- 2012
- Alessandro Abate, Stéphane Vincent, Roel Dobbe, Alberto Silletti, Neal Master, Jeffrey D. Axelrod, Claire J. Tomlin:
A Mathematical Model to Study the Dynamics of Epithelial Cellular Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 9(6): 1607-1620 (2012) - Lipi R. Acharya, Thair Judeh, Zhansheng Duan, Michael G. Rabbat, Dongxiao Zhu:
GSGS: A Computational Approach to Reconstruct Signaling Pathway Structures from Gene Sets. IEEE ACM Trans. Comput. Biol. Bioinform. 9(2): 438-450 (2012) - Tatsuya Akutsu
, Sven Kosub
, Avraham A. Melkman
, Takeyuki Tamura:
Finding a Periodic Attractor of a Boolean Network. IEEE ACM Trans. Comput. Biol. Bioinform. 9(5): 1410-1421 (2012) - Kyle H. Ambert, Aaron M. Cohen:
k-Information Gain Scaled Nearest Neighbors: A Novel Approach to Classifying Protein-Protein Interaction-Related Documents. IEEE ACM Trans. Comput. Biol. Bioinform. 9(1): 305-310 (2012) - Mohammad Shafkat Amin, Russell L. Finley Jr.
, Hasan M. Jamil
:
Top-k Similar Graph Matching Using TraM in Biological Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 9(6): 1790-1804 (2012) - Sandro Andreotti
, Gunnar W. Klau
, Knut Reinert
:
Antilope - A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem. IEEE ACM Trans. Comput. Biol. Bioinform. 9(2): 385-394 (2012) - Ulavappa B. Angadi, M. Venkatesulu:
Structural SCOP Superfamily Level Classification Using Unsupervised Machine Learning. IEEE ACM Trans. Comput. Biol. Bioinform. 9(2): 601-608 (2012) - Nadeem Ansari, Riyue Bao, Calin Voichita, Sorin Draghici
:
Detecting Phenotype-Specific Interactions between Biological Processes from Microarray Data and Annotations. IEEE ACM Trans. Comput. Biol. Bioinform. 9(5): 1399-1409 (2012) - Giuliano Armano, Filippo Ledda:
Exploiting Intrastructure Information for Secondary Structure Prediction with Multifaceted Pipelines. IEEE ACM Trans. Comput. Biol. Bioinform. 9(3): 799-808 (2012) - Wendy Ashlock, Suprakash Datta:
Distinguishing Endogenous Retroviral LTRs from SINE Elements Using Features Extracted from Evolved Side Effect Machines. IEEE ACM Trans. Comput. Biol. Bioinform. 9(6): 1676-1689 (2012) - Hossam M. Ashtawy, Nihar R. Mahapatra:
A Comparative Assessment of Ranking Accuracies of Conventional and Machine-Learning-Based Scoring Functions for Protein-Ligand Binding Affinity Prediction. IEEE ACM Trans. Comput. Biol. Bioinform. 9(5): 1301-1313 (2012) - Silvana Badaloni, Barbara Di Camillo, Francesco Sambo:
Qualitative Reasoning for Biological Network Inference from Systematic Perturbation Experiments. IEEE ACM Trans. Comput. Biol. Bioinform. 9(5): 1482-1491 (2012) - Jiri Barnat, Lubos Brim
, Adam Krejci, Adam Streck, David Safránek
, Martin Vejnar, Tomas Vejpustek:
On Parameter Synthesis by Parallel Model Checking. IEEE ACM Trans. Comput. Biol. Bioinform. 9(3): 693-705 (2012) - Vincenzo Belcastro
, Francesco Gregoretti
, Velia Siciliano, Michele Santoro, Giovanni D'Angelo, Gennaro Oliva
, Diego di Bernardo
:
Reverse Engineering and Analysis of Genome-Wide Gene Regulatory Networks from Gene Expression Profiles Using High-Performance Computing. IEEE ACM Trans. Comput. Biol. Bioinform. 9(3): 668-678 (2012) - Manuele Bicego, Pietro Lovato, Alessandro Perina, Marianna Fasoli
