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Haitham Gabr and Tamer Kahveci have co-authored a paper with the Gilbert Lab at the Genome Research journal. The title of their paper is "Dynamic changes in replication timing and gene expression during human development". (06/2015)
The Bioinformatics Lab is awarded a three year NSF grant, titled "Inferring the genetic architecture of gene expression in prostate cancer" in a collaborative project. (05/2015)
Haitham Gabr's paper with Tamer Kahveci has been accepted for publication in BMC Bioinformatics. The title of the paper is "Signal reachability facilitates characterization of probabilistic signaling networks". (04/2015)
Ahmet Ay's paper with Dihong Gong and Tamer Kahveci has been accepted for publication in BMC Bioinformatics. The title of the paper is "Hierarchical Decomposition of Dynamically Evolving Regulatory Networks". (03/2015)
The Bioinformatics Lab is awarded a one year project titled "Integrating Omics Data with Domain Specific Knowledge for Predicting Cellular Sensitivity to Chemotherapy And Radiotherapy". (02/2015)
Tamer Kahveci has co-authored a paper with the mouse ENCODE Consortium, which is accepted to the Nature journal. The title of their paper is "An Integrated and Comparative Encyclopedia of DNA Elements in the Mouse Genome". (10/2014)
Tamer Kahveci has co-authored a paper with Gilbert Lab, which is accepted to the Nature journal. The title of their paper is "Topologically-associating domains are stable units of replication-timing regulation". (09/2014)
Md Mahmudul Hasan's paper with Tamer Kahveci is accepted to the 8th International Workshop on Biomolecular Network Analysis (IWBNA 2014) at ACM-BCB 2014. The title of their paper is "Incremental Network Querying in Biological Networks". (07/2014)
Rasha Elhesha's paper with Ryan Cobb and Tamer Kahveci is accepted to the International Conference on Bioinformatics and Computational Biology (ACM-BCB) 2014. The title of their paper is "Extracting phylogenetic signals from gene trees and its significance for species tree construction". (07/2014)
Haitham Gabr's paper with Andrei Todor, Alin Dobra and Tamer Kahveci is accepted to the IEEE/ACM Transactions on Computational Biology and Bioinformatics. The title of their paper is "Reachability analysis in probabilistic biological networks". (07/2014)
The Bioinformatics Lab is awarded a one year project titled "Integrating Omics Data with Domain Specific Knowledge for Predicting Cellular Sensitivity to Chemotherapy And Radiotherapy". (06/2014)
Ahmet Ay paper with Dihong Gong and Tamer Kahveci is accepted to the Cancer Informatics Journal. The title of their paper is "Network-based prediction of cancer under genetic storm". (06/2014)
The Bioinformatics Lab is awarded a one year project titled "Identification of phylogenetic and functional networks of prokaryotes that control methane production in peatlands". (06/2014)
Haitham Gabr's paper with Tamer Kahveci is accepted to the IEEE ICCABS conference. The title of their paper is "Characterization of probabilistic signaling networks through signal propagation". (05/2014)
Tamer Kahveci is the Workshops chair of the International Conference on Bioinformatics and Computational Biology (ACM-BCB) 2014.
Andrei Todor's paper with Haitham Gabr, Alin Dobra and Tamer Kahveci is accepted to the International Conference on Intelligent Systems for Molecular Biology (ISMB). The title of their paper is "Large scale analysis of signal reachability". (08/2013)
Tamer Kahveci is the PC co-chair of the Workshop on Epigenomics and Cell Function (ECF) 2013 with David Gilbert.
