Tamer Kahveci

IEEE ACM Trans. Comput. Biol. Bioinform., 2020

Stability Analysis of Biological Networks' Diffusion State.

[BibT_eX]

[DOI]

Volkan Altuntas

Murat Gök

IEEE ACM Trans. Comput. Biol. Bioinform., 2020

A method to assess COVID-19 infected numbers in Italy during peak pandemic period.

[BibT_eX]

[DOI]

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2020

2019

Guest Editorial on the Special Issue on Informatics on Biomedical Data Learning, Reasoning, and Representation.

[BibT_eX]

[DOI]

IEEE J. Biomed. Health Informatics, 2019

Guest Editorial for the ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics.

[BibT_eX]

[DOI]

Amarda Shehu

Giuseppe Pozzi

IEEE ACM Trans. Comput. Biol. Bioinform., 2019

A New Algorithm for Counting Independent Motifs in Probabilistic Networks.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2019

Selected research articles from the 2018 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC).

[BibT_eX]

[DOI]

BMC Bioinform., 2019

Characterizing building blocks of resource constrained biological networks.

[BibT_eX]

[DOI]

BMC Bioinform., 2019

Aligning optical maps to de Bruijn graphs.

[BibT_eX]

[DOI]

Bioinform., 2019

Finding Conserved Patterns in Multilayer Networks.

[BibT_eX]

[DOI]

Proceedings of the 10th ACM International Conference on Bioinformatics, 2019

Co-evolving Patterns in Temporal Networks of Varying Evolution.

[BibT_eX]

[DOI]

Proceedings of the 10th ACM International Conference on Bioinformatics, 2019

2018

Index Structures for Biological Sequences.

[BibT_eX]

[DOI]

Proceedings of the Encyclopedia of Database Systems, Second Edition, 2018

Construction of Signaling Pathways with RNAi Data and Multiple Reference Networks.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2018

Identification of jointly correlated gene sets.

[BibT_eX]

[DOI]

J. Bioinform. Comput. Biol., 2018

Counting motifs in dynamic networks.

[BibT_eX]

[DOI]

BMC Syst. Biol., 2018

Selected research articles from the 2017 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC).

[BibT_eX]

[DOI]

BMC Bioinform., 2018

ProMotE: an efficient algorithm for counting independent motifs in uncertain network topologies.

[BibT_eX]

[DOI]

Yuanfang Ren

Aisharjya Sarkar

BMC Bioinform., 2018

Shortest path counting in probabilistic biological networks.

[BibT_eX]

[DOI]

Yuanfang Ren

Ahmet Ay

BMC Bioinform., 2018

Identification of Co-evolving Temporal Networks.

[BibT_eX]

[DOI]

Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

ANCA: Alignment-based Network Construction Algorithm.

[BibT_eX]

[DOI]

Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

2017

Motif centrality in food web networks.

[BibT_eX]

[DOI]

Rasha Elhesha

Benjamin Baiser

J. Complex Networks, 2017

Selected research articles from the 2016 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC).

[BibT_eX]

[DOI]

Byung-Jun Yoon

Xiaoning Qian

BMC Bioinform., 2017

CNB-MAC'17: The Fourth International Workshop on Computational Network Biology: Modeling, Analysis, and Control.

[BibT_eX]

[DOI]

Byung-Jun Yoon

Xiaoning Qian

Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

Highlights Talks at ACM BCB 2017.

[BibT_eX]

[DOI]

Amarda Shehu

Giuseppe Pozzi

Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

2016

Identifying the topology of signaling networks from partial RNAi data.

[BibT_eX]

[DOI]

BMC Syst. Biol., 2016

Identification of large disjoint motifs in biological networks.

[BibT_eX]

[DOI]

Rasha Elhesha

BMC Bioinform., 2016

Counting independent motifs in probabilistic networks.

[BibT_eX]

[DOI]

Proceedings of the 7th ACM International Conference on Bioinformatics, 2016

2015

Signal reachability facilitates characterization of probabilistic signaling networks.

[BibT_eX]

[DOI]

BMC Bioinform., December, 2015

Reachability Analysis in Probabilistic Biological Networks.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2015

Computing interaction probabilities in signaling networks.

