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3. BCB 2012: Orlando, FL, USA
- Sanjay Ranka, Tamer Kahveci, Mona Singh:
ACM International Conference on Bioinformatics, Computational Biology and Biomedicine, BCB' 12, Orlando, FL, USA - October 08 - 10, 2012. ACM 2012, ISBN 978-1-4503-1670-5 - Huey-Eng Chua, Sourav S. Bhowmick
, Lisa Tucker-Kellogg
STEROID: in silico heuristic target combination identification for disease-related signaling networks. 4-11 - Nicola Prezza, Cristian Del Fabbro
ERNE-BS5: aligning BS-treated sequences by multiple hits on a 5-letters alphabet. 12-19 - Min Wu
NetPipe: a network-based pipeline for discovery of genes and protein complexes regulating meiotic recombination hotspots. 20-27 - K. S. M. Tozammel Hossain
Improved multiple sequence alignments using coupled pattern mining. 28-35 - Jeffrey R. Van Voorst, Yiying Tong, Leslie A. Kuhn:
ArtSurf: a method for deformable partial matching of protein small-molecule binding sites. 36-43 - Shuvra Kanti Nath, Shawna L. Thomas, Chinwe Ekenna, Nancy M. Amato:
A multi-directional rapidly exploring random graph (mRRG) for protein folding. 44-51 - Meng Lu, Jianhua Z. Huang, Xiaoning Qian:
Supervised logistic principal component analysis for pathway based genome-wide association studies. 52-59 - Jintao Zhang, Gerald H. Lushington
Multi-target protein-chemical interaction prediction using task-regularized and boosted multi-task learning. 60-67 - Ahsanur Rahman
Reverse engineering molecular hypergraphs. 68-75 - Saradindu Kar, Deepak Vijayakeerthi, Ashish V. Tendulkar, Balaraman Ravindran
Functional site prediction by exploiting correlations between labels of interacting residues. 76-83 - Reginaldo Kuroshu:
Non-overlapping clone pooling for high-throughput sequencing. 84-89 - Ming-Chi Tsai, Guy E. Blelloch, Russell Schwartz
Coalescent-based method for learning parameters of admixture events from large-scale genetic variation data. 90-97 - Hagit Shatkay, Ramya Narayanaswamy, Santosh S. Nagaral, Na Harrington, M. V. Rohith, Gowri Somanath, Ryan Tarpine, Kyle Schutter, Tim Johnstone, Dorothea Blostein, Sorin Istrail, Chandra Kambhamettu:
OCR-based image features for biomedical image and article classification: identifying documents relevant to cis-regulatory elements. 98-104 - Chen-Ping Fu, Catherine E. Welsh, Fernando Pardo-Manuel de Villena, Leonard McMillan
Inferring ancestry in admixed populations using microarray probe intensities. 105-112 - Jennifer D'Souza, Vincent Ng:
Anaphora resolution in biomedical literature: a hybrid approach. 113-122 - Yijie Wang, Xiaoning Qian:
Functional module identification by block modeling using simulated annealing with path relinking. 123-130 - Kevin Molloy, Amarda Shehu
Biased decoy sampling to aid the selection of near-native protein conformations. 131-138 - Dino Franklin:
Protein blocks versus hydrogen bonds based alphabets for protein structure classification. 139-146 - Wenxuan Gao, Lijia Ma, Christopher Brown, Matthew Slattery, Philip S. Yu, Robert L. Grossman, Kevin P. White:
Discovering geometric patterns in genomic data. 147-154 - Yao-ming Huang, Christopher Bystroff:
Exploring objective functions and cross-terms in the optimization of an energy function for protein design. 155-162 - Ruibang Luo
Efficient SNP-sensitive alignment and database-assisted SNP calling for low coverage samples. 163-169 - Leandro A. Loss, George Bebis, Hang Chang, Manfred Auer, Purbasha Sarkar, Bahram Parvin:
Automatic segmentation and quantification of filamentous structures in electron tomography. 170-177 - Yuan Zhang, Yanni Sun