Andrei Todor's paper with Alin Dobra and Tamer Kahveci is accepted to the IEEE/ACM Transactions on Computational Biology and Bioinformatics Journal. The title of their paper is "Characterizing topology of probabilistic biological networks". (08/2013)
The Bioinformatics Lab is awarded a two year NSF grant, titled "CIF: EAGER: Modeling and Querying of Probabilistic Biological Networks". (08/2013)
Mahmudul Hasan's paper with Yusuf Kavurucu and Tamer Kahveci is accepted to the BMC Systems Biology Journal. The title of their paper is "A scalable method for discovering significant subnetworks". (08/2013)
The Bioinformatics Lab is awarded a three year NSF grant, titled "ABI Innovation: Querying massive dynamic biological network databases". (07/2013)
Tamer Kahveci will be giving a highlight talk at the International Conference on Bioinformatics and Computational Biology (ACM-BCB). The title of his talk is "Large scale signaling network reconstruction". (07/2013)
Mahmudul Hasan's paper with Tamer Kahveci is accepted to the International Conference on Bioinformatics and Computational Biology (ACM-BCB). The title of their paper is "Color distribution can accelerate network alignment". (07/2013)
Haitham Gabr's paper with Andrei Todor, Helia Zandi, Alin Dobra and Tamer Kahveci is accepted to the International Conference on Bioinformatics and Computational Biology (ACM-BCB). The title of their paper is "PReach: Reachability in Probabilistic Signaling Networks". (07/2013)
Zane has received the UF-HHMI Science for Life intramural research award. We wish him success at his research career. (04/2013)
Andrei defended his thesis proposal. The title of his thesis is "Probabilistic Biological Networks". (04/2013)
Gunhan defended his thesis. The title of his thesis is "Querying Large Biological Network Datasets". (04/2013)
Nirmalya's paper with Tamer Kahveci, Sanjay Ranka and Jesse Gregory lab is accepted to the PLoS ONE Journal. The title of their paper is "Metabolomic Analysis Reveals Extended Metabolic Consequences of Marginal Vitamin B-6 Deficiency in Healthy Human Subjects". (04/2013)
Saad Sheik's paper with Tamer Kahveci, Sanjay Ranka and Gordon Burleigh is accepted to the Bioinformatics Journal. The title of their paper is "Stability Analysis of Phylogenetic Trees". (11/2012)
Andrei Todor's paper with Alin Dobra and Tamer Kahveci is accepted to the IEEE/ACM Transactions on Computational Biology and Bioinformatics Journal. The title of their paper is "Probabilistic Biological Network Alignment". (10/2012)
Gunhan Gulsoy's paper with Nirmalya Bandhyopadhyay and Tamer Kahveci is accepted to the Journal "BMC:Bioinformatics". The title of their paper is "HIDEN: Hierarchical decomposition of regulatory networks". (09/2012)
Tamer Kahveci's paper with Seyedsasan Hashemikhabir, Eyup Serdar Ayaz, Yusuf Kavurucu and Tolga Can is accepted to the IEEE/ACM Transactions on Computational Biology and Bioinformatics Journal. The title of their paper is "Large scale signaling network reconstruction". (09/2012)
Haitham Gabr's paper with Alin Dobra and Tamer Kahveci is accepted to the Pacific Symposium on Biocomputing (PSB). The title of their paper is "From uncertain protein interaction networks to signaling pathways through intensive color coding". (09/2012)
Tamer Kahveci's is the PC co-chair of the ACM-BCB 2012 conference along with Mona Singh.
Mahmudul Hasan's paper with Yusuf Kavurucu and Tamer Kahveci is accepted to the IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM). The title of their paper is "SiS: Significant Subnetworks in Massive Number of Network Topologies". (07/2012)
Andrei Todor's paper with Alin Dobra and Tamer Kahveci is accepted to the IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM). The title of their paper is "Uncertain interactions affect degree distribution of biological networks". (07/2012)
Tamer Kahveci's paper with Avinash Ramu and Gordon Burleigh is accepted to the BMC Bioinformatics Journal. The title of their paper is "A scalable method for identifying frequent subtrees in sets of large phylogenetic trees". (07/2012)
Gunhan Gulsoy's paper with Bhavik Gandhi and Tamer Kahveci is accepted to the Journal of Bioinformatics and Computational Biology (JBCB). The title of their paper is "TOPAC: Alignment of gene regulatory networks using topology aware coloring". (01/2012)
