23 Result(s)

Article

Metabolic network alignment in large scale by network compression

Metabolic network alignment is a system scale comparative analysis that discovers important similarities and differences across different metabolisms and organisms. Although the problem of aligning metabolic n...

Ferhat Ay, Michael Dang, Tamer Kahveci in BMC Bioinformatics (2012)

Article

CMRF: analyzing differential gene regulation in two group perturbation experiments

Microarray experiments often measure expressions of genes taken from sample tissues in the presence of external perturbations such as medication, radiation, or disease. The external perturbation can change the...

Nirmalya Bandyopadhyay, Manas Somaiya, Sanjay Ranka, Tamer Kahveci in BMC Genomics (2012)

Article

HIDEN: Hierarchical decomposition of regulatory networks

Transcription factors regulate numerous cellular processes by controlling the rate of production of each gene. The regulatory relations are modeled using transcriptional regulatory networks. Recent studies hav...

Günhan Gülsoy, Nirmalya Bandhyopadhyay, Tamer Kahveci in BMC Bioinformatics (2012)

Article

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

We consider the problem of finding the maximum frequent agreement subtrees (MFASTs) in a collection of phylogenetic trees. Existing methods for this problem often do not scale beyond datasets with around 100 t...

Avinash Ramu, Tamer Kahveci, J Gordon Burleigh in BMC Bioinformatics (2012)

Article

A scalable method for discovering significant subnetworks

Study of biological networks is an essential first step to understand the complex functions they govern in different organisms. The topology of interactions that define how biological networks operate is often...

Md Mahmudul Hasan, Yusuf Kavurucu, Tamer Kahveci in BMC Systems Biology (2013)

Article

Topologically associating domains are stable units of replication-timing regulation

A study of DNA replication timing in mouse and human cells reveals that replication domains (domains of the genome which replicate at the same time) share a correlation with topologically associating domains; ...

Benjamin D. Pope, Tyrone Ryba, Vishnu Dileep, Feng Yue, Weisheng Wu, Olgert Denas… in Nature (2014)

Article

A comparative encyclopedia of DNA elements in the mouse genome

The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater in...

Feng Yue, Yong Cheng, Alessandra Breschi, Jeff Vierstra, Weisheng Wu, Tyrone Ryba… in Nature (2014)

Article

Hierarchical decomposition of dynamically evolving regulatory networks

Gene regulatory networks describe the interplay between genes and their products. These networks control almost every biological activity in the cell through interactions. The hierarchy of genes in these netwo...

Ahmet Ay, Dihong Gong, Tamer Kahveci in BMC Bioinformatics (2015)

Article

Indexing a protein-protein interaction network expedites network alignment

Network query problem aligns a small query network with an arbitrarily large target network. The complexity of this problem grows exponentially with the number of nodes in the query network if confidence in th...

Md Mahmudul Hasan, Tamer Kahveci in BMC Bioinformatics (2015)

Article

Computing interaction probabilities in signaling networks

Biological networks inherently have uncertain topologies. This arises from many factors. For instance, interactions between molecules may or may not take place under varying conditions. Genetic or epigenetic m...

Haitham Gabr, Juan Carlos Rivera-Mulia… in EURASIP Journal on Bioinformatics and Syst… (2015)

Article

Signal reachability facilitates characterization of probabilistic signaling networks

Studying biological networks is of extreme importance in understanding cellular functions. These networks model interactions between molecules in each cell. A large volume of research has been done to uncover ...

Haitham Gabr, Tamer Kahveci in BMC Bioinformatics (2015)

Article

Identifying the topology of signaling networks from partial RNAi data

Methods for inferring signaling networks using single gene knockdown RNAi experiments and reference networks have been proposed in recent years. These methods assume that RNAi information is available for all ...

Yuanfang Ren, Qiyao Wang, Md Mahmudul Hasan, Ahmet Ay, Tamer Kahveci in BMC Systems Biology (2016)

Article

Identification of large disjoint motifs in biological networks

Biological networks provide great potential to understand how cells function. Network motifs, frequent topological patterns, are key structures through which biological networks operate. Finding motifs in biol...

Rasha Elhesha, Tamer Kahveci in BMC Bioinformatics (2016)

Article

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

Byung-Jun Yoon, **aoning Qian, Tamer Kahveci in BMC Bioinformatics (2017)

Article

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

Byung-Jun Yoon, **aoning Qian, Tamer Kahveci, Ranadip Pal in BMC Bioinformatics (2018)

Article

Counting motifs in dynamic networks

A network motif is a sub-network that occurs frequently in a given network. Detection of such motifs is important since they uncover functions and local properties of the given biological network. Finding moti...

Kingshuk Mukherjee, Md Mahmudul Hasan, Christina Boucher… in BMC Systems Biology (2018)

Article

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

Identifying motifs in biological networks is essential in uncovering key functions served by these networks. Finding non-overlap** motif instances is however a computationally challenging task. The fact that...

Yuanfang Ren, Aisharjya Sarkar, Tamer Kahveci in BMC Bioinformatics (2018)

Article

Shortest path counting in probabilistic biological networks

Biological regulatory networks, representing the interactions between genes and their products, control almost every biological activity in the cell. Shortest path search is critical to apprehend the structure...

Yuanfang Ren, Ahmet Ay, Tamer Kahveci in BMC Bioinformatics (2018)

Article

Identification of co-evolving temporal networks

Biological networks describes the mechanisms which govern cellular functions. Temporal networks show how these networks evolve over time. Studying the temporal progression of network topologies is of utmost im...

Rasha Elhesha, Aisharjya Sarkar, Christina Boucher, Tamer Kahveci in BMC Genomics (2019)