Journal of Bioinformatics and Computational Biology Vol. 10, No. 6 (2012) 1299001 (8 pages) c Imperial College Press # .

DOI: 10.1142/S0219720012990016

AUTHOR INDEX Volume 10 (2012)

J. Bioinform. Comput. Biol. 2012.10. Downloaded from www.worldscientific.com by 85.74.84.134 on 10/23/12. For personal use only.

Abnizova, I., Leonard, S., Skelly, T., Brown, A., Jackson, D., Gourtovaia, M., Qi, G., te Boekhorst, R., Faruque, N., Lewis, K. and Cox, T., Analysis of Context-Dependent Errors for Illumina Sequencing Akbal-Delibas, B., see Hashmi, I. Akbal-Delibas, B., Hashmi, I., Shehu, A. and Haspel, N., An Evolutionary Conservation-Based Method for Rening and Reranking Protein Complex Structures Aksianov, E. and Alexeevski, A., SheeP: A Tool for Description of -Sheets in Protein 3D Structures Alexeevski, A., see Aksianov, E. Al Nasr, K., see Biswas, A. Amos, C. I., see Gorlova, O. Y. Ananthasubramanian, S., see Ganapathiraju, M. K. Arnold, N., see Krivan, W. Awad, S., Panchy, N., Ng, S.-K. and Chen, J., Inferring the Regulatory Interaction Models of Transcription Factors in Transcriptional Regulatory Networks Bandyopadhyay, P., see Meher, B. R. Bandyopadhyay, S., see Chen, B. Y. Banerjee, R., see Limaye, B. Barillot, E., see Martignetti, L. Batagov, A., see Sirota, F. L. Batuwita, R. and Palade, V., Adjusted Geometric-Mean: A Novel Performance Measure for Imbalanced Bioinformatics Datasets Learning Bayaskar, A., see Limaye, B. Bederman, I., see Cakmak, A. Benson, N. C. and Daggett, V., A Chemical Group Graph Representation for Ecient High-Throughput Analysis of Atomistic Protein Simulations Bereg, S., see Sheng, R.
1299001-1

2 (2012) 1241005 2 (2012) 1242008

3 (2012) 1242002 2 2 2 2 2 2 (2012) (2012) (2012) (2012) (2012) (2012) 1241003 1241003 1242006 1241008 1250016 1250009

5 5 5 5 5 5

(2012) (2012) (2012) (2012) (2012) (2012)

1250012 1250018 1242004 1250006 1241001 1250020

4 (2012) 1250003 4 (2012) 1250006 4 (2012) 1240003

4 (2012) 1250008 4 (2012) 1250017

Author Index

Bernauer, J., see Sim, A. Y. L. Berry, V., see Gambette, P. Bhandari, A., see Limaye, B. Biswas, A., Si, D., Al Nasr, K., Ranjan, D., Zubair, M. and He, J., Improved Eciency in Cryo-EM Secondary Structure Topology Determination from Inaccurate Data te Boekhorst, R., see Abnizova, I. Bonett, S., see Huang, Y. Borozdenko, D. A., see Terentiev, A. A. Boyd, S. and Haghighi, M., A Fast Method for Large-Scale Multichromosomal Breakpoint Median Problems Brown, A., see Abnizova, I. Bucher, P., see Dimitrieva, S. Byun, J., see Gorlov, I. P. Cakmak, A., Qi, X., Cicek, A. E., Bederman, I., Henderson, L., Drumm, M. and Ozsoyoglu, G., A New Metabolomics Analysis Technique: Steady-State Metabolic Network Dynamics Analysis Carter, D., see Krivan, W. Casagrande, A. and Fabris, F., Family Fingerprints: A Global Approach to Structural Classication Chen, B. Y. and Bandyopadhyay, S., A Regionalizable Statistical Model of Intersecting Regions in ProteinLigand Binding Cavities Chen, J., see Awad, S. Chen, J., see Jiao, Y. Chen, Y. and Li, J., Generation of Synthetic Data and Experimental Designs in Evaluating Interactions for Association Studies Cheng, J., Eickholt, J., Wang, Z. and Deng, X., Recursive Protein Modeling: A Divide and Conquer Strategy for Protein Structure Prediction and Its Case Study in CASP9 Chong, K. F. and Leong, H. W., Tutorial on De Novo Peptide Sequencing Using MS/MS Mass Spectrometry Chumakov, M., see Volokhina, I. Cicek, A. E., see Cakmak, A. Cicek, A. E. and Ozsoyoglu, G., Observation Conict Resolution in Steady-State Metabolic Network Dynamics Analysis Cox, T., see Abnizova, I. Daggett, V., see Benson, N. C.
1299001-2

4 (2012) 1241010 4 (2012) 1250004 4 (2012) 1250006

J. Bioinform. Comput. Biol. 2012.10. Downloaded from www.worldscientific.com by 85.74.84.134 on 10/23/12. For personal use only.