, Massimo Delledonne
, Mario Pezzotti, Annalisa Polverari, Vittorio Murino
:
Investigating Topic Models' Capabilities in Expression Microarray Data Classification. IEEE ACM Trans. Comput. Biol. Bioinform. 9(6): 1831-1836 (2012) - Damian Bogdanowicz, Krzysztof Giaro
:
Matching Split Distance for Unrooted Binary Phylogenetic Trees. IEEE ACM Trans. Comput. Biol. Bioinform. 9(1): 150-160 (2012) - Shahid H. Bokhari, Laura W. Pomeroy, Daniel Janies:
Reassortment Networks and the Evolution of Pandemic H1N1 Swine-Origin Influenza. IEEE ACM Trans. Comput. Biol. Bioinform. 9(1): 214-227 (2012) - Maria Luisa Bonet
, Simone Linz
, Katherine St. John
:
The Complexity of Finding Multiple Solutions to Betweenness and Quartet Compatibility. IEEE ACM Trans. Comput. Biol. Bioinform. 9(1): 273-285 (2012) - Nicolas Bonnel, Pierre-Francois Marteau:
LNA: Fast Protein Structural Comparison Using a Laplacian Characterization of Tertiary Structure. IEEE ACM Trans. Comput. Biol. Bioinform. 9(5): 1451-1458 (2012) - Christina Boucher, Mohamed Omar:
On the Hardness of Counting and Sampling Center Strings. IEEE ACM Trans. Comput. Biol. Bioinform. 9(6): 1843-1846 (2012) - Mark Burkitt, Dawn C. Walker, Daniela M. Romano
, Alireza Fazeli
:
Constructing Complex 3D Biological Environments from Medical Imaging Using High Performance Computing. IEEE ACM Trans. Comput. Biol. Bioinform. 9(3): 643-654 (2012) - Alhadi Bustamam
, Kevin Burrage
, Nicholas A. Hamilton
:
Fast Parallel Markov Clustering in Bioinformatics Using Massively Parallel Computing on GPU with CUDA and ELLPACK-R Sparse Format. IEEE ACM Trans. Comput. Biol. Bioinform. 9(3): 679-692 (2012) - Barbara Di Camillo, Marco Falda
, Gianna Toffolo, Claudio Cobelli:
SimBioNeT: A Simulator of Biological Network Topology. IEEE ACM Trans. Comput. Biol. Bioinform. 9(2): 592-600 (2012) - Ricardo J. G. B. Campello
, Davoud Moulavi, Jörg Sander
:
A Simpler and More Accurate AUTO-HDS Framework for Clustering and Visualization of Biological Data. IEEE ACM Trans. Comput. Biol. Bioinform. 9(6): 1850-1852 (2012) - Gizem Çavuslar, Bülent Çatay, Mehmet Serkan Apaydin
:
A Tabu Search Approach for the NMR Protein Structure-Based Assignment Problem. IEEE ACM Trans. Comput. Biol. Bioinform. 9(6): 1621-1628 (2012) - Raymond H. Chan, Tony H. Chan, Hau Man Yeung, Roger Wei Wang:
Composition Vector Method Based on Maximum Entropy Principle for Sequence Comparison. IEEE ACM Trans. Comput. Biol. Bioinform. 9(1): 79-87 (2012) - Ruchi Chaudhary, J. Gordon Burleigh, David Fernández-Baca:
Fast Local Search for Unrooted Robinson-Foulds Supertrees. IEEE ACM Trans. Comput. Biol. Bioinform. 9(4): 1004-1013 (2012) - Yi-Ping Phoebe Chen
:
Guest Editorial: Application and Development of Bioinformatics. IEEE ACM Trans. Comput. Biol. Bioinform. 9(5): 1265 (2012) - Zhi-Zhong Chen, Fei Deng, Lusheng Wang
:
Simultaneous Identification of Duplications, Losses, and Lateral Gene Transfers. IEEE ACM Trans. Comput. Biol. Bioinform. 9(5): 1515-1528 (2012) - Xin Chen, Xiaohua Hu, Tze Yee Lim
, Xiajiong Shen, E. K. Park, Gail L. Rosen
:
Exploiting the Functional and Taxonomic Structure of Genomic Data by Probabilistic Topic Modeling. IEEE ACM Trans. Comput. Biol. Bioinform. 9(4): 980-991 (2012)