Lin, Shiwei Sun, Chungong Yu and Dongbo Bu. A training-set-free stochastic model for peptide identification
72 Hans-Juergen Thiesen, Peter Lorenz, Ziliang Qian, Yixue Li, Michael Kreutzer and Michael Glocker. In silico characterization of peptide epitopes recognized by autoantibodies present in IVIG sample preparations.
73 Niko Beerenwinkel, Nicholas Eriksson, Volker Roth and Osvaldo Zagordi. Ultra-deep sequencing of genetically heterogeneous samples
74 Dong Tong and Robert Mintram. Microarray gene recognition using multiobjetive evolutionary techniques
75 Marcel Martin and Sven Rahmann. A heuristic clustering algorithm using graph transitivity
76 Sebastian Boecker and Florian Rasche. Analysis of metabolite tandem mass Spectra
77 Sang Yup Lee, Jin Hwan Park, Kwang Ho Lee and Tae Yong Kim. L-valine production by systematically engineered Escherichia coli
78 Sang Yup Lee and Tae Yong Kim. Deciphering the evolution and metabolism of Mannheimia succiniciproducens
MBEL55E by genome-scale analysis
79 Duygu Tas, Kemal Kilic and Ugur Sezerman. A new probabilistic approach for simplified partial digest problem
80 Elvin Coban, Kemal Kilic and Ugur Sezerman. Constraint programming applied to simplified partial digest problem with errors
81 HsinNan Lin and WenLian Hsu. GACOT -- A genetic algorithm for the physical mapping problem with noisy data
82 Tobias Marschall and Sven Rahmann. Probabilistic arithmetic automata and their application to pattern matching statistics
83 Tae Yong Kim, Soo Yun Moon, Soon Ho Hong and Sang Yup Lee. Metabolic engineering of Escherichia coli for the production of malic acid
84 Tae Yong Kim, Hyung Rok Choi and Sang Yup Lee. Metabolic pathway analysis and its optimization for producing succinic acid in
Mannheimia succiniciproducens MBEL55E
86 Fang Rong Hsu and Wei-Chung Shia. A decision support system for the cardiovascular disease using bioinformatics approach
87 Sang Yup Lee, Kwang Ho Lee, Jin Hwan Park and Tae Yong Kim. Metabolic engineering of Escherichia coli for L-threonine production based on
systems biology
88 Tae Yong Kim, Hyun Uk Kim, Joon Haeng Rhee and Sang Yup Lee. Application of genome-scale metabolic model of Vibrio vulnificus CMCP6 for in silico drug targeting
89 Roel Verhaak, Laura MacConaill and
Matthew Meyerson.
Pathogen discovery by combination of computational substraction and
pyrosequencing technology
90 Thasso Griebel, Malte Brinkmeyer
and Sebastian Boecker.
EPoS: A modular framework for phylogenetic analysis
91 S. Avinash Kumar, S. Sundar Raman, R. Parthasarathi, V. Subramanian A triad based approach to sequence comparison of various types of collagen
92 Sumeet Dua and Shirin Lakhani. Structural classification using mining of frequent patterns in concave protein surfaces
93 Ankit Rakha, Mitra Basu, Rao Kosaraju HLA class I peptides: Exploiting positional information for identification and classification
94 John Thomas, Naren Ramakrishnan and Chris Bailey-Kellogg. Protein design by sampling an undirected graphical model of residue constraints
95 Wei Wang, Youling Guo, Yuexian Zou and Tianrui Wu. A novel algorithm for tag SNP selection based on pairwise linkage disequilibrium
96 Valentina Boeva, Julien Clément,
Mireille Régnier, Mikhail Roytberg and
Vsevolod Makeev.
Exact p-value calculation for clusters of TFBSs: Application in computational
annotation of regulatory sites
97 Mario Albrecht, Christoph Welsch,
Francisco S. Domingues, Gabriele Mayr,
Andreas Schlicker, Stefan Zeuzem
and Thomas Lengauer.
Residue interaction networks for analyzing resistance mutations in HCV protein structures
98 Johan Rung, Ghislain Rocheleau, Alexander Mazur, Christian Dina, Constantin Polychronakos, Philippe Froguel and Rob Sladek. A two-stage genome-wide association study of Type 2 Diabetes Mellitus in
a French population
99

Gerard Wong, Kylie Gorringe, Ian Campbell, Izhak Haviv, Christopher Leckie, Adam Kowalczyk.

