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2013

2013 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSiPS 2013, Houston, TX, USA, November 17-19, 2013IEEE, 2013. [doi]

Exploiting the cancer and diabetes metabolic connection for therapeutic purposesOsama A. Arshad, Priyadharshini S. Venkatasubramami, Aniruddha Datta, Jijayanagaram Venkatraj. gensips 2013: 44 [doi]

Improved branch-and-bound algorithm for U-curve optimizationEsmaeil Atashpaz-Gargari, Ulisses Braga-Neto, Edward R. Dougherty. gensips 2013: 100-101 [doi]

Identifying RNAseq-based coding-noncoding co-expression interactions in breast cancerNilanjana Banerjee, Sonia Chothani, Lyndsay Harris, Nevenka Dimitrova. gensips 2013: 11-14 [doi]

Inference of genetic regulatory networks with unknown covariance structureBelhassen Bayar, Nidhal Bouaynaya, Roman Shterenberg. gensips 2013: 74-77 [doi]

Quantifying the inference power of a drug screen for predictive analysisNoah Berlow, Saad Haider, Ranadip Pal, Charles Keller. gensips 2013: 49-52 [doi]

Integrative sparse Bayesian analysis of high-dimensional multi-platform genomic data in glioblastomaAnindya Bhadra, Veerabhadran Baladandayuthapani. gensips 2013: 1-4 [doi]

Optimal Bayesian MMSE estimation of the coefficient of determination for discrete predictionTing Chen, Ulisses Braga-Neto. gensips 2013: 66-69 [doi]

Characterization of conditions for competing endogenous RNA regulation in GBMYu-Chiao Chiu, Eric Y. Chuang, Tzu-Hung Hsiao, Yidong Chen. gensips 2013: 23 [doi]

Semi-supervised classification using sparse representation for cancer recurrence predictionYan Cui, Xiaodong Cai, Zhong Jin. gensips 2013: 102-105 [doi]

An HMM-based Exome Peak-finding package for RNA epigenome sequencing dataXiaodong Cui, Jia Meng, Manjeet K. Rao, Yidong Chen, Ufei Huang. gensips 2013: 85 [doi]

Optimal neyman-pearson classification under Bayesian uncertainty modelsLori A. Dalton. gensips 2013: 90-91 [doi]

On the optimality of k-means clusteringLori A. Dalton. gensips 2013: 70-71 [doi]

Designing experiments for optimal reduction of uncertainty in gene regulatory networksRoozbeh Dehghannasiri, Byung-Jun Yoon, Edward R. Dougherty. gensips 2013: 88-89 [doi]

Effect of separate sampling on classification and the minimax criterionMohammad Shahrokh Esfahani, Edward R. Dougherty. gensips 2013: 72-73 [doi]

NetceRNA: An algorithm for construction of phenotype-specific regulation networks via competing endogenous RNAsMario Flores, Yufei Huang, Yidong Chen. gensips 2013: 24-27 [doi]

A structure-based approach to predicting in vitro transcription factor-DNA interactionZhen Gao, Jianhua Ruan. gensips 2013: 9 [doi]

Bayesian multivariate Poisson model for RNA-seq classificationJason M. Knight, Ivan Ivanov, Edward R. Dougherty. gensips 2013: 96-97 [doi]

DBComposer: An R package for integrative analysis and management of gene expression microarray dataLingjia Kong, Kaisa-Leena Aho, Kirsi Granberg, Christophe Roos, Reija Autio. gensips 2013: 92-93 [doi]

Prediction of drug-target interactions using popular Collaborative Filtering methodsArezou Koohi. gensips 2013: 58-61 [doi]

Active learning for Bayesian network models of biological networks using structure priorsAntti Larjo, Harri Lähdesmaki. gensips 2013: 78-81 [doi]

Drug effect study on proliferation and survival pathways on cell line-based platform: A stochastic hybrid systems approachXiangfang Li, Lijun Qian, Michael L. Bittner, Edward R. Dougherty. gensips 2013: 54-57 [doi]

