1. Huey Eng Chua, Sourav S Bhowmick, Lisa Tucker-Kellogg and C Forbes Dewey Jr. STEROID: In Silico Heuristic Target Combination Identification for Disease-Related Signaling Networks


2. Nicola Prezza, Cristian Del Fabbro, Francesco Vezzi, Emanuele De Paoli and Alberto Policriti. ERNE-BS5: aligning BS-treated sequences by multiple hits on a 5-letters alphabet

3. Min Wu, Chee Keong Kwoh, Xiaoli Li and Jie Zheng. NetPipe: A Network-based Pipeline for Discovery of Genes and Protein Complexes Regulating Meiotic Recombination Hotspots

4. K. S. M. Tozammel Hossain, Debprakash Patnaik, Srivatsan Laxman, Prateek Jain, Chris Bailey-Kellogg and Naren Ramakrishnan. Improved Multiple Sequence Alignments using Coupled Pattern Mining

5. Jeffrey Van Voorst, Yiying Tong and Leslie Kuhn. ArtSurf: A Method for Deformable Partial Matching of Protein Small-Molecule Binding Sites

6. Shuvra Nath, Chinwe Ekenna, Hsin-Yi Yeh, Shawna Thomas and Nancy Amato. Multi-Directional Rapidly Exploring Random Graphs for Modeling Protein Folding

7. Meng Lu, Jianhua Huang and Xiaoning Qian. Supervised Logistic Principal Component Analysis for Pathway Based Genome-Wide Association Studies

8. Jintao Zhang, Gerald Lushington and Jun Huan. Multi-target protein-chemical interaction prediction using task-regularized and boosted multi-task learning

9. Ahsanur Rahman, Christopher L. Poirel, David J. Badger and T. M. Murali. Reverse Engineering Molecular Hypergraphs

10. Saradindu Kar, Deepak Vijayakeerthi, Balaraman Ravindran and Ashish V. Tendulkar. Functional Site Prediction by Exploiting Correlations between Labels of Interacting Residues

11. Reginaldo Kuroshu. Non-overlapping clone pooling for high-throughput sequencing

12. Ming-Chi Tsai, Guy Blelloch, R Ravi and Russell Schwartz. Coalescent-based Method for Learning Parameters of Admixture Events from Large-Scale Genetic Variation Data

13. Hagit Shatkay, Ramya Narayanaswamy, Santosh Nagaral, Na Harrington, Dorothea Blostein, Ryan Tarpine, Kyle Schutter, Rohith Mv, Gowri Somanath, Sorin Istrail and Chandra Kambahmettu. OCR-based Image Features for Biomedical Image and Article Classification: Identifying Documents relevant to Cis-Regulatory Elements

14. Chen-Ping Fu, Catherine E. Welsh, Fernando Pardo-Manuel de Villena and Leonard McMillan. Ancestry Inference of Admixed Populations with Microarray Probe Intensities

15. Jennifer D'Souza and Vincent Ng. Anaphora Resolution in Biomedical Literature: A Hybrid Approach

16. Yijie Wang and Xiaoning Qian. Functional Module Identification by Block Modeling using Simulated Annealing with Path Relinking

17. Kevin Molloy and Amarda Shehu. Biased Decoy Sampling to Aid the Selection of Near-native Protein Conformations

18. Dino Franklin. Protein Blocks Versus Hydrogen Bonds Based Alphabets For Protein Structure Classification

19. Wenxuan Gao, Robert Grossman, Philip Yu, Christopher Brown, Matthew Slattery, Lijia Ma and Kevin White. Discovering Geometric Patterns in Genomic Data

20. Yao-Ming Huang and Chris Bystroff. Exploring objective functions and cross-terms in the optimization of an energy function for protein design

21. Ruibang Luo, Chi Man Liu, Thomas Wong, Chang Yu, Tak-Wah Lam, Siu Ming Yiu, Ruiqiang Li and Hingfung Ting. Efficient SNP-sensitive alignment and database-assisted SNP calling for low coverage samples