[BibT_eX]

[DOI]

Juan Carlos Rivera-Mulia

David M. Gilbert

EURASIP J. Bioinform. Syst. Biol., 2015

Indexing a protein-protein interaction network expedites network alignment.

[BibT_eX]

[DOI]

BMC Bioinform., 2015

Hierarchical decomposition of dynamically evolving regulatory networks.

[BibT_eX]

[DOI]

Ahmet Ay

Dihong Gong

BMC Bioinform., 2015

Construction of signaling networks with incomplete RNAi data.

[BibT_eX]

[DOI]

Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015

Counting motifs in probabilistic biological networks.

[BibT_eX]

[DOI]

Proceedings of the 6th ACM Conference on Bioinformatics, 2015

Estimating reachability in dense biological networks.

[BibT_eX]

[DOI]

Proceedings of the 6th ACM Conference on Bioinformatics, 2015

Multiple reference networks improve accuracy of signaling network construction.

[BibT_eX]

[DOI]

Proceedings of the 6th ACM Conference on Bioinformatics, 2015

2014

Topologically associating domains are stable units of replication-timing regulation Open.

[BibT_eX]

[DOI]

Nat., 2014

Large scale analysis of signal reachability.

[BibT_eX]

[DOI]

Bioinform., 2014

Characterization of probabilistic signaling networks through signal propagation.

[BibT_eX]

[DOI]

Proceedings of the IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences, 2014

Incremental network querying in biological networks.

[BibT_eX]

[DOI]

Proceedings of the 5th ACM Conference on Bioinformatics, 2014

Extracting phylogenetic signals from multi-labeled gene trees and its significance for species tree construction.

[BibT_eX]

[DOI]

Proceedings of the 5th ACM Conference on Bioinformatics, 2014

2013

Characterizing the Topology of Probabilistic Biological Networks.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2013

Probabilistic Biological Network Alignment.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2013

Guest Editorial for ACM BCB.

[BibT_eX]

[DOI]

Mona Singh

IEEE ACM Trans. Comput. Biol. Bioinform., 2013

Making massive probabilistic databases practical.

[BibT_eX]

[DOI]

CoRR, 2013

A scalable method for discovering significant subnetworks.

[BibT_eX]

[DOI]

Yusuf Kavurucu

BMC Syst. Biol., 2013

Stability analysis of phylogenetic trees.

[BibT_eX]

[DOI]

Bioinform., 2013

From Uncertain Protein Interaction Networks to Signaling Pathways Through Intensive Color Coding.

[BibT_eX]

[DOI]

Proceedings of the Biocomputing 2013: Proceedings of the Pacific Symposium, 2013

Reachability analysis in large probabilistic biological networks.

[BibT_eX]

[DOI]

Proceedings of the ACM Conference on Bioinformatics, 2013

Color distribution can accelerate network alignment.

[BibT_eX]

[DOI]

Proceedings of the ACM Conference on Bioinformatics, 2013

PReach: Reachability in Probabilistic Signaling Networks.

[BibT_eX]

[DOI]

Proceedings of the ACM Conference on Bioinformatics, 2013

2012

Large-Scale Signaling Network Reconstruction.

[BibT_eX]

[DOI]

Seyedsasan Hashemikhabir

IEEE ACM Trans. Comput. Biol. Bioinform., 2012

Topac: Alignment of gene Regulatory Networks Using Topology-Aware Coloring.

[BibT_eX]

[DOI]

Bhavik Gandhi

J. Bioinform. Comput. Biol., 2012

A scalable method for identifying frequent subtrees in sets of large phylogenetic trees.

[BibT_eX]

[DOI]

Avinash Ramu

J. Gordon Burleigh

BMC Bioinform., 2012

HIDEN: Hierarchical decomposition of regulatory networks.

[BibT_eX]

[DOI]

BMC Bioinform., 2012

Metabolic network alignment in large scale by network compression.

[BibT_eX]

[DOI]

Michael Dang

BMC Bioinform., 2012

SSLPred : Predicting Synthetic Sickness Lethality.

[BibT_eX]

[DOI]

Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012

Inferring gene functions from metabolic reactions.

[BibT_eX]

[DOI]

Proceedings of the Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics, 2012

Uncertain interactions affect degree distribution of biological networks.

