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AUTHOR INDEX

Volume 10 (2012)

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 2 (2012) 1241005

Akbal-Delibas, B., see Hashmi, I. 2 (2012) 1242008

Akbal-Delibas, B., Hashmi, I., Shehu, A. and Haspel, N., An

Evolutionary Conservation-Based Method for Rening and

Reranking Protein Complex Structures 3 (2012) 1242002

Aksianov, E. and Alexeevski, A., SheeP: A Tool for

Description of-Sheets in Protein 3D Structures 2 (2012) 1241003

Alexeevski, A., see Aksianov, E. 2 (2012) 1241003

Al Nasr, K., see Biswas, A. 2 (2012) 1242006

Amos, C. I., see Gorlova, O. Y. 2 (2012) 1241008

Ananthasubramanian, S., see Ganapathiraju, M. K. 2 (2012) 1250016

Arnold, N., see Krivan, W. 2 (2012) 1250009

Awad, S., Panchy, N., Ng, S.-K. and Chen, J., Inferring the

Regulatory Interaction Models of Transcription Factors in

Transcriptional Regulatory Networks 5 (2012) 1250012

Bandyopadhyay, P., see Meher, B. R. 5 (2012) 1250018

Bandyopadhyay, S., see Chen, B. Y. 5 (2012) 1242004

Banerjee, R., see Limaye, B. 5 (2012) 1250006

Barillot, E., see Martignetti, L. 5 (2012) 1241001

Batagov, A., see Sirota, F. L. 5 (2012) 1250020

Batuwita, R. and Palade, V., Adjusted Geometric-Mean: A

Novel Performance Measure for Imbalanced Bioinformatics

Datasets Learning 4 (2012) 1250003

Bayaskar, A., see Limaye, B. 4 (2012) 1250006

Bederman, I., see Cakmak, A. 4 (2012) 1240003

Benson, N. C. and Daggett, V., A Chemical Group Graph

Representation for Ecient High-Throughput Analysis of

Atomistic Protein Simulations 4 (2012) 1250008

Bereg, S., see Sheng, R. 4 (2012) 1250017

Journal of Bioinformatics and Computational BiologyVol. 10, No. 6 (2012) 1299001 (8 pages)#.c Imperial College PressDOI: 10.1142/S0219720012990016

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Bernauer, J., see Sim, A. Y. L. 4 (2012) 1241010

Berry, V., see Gambette, P. 4 (2012) 1250004Bhandari, A., see Limaye, B. 4 (2012) 1250006

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 3 (2012) 1242006

te Boekhorst, R., see Abnizova, I. 3 (2012) 1241005

Bonett, S., see Huang, Y. 3 (2012) 1242007

Borozdenko, D. A., see Terentiev, A. A. 3 (2012) 1241012

Boyd, S. and Haghighi, M., A Fast Method for Large-ScaleMultichromosomal Breakpoint Median Problems 1 (2012) 1240008

Brown, A., see Abnizova, I. 1 (2012) 1241005

Bucher, P., see Dimitrieva, S. 1 (2012) 1241007

Byun, J., see Gorlov, I. P. 1 (2012) 1241013

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 1 (2012) 1240003

Carter, D., see Krivan, W. 1 (2012) 1250009Casagrande, A. and Fabris, F., Family Fingerprints: A Global

Approach to Structural Classication 3 (2012) 1242001

Chen, B. Y. and Bandyopadhyay, S., A Regionalizable

Statistical Model of Intersecting Regions in

ProteinLigand Binding Cavities 3 (2012) 1242004

Chen, J., see Awad, S. 3 (2012) 1250012

Chen, J., see Jiao, Y. 3 (2012) 1271002

Chen, Y. and Li, J., Generation of Synthetic Data and

Experimental Designs in Evaluating Interactions forAssociation Studies 1 (2012) 1240005

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 3 (2012) 1242003

Chong, K. F. and Leong, H. W., Tutorial on De Novo Peptide

Sequencing Using MS/MS Mass Spectrometry 6 (2012) 1231002

Chumakov, M., see Volokhina, I. 6 (2012) 1241009

Cicek, A. E., see Cakmak, A. 6 (2012) 1240003

Cicek, A. E. and Ozsoyoglu, G., Observation ConictResolution in Steady-State Metabolic Network Dynamics

Analysis 1 (2012) 1240004

Cox, T., see Abnizova, I. 1 (2012) 1241005

Daggett, V., see Benson, N. C. 1 (2012) 1250008

Author Index

1299001-2

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Dahale, S., see Limaye, B. 1 (2012) 1250006