SeqBBS: A change-point model based algorithm and R package for searching CNV regions via the ratio of sequencing readsHua Li, Jim Vallandingham, Jie Chen. gensips 2013: 40-43 [doi]

On the modeling of heterogeneity in cancer tissueAnwoy Kumar Mohanty, Aniruddha Datta, Jijayanagaram Venkatraj. gensips 2013: 10 [doi]

ROBNCA: Robust Network Component Analysis for recovering transcription factor activitiesAmina Noor, Aitzaz Ahmad, Erchin Serpedin, Mohamed N. Nounou, Hazem N. Nounou. gensips 2013: 19-22 [doi]

Integrative analysis of multi-modal correlated imaging-genomics data in glioblastomaRolando J. Olivares, Arvind Rao, Ganesh Rao, Jeffrey S. Morris, Veerabhadran Baladandayuthapani. gensips 2013: 5-8 [doi]

Phenotypically constrained Boolean network inference with prescribed steady statesXiaoning Qian, Edward R. Dougherty. gensips 2013: 82-83 [doi]

Boolean model to experimental validation: A preliminary attemptS. Sridharan, A. Datta, J. Venkatraj. gensips 2013: 94-95 [doi]

A generic model of transcriptional regulatory networks: Application to plants under abiotic stressAlain B. Tchagang, Sieu Phan, Fazel Famili, Youlian Pan, Adrian Cutler, Jitao Zou. gensips 2013: 28-31 [doi]

Modeling hypoxia stress response pathwaysRajani Varghese, Sriram Sridharan, Aniruddha Datta, Jijayanagaram Venkatraj. gensips 2013: 84 [doi]

Supersonic MiBBilal Wajid, Ali Riza Ekti, Amina Noor, Erchin Serpedin, Muhammad Naeem Ayyaz, Hazem N. Nounou, Mohamed N. Nounou. gensips 2013: 86-87 [doi]

A multivariate random forest based framework for drug sensitivity predictionQian Wan, Ranadip Pal. gensips 2013: 53 [doi]

Identifying cancer biomarkers through a network regularized Cox modelYing-Wooi Wan, John Nagorski, Genevera I. Allen, Zhaohui Li, Zhandong Liu. gensips 2013: 36-39 [doi]

An approach for assessing RNA-seq quantification algorithms in replication studiesPo-Yen Wu, John H. Phan, May D. Wang. gensips 2013: 15-18 [doi]

Parameter distribution estimation in first order ODETianyi Yang, Nguyen Nguyen, Yufang Jin, Merry Lindsey. gensips 2013: 62-65 [doi]

Deciphering chemically-induced reversible neurotoxicity by reconstructing perturbed pathways from time series microarray gene expression dataYi Yang, Si Li, Andrew S. Maxwell, Natalie D. Barker, Yan Peng, Ying Li, Haoni Li, Xi Wu, Peng Li, Tao Huang, Chenhua Zhang, Nan Wang, Edward J. Perkins, Chaoyang Zhang, Ping Gong. gensips 2013: 45-48 [doi]

Compromised intervention policies for phenotype alterationMohammadmahdi R. Yousefi. gensips 2013: 32-35 [doi]

Effect of mixing probabilities on the bias of cross-validation under separate samplingAmin Zollanvari, Ulisses Braga-Neto, Edward R. Dougherty. gensips 2013: 98-99 [doi]

2012

An investigation of clinical outcome prediction from integrative genomic profiles in ovarian cancerLin Zhang 0015, Hui Liu, Tzu-Hung Hsiao, Yidong Chen, Yufei Huang. gensips 2012: 103-106 [doi]

Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSiPS 2012, Washington, DC, USA, December 2-4, 2012IEEE, 2012. [doi]

Feature ranking based on synergy networks to identify prognostic markers in DPT-1Amin Ahmadi-Adl, Xiaoning Qian, Ping Xu, Kendra Vehik, Jeffrey P. Krischer. gensips 2012: 66-69 [doi]