[BibT_eX]

[DOI]

Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine, 2012

SiS: Significant subnetworks in massive number of network topologies.

[BibT_eX]

[DOI]

Yusuf Kavurucu

Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine, 2012

2011

TRIAL: A Tool for Finding Distant Structural Similarities.

[BibT_eX]

[DOI]

Bin Song

Chris Jermaine

IEEE ACM Trans. Comput. Biol. Bioinform., 2011

Manipulating the Steady State of Metabolic Pathways.

[BibT_eX]

[DOI]

Bin Song

I. Esra Büyüktahtakin

IEEE ACM Trans. Comput. Biol. Bioinform., 2011

SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings.

[BibT_eX]

[DOI]

Manolis Kellis

J. Comput. Biol., 2011

RINQ: Reference-based Indexing for Network Queries.

[BibT_eX]

[DOI]

Bioinform., 2011

Identifying differentially regulated genes.

[BibT_eX]

[DOI]

Manas Somaiya

Proceedings of the IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, 2011

Topology aware coloring of gene regulatory networks.

[BibT_eX]

[DOI]

Bhavik Gandhi

Proceedings of the ACM International Conference on Bioinformatics, 2011

A novel framework for large scale metabolic network alignments by compression.

[BibT_eX]

[DOI]

Michael Dang

Proceedings of the ACM International Conference on Bioinformatics, 2011

2010

GBA Manager: An Online Tool for Querying Low-Complexity Regions in Proteins.

[BibT_eX]

[DOI]

J. Comput. Biol., 2010

SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings.

[BibT_eX]

[DOI]

Proceedings of the Research in Computational Molecular Biology, 2010

Surrogate ranking for very expensive similarity queries.

[BibT_eX]

[DOI]

Proceedings of the 26th International Conference on Data Engineering, 2010

Finding steady states of large scale regulatory networks through partitioning.

[BibT_eX]

[DOI]

Proceedings of the 2010 IEEE International Workshop on Genomic Signal Processing and Statistics, 2010

Finding Dynamic Modules of Biological Regulatory Networks.

[BibT_eX]

[DOI]

Proceedings of the 10th IEEE International Conference on Bioinformatics and Bioengineering, 2010

Enzymatic target identification with dynamic states.

[BibT_eX]

[DOI]

Bin Song

Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 2010

RepFrag: a graph based method for finding repeats and transposons from fragmented genomes.

[BibT_eX]

[DOI]

A. Mark Settles

Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 2010

Functional similarities of reaction sets in metabolic pathways.

[BibT_eX]

[DOI]

Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 2010

2009

Index Structures for Biological Sequences.

[BibT_eX]

[DOI]

Proceedings of the Encyclopedia of Database Systems, 2009

A Fast and Accurate Algorithm for Comparative Analysis of metabolic Pathways.

[BibT_eX]

[DOI]

Valérie de Crécy-Lagard

J. Bioinform. Comput. Biol., 2009

Double iterative optimisation for metabolic network-based drug target identification.

[BibT_eX]

[DOI]

Int. J. Data Min. Bioinform., 2009

Inferring progression models for CGH data.

[BibT_eX]

[DOI]

Jun Liu

Michael Baudis

Bioinform., 2009

Pathway-Based Feature Selection Algorithm for Cancer Microarray Data.

[BibT_eX]

[DOI]

Adv. Bioinformatics, 2009

2008

Reference-based indexing for metric spaces with costly distance measures.

[BibT_eX]

[DOI]

Christopher M. Jermaine

Deepak Lachwani

VLDB J., 2008

A novel genome-scale repeat finder geared towards transposons.

[BibT_eX]

[DOI]

Xuehui Li

A. Mark Settles

Bioinform., 2008

Mining Metabolic Networks for Optimal Drug Targets.

[BibT_eX]

[DOI]

Proceedings of the Biocomputing 2008, 2008

Classification and feature selection algorithms for multi-class CGH data.

[BibT_eX]

[DOI]

Jun Liu

Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

2007

QOMA: quasi-optimal multiple alignment of protein sequences.

[BibT_eX]

[DOI]

Xu Zhang

Bioinform., 2007

Markers improve clustering of CGH data.