3 3 3 3 1 1 1 1

(2012) (2012) (2012) (2012) (2012) (2012) (2012) (2012)

1242006 1241005 1242007 1241012 1240008 1241005 1241007 1241013

1 (2012) 1240003 1 (2012) 1250009 3 (2012) 1242001

3 (2012) 1242004 3 (2012) 1250012 3 (2012) 1271002

1 (2012) 1240005

3 (2012) 1242003 6 (2012) 1231002 6 (2012) 1241009 6 (2012) 1240003

1 (2012) 1240004 1 (2012) 1241005 1 (2012) 1250008

Author Index

Dahale, S., see Limaye, B. Datta, A., see Limaye, B. De, R. K. and Tomar, N., Modeling the Optimal Central Carbon Metabolic Pathways Under Feedback Inhibition Using Flux Balance Analysis Deng, X., see Cheng, J. Dimitrieva, S. and Bucher, P., Practicality and Time Complexity of a Sparsied RNA Folding Algorithm Dong, G., see Han, Q. Drumm, M., see Cakmak, A. Eickholt, J., see Cheng, J. Eisenhaber, B., see Sirota, F. L. Eisenhaber, F., see Sirota, F. L. Eisenhaber, F., A Decade After the First Full Human Genome Sequencing: When Will We Understand our own Genome? Fabris, F., see Casagrande, A. Faruque, N., see Abnizova, I. Gadhari, R., see Limaye, B. Gambette, P., Berry, V. and Paul, C., Quartets and Unrooted Phylogenetic Networks Ganapathiraju, M. K., Mitchell, A. D., Thahir, M., Motwani, K. and Ananthasubramanian, S., Suite of Tools for Statistical N-Gram Language Modeling for Pattern Mining in Whole Genome Sequences Gandhi, B., see Glsoy, G. Gavane, V., see Limaye, B. Gorlov, I. P., see Gorlova, O. Y. Gorlov, I. P., Byun, J., Zhao, H., Logothetis, C. J. and Gorlova, O. Y., Beyond Comparing Means: The Usefulness of Analyzing Interindividual Variation in Gene Expression for Identifying Genes Associated with Cancer Development Gorlova, O. Y., see Gorlov, I. P. Gorlova, O. Y., Ying, J., Amos, C. I., Spitz, M. R., Peng, B. and Gorlov, I. P., Derived SNP Alleles Are Used More Frequently than Ancestral Alleles as Risk-Associated Variants in Common Human Diseases Gourtovaia, M., see Abnizova, I. Glsoy, G., Gandhi, B. and Kahveci, T., TOPAC: Alignment of Gene Regulatory Networks Using Topology-Aware Coloring
1299001-3

1 (2012) 1250006 1 (2012) 1250006

6 (2012) 1250019 6 (2012) 1242003 2 2 2 2 2 2 (2012) (2012) (2012) (2012) (2012) (2012) 1241007 1250005 1240003 1242003 1250020 1250020

J. Bioinform. Comput. Biol. 2012.10. Downloaded from www.worldscientific.com by 85.74.84.134 on 10/23/12. For personal use only.

5 5 5 5

(2012) (2012) (2012) (2012)

1271001 1242001 1241005 1250006

4 (2012) 1250004

6 6 6 6

(2012) (2012) (2012) (2012)