Datta, A., see Limaye, B. 1 (2012) 1250006De, R. K. and Tomar, N., Modeling the Optimal Central

Carbon Metabolic Pathways Under Feedback Inhibition

Using Flux Balance Analysis 6 (2012) 1250019

Deng, X., see Cheng, J. 6 (2012) 1242003

Dimitrieva, S. and Bucher, P., Practicality and Time

Complexity of a Sparsied RNA Folding Algorithm 2 (2012) 1241007

Dong, G., see Han, Q. 2 (2012) 1250005

Drumm, M., see Cakmak, A. 2 (2012) 1240003

Eickholt, J., see Cheng, J. 2 (2012) 1242003Eisenhaber, B., see Sirota, F. L. 2 (2012) 1250020

Eisenhaber, F., see Sirota, F. L. 2 (2012) 1250020

Eisenhaber, F., A Decade After the First Full Human

Genome Sequencing: When Will We Understand our own

Genome? 5 (2012) 1271001

Fabris, F., see Casagrande, A. 5 (2012) 1242001

Faruque, N., see Abnizova, I. 5 (2012) 1241005

Gadhari, R., see Limaye, B. 5 (2012) 1250006

Gambette, P., Berry, V. and Paul, C., Quartets and UnrootedPhylogenetic Networks 4 (2012) 1250004

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 6 (2012) 1250016

Gandhi, B., see Glsoy, G. 6 (2012) 1240001

Gavane, V., see Limaye, B. 6 (2012) 1250006

Gorlov, I. P., see Gorlova, O. Y. 6 (2012) 1241008

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 2 (2012) 1241013

Gorlova, O. Y., see Gorlov, I. P. 2 (2012) 1241013

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 2 (2012) 1241008Gourtovaia, M., see Abnizova, I. 2 (2012) 1241005

Glsoy, G., Gandhi, B. and Kahveci, T., TOPAC: Alignment

of Gene Regulatory Networks Using Topology-Aware

Coloring 1 (2012) 1240001

Author Index

1299001-3

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Gusev, Y., see Volokhina, I. 1 (2012) 1241009

Habib, M. and To, T.-H., Constructing a MinimumPhylogenetic Network from a Dense Triplet Set 5 (2012) 1250013

Haghighi, M., see Boyd, S. 5 (2012) 1240008

Han, Q. and Dong, G., Using Attribute Behavior Diversity to

Build Accurate Decision Tree Committees for Microarray

Data 4 (2012) 1250005

Hardy, J., see Jagodzinski, F. 4 (2012) 1242010

Hashmi, I., see Akbal-Delibas, B. 4 (2012) 1242002

Hashmi, I., Akbal-Delibas, B., Haspel, N. and Shehu, A.,

Guiding Protein Docking with Geometric and EvolutionaryInformation 3 (2012) 1242008

Haspel, N., see Akbal-Delibas, B. 3 (2012) 1242002

Haspel, N., see Hashmi, I. 3 (2012) 1242008

He, J., see Biswas, A. 3 (2012) 1242006

Henderson, L., see Cakmak, A. 3 (2012) 1240003

Hendi, S. F., see Olson, B. 3 (2012) 1242005

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 Structuresand Its Application to Structural Repeat Detection 4 (2012) 1250001

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 3 (2012) 1242007

Imoto, S., see Sharma, A. 3 (2012) 1250010

Inamdar, H., see Limaye, B. 3 (2012) 1250006

Jackson, D., see Abnizova, I. 3 (2012) 1241005

Jagodzinski, F., Hardy, J. and Streinu, I., Using Rigidity

Analysis to Probe Mutation-Induced Structural Changes inProteins 3 (2012) 1242010

Jain, S., see Limaye, B. 3 (2012) 1250006

Jernigan, R., see Huang, Y. 3 (2012) 1242007

Ji, X., see Hua, L. 3 (2012) 1250001

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 6 (2012) 1271002

Joshi, R., see Limaye, B. 6 (2012) 1250006Kahveci, T., see Glsoy, G. 6 (2012) 1240001

Kamzolova, S. G., see Osypov, A. A. 6 (2012) 1241004

Khaladkar, M., see Hua, L. 6 (2012) 1250001

Author Index

1299001-4

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Kimura, K., Koike, A. and Nakai, K., A Bit-Parallel Dynamic

Programming Algorithm Suitable for DNA SequenceAlignment 4 (2012) 1250002

Kirys, T., see Ruvinsky, A. M. 4 (2012) 1241002

Kloczkowski, A., see Huang, Y. 4 (2012) 1242007

Koike, A., see Kimura, K. 4 (2012) 1250002

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 5 (2012) 1250009

Krutinin, G. G., see Osypov, A. A. 5 (2012) 1241004Krutinina, E. A., see Osypov, A. A. 5 (2012) 1241004