PseudoDomain: identification of processed pseudogenes based on protein domain classification. 178-185 - Mehmet Umut Caglar, Ranadip Pal
Complexity reduction of stochastic master equation simulation based on Kronecker product analysis. 186-193 - Sinan Erten, Marzieh Ayati
Algorithms for detecting complementary SNPs within a region of interest that are associated with diseases. 194-201 - Guo-Xian Yu, Guoji Zhang, Huzefa Rangwala, Carlotta Domeniconi, Zhiwen Yu:
Protein function prediction using weak-label learning. 202-209 - Kang Li, Nan Du, Aidong Zhang:
Detecting ECG abnormalities via transductive transfer learning. 210-217 - Sonal Kothari, Adeboye O. Osunkoya, John H. Phan, May D. Wang
Biological interpretation of morphological patterns in histopathological whole-slide images. 218-225 - Vinodh N. Rajapakse, Wojciech Czaja, Yves Pommier, William C. Reinhold, Sudhir Varma:
Predicting expression-related features of chromosomal domain organization with network-structured analysis of gene expression and chromosomal location. 226-233 - Chanchala Kaddi, R. Mitchell Parry, May D. Wang
Multivariate hypergeometric similarity measure. 234-241 - Brian Y. Chen, Debdas Paul
A volumetric method for representing and comparing regions of electrostatic focusing in molecular structure. 242-249 - Nan Du, Yuan Zhang, Kang Li, Jing Gao, Supriya D. Mahajan, Bindukumar B. Nair, Stanley A. Schwartz, Aidong Zhang:
Evolutionary analysis of functional modules in dynamic PPI networks. 250-257 - Oben M. Tataw, G. Venugopala Reddy, Amit K. Roy-Chowdhury:
Alignment of real-time live-cell growth data for quantitative analysis of growth at the shoot apex of Arabidopsis thaliana: deducing the relationship between primordia growth, gene expression and cell behaviors. 258-265 - Junjie Li, Sanjay Ranka
Parallel syntenic alignment on GPUs. 266-273 - Liang Ge, Jing Gao, Nan Du, Aidong Zhang:
Finding informative genes for prostate cancer: a general framework of integrating heterogeneous sources. 274-281 - Iman Rezaeian, Luis Rueda:
A new algorithm for finding enriched regions in ChIP-Seq data. 282-288 - Jung-Jae Kim
Hybrid pattern matching for complex ontology term recognition. 289-296 - Min Wu
Integration of genomic and epigenomic features to predict meiotic recombination hotspots in human and mouse. 297-304 - Shuo Wang, Yang Cao:
Efficient implementation of the hybrid method for stochastic simulation of biochemical systems. 305-312 - Jie Liu, Elizabeth S. Burnside, Humberto J. Vidaillet, David Page:
A collective ranking method for genome-wide association studies. 313-320 - Tyson J. Lipscomb, Anqi Zou, Samuel S. Cho:
Parallel verlet neighbor list algorithm for GPU-optimized MD simulations. 321-328 - Yang Ruan, Saliya Ekanayake, Mina Rho, Haixu Tang, Seung-Hee Bae, Judy Qiu, Geoffrey C. Fox:
DACIDR: deterministic annealed clustering with interpolative dimension reduction using a large collection of 16S rRNA sequences. 329-336 - Wei Zhang
Signed network propagation for detecting differential gene expressions and DNA copy number variations. 337-344 - Swakkhar Shatabda
Memory-based local search for simplified protein structure prediction. 345-352 - Mengfei Cao, Lenore J. Cowen:
Remote homology detection on alpha-structural proteins using simulated evolution. 353-360 - Hui Li, Cathy Buyea, Xiaoyi Li, Murali Ramanathan, Lawrence Bone, Aidong Zhang:
3D bone microarchitecture modeling and fracture risk prediction. 361-368 - Serghei Mangul, Adrian Caciula, Sahar Al Seesi
An integer programming approach to novel transcript reconstruction from paired-end RNA-Seq reads. 369-376 - James Lindsay, Hamed Salooti, Alexander Zelikovsky