1250016 1240001 1250006 1241008

2 (2012) 1241013 2 (2012) 1241013

2 (2012) 1241008 2 (2012) 1241005

1 (2012) 1240001

Author Index

Gusev, Y., see Volokhina, I. Habib, M. and To, T.-H., Constructing a Minimum Phylogenetic Network from a Dense Triplet Set Haghighi, M., see Boyd, S. Han, Q. and Dong, G., Using Attribute Behavior Diversity to Build Accurate Decision Tree Committees for Microarray Data Hardy, J., see Jagodzinski, F. Hashmi, I., see Akbal-Delibas, B. Hashmi, I., Akbal-Delibas, B., Haspel, N. and Shehu, A., Guiding Protein Docking with Geometric and Evolutionary Information Haspel, N., see Akbal-Delibas, B. Haspel, N., see Hashmi, I. He, J., see Biswas, A. Henderson, L., see Cakmak, A. Hendi, S. F., see Olson, B. Hua, L., Wang, J. T. L., Ji, X., Malhotra, A., Khaladkar, M., Shapiro, B. A. and Zhang, K., A Method for Discovering Common Patterns from Two RNA Secondary Structures and Its Application to Structural Repeat Detection Huang, Y., Bonett, S., Kloczkowski, A., Jernigan, R. and Wu, Z., P.R.E.S.S. An R-Package for Exploring Residual-Level Protein Structural Statistics Imoto, S., see Sharma, A. Inamdar, H., see Limaye, B. Jackson, D., see Abnizova, I. Jagodzinski, F., Hardy, J. and Streinu, I., Using Rigidity Analysis to Probe Mutation-Induced Structural Changes in Proteins Jain, S., see Limaye, B. Jernigan, R., see Huang, Y. Ji, X., see Hua, L. Jiao, Y., Rosa, B. A., Oh, S., Montgomery, B. L., Qin, W. and Chen, J., Detection and Decomposition: Treatment-Induced Cyclic Gene Expression Disruption in High-Throughput Time-Series Datasets Joshi, R., see Limaye, B. Kahveci, T., see Glsoy, G. Kamzolova, S. G., see Osypov, A. A. Khaladkar, M., see Hua, L.
1299001-4

1 (2012) 1241009 5 (2012) 1250013 5 (2012) 1240008

4 (2012) 1250005 4 (2012) 1242010 4 (2012) 1242002

J. Bioinform. Comput. Biol. 2012.10. Downloaded from www.worldscientific.com by 85.74.84.134 on 10/23/12. For personal use only.

3 3 3 3 3 3

(2012) (2012) (2012) (2012) (2012) (2012)

1242008 1242002 1242008 1242006 1240003 1242005

4 (2012) 1250001

3 3 3 3

(2012) (2012) (2012) (2012)

1242007 1250010 1250006 1241005

3 3 3 3

(2012) (2012) (2012) (2012)

1242010 1250006 1242007 1250001

6 6 6 6 6

(2012) (2012) (2012) (2012) (2012)

1271002 1250006 1240001 1241004 1250001

Author Index

Kimura, K., Koike, A. and Nakai, K., A Bit-Parallel Dynamic Programming Algorithm Suitable for DNA Sequence Alignment Kirys, T., see Ruvinsky, A. M. Kloczkowski, A., see Huang, Y. Koike, A., see Kimura, K. Krivan, W., Arnold, N., Morales, C. and Carter, D., FlexGrePPS Flexible Greedy Peptide Pool Search: Computation of Near-Optimal Sets of Degenerate Polypeptides for Antigenic Screening Krutinin, G. G., see Osypov, A. A. Krutinina, E. A., see Osypov, A. A. Lavor, C., see Mucherino, A. Leonard, S., see Abnizova, I. Leong, H. W., see Chong, K. F. Levitt, M., see Sim, A. Y. L. Levtsova, O. V., see Terentiev, A. A. Lewis, K., see Abnizova, I. Li, J., see Chen, Y. Li, W., Volcano Plots in Analyzing Dierential Expressions with mRNA Microarrays Liberti, L., see Mucherino, A. Limaye, B., Banerjee, R., Datta, A., Inamdar, H., Vats, P., Dahale, S., Bhandari, A., Ramakrishnan, E. P., Tupakula, R., Malviya, S., Bayaskar, A., Gadhari, R., Jain, S., Gavane, V., Mahajan, R., Sunitha, K. and Joshi, R., Anvaya: A Workows Environment for Automated Genome Analysis Liu, B. and Thiagarajan, P. S., Modeling and Analysis of Biopathways Dynamics Liu, Y., see Shen, C. Logothetis, C. J., see Gorlov, I. P. Mahajan, R., see Limaye, B. Malhotra, A., see Hua, L. Malviya, S., see Limaye, B. Martignetti, L., Zinovyev, A. and Barillot, E., Identication of Shortened 3 0 Untranslated Regions from Expression Arrays Maurer-Stroh, S., see Sirota, F. L. Maximenko, D. M., see Terentiev, A. A. Mazilov, S., see Volokhina, I.
1299001-5

4 4 4 4

(2012) (2012) (2012) (2012)

1250002 1241002 1242007 1250002

J. Bioinform. Comput. Biol. 2012.10. Downloaded from www.worldscientific.com by 85.74.84.134 on 10/23/12. For personal use only.