22. Leandro Loss, Hang Chang, Purbasha Sarkar, Manfred Auer and Bahram Parvin. Automatic Segmentation and Quantification of Filamentous Structures in Electron Tomography

23. Yuan Zhang and Yanni Sun. PseudoDomain: identification of processed pseudogenes based on protein domain classification

24. Mehmet Umut Caglar and Ranadip Pal. Complexity reduction of Stochastic Master Equation Simulation based on Kronecker Product Analysis

25. Sinan Erten, Marzieh Ayati, Yu Liu, Mark R. Chance and Mehmet Koyuturk. Algorithms for Detecting Complementary SNPs within a Region of Interest That Are Associated with Diseases

26. Guoxian Yu, Guoji Zhang, Huzefa Rangwala, Carlotta Domeniconi and Zhiwen Yu. Protein Function Prediction using Weak-label Learning

27. Kang Li, Nan Du and Aidong Zhang. Detecting ECG Abnormalities via Transductive Transfer Learning

28. Sonal Kothari, John H. Phan, Adeboye O. Osunkoya and May D. Wang. Biological Interpretation of Morphological Patterns in Histopathological Whole-Slide Images

29. Vinodh Rajapakse, Wojciech Czaja, William Reinhold, Yves Pommier and Sudhir Varma. Predicting expression-related features of chromosomal domain organization with network-structured analysis of gene expression and chromosomal location

30. Chanchala Kaddi, R. Mitchell Parry and May D. Wang. Multivariate Hypergeometric Similarity Measure

31. Debdas Paul and Brian Chen. A Volumetric Method for Representing and Comparing Regions of Electrostatic Focusing in Molecular Structure

32. Nan Du, Yuan Zhang, Kang Li, Jing Gao and Aidong Zhang. Evolutionary Analysis of Functional Modules in Dynamic PPI Networks

33. Oben M Tataw, A. K. Row-Chowdhurry and G.V. Reddy. Alignment of Real-Time Live-Cell Growth Data for Quantitative Analysis of Growth at the Shoot Apex of Arabidopsis thaliana



34. Junjie Li, Sanjay Ranka and Sartaj Sahni. Parallel Syntenic Alignment on GPUs

35. Liang Ge, Jing Gao, Nan Du and Aidong Zhang. Finding Informative Genes for Prostate Cancer: A General Framework of Integrating Heterogeneous Sources

36. Iman Rezaeian and Luis Rueda. A New Algorithm for Finding Enriched Regions in ChIP-Seq Data

37. Jung-Jae Kim and Luu Anh Tuan. Hybrid pattern matching for complex ontology term recognition

38. Min Wu, Chee Keong Kwoh, Teresa M. Przytycka, Jing Li and Jie Zheng. Integration of Genomic and Epigenomic Features to Predict Meiotic Recombination Hotspots in Human and Mouse

39. Shuo Wang and Yang Cao. Efficient Implementation of the Hybrid Method for Stochastic Simulation of Biochemical Systems

40. Jie Liu, Humberto Vidaillet, Elizabeth Burnside and David Page. SNPRank: An Efficient Ranking Method for Genome-wide Association Studies

41. Tyson Lipscomb, Anqi Zou and Samuel Cho. Parallel Verlet Neighbor List Algorithm for GPU-Optimized MD Simulations

42. Yang Ruan, Saliya Ekanayake, Mina Rho, Haixu Tang, Seung-Hee Bae, Judy Qiu and Geoffrey C. Fox. DACIDR: Deterministic Annealed Clustering with Interpolative Dimension Reduction using Large Collection of 16S rRNA Sequences

43. Wei Zhang, Nicholas Johnson, Baolin Wu and Rui Kuang. Signed Network Propagation for Detecting Differential Gene Expressions and DNA Copy Number Variations

44. Swakkhar Shatabda, M.A.Hakim Newton, Duc Nghia Pham and Abdul Sattar. Memory-Based Local Search for Simplified Protein Structure Prediction

