30 Result(s)

Article

Selected Research Articles from the 2019 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC)

Byung-Jun Yoon, **aoning Qian, Tamer Kahveci, Ranadip Pal in BMC Genomics (2020)

Article

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

Byung-Jun Yoon, **aoning Qian, Tamer Kahveci, Ranadip Pal in BMC Bioinformatics (2019)

Article

Characterizing building blocks of resource constrained biological networks

Identification of motifs–recurrent and statistically significant patterns–in biological networks is the key to understand the design principles, and to infer governing mechanisms of biological systems. This, h...

Yuanfang Ren, Ahmet Ay, Alin Dobra, Tamer Kahveci in BMC Bioinformatics (2019)

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)

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

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

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

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

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

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

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

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

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

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

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

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)