OBGene: Optimal barcode generator for NGS experimentsEsmaeil Atashpaz-Gargari, Mohammad Shahrokh Esfahani, Richard Metz, Charles D. Johnson. gensips 2012: 90-94 [doi]

A comparison of periodicity profile methods for sequence analysisManas Bellani, Julien Epps, Gavin A. Huttley. gensips 2012: 78-81 [doi]

Multiclass cancer-microarray classification algorithm with pair-against-all redundancyMattia Bosio, Pau Bellot Pujalte, Philippe Salembier, Albert Oliveras-Vergés. gensips 2012: 111-112 [doi]

Utilizing RNA-Seq data for cancer network inferenceYing Cai, Bernard Fendler, Gurinder S. Atwal. gensips 2012: 46-49 [doi]

A statistical test for intrinsically multivariate predictive genesTing Chen, Ulisses Braga-Neto. gensips 2012: 151-154 [doi]

An SILAC quantification algorithm for LC-FTMSJian Cui, Xuepo Ma, Xiaolin Zhang, William Haskins, Jiangiu (Michelle) Zhang. gensips 2012: 199-202 [doi]

Optimal Bayesian classification and its application to gene regulatory networksLori A. Dalton, Edward R. Dougherty. gensips 2012: 164-167 [doi]

Information theoretic feature selection for high dimensional metagenomic dataGregory Ditzler, Gail Rosen, Robi Polikar. gensips 2012: 143-146 [doi]

NMF based approach for finding recurrent aberrations in DNA copy number dataMohammed Elhenawy, Guoqiang Yu. gensips 2012: 82-85 [doi]

A non-parametric approach for estimating stromal contamination in cancer samplesMohammed Elhenawy, Xuchu Hou, Guoqiang Yu. gensips 2012: 126-129 [doi]

A new algorithm for predicting competing endogenous rnasMario Flores, Yufei Huang. gensips 2012: 118-121 [doi]

Latent feature decompositions for integrative analysis of diverse high-throughput genomic dataKarl B. Gregory, Kevin R. Coombes, Amin Momin, Luc Girard, Lauren A. Byers, Steven Lin, Michael Peyton, John V. Heymach, John D. Minna, Veerabhadran Baladandayuthapani. gensips 2012: 130-134 [doi]

Inferring gene functions from metabolic reactionsGünhan Gülsoy, Tamer Kahveci. gensips 2012: 159-163 [doi]

Combination therapy design for targeted therapeutics from a drug-protein interaction perspectiveSaad Haider, Noah Berlow, Ranadip Pal, Lara E. Davis, Charles Keller. gensips 2012: 58-61 [doi]

Accurate identification of significant aberrations in contaminated cancer genomeXuchu Hou, Guoqiang Yu, Xiguo Yuan, Bai Zhang, Ie-Ming Shih, Zhen Zhang, Robert Clarke, Subha Madhavan. gensips 2012: 74-77 [doi]

Identification of functional genomic regions with copy number alteration in liver cancerTzu-Hung Hsiao, Hung-I Harry Chen, Yidong Chen. gensips 2012: 155-158 [doi]

Hierarchical Bayesian methods for integration of various types of genomics dataElizabeth M. Jennings, Jeffrey S. Morris, Raymond J. Carroll, Ganiraju Manyam, Veerabhadran Baladandayuthapani. gensips 2012: 5-8 [doi]

External control of probabilistic boolean networks using inhomogeneous Markov chainsTimothy M. Josserand. gensips 2012: 180-182 [doi]

Finding robust pathway markers for cancer classificationNavadon Khunlertgit, Byung-Jun Yoon. gensips 2012: 147-150 [doi]

Determining gene function in boolean networks using boolean satisfiabilityPey-Chang Kent Lin, Sunil P. Khatri. gensips 2012: 176-179 [doi]

Integrative analysis of methylation and gene expression data in TCGAYihua Liu, Peng Qiu. gensips 2012: 1-4 [doi]