45. Mengfei Cao and Lenore Cowen. Remote Homology Detection on Alpha-Structural Proteins Using Simulated Evolution

46. Hui Li, Xiaoyi Li, Lawrence Bone, Cathy Buyea, Murali Ramanathan and Aidong Zhang. 3D Bone Microarchitecture Modeling and Fracture Risk Prediction

47. Serghei Mangul, Adrian Caciula, Sahar Al Seesi, Dumitru Brinza, Abdul Rouf Banday, Rahul N. Kanadia, Ion Mandoiu and Alex Zelikovsky. An Integer Programming Approach to Novel Transcript Reconstruction from Paired-End RNA-Seq Reads

48. James Lindsay, Hamed Salooti, Alex Zelikovsky and Ion Mandoiu. Scalable Genome Scaffolding using Integer Linear Programming

49. Minmei Hou, Louxin Zhang and Robert Harris. Alignment seeding strategies using contiguous pyrimidine purine matches

50. Daehan Won, Chun-An Chou, W. Art Chaovalitwongse, Tanya Y. Berger-Wolf, Bhaskar Dasgupta, Ashfaq A. Khokhar, Mary V. Ashley, Jason Palagi and Marco Maggioni. An integrated optimization framework for inferring two-generation kinships and parental genotypes from microsatellite samples

51. Watson Wei Khong Chua and Jung-Jae Kim. Semantic Querying over Knowledge in Biomedical Text Corpora Annotated with Multiple Ontologies

52. Filip Jagodzinski and Ileana Streinu. Towards Biophysical Validation of Constraint Modeling for Rigidity Analysis of Proteins

53. Yongwook Choi. A fast computation of pairwise sequence alignment scores between a protein and a set of variants of another protein

54. Jianhua Ruan, Md. Jamiul Jahid, Fei Gu, Chengwei Lei, Yi-Wen Huang, Ya-Ting Hsu, David G. Mutch, Chun-Liang Chen, Nameer B. Kirma and Tim H. Huang. Network-based classification of recurrent endometrial cancers using high-throughput DNA methylation data

55. Yasser El-Manzalawy, Drena Dobbs and Vasant Honavar. Predicting Protective Bacterial Antigens Using Random Forest Classifiers

56. Janusz Slawek and Tomasz Arodz. ADANET: Inferring Gene Regulatory Networks using Ensemble Classifiers

57. M. Oguzhan Kulekci. On enumerating the DNA sequences

58. Ayat Hatem, Kamer Kaya and Umit Catalyurek. Microarray vs. RNA-Seq: A comparison for active subnetwork discovery

59. Kasra Manavi, Bridget Wilson and Lydia Tapia. Simulation and Analysis of Antibody Aggregation on Cell Surfaces Using Motion Planning and Graph Analysis

60. Wei Cheng, Xiang Zhang, Wei Wang, Yubao Wu, Xiaolin Yin, Jing Li and David Heckerman. Inferring novel associations between SNP sets and gene sets in eQTL study using sparse graphical model

61. Thair Judeh, Tin Chi Nguyen and Dongxiao Zhu. QSEA for fuzzy subgraph querying of KEGG pathways

62. Daniel Ryan and Dimitris Papamichail. Rational design of Orthogonal Libraries of Protein Coding Genes

63. Kamal Al Nasr, Lin Chen, Dong Si, Desh Ranjan, Muhammad Zubair and Jing He. Protein Structure Prediction from Cryo-Electron Microscopy Volume Data at the Medium Resolution

64. Sanjoy Dey, Gowtham Atluri, Michael Steinbach, Kelvin Lim, Angus MacDonald and Vipin Kumar. A pattern mining based integrative framework for biomarker discovery


1. Wajdi Dhifli, Rabie Saidi and Engelbert Mephu Nguifo. A Novel Approach for Mining Representative Spatial Motifs of Proteins