Scalable genome scaffolding using integer linear programming. 377-383 - Minmei Hou, Louxin Zhang, Robert S. Harris:
Alignment seeding strategies using contiguous pyrimidine purine matches. 384-391 - Daehan Won, Chun-An Chou, Wanpracha Art Chaovalitwongse, Tanya Y. Berger-Wolf
An integrated optimization framework for inferring two generation kinships and parental genotypes from microsatellite samples. 392-399 - Watson Wei Khong Chua, Jung-Jae Kim
Semantic querying over knowledge in biomedical text corpora annotated with multiple ontologies. 400-407 - Filip Jagodzinski, Ileana Streinu:
Towards biophysical validation of constraint modeling for rigidity analysis of proteins. 408-413 - Yongwook Choi
A fast computation of pairwise sequence alignment scores between a protein and a set of single-locus variants of another protein. 414-417 - Jianhua Ruan
Network-based classification of recurrent endometrial cancers using high-throughput DNA methylation data. 418-425 - Yasser El-Manzalawy, Drena Dobbs
Predicting protective bacterial antigens using random forest classifiers. 426-433 - Janusz Slawek, Tomasz Arodz:
ADANET: inferring gene regulatory networks using ensemble classifiers. 434-441 - M. Oguzhan Külekci
On enumerating the DNA sequences. 442-449 - Ayat Hatem, Kamer Kaya, Ümit V. Çatalyürek
Microarray vs. RNA-Seq: a comparison for active subnetwork discovery. 450-457 - Kasra Manavi, Bridget S. Wilson, Lydia Tapia:
Simulation and analysis of antibody aggregation on cell surfaces using motion planning and graph analysis. 458-465 - Wei Cheng, Xiang Zhang, Yubao Wu
Inferring novel associations between SNP sets and gene sets in eQTL study using sparse graphical model. 466-473 - Thair Judeh, Tin Chi Nguyen
QSEA for fuzzy subgraph querying of KEGG pathways. 474-481 - Daniel Ryan, Dimitris Papamichail:
Rational design of orthogonal libraries of protein coding genes. 482-489 - Kamal Al-Nasr, Lin Chen, Dong Si, Desh Ranjan, Mohammad Zubair, Jing He
Building the initial chain of the proteins through de novo modeling of the cryo-electron microscopy volume data at the medium resolutions. 490-497 - Sanjoy Dey, Kelvin O. Lim
A pattern mining based integrative framework for biomarker discovery. 498-505 - Wajdi Dhifli
A novel approach for mining representative spatial motifs of proteins. 506-508 - Jens-Peter Volkmer, Debashis Sahoo, Robert K. Chin:
Systems biology approach to identify markers of differentiation in bladder cancer. 509 - Yoram Shotland:
454 and SOLiD™ complementary used to filter and build the draft genome of highly abundant cyanobacteria in biological desert crust. 510-512 - Shaherin Basith, Sangdun Choi:
An in-depth analysis of the molecular dynamics and structural aspects of IKB proteins. 513-514 - Qi Ma, Wen Liu, Michael G. Rosenfeld:
mHMM (multivariate hidden Markov model) application in studying BRD4 and JMJD6 function cooperatively on promoter-proximal polymerase-II (Pol II) pausing release. 515 - Vijayakumar Gosu, Sangdun Choi:
Phylogenetic and functional divergence analysis of vertebrate IRAK family members. 516-517 - Michael Hall, Mina Maleki, Luis Rueda:
Multi-level structural domain-domain interactions for prediction of obligate and non-obligate protein-protein interactions. 518-520 - Marie De Laet, Yves Dehouck, Dimitri Gilis, Marianne Rooman:
Identification of protein stability patches that pinpoint key structural or functional sites. 521-523 - Satoshi Mizuta, Taro Mori:
Searching for the relics of primitive codons. 524-526 - Yi-Cheng Tu, Shaoping Chen, Sagar Pandit, Anand Kumar, Vladimir Grupcev:
Efficient SDH computation in molecular simulations data. 527-529 - Aditya Reddy Kolli