Logistic principal component analysis for rare variants in gene-environment interaction analysisMeng Lu, Hye-Seung Lee, David Hadley, Jianhua Z. Huang, Xiaoning Qian. gensips 2012: 122-125 [doi]

Sparse Bayesian graphical models for RPPA time course dataRiten Mitra, Peter Müller, Yuan Ji, Gordon B. Mills, Yiling Lu. gensips 2012: 113-117 [doi]

Determining the relative prevalence of different subpopulations in heterogeneous cancer tissueAnwoy Kumar Mohanty, Aniruddha Datta, Jijayanagaram Venkatraj. gensips 2012: 95-96 [doi]

Fast DNA barcode generating algorithm using Radix Coding methodAmir Nikooienejad, Richard Metz, Byung-Jun Yoon, Charles D. Johnson. gensips 2012: 26-30 [doi]

Anticancer drug sensitivity analysis: An integrated approach applied to Erlotinib sensitivity prediction in the CCLE databaseRanadip Pal, Noah Berlow, Saad Haider. gensips 2012: 9-12 [doi]

Improving the flexibility of RNA-Seq data analysis pipelinesJohn H. Phan, Po-Yen Wu, May D. Wang. gensips 2012: 70-73 [doi]

Detection of short exons in DNA sequences using complex wavelet transform of structural featuresIvo Provaznik, Vladimira Kubicova, Helena Skutkova, Jiri Nedved, Ewaryst Tkacz, Petr Babula, René Kizek. gensips 2012: 107-110 [doi]

A new phenotypically constrained control policy in boolean networks based on basins of attractionXiaoning Qian. gensips 2012: 54-57 [doi]

Toward exhaustive gating of flow cytometry dataPeng Qiu. gensips 2012: 183-186 [doi]

Normalization of LC-MS data using Gaussian processMohammad R. Nezami Ranjbar, Mahlet G. Tadesse, Yue Joseph Wang, Habtom W. Ressom. gensips 2012: 187-190 [doi]

Inference of time-varying gene networks using constrained and smoothed Kalman filteringGhulam Rasool, Nidhal Bouaynaya. gensips 2012: 172-175 [doi]

Detection and clustering of palindrome in genome sequences by DCT-II methodAhsan Zaigam Rizvi, C. Bhattacharya. gensips 2012: 97-98 [doi]

Network-based methods to identify highly discriminating subsets of biomarkersSeyed Javad Sajjadi, Xiaoning Qian, Bo Zeng. gensips 2012: 139-142 [doi]

Design of short barcodes for next generation sequencing of DNA and RNASteffen Schober, Katharina Mir, Klaus Neuhaus, Martin Bossert. gensips 2012: 31-34 [doi]

A message passing algorithm for reference-guided sequence assembly from high-throughput sequencing dataXiaohu Shen, Haris Vikalo. gensips 2012: 35-37 [doi]

Inferring weighted and directed gene interaction networks from gene expression data using the phi-mixing coefficientNitin K. Singh, Mehmet Eren Ahsen, Shiva Mankala, M. Vidyasagar, Michael A. White. gensips 2012: 168-171 [doi]

Integrating multi-platform genomic data using hierarchical Bayesian relevance vector machinesSanvesh Srivastava, Wenyi Wang, Pascal O. Zinn, Rivka R. Colen, Veerabhadran Baladandayuthapani. gensips 2012: 18-21 [doi]

Robust MS serum sample classification in proteomics by the use of inverse problemsPascal Szacherski, Jean-François Giovannelli, Laurent Gerfault, Audrey Giremus, Pierre Grangeat. gensips 2012: 191-194 [doi]

MiB: A comparative assembly processing pipelineBilal Wajid, Erchin Serpedin, Mohamed N. Nounou, Hazem N. Nounou. gensips 2012: 86-89 [doi]

Integration of multiple data sources for identifying functional modules using Bayesian networkJinlian Wang, Hongyan Yuan, Mahlet G. Tadesse, Habtom W. Ressom. gensips 2012: 13-17 [doi]