5 5 5 5 5 5 5 5 5 5

(2012) (2012) (2012) (2012) (2012) (2012) (2012) (2012) (2012) (2012)

1250009 1241004 1241004 1242009 1241005 1231002 1241010 1241012 1241005 1240005

6 (2012) 1231003 6 (2012) 1242009

4 (2012) 1250006 4 4 4 4 4 4 (2012) (2012) (2012) (2012) (2012) (2012) 1231001 1240007 1241013 1250006 1250001 1250006

2 2 2 2

(2012) (2012) (2012) (2012)

1241001 1250020 1241012 1241009

Author Index

Meher, B. R., Satish Kumar, M. V., Sharma, S. and Bandyopadhyay, P., Conformational Dynamics of HIV-1 Protease: A Comparative Molecular Dynamics Simulation Study with Multiple Amber Force Fields Mitchell, A. D., see Ganapathiraju, M. K. Miyano, S., see Sharma, A. Moldogazieva, N. T., see Terentiev, A. A. Molloy, K., see Olson, B. Montgomery, B. L., see Jiao, Y. Morales, C., see Krivan, W. Motwani, K., see Ganapathiraju, M. K. Mucherino, A., Lavor, C. and Liberti, L., Exploiting Symmetry Properties of the Discretizable Molecular Distance Geometry Problem Nakai, K., see Kimura, K. Ng, S.-K., see Awad, S. Novoselova, N. and Tom, I., Entropy-Based Cluster Validation and Estimation of the Number of Clusters in Gene Expression Data Odibat, O. and Reddy, C. K., Ranking Dierential Hubs in Gene Co-Expression Networks Oh, S., see Jiao, Y. Olson, B., Molloy, K., Hendi, S. F. and Shehu, A., Guiding Probabilistic Search of the Protein Conformational Space with Structural Proles Osypov, A. A., Krutinin, G. G., Krutinina, E. A. and Kamzolova, S. G., DEPPDB DNA Electrostatic Potential Properties Database. Electrostatic Properties of Genome DNA Elements Ozsoyoglu, G., see Cakmak, A. Ozsoyoglu, G., see Cicek, A. E. Palade, V., see Batuwita, R. Panchy, N., see Awad, S. Paul, C., see Gambette, P. Peng, B., see Gorlova, O. Y. Qi, G., see Abnizova, I. Qi, X., see Cakmak, A. Qin, W., see Jiao, Y. Radulescu, O., see Vakulenko, S. A. Ramakrishnan, E. P., see Limaye, B. Rangwala, H., see Rasheed, Z. Ranjan, D., see Biswas, A.
1299001-6

J. Bioinform. Comput. Biol. 2012.10. Downloaded from www.worldscientific.com by 85.74.84.134 on 10/23/12. For personal use only.

6 6 6 6 6 6 6 6

(2012) (2012) (2012) (2012) (2012) (2012) (2012) (2012)

1250018 1250016 1250010 1241012 1242005 1271002 1250009 1250016

3 (2012) 1242009 3 (2012) 1250002 3 (2012) 1250012

5 (2012) 1250011 1 (2012) 1240002 1 (2012) 1271002

3 (2012) 1242005

2 2 2 2 2 2 2 2 2 2 2 2 2 2

(2012) (2012) (2012) (2012) (2012) (2012) (2012) (2012) (2012) (2012) (2012) (2012) (2012) (2012)

1241004 1240003 1240004 1250003 1250012 1250004 1241008 1241005 1240003 1271002 1241011 1250006 1250015 1242006