Lavor, C., see Mucherino, A. 5 (2012) 1242009

Leonard, S., see Abnizova, I. 5 (2012) 1241005

Leong, H. W., see Chong, K. F. 5 (2012) 1231002

Levitt, M., see Sim, A. Y. L. 5 (2012) 1241010

Levtsova, O. V., see Terentiev, A. A. 5 (2012) 1241012

Lewis, K., see Abnizova, I. 5 (2012) 1241005

Li, J., see Chen, Y. 5 (2012) 1240005

Li, W., Volcano Plots in Analyzing Dierential Expressionswith mRNA Microarrays 6 (2012) 1231003

Liberti, L., see Mucherino, A. 6 (2012) 1242009

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 4 (2012) 1250006

Liu, B. and Thiagarajan, P. S., Modeling and Analysis ofBiopathways Dynamics 4 (2012) 1231001

Liu, Y., see Shen, C. 4 (2012) 1240007

Logothetis, C. J., see Gorlov, I. P. 4 (2012) 1241013

Mahajan, R., see Limaye, B. 4 (2012) 1250006

Malhotra, A., see Hua, L. 4 (2012) 1250001

Malviya, S., see Limaye, B. 4 (2012) 1250006

Martignetti, L., Zinovyev, A. and Barillot, E., Identication

of Shortened 3 0 Untranslated Regions from Expression

Arrays 2 (2012) 1241001Maurer-Stroh, S., see Sirota, F. L. 2 (2012) 1250020

Maximenko, D. M., see Terentiev, A. A. 2 (2012) 1241012

Mazilov, S., see Volokhina, I. 2 (2012) 1241009

Author Index

1299001-5

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Meher, B. R., Satish Kumar, M. V., Sharma, S. and

Bandyopadhyay, P., Conformational Dynamics of HIV-1Protease: A Comparative Molecular Dynamics Simulation

Study with Multiple Amber Force Fields 6 (2012) 1250018

Mitchell, A. D., see Ganapathiraju, M. K. 6 (2012) 1250016

Miyano, S., see Sharma, A. 6 (2012) 1250010

Moldogazieva, N. T., see Terentiev, A. A. 6 (2012) 1241012

Molloy, K., see Olson, B. 6 (2012) 1242005

Montgomery, B. L., see Jiao, Y. 6 (2012) 1271002

Morales, C., see Krivan, W. 6 (2012) 1250009

Motwani, K., see Ganapathiraju, M. K. 6 (2012) 1250016Mucherino, A., Lavor, C. and Liberti, L., Exploiting

Symmetry Properties of the Discretizable Molecular

Distance Geometry Problem 3 (2012) 1242009

Nakai, K., see Kimura, K. 3 (2012) 1250002

Ng, S.-K., see Awad, S. 3 (2012) 1250012

Novoselova, N. and Tom, I., Entropy-Based Cluster

Validation and Estimation of the Number of Clusters in

Gene Expression Data 5 (2012) 1250011

Odibat, O. and Reddy, C. K., Ranking Dierential Hubs inGene Co-Expression Networks 1 (2012) 1240002

Oh, S., see Jiao, Y. 1 (2012) 1271002

Olson, B., Molloy, K., Hendi, S. F. and Shehu, A., Guiding

Probabilistic Search of the Protein Conformational Space

with Structural Proles 3 (2012) 1242005

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 2 (2012) 1241004Ozsoyoglu, G., see Cakmak, A. 2 (2012) 1240003

Ozsoyoglu, G., see Cicek, A. E. 2 (2012) 1240004

Palade, V., see Batuwita, R. 2 (2012) 1250003

Panchy, N., see Awad, S. 2 (2012) 1250012

Paul, C., see Gambette, P. 2 (2012) 1250004

Peng, B., see Gorlova, O. Y. 2 (2012) 1241008

Qi, G., see Abnizova, I. 2 (2012) 1241005

Qi, X., see Cakmak, A. 2 (2012) 1240003

Qin, W., see Jiao, Y. 2 (2012) 1271002Radulescu, O., see Vakulenko, S. A. 2 (2012) 1241011

Ramakrishnan, E. P., see Limaye, B. 2 (2012) 1250006

Rangwala, H., see Rasheed, Z. 2 (2012) 1250015

Ranjan, D., see Biswas, A. 2 (2012) 1242006

Author Index

1299001-6

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Rasheed, Z. and Rangwala, H., Metagenomic Taxonomic