Detecting Significant Micro-Regions of DNA Aberration in High Density SNP Array Data

101 Marc Delarue and Patrice Koehl. Biomolecular electrostatics: Beyond the Poisson-Boltzmann centric view
102 Hao Zhao and Guillaume Bourque. Prediction and analysis of reliable rearrangement events in mammalian evolution
103 Maryam Nikoosaleh, Armin Madadkar Sobhani and Bahram Goliaei. Camel alpha-lactalbumin 3D structure prediction
104 Chi Ho Lin, Guillaume Bourque and Patrick Tan. Comparative analysis of Burkholderia species reveals an association between large-scale genome rearrangements and fine-scale nucleotide variation in prokaryotes
105 Ron Zhu, Yuelin Zhu and Wei Xu. EzArray: a web-based highly automated Affymetrix expression array data management and analysis system
106 Holger Froehlich, Mark Fellmann, Annemarie Poustka, Holger Sueltmann and Tim Beissbarth. Estimating signaling networks through nested effects models
107 Utz J. Pape and Martin Vingron. Statistics for co-occurrence of DNA motifs
108 Mohamed Helmy, Masaru Tomita, Masa Tsuchiya and Kumar Selvarajoo. Computational simulations suggest transcription factors AP-1 and NF-κB are
key regulators of TLR3 signaling.
109 Lee Hazelwood and John Hancock. Modelling metabolic processes in insulin-secreting pancreatic β-cells
110 Christine Steinhoff, Matteo Pardo and Martin Vingron. Unsupervised joint analysis of arrayCGH, gene expression data and supplementary features
111 Huiqing Liu and Gyan Bhanot. A procedure to identify microRNA gene targets in human kidney cancer
112 Trupti Joshi, Chao Zhang, Guan Ning Lin
and Dong Xu.
An integrated probabilistic approach for gene function prediction using multiple sources of high-throughput data
113 Amit Nagal and Om Prakash Jangir. Computational studies of Lens regeneration under influence of Vitamin A and its metabolite
114 Narendra Kumar and Debasisa Mohanty. Structure based approach for predicting kinase substrates: Role of solvent accessibility of the site of phosphorylation.
115 Jayasree Ganugapati, Ravindra Babu Potti and Ashok Chakravarthy. In silico modeling of pesticidal crystal-like protein cry16Aa from Clostridium bifermentans
116 Gabriela Alexe, Erhan Bilal, Nilay Sethi,
Lyndsay Harris, Vasisht Tadigotla,
Shridar Ganesan and Gyan Bhanot.
Patterns of differential over-expression of the oncogene IKBKE in HER2+ and basal breast cancer
117 Kok Siong Ang and Rudiyanto Gunawan. Parameter estimation in oscillatory biological systems
118 Suresh Kumar Poovathingal, Rudiyanto Gunawan and Gruber Jan. Aging studies: A stochastic approach
119 Faraaz Noor Khan Yusufi, Satty Ganeswara Reddy, May May Lee and Dong-Yup Lee. GlycoVault: An online storage and visualization system for glycan structures
120 Jong Myoung Park, Hongseok Yun and Sang Yup Lee. MFAML: Metabolic Flux Analysis Markup Language
121 Jong Myoung Park, Hongseok Yun, Jeong Wook Lee, Joonwoo Jeong, Jaesung Chung and Sang Yup Lee. EcoProDB: The protein database for Escherichia coli
122 Jong Myoung Park, Choamun Yun, Hongseok Yun, Sunwon Park and Sang Yup Lee. Development of an integrative online tool for modeling and simulation of cellular networks
123 Noel Faux, Richard Tothill, Justin Bedo, David Bowtell and Adam Kowalczyk. Gene expression profiling for the classification of unknown primary
124 Janusz Dutkowski and Jerzy Tiuryn. Inference of protein-protein interactions - an evolutionary approach
125 Xing Yi Woo, Edison Tak-Bun Liu and Guillaume Bourque. Integrative analysis of transcriptome and genomic aberration map in cancer
126 Fang Rong Hsu and Wen Chun Lo. Discovery of novel relationship among single nucleotide polymorphisms, alternative splicing events and tumor
127 Pratap Dey, Arathi Raghunath, Sangjukta Kashyap, Jignesh Bhate and Usha Mahadevan. Role of interaction databases in studying cross-talks between pathways
128 Fang Rong Hsu, Dung-Lin Hsieh and Shao-Peng Yeh. AVATAR II:An alternative splicing database using three alignment tools
131 Lawrence Buckingham, Xin-Yi Chua, James Hogan, Paul Roe and Jiro Sumitomo. Large-scale comparative studies in GPFlow
132 Vincent Piras, Alessandro Giuliani, Naoki Fujikawa, Masaru Tomita, Kumar Selvarajoo and Masa Tsuchiya. Is transcription factors mediated gene regulation hard wired? A microarray based statistical estimate
133 Sangjukta Kashyap, Arathi Raghunath, Usha Mahadevan, Pratap Dey and Jignesh Bhate. Contrast interaction database -A novel approach to study contextual relevance
of interactions
134 Dang Hung Tran, Kenji Satou and
Tu Bao Ho.