Nirmalya Bandyopadhyay graduated in Fall 2011. He has joined the Bader Research Lab at Johns Hopkins University as a post doctoral researcher. Congratulations. (01/2012)
Nirmalya Bandyopadhyay's paper with Manas Somaiya, Sanjay Ranka and Tamer Kahveci is accepted to the BMC Genomics. The title of the paper is "CMRF : Analyzing Differential Gene Regulation in Two Group Perturbation Experiments". (10/2011)
Nirmalya Bandyopadhyay's paper with Sanjay Ranka and Tamer Kahveci is accepted to the Pacific Symposium on Biocomputing (PSB). The title of the paper is "SSLPred : Predicting Synthetic Sickness Lethality". (09/2011)
Ferhat Ay graduated in Summer 2011. He has joined the Noble Research Lab at University of Washington as a post doctoral researcher. Congratulations. (08/2011)
Gunhan Gulsoy's paper with Bhavik Gandhi and Tamer Kahveci is accepted to the International Conference on Bioinformatics and Computational Biology (ACM-BCB). The title of their paper is "Topology aware coloring of gene regulatory networks". (04/2011)
Nirmalya Bandyopadhyay's book chapter with Bin Song, Esra Buyuktahtakin, Sanjay Ranka and Tamer Kahveci is accepted for the book Bioinformatics / Book 2 from Intech. The title of their book chapter is "Identifying enzyme knockout strategies on multiple enzyme associations". (04/2011)
Michael Dang's paper with Ferhat Ay and Tamer Kahveci is accepted to the International Conference On Bioinformatics and Computational Biology (ACM-BCB). The title of the paper is "A Novel Framework for Large Scale Metabolic Network Alignments by Compression". (04/2011)
Ferhat Ay received the prestigious 2011 UF-HHMI Science for Life Graduate Student Mentor Award. This award is given annualy for graduate students who participate in research and publication opportunities in the life sciences in collaboration with undergraduates. (03/2011)
Gunhan Gulsoy's paper with Tamer Kahveci is accepted to the International Conference on Intelligent Systems for Molecular Biology (ISMB). The title of the paper is "RINQ: Reference-based Indexing for Network Queries". (03/2011)
Nirmalya Bandyopadhyay has advanced to candidacy. Congratulations. (02/2011)
Tamer Kahveci's joint paper with Basma El Yacoubi, Isabelle Hatin, Christopher Deutsch, Jean-Pierre Rousset, Dirk Iwata-Reuyl, Alexey G Murzin and Valerie de Crecy-Lagard is accepted to the European Molecular Biology Organisation Journal (EMBOJ). The title of their paper is "A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification". (02/2011)
Nirmalya Bandyopadhyay's paper with Manas Somiya, Sanjay Ranka and Tamer Kahveci is accepted to the IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS). The title of their paper is "Identifying Differentially Regulated Genes". (01/2011)
Ferhat Ay's collaborative paper (co-first author) with Manolis Kellis' Lab in MIT CSAIL and the modENCODE Consortium is accepted to Science. The title of their paper is "Identification of functional elements and regulatory circuits in Drosophila modENCODE". (11/2010)
The Bioinformatics Lab got two year NSF grant, titled "CiC: EAGER: Inferring Pattern and Processes of Genome Evolution Through Cloud Computing" in a collaborative project. (10/2010)
Ferhat Ay, Gunhan Gulsoy and Tamer Kahveci's paper is accepted to the IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS). The title of their paper is "Finding Steady States of Large Scale Regulatory Networks through Partitioning". (10/2010)
UF CISE PhD student Bin Song and her co-supervisors Associate Professor Tamer Kahveci and Professor Sanjay Ranka received the Best Student Paper Award for their research paper titled "Enzymatic target identification with dynamic states" at the ACM International Conference On Bioinformatics and Computational Biology (ACM-BCB), 2010. (08/2010) (More)
Nirmalya Bandyopadhyay's paper with Manas Somiya, Sanjay Ranka and Tamer Kahveci is accepted to the International Conference on Computational Systems Biology (CSB). The title of their paper is "Modeling Perturbations using Gene Networks". (05/2010)
Bin Song's paper with Sanjay Ranka and Tamer Kahveci is accepted to the International Conference On Bioinformatics and Computational Biology (ACM-BCB). The title of their paper is "Enzymatic target identification with dynamic states". (05/2010)