Classication Using Extreme Learning Machines 5 (2012) 1250015Reddy, C. K., see Odibat, O. 5 (2012) 1240002

Rosa, B. A., see Jiao, Y. 5 (2012) 1271002

Ruvinsky, A. M., Kirys, T., Tuzikov, A. V. and Vakser, I. A.,

Structure Fluctuations and Conformational Changes in

Protein Binding 2 (2012) 1241002

Satish Kumar, M. V., see Meher, B. R. 2 (2012) 1250018

Schneider, G., see Sirota, F. L. 2 (2012) 1250020

Schwander, O., see Sim, A. Y. L. 2 (2012) 1241010

Shaitan, K. V., see Terentiev, A. A. 2 (2012) 1241012Shapiro, B. A., see Hua, L. 2 (2012) 1250001

Sharma, A., Imoto, S. and Miyano, S., A Between-Class

Overlapping Filter-Based Method for Transcriptome Data

Analysis 5 (2012) 1250010

Sharma, S., see Meher, B. R. 5 (2012) 1250018

Shavlik, J., see Soni, A. 5 (2012) 1240009

Shehu, A., see Akbal-Delibas, B. 5 (2012) 1242002

Shehu, A., see Olson, B. 5 (2012) 1242005

Shehu, A., see Hashmi, I. 5 (2012) 1242008Shen, C. and Liu, Y., A Tripartite Clustering Analysis on

MicroRNA, Gene and Disease Model 1 (2012) 1240007

Sheng, R. and Bereg, S., Approximating Metrics with Planar

Boundary-Labeled Phylogenetic Networks 6 (2012) 1250017

Si, D., see Biswas, A. 6 (2012) 1242006

Sim, A. Y. L., Schwander, O., Levitt, M. and Bernauer, J.,

Evaluating Mixture Models for Building RNA Knowledge-

Based Potentials 2 (2012) 1241010

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 6 (2012) 1250020

Skelly, T., see Abnizova, I. 6 (2012) 1241005

Soni, A. and Shavlik, J., Probabilistic Ensembles for

Improved Inference in Protein-Structure Determination 1 (2012) 1240009

Spitz, M. R., see Gorlova, O. Y. 1 (2012) 1241008

Streinu, I., see Jagodzinski, F. 1 (2012) 1242010

Sunitha, K., see Limaye, B. 1 (2012) 1250006Tang, Y. and Wang, F., Neural System Modeling and

Simulation Using Hybrid Functional Petri Net 1 (2012) 1240006

Author Index

1299001-7

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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 Alpha-

Fetoprotein Complexed with Diethylstilbestrol: Docking

and Molecular Dynamics Simulation Study 2 (2012) 1241012

Thahir, M., see Ganapathiraju, M. K. 2 (2012) 1250016

Thiagarajan, P. S., see Liu, B. 2 (2012) 1231001

To, T.-H., see Habib, M. 2 (2012) 1250013

Tom, I., see Novoselova, N. 2 (2012) 1250011

Tomar, N., see De, R. K. 2 (2012) 1250019

Tupakula, R., see Limaye, B. 2 (2012) 1250006Tuzikov, A. V., see Ruvinsky, A. M. 2 (2012) 1241002

Vakser, I. A., see Ruvinsky, A. M. 2 (2012) 1241002

Vakulenko, S. A. and Radulescu, O., Flexible and Robust

Networks 2 (2012) 1241011

Vats, P., see Limaye, B. 2 (2012) 1250006

Volokhina, I., Gusev, Y., Mazilov, S. and Chumakov, M.,

VirE2-Dependent Pores for ssDNA Transfer Across

Articial and Cell Membranes 2 (2012) 1241009

Wang, F., see Tang, Y. 2 (2012) 1240006Wang, J. T. L., see Hua, L. 2 (2012) 1250001

Wang, Z., see Cheng, J. 2 (2012) 1242003

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 4 (2012) 1203002

Wu, Z., see Huang, Y. 4 (2012) 1242007

Xu, J., A New Method for Nonhomogeneous Time Course

Expression Analysis 4 (2012) 1250007Ying, J., see Gorlova, O. Y. 4 (2012) 1241008

Zhang, K., see Hua, L. 4 (2012) 1250001

Zhao, H., see Gorlov, I. P. 4 (2012) 1241013

Zinovyev, A., see Martignetti, L. 4 (2012) 1241001

Zubair, M., see Biswas, A. 4 (2012) 1242006

Author Index

1299001-8

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