Author Index

Rasheed, Z. and Rangwala, H., Metagenomic Taxonomic Classication Using Extreme Learning Machines Reddy, C. K., see Odibat, O. Rosa, B. A., see Jiao, Y. Ruvinsky, A. M., Kirys, T., Tuzikov, A. V. and Vakser, I. A., Structure Fluctuations and Conformational Changes in Protein Binding Satish Kumar, M. V., see Meher, B. R. Schneider, G., see Sirota, F. L. Schwander, O., see Sim, A. Y. L. Shaitan, K. V., see Terentiev, A. A. Shapiro, B. A., see Hua, L. Sharma, A., Imoto, S. and Miyano, S., A Between-Class Overlapping Filter-Based Method for Transcriptome Data Analysis Sharma, S., see Meher, B. R. Shavlik, J., see Soni, A. Shehu, A., see Akbal-Delibas, B. Shehu, A., see Olson, B. Shehu, A., see Hashmi, I. Shen, C. and Liu, Y., A Tripartite Clustering Analysis on MicroRNA, Gene and Disease Model Sheng, R. and Bereg, S., Approximating Metrics with Planar Boundary-Labeled Phylogenetic Networks Si, D., see Biswas, A. Sim, A. Y. L., Schwander, O., Levitt, M. and Bernauer, J., Evaluating Mixture Models for Building RNA KnowledgeBased Potentials Sirota, F. L., Batagov, A., Schneider, G., Eisenhaber, B., Eisenhaber, F. and Maurer-Stroh, S., Beware of Moving Targets: Reference Proteome Content Fluctuates Substantially Over the Years Skelly, T., see Abnizova, I. Soni, A. and Shavlik, J., Probabilistic Ensembles for Improved Inference in Protein-Structure Determination Spitz, M. R., see Gorlova, O. Y. Streinu, I., see Jagodzinski, F. Sunitha, K., see Limaye, B. Tang, Y. and Wang, F., Neural System Modeling and Simulation Using Hybrid Functional Petri Net

5 (2012) 1250015 5 (2012) 1240002 5 (2012) 1271002

J. Bioinform. Comput. Biol. 2012.10. Downloaded from www.worldscientific.com by 85.74.84.134 on 10/23/12. For personal use only.

2 2 2 2 2 2

(2012) (2012) (2012) (2012) (2012) (2012)

1241002 1250018 1250020 1241010 1241012 1250001

5 5 5 5 5 5

(2012) (2012) (2012) (2012) (2012) (2012)

1250010 1250018 1240009 1242002 1242005 1242008

1 (2012) 1240007 6 (2012) 1250017 6 (2012) 1242006

2 (2012) 1241010

6 (2012) 1250020 6 (2012) 1241005 1 1 1 1 (2012) (2012) (2012) (2012) 1240009 1241008 1242010 1250006

1 (2012) 1240006

1299001-7

Author Index

Terentiev, A. A., Moldogazieva, N. T., Levtsova, O. V., Maximenko, D. M., Borozdenko, D. A. and Shaitan, K. V., Modeling of Three Dimensional Structure of Human AlphaFetoprotein Complexed with Diethylstilbestrol: Docking and Molecular Dynamics Simulation Study Thahir, M., see Ganapathiraju, M. K. Thiagarajan, P. S., see Liu, B. To, T.-H., see Habib, M. Tom, I., see Novoselova, N. Tomar, N., see De, R. K. Tupakula, R., see Limaye, B. Tuzikov, A. V., see Ruvinsky, A. M. Vakser, I. A., see Ruvinsky, A. M. Vakulenko, S. A. and Radulescu, O., Flexible and Robust Networks Vats, P., see Limaye, B. Volokhina, I., Gusev, Y., Mazilov, S. and Chumakov, M., VirE2-Dependent Pores for ssDNA Transfer Across Articial and Cell Membranes Wang, F., see Tang, Y. Wang, J. T. L., see Hua, L. Wang, Z., see Cheng, J. Wong, L., A Short Introduction to Some Recent Progress in Phylogenetic Network Reconstruction, Genome Mapping, Gene Expression Analysis, Molecular Dynamic Simulation, and Other Problems in Bioinformatics Wu, Z., see Huang, Y. Xu, J., A New Method for Nonhomogeneous Time Course Expression Analysis Ying, J., see Gorlova, O. Y. Zhang, K., see Hua, L. Zhao, H., see Gorlov, I. P. Zinovyev, A., see Martignetti, L. Zubair, M., see Biswas, A.

J. Bioinform. Comput. Biol. 2012.10. Downloaded from www.worldscientific.com by 85.74.84.134 on 10/23/12. For personal use only.

2 2 2 2 2 2 2 2 2

(2012) (2012) (2012) (2012) (2012) (2012) (2012) (2012) (2012)

1241012 1250016 1231001 1250013 1250011 1250019 1250006 1241002 1241002

2 (2012) 1241011 2 (2012) 1250006

2 2 2 2

(2012) (2012) (2012) (2012)

1241009 1240006 1250001 1242003

4 (2012) 1203002 4 (2012) 1242007 4 4 4 4 4 4 (2012) (2012) (2012) (2012) (2012) (2012) 1250007 1241008 1250001 1241013 1241001 1242006

1299001-8