A computational metabolic model of the NG108-15 cell for high content drug screening with electrophysiological readout. 530-532 - Eric Bareke
A novel mathematical basis for predicting somatic single nucleotide variants from next-generation sequencing. 533-535 - Jhih-rong Lin, Jianjun Hu:
Nuclear localization signal prediction based on sequential pattern mining. 536-538 - Nam S. Vo
Pattern analysis: a web-based tool for analyzing response patterns in low-replication, many-treatment gene expression data. 539-541 - Pascal St-Onge, Robert Hamon, Virginie Saillour, Jasmine Healy, Patrick Beaulieu, Daniel Sinnett:
ngALL database: a flexible framework for the management and integration of childhood leukemia next generation sequencing data. 542-544 - Daniel T. Yehdego, Boyu Zhang, Michela Taufer
Secondary structure predictions for long RNA sequences based on inversion excursions: preliminary results. 545-547 - Jeffrey R. Van Voorst, Barry C. Finzel:
Rapid efficient macromolecular substructure searching in a cloud. 548-550 - Jingyao Li, Hongbao Cao, Yu-Ping Wang:
Classification of multicolor fluorescence in-situ hybridization (M-FISH) image using regularized multinomial logistic regression. 551-554 - Junbo Duan, Ji-Gang Zhang, Hongbao Cao, Hong-Wen Deng, Yu-Ping Wang:
Copy number variation estimation from multiple next-generation sequencing samples. 555-557 - Lariza Laura de Oliveira, Renato Tinós
Entropy-based evaluation function for the investigation of genetic code adaptability. 558-560 - Sérgio Nery Simões, David Correa Martins Jr., Helena Paula Brentani
Shortest paths ranking methodology to identify alterations in PPI networks of complex diseases. 561-563 - Bingqing Xie, Gady Agam, Dinanath Sulakhe, Natalia Maltsev, Bhadrachalam Chitturi, T. Conrad Gilliam:
Prediction of candidate genes for neuropsychiatric disorders using feature-based enrichment. 564-566 - Yuan Zhang, Liang Ge, Nan Du, Guoqiang Fan, Kebin Jia, Aidong Zhang:
A graph-based cluster ensemble method to detect protein functional modules from multiple information sources. 567-569 - Marcelo Filipe Breda de Moraes, Nilson Nicolau Junior, Silvana Giuliatti
Macromolecular modeling of protein structure - SCI1 of Nicotiana tabacum L. 570-572 - Craig A. Finch, James J. Hickman:
A continuum hard-sphere model of protein adsorption. 573-575 - Andrew Gallant, Mark D. M. Leiserson, Maxim Kachalov, Lenore J. Cowen, Benjamin J. Hescott:
Genecentric: a package to uncover graph-theoretic structure in high-throughput epistasis data. 576-578 - Nam S. Vo
Predicting possible directed-graph patterns of gene expressions in studies involving multiple treatments. 579-581 - Sajid Marhon
A brief comparison of DSP and HMM methods for gene finding. 582-584 - Clemente Aguilar-Bonavides, Ming-Ying Leung
Computational tool for large-scale GPIomic analysis. 585-587 - Parag S. Chandakkar, Ragav Venkatesan, Baoxin Li, Helen K. Li:
A machine-learning approach to retrieving diabetic retinopathy images. 588-589 - Brian S. Olson, Amarda Shehu
An evolutionary search framework to efficiently sample local minima in the protein conformational space. 590 - Paul E. Anderson, Michael Peterson:
Empirical metabolite identification via GA feature selection and Bayes classification. 591-593 - Jeremy C. Morgan, Robert W. Chapman, Paul E. Anderson:
A next generation sequence processing and analysis platform with integrated cloud-storage and high performance computing resources. 594 - Edward Pharr, Aspen Olmsted
gLIMS: Google cloud-based laboratory information management system for NMR metabolomics. 595-597 - Shivapriya Chithambaram, Ramanandan Prabhakaran, Xuhua Xia