Finding microRNA-mRNA modules based on rule induction
135 V Jayaraj, R Suhanya, M Vijayasarathy and E Rajasekaran. Computational studies on role of large hydrophobic residues in proteins
136 Anne Bergeron, Julia Mixtacki and Jens Stoye. HP distance via double cut and join distance
137 Yaotao Qiao, Shiwei Sun, Gongjin Dong, Yu Lin, Chungong Yu and Dongbo Bu. A novel scoring scheme to evaluate the Mmatch of the peptide and mass spectrum
138 Yuriy Orlov. Sequence complexity measures for alignment-free genome comparisons
139 Chia-Lang Hsu, Yen-Hua Huang and Ueng-Cheng Yang. A gene ontology-based method to present pathway relations
140 Armando Solis and Shalom Rackovsky. Information-guided knowledge-based potential functions for protein structure prediction
141 Rajaraman Kanagasabai and Christopher Baker. Extraction and mapping of protein mutations via ontology-centric knowledge integration
142 Przemek Biecek, Adam Zagdanski,
Rafal Kustra and Stanislaw Cebrat.
Improving the detection performance for gene set functional enrichment
and transcription factor binding sites analysis
144 Brian Parker, Jiayu Wen and Georg Weiller. Structural strand asymmetry for transcription orientation prediction in unaligned non-coding RNA sequences
145 Xin Li and Jing Li. Zero recombinant haplotype inference with missing
146 Jia-Ming Chang, Emily Chia-Yu Su,
Allan Lo, Hua-Sheng Chiu, Ting-Yi Sung
and WenLian Hsu.
A document classification strategy to predict protein subcellular localization using sequence motifs and evolutionary information
147 Alvin Ng and Jagath Rajapakse. Statistical analysis of macrophage cell morphology after microtubule disruption
148 Reetal Pai, James Sacchettini and Thomas Ioerger. Fragment-based analysis of protein-ligand interactions using localized
stereochemical features
149 Namit Bharija and Avinash Kumar Shanmugam. QSAR studies of anti influenza Neuraminidase inhibitors [Oseltamivir]
150 Sandro Andreotti, Juergen Kleffe and Paul Wrede. De novo design of peptides: potential vaccines against the influenza A virus
151 Merlin V. A James, James G Evans, Paul Matsudaira, Roy E Welsch and Jagath Rajapakse. Size-specific and brightness-weighted cell tracking in 2D images
152 Chi-Yong Cho, Dae-Soo Kim, Jae-Won Huh, Heui-Soo Kim, DoHoon Lee and Hwan-Gue Cho EVOG : Evolution Visualizer for Overlapping Genes
153 Meng-Chang Hsiao, Chien-Ming Chen, Tun-Wen Pai, Wen-Shyong Tzou, and Ron-Shan Chen A study of microsatellites dominating mammalian size variation
154 Duygu Ucar, Fatih Altiparmak, Hakan Ferhatosmanoglu and Srinivasan Parthasarathy. Investigating the promise of extrinsic similarity measures for gene expression analysis
155 Sharlee Climer, Alan Templeton and
Weixiong Zhang.
A dense graph model for haplotype inference
156 Neil D. Clarke, Hock Chuan Yeo, Zhen Xuan Yeo, and Ye Li Large scale inference of condition-specific regulation using gene expression data and
the predicted transcription factor occupancy of promoters

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