2. Jens-Peter Volkmer, Debashis Sahoo, Robert Chin, Philip Ho, Chad Tang, Antonina Kurtova, Stephen Willingham, Senthil Pazhanisamy, Humberto Contreras-Trujillo, Theresa Storm, Yair Lotan, Andrew Beck, Benjamin Chung, Ash Alizadeh, Guilherme Godoy, Seth Lerner, Matt van de Rijn, Linda Shortliffe, Irving Weissman and Keith Chan. Systems Biology Approach to Identify Markers of Differentiation in Bladder Cancer

3. Yoram Shotland. 454 and SOLiD Complementary Used to Filter and Build the Draft Genome of Highly Abundant Cyanobacteria in Biological Desert Crust

4. Shaherin Basith and Sangdun Choi. An In-depth Analysis of the Molecular Dynamics and Structural Aspects of IKB Proteins

5. Qi Ma, Wen Liu and 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

6. Vijayakumar Gosu and Sangdun Choi. Phylogenetic and Functional Divergence Analysis of Vertebrate IRAK Family Members

7. Michael Hall, Mina Maleki and Luis Rueda. Multi-level Structural Domain-domain Interactions for Prediction of Obligate and Non-obligate Protein-protein Interactions

8. De Laet Marie, Dehouck Yves, Gilis Dimitri and Rooman Marianne. Identification of Protein Stability Patches that Pinpoint Key Structural or Functional Sites

9. Satoshi Mizuta and Taro Mori. Searching for the Relics of Primitive Codons

10. Yi-Cheng Tu, Shaoping Chen, Sagar Pandit, Anand Kumar and Vladimir Grupcev. Efficient SDH Computation in Molecular Simulations Data

11. Aditya Reddy Kolli, Frank Sommerhage, Peter Molnar, Jonathan E. Hood, Jerry J. Jenkins, Faraz Hussain, Arup K. Ghosh, Sumit Kumar Jha and James J. Hickman. A Computational Metabolic Model of the NG108-15 Cell for High Content Drug Screening with Electrophysiological Readout

12. Eric Bareke, Jean-Francois Spinella, Ramon Vidal, Jasmine Healy, Daniel Sinnett and Miklos Csuros. A Novel Mathematical Basis for Predicting Somatic Single Nucleotide Variants from Next-generation Sequencing

13. Jhih-Rong Lin and Jianjun Hu. Nuclear Localization Signal Prediction Based on Sequential Pattern Mining

14. Nam S. Vo and Vinhthuy Phan. Pattern Analysis: a Web-based Tool for Analyzing Response Patterns in Low-replication, Many-treatment Gene Expression Data

15. Pascal St-Onge, Virginie Saillour, Patrick Beaulieu, Robert Hamon, Jasmine Healy and Daniel Sinnett. ngALL Database : A Flexible Framework for the Management and Integration of Childhood Leukemia Next Generation Sequencing data

16. Daniel T. Yehdego, Vikram Kumar Reddy Kodimala, Sameera Viswakula, Boyu Zhang, Rahulsimham Vegesna, Kyle L. Johnson, Michela Taufer and Ming-Ying Leung. Secondary Structure Predictions for Long RNA Sequences Based on Inversion Excursions-Preliminary Results

17. Jeffrey R. Van Voorst and Barry C. Finzel. Rapid Efficient Macromolecular Substructure Searching in a Cloud

18. Jingyao Li, Hongbao Cao and Yu-Ping Wang. Classification of Multicolor Fluorescence In-Situ Hybridization (M-FISH) Image Using Regularized Multinomial Logistic Regression

19. Junbo Duan, Ji-Gang Zhang, Hongbao Cao, Hong-Wen Deng and Yu-Ping Wang. Copy Number Variation Estimation from Multiple Next-generation Sequencing Samples

20. Lariza Laura de Oliveira and Renato Tinos. Entropy-based Evaluation Function for the Investigation of Genetic Code Adaptability

21. Sergio Nery Simoes, David Correa Martins Jr, Helena Brentani and Ronaldo Fumio Hashimoto. Shortest Paths Ranking Methodology to Identify Alterations in PPI Networks of Complex Diseases