[BibT_eX]

[DOI]

Jun Liu

Bioinform., 2007

An Iterative Algorithm for Metabolic Network-Based Drug Target Identification.

[BibT_eX]

[DOI]

Padmavati Sridhar

Proceedings of the Biocomputing 2007, 2007

Quality-Based Similarity Search for Biological Sequence Databases.

[BibT_eX]

Xuehui Li

Proceedings of the International Conference on Bioinformatics & Computational Biology, 2007

QOMA2: Optimizing the alignment of many sequences.

[BibT_eX]

[DOI]

Xu Zhang

Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007

2006

Distance-based clustering of CGH data.

[BibT_eX]

[DOI]

Bioinform., 2006

A Novel algorithm for identifying low-complexity regions in a protein sequence.

[BibT_eX]

[DOI]

Xuehui Li

Bioinform., 2006

Reference-based Indexing of Sequence Databases.

[BibT_eX]

[DOI]

Deepak Lachwani

Christopher M. Jermaine

Proceedings of the 32nd International Conference on Very Large Data Bases, 2006

A New Approach for Alignment of Multiple Proteins.

[BibT_eX]

[DOI]

Xu Zhang

Proceedings of the Biocomputing 2006, 2006

Finding Data Broadness Via Generalized Nearest Neighbors.

[BibT_eX]

[DOI]

Proceedings of the Advances in Database Technology, 2006

2005

Workload Characterization of Bioinformatics Applications.

[BibT_eX]

[DOI]

Proceedings of the 13th International Symposium on Modeling, 2005

Highly Scalable and Accurate Seeds for Subsequence Alignment.

[BibT_eX]

[DOI]

Abhijit Pol

Proceedings of the Fifth IEEE International Symposium on Bioinformatic and Bioengineering (BIBE 2005), 2005

Approximate Global Alignment of Sequences.

[BibT_eX]

[DOI]

Venkatakrishnan Ramaswamy

Han Tao

Tao Li

Proceedings of the Fifth IEEE International Symposium on Bioinformatic and Bioengineering (BIBE 2005), 2005

2004

Optimizing Similarity Search for Arbitrary Length Time Series Queries.

[BibT_eX]

[DOI]

IEEE Trans. Knowl. Data Eng., 2004

Index-based Similarity Search for Protein Structure Databases.

[BibT_eX]

[DOI]

J. Bioinform. Comput. Biol., 2004

Progressive Searching of Biological Sequences.

[BibT_eX]

[DOI]

IEEE Data Eng. Bull., 2004

Speeding up whole-genome alignment by indexing frequency vectors.

[BibT_eX]

[DOI]

Vebjorn Ljosa

Bioinform., 2004

ProGreSS: Simultaneous Searching of Protein Databases by Sequence and Structure.

[BibT_eX]

[DOI]

Proceedings of the Biocomputing 2004, 2004

2003

MAP: Searching Large Genome Databases.

[BibT_eX]

[DOI]

Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

PSI: indexing protein structures for fast similarity search.

[BibT_eX]

[DOI]

Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003

Fast alignment of large genome databases.

[BibT_eX]

[DOI]

Proceedings of the 19th International Conference on Data Engineering, 2003

Joining Massive High-Dimensional Datasets.

[BibT_eX]

[DOI]

Christian A. Lang

Proceedings of the 19th International Conference on Data Engineering, 2003

Genome on Demand: Interactive Substring Searching.

[BibT_eX]

[DOI]

Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003

Towards Index-based Similarity Search for Protein Structure Databases.

[BibT_eX]

[DOI]

Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003

2002

Similarity Searching for Multi-Attribute Sequences.

[BibT_eX]

[DOI]

Aliekber Gürel

Proceedings of the 14th International Conference on Scientific and Statistical Database Management, 2002

An Efficient Index Structure for Shift and Scale Invariant Search of Multi-Attribute Time Sequences.

[BibT_eX]

[DOI]

Aliekber Gürel

Proceedings of the 18th International Conference on Data Engineering, San Jose, CA, USA, February 26, 2002

2001

Efficient Index Structures for String Databases.

[BibT_eX]

[DOI]

Proceedings of the VLDB 2001, 2001

Variable Length Queries for Time Series Data.

[BibT_eX]

[DOI]