A comparative study of methods for detecting small somatic variants in disease-normal paired next generation sequencing dataQingguo Wang, Zhongming Zhao. gensips 2012: 38-41 [doi]

Integration of imaging and systems biology to study treatment of medulloblastomaSean S. Wang, Olga C. Rodriguez, Ye Tian, Shaozhen Ye, Emanual F. Petricoin, Chris Albanese. gensips 2012: 22-25 [doi]

An evaluation for merging signaling pathways by using protein-protein interaction dataXiaogang Wu, Jake Y. Chen. gensips 2012: 203-206 [doi]

Cell type specific analysis of human transcriptome dataXiaoxiao Xu, Arye Nehorai, Joseph Dougherty. gensips 2012: 99-100 [doi]

A Bayesian model for SNP discovery based on next-generation sequencing dataYanxun Xu, Xiaofeng Zheng, Yuan Yuan, Marcos R. Estecio, Jean-Pierre Issa, Yuan Ji, Shoudan Liang. gensips 2012: 42-45 [doi]

Genome-wide meta-regression of gene-environment interactionXiaoxiao Xu, Gang Shi, Arye Nehorai. gensips 2012: 62-65 [doi]

A Bayesian graphical model for integrative analysis of TCGA dataYanxun Xu, Jie Zhang, Yuan Yuan, Riten Mitra, Peter Müller, Yuan Ji. gensips 2012: 135-138 [doi]

Optimal therapeutic methods with random-length response in probabilistic boolean networksMohammadmahdi R. Yousefi, Aniruddha Datta, Edward R. Dougherty. gensips 2012: 50-53 [doi]

Comprehensive analyses of tumor suppressor genes in protein-protein interaction networks: A topological perspectiveMin Zhao, Jingchun Sun, Zhongming Zhao. gensips 2012: 101-102 [doi]

Variability assessment of LC-MS experiments and its application to experimental design and difference detectionYi Zhao, Tsung-Heng Tsai, Cristina Di Poto, Lewis K. Pannell, Mahlet G. Tadesse, Habtom W. Ressom. gensips 2012: 195-198 [doi]

2011

2011 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSiPS 2011, San Antonio, TX, USA, December 4-6, 2011IEEE, 2011. [doi]

A novel approach for tumor sensitivity prediction and combination therapy design for targeted drugsNoah Berlow, Ranadip Pal. gensips 2011: 36-37 [doi]

A novel critical time analysis approach for genetic regulatory networksSonal Bhattacharya, Ranadip Pal. gensips 2011: 29-32 [doi]

Identification of biomarkers in breast cancer metastasis by integrating protein-protein interaction network and gene expression dataMd. Jamiul Jahid, Jianhua Ruan. gensips 2011: 60-63 [doi]

Comparative copy number variation from whole genome sequencingAngel Janevski, Vinay Varadan, Sitharthan Kamalakaran, Nilanjana Banerjee, Nevenka Dimitrova. gensips 2011: 123-126 [doi]

A scalable, flexible workflow for MethylCap-seq data analysisBenjamin Rodriguez, Hok-Hei Tam, David Frankhouser, Michael Trimarchi, Mark Murphy, Chris Kuo, Deval Parikh, Bryan Ball, Sebastian Schwind, John Curfman, William Blum, Guido Marcucci, Pearlly Yan, Ralf Bundschuh. gensips 2011: 1-4 [doi]

Revision of the variational Bayesian method for uncovering genes regulatory networkManuel Sanchez-Castillo, Isabel M. Tienda-Luna, David Blanco-Navarro, Maria Carmen Carrion Perez. gensips 2011: 206-209 [doi]

Mathematical modeling of macrophage activation in left ventricular remodeling post-myocardial infarctionYunji Wang, Yufang Jin, Yonggang Ma, Ganesh V. Halade, Merry L. Linsey. gensips 2011: 202-205 [doi]

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