22. Bingqing Xie, Dinanath Sulakhe, Bhadrachalam Chitturi, Gady Agam, Natalia Maltsev and T. Conrad Gilliam. Prediction of Candidate Genes for Neuropsychiatric Disorders Using Feature-based Enrichment

23. Yuan Zhang, Liang Ge, Nan Du, Guoqiang Fan, Kebin Jia and Aidong Zhang. A Graph-based Cluster Ensemble Method to Detect Protein Functional Modules from Multiple Information Sources

24. Marcelo Filipe Breda de Moraes, Nilson Nicolau Junior and Silvana Giuliatti. Macromolecular Modeling of Protein Structure - SCI1 of Nicotiana tabacum L.

25. Craig A. Finch and James J. Hickman. A Continuum Hard-Sphere Model of Protein Adsorption

26. Andrew Gallant, Mark D.M. Leiserson, Maxim Kachalov, Lenore J. Cowen and Benjamin J. Hescott. Genecentric: A Package to Uncover Graph-theoretic Structure in High-throughput Epistasis Data

27. Nam S. Vo, Vinhthuy Phan and Thomas Sutter. Predicting Possible Directed-graph Patterns of Gene Expressions in Studies Involving Multiple Treatments

28. Sajid A. Marhon and Stefan C. Kremer. A Brief Comparison of DSP and HMM Methods for Gene Finding

29. Clemente Aguilar-Bonavides, Ming-Ying Leung, Ernesto S. Nakayasu, Felipe Gazos-Lopes and Igor C. Almeida. Computational Tool for the Automated Large-Scale GPIomic Analysis

30. Parag S. Chandakkar, Ragav Venkatesan, Baoxin Li and Helen K. Li. A Machine-learning Approach to Retrieving Diabetic Retinopathy Images

31. Brian Olson and Amarda Shehu. An Evolutionary Search Framework to Efficiently Sample Local Minima in the Protein Conformational Space

32. Paul Anderson and Michael Peterson. Empirical Metabolite Identification via GA Feature Selection and Bayes Classification

33. Jeremy C. Morgan, Robert W. Chapman and Paul E. Anderson. A Next Generation Sequence Processing and Analysis Platform with Integrated Cloud-storage and High Performance Computing Resources

34. Edward Pharr, Aspen Olmsted and Paul E. Anderson. gLIMS: Google Cloud-based Laboratory Information Management System for NMR Metabolomics

35. Shivapriya Chithambaram, Ramanandan Prabhakaran and Xuhua Xia. A Comparative Study of cCodon Adaptation in ssDNA and dsDNA Phages

36. Herbert H. Tsang and Denny C. Dai. RNA-DV: an Interactive Tool for Editing and Visualizing RNA Secondary Structures

37. Xi Gao and Tomasz Arodz. Robust Differential Co-Expression Discovery: an Insight into Pharmacodynamics of Tyrosine Kinase Inhibitor

38. Emily Flynn, Filip Jagodzinski and Ileana Streinu. Towards Sequence-Based DNA Flexibility Analysis

39. Jie Li, Vishakha Sharma, Narayan Ganesan and Adriana Compagnoni. Simulation and Study of Large-Scale Bacteria-Materials Interactions via BioScape Enabled by GPUs

40. Peter Bajcsy, Joe Chalfoun and Mary Brady. How to Select Microscopy Image Similarity Metrics?

41. Nicholas Johnson, Gang Fang and Rui Kuang. Approximate Subspace Pattern Mining for Mapping Copy-Number Variations

42. Jan Lorenz Soliman, Aldrin Montana, Kevin Webb, Alex Dekhtyar, Michael Black, Chris Kitts, Jennifer Vanderkellen, Emily Neal and Anya Goodman. Microbial Source Tracking by Molecular Fingerprinting

43. Mahmood A Rashid, Swakkhar Shatabda, M.A.Hakim Newton, Md Tamjidul Hoque, Duc Nghia Pham and Abdul Sattar. Random-Walk: a Stagnation Recovery Technique for Simplified Protein Structure Prediction