A comparative study of codon adaptation in ssDNA and dsDNA phages. 598-600 - Herbert H. Tsang
RNA-DV: an interactive tool for editing and visualizing RNA secondary structures. 601-603 - Xi Gao, Tomasz Arodz:
Robust differential co-expression discovery: an insight into pharmacodynamics of tyrosine kinase inhibitor. 604-606 - Emily Flynn, Filip Jagodzinski, Ileana Streinu:
Towards sequence-based DNA flexibility analysis. 607-609 - Jie Li, Vishakha Sharma, Narayan Ganesan, Adriana B. Compagnoni:
Simulation and study of large-scale bacteria-materials interactions via BioScape enabled by GPUs. 610-612 - Peter Bajcsy, Joe Chalfoun, Mary Brady:
How to select microscopy image similarity metrics? 613-615 - Nicholas Johnson, Gang Fang, Rui Kuang:
Approximate subspace pattern mining for mapping copy-number variations. 616 - Jan Lorenz Soliman, Alex Dekhtyar, Jennifer Vanderkelen, Aldrin Montana
Microbial source tracking by molecular fingerprinting. 617-619 - Mahmood A. Rashid
Random-walk: a stagnation recovery technique for simplified protein structure prediction. 620-622
Workshop ICIW
- Xinyue Liu, Luke J. Tallon, Lisa Sadzewicz, Elena N. Klyushnenkova, Yurij Ionov:
Serum antibody repertoire profiling using virtual antigen screen. 623-624 - Magdalena Feldhahn, Karin Schilbach, Pierre Dönnes, Hans-Georg Rammensee, Benjamin Schubert, Oliver Kohlbacher
miHA-match: computational detection of tissue-specific minor histocompatibility antigens. 625-626 - Gaurav Pandey, Ariella Cohain, Jennifer Miller, Miriam Merad:
Decoding dendritic cell function through module and network analysis. 627-628 - Salvador Eugenio C. Caoili:
Using quantitative dose-response data to benchmark B-cell epitope prediction for antipeptide antibodies. 629-636 - Andres H. Gutiérrez, Leonard Moise, Frances Terry, Kristen Dasilva, Chris Bailey-Kellogg, William D. Martin, Anne S. De Groot
Immunoinformatic analysis of Chinese hamster ovary (CHO) protein contaminants in therapeutic protein formulations. 637-642
Workshop BNA-M
- Vijender Chaitankar, Preetam Ghosh
Genome scale inference of transcriptional regulatory networks using mutual information on complex interactions. 643-648 - Pietro Hiram Guzzi, Pierangelo Veltri
Unraveling multiple miRNA-mRNA associations through a graph-based approach. 649-654 - Yuan Zhang, Nan Du, Liang Ge, Kebin Jia, Aidong Zhang:
A collective NMF method for detecting protein functional module from multiple data sources. 655-660
Workshop ParBio
- Steven Hill, Bismita Srichandan, Rajshekhar Sunderraman:
An iterative MapReduce approach to frequent subgraph mining in biological datasets. 661-666 - Fahad Saeed, Jason D. Hoffert, Trairak Pisitkun, Mark A. Knepper:
High performance phosphorylation site assignment algorithm for mass spectrometry data using multicore systems. 667-672 - Neelam N. Deshpande, John A. Springer:
Parallelization of the spectral deconvolution stage of the proteomic discovery process. 673-676 - Pietro Cinaglia
A system for acquiring and management of ECG signals by using mobile devices: a support for first intervention in heart attacks. 677-682
Workshop RSBC
- Rabie Saidi
Feature extraction in protein sequences classification: a new stability measure. 683-689 - Ruijin Wu, Aysegul Ozkan, Antonette Bennett, Mavis Agbandje-McKenna, Meera Sitharam:
Robustness measure for an adeno-associated viral shell self-assembly is accurately predicted by configuration space atlasing using EASAL. 690-695 - Vitor H. P. Louzada, Fabrício Martins Lopes, Ronaldo Fumio Hashimoto
A Monte Carlo approach to measure the robustness of Boolean networks. 696-699
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