Ferhat Ay's paper with Tamer Kahveci is accepted to the International Conference On Bioinformatics and Computational Biology (ACM-BCB). The title of their paper is "Functional Similarities of Reaction Sets in Metabolic Pathways". (05/2010)
Nirmalya Bandyopadhyay's paper with Mark Settles and Tamer Kahveci is accepted to the International Conference On Bioinformatics and Computational Biology (ACM-BCB). The title of their paper is "RepFrag: A Graph based Method for Finding Repeats and Transposons from Fragmented Genomes". (05/2010)
Ferhat Ay's joint paper with Thang N. Dinh, My T. Thai, Tamer Kahveci is accepted to the IEEE International Conference on Bioinformatics and Bioengineering (BIBE). The title of their paper is "Finding Dynamic Modules of Biological Regulatory Networks". (03/2010)
Ferhat Ay's paper with Tamer Kahveci is accepted to the International Conference on Research in Computational Biology (RECOMB). The title of their paper is "SubMAP: Aligning metabolic pathways with subnetwork mappings". (12/2009)
Nirmalya Bandyopadhyay's paper with Sanjay Ranka, Y. Sun, Steve Goodison and Tamer Kahveci is accepted to the Journal of Advances in Bioinformatics. The title of their paper is "Pathway based Feature Selection Algorithm for Cancer Microarray Data". (11/2009)
The Bioinformatics Lab got four year NSF grant, titled "Sequencing Gators: Building a Genome Science Curriculum at the University of Florida and Beyond" in a collaborative project. (09/2009)
Dr. Kahveci's joint paper with Fei Xu, Ravi Jampani, Mingxi Wu, Chris Jermaine is accepted to the International Conference on Data Engineering (ICDE). The title of this paper is "Surrogate Ranking for Very Expensive Similarity Queries". (09/2009)
Ferhat Ay's paper with Fei Xu and Tamer Kahveci is accepted to the RECOMB satellite workshop on Systems Biology and Regulatory genomics (RECOMB SB-RG-DREAM). The title of their paper is "Scalable Steady State Analysis of Boolean Biological Regulatory Networks". (09/2009)
Bin Song's paper with Esra Buyuktahtakin, Sanjay Ranka and Tamer Kahveci is accepted to the IEEE/ACM Transactions on Computational Biology and Bioinformatics. The title of their paper is "Manipulating the steady state of metabolic pathways" (08/2009)
Nirmalya Bandyopadhyay's paper with Tamer Kahveci is accepted to the Journal of Computational Biology. The title of their paper is "GBA Manager : An online tool for querying low complexity regions in proteins" (08/2009)
Jun Liu's paper with Nirmalya Bandyopadhyay, Sanjay Ranka, Michael Baudis and Tamer Kahveci is accepted to the Bioinformatics journal. The title of their paper is "Inferring Progression Models for CGH data" (06/2009)
The Bioinformatics Lab got five year NSF grant, titled "CAREER: New technologies for querying pathway databases". (02/2009)
Jayendra Venkateswaran and Bin Song's paper is accepted to the IEEE/ACM Transactions on Computational Biology and Bioinformatics. The title of their paper is "TRIAL: A Tool for Finding Distant Structural Similarities" (02/2009)
Ferhat Ay's paper is accepted to the Journal of Bioinformatics and Computational Biology. The title of his paper is "A Fast And Accurate Algorithm For Comparative Analysis Of Metabolic Pathways" (12/2008)
Nirmalya Bandyopadhyay has released the first version of GBA Manager. This is an online tool that identifies low complexity regions in protein sequences. (12/2008)
Ferhat Ay received the prestigious Alec Courtelis Award by UFIC. This award is given annually to three outstanding international graduate students showing excellent academic achievement and significant contribution to the department and UF community. (11/2008)
UF CISE PhD student Ferhat Ay, his supervisor Assistant Professor Tamer Kahveci and their collaborator Assistant Professor Valerie de-Crecy Lagard (UF - Dept of Microbiology and Cell Science) received the Best Paper Award for their research paper titled "Consistent Alignment of Metabolic Pathways without Abstraction" at the International Conference of Computational Systems Biology (CSB) 2008. (08/2008) (More)
The Bioinformatics Lab got a three year NSF grant, titled "EMT/BSSE: Biological networks as a communication model for entities with complex interactions". (07/2008)
Jun Liu's paper is accepted to ISMB 2008. The title of his paper is "Classification and Feature Selection Algorithms for Multi-class CGH data" (03/2008)
Tamer Kahveci
Last modified: Thu Sep 22 17:24:04 EDT 2016