Tamer Kahveci

Tamer Kahveci

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Tamer Kahveci

Publications by authors named "Tamer Kahveci"

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

IEEE/ACM Trans Comput Biol Bioinform 2018 Jul-Aug;15(4):1079-1091

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http://dx.doi.org/10.1109/TCBB.2017.2710129DOI Listing
May 2019

Aligning Optical Maps to De Bruijn Graphs.

Bioinformatics 2019 Jan 30. Epub 2019 Jan 30.

Department of Computer and Information Science and Engineering, College of Engineering, University of Florida, Gainesville, FL.

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http://dx.doi.org/10.1093/bioinformatics/btz069DOI Listing
January 2019

Shortest path counting in probabilistic biological networks.

BMC Bioinformatics 2018 Dec 4;19(1):465. Epub 2018 Dec 4.

Department of Computer and Information Science and Engineering, University of Florida, Gainesville, 32611, FL, USA.

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https://bmcbioinformatics.biomedcentral.com/articles/10.1186
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http://dx.doi.org/10.1186/s12859-018-2480-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6278053PMC
December 2018

Stability Analysis of Biological Networks' Diffusion State.

IEEE/ACM Trans Comput Biol Bioinform 2018 Nov 19. Epub 2018 Nov 19.

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http://dx.doi.org/10.1109/TCBB.2018.2881887DOI Listing
November 2018

Identification of jointly correlated gene sets.

J Bioinform Comput Biol 2018 Oct;16(5):1840019

* Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611, USA.

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http://dx.doi.org/10.1142/S021972001840019XDOI Listing
October 2018

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

BMC Bioinformatics 2018 06 26;19(1):242. Epub 2018 Jun 26.

Department of Computer & Information Science & Engineering, University of Florida, Gainesville, 32611, FL, USA.

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http://dx.doi.org/10.1186/s12859-018-2236-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6020255PMC
June 2018

Counting motifs in dynamic networks.

BMC Syst Biol 2018 04 11;12(Suppl 1). Epub 2018 Apr 11.

Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, USA.

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http://dx.doi.org/10.1186/s12918-018-0533-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5907309PMC
April 2018

A new algorithm for counting independent motifs in probabilistic networks.

IEEE/ACM Trans Comput Biol Bioinform 2018 Apr 2. Epub 2018 Apr 2.

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http://dx.doi.org/10.1109/TCBB.2018.2821666DOI Listing
April 2018

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

BMC Bioinformatics 2018 03 21;19(Suppl 3):69. Epub 2018 Mar 21.

Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, TX, 79409-3102, USA.

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http://dx.doi.org/10.1186/s12859-018-2058-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5872518PMC
March 2018

Integrating Domain Specific Knowledge and Network Analysis to Predict Drug Sensitivity of Cancer Cell Lines.

PLoS One 2016 8;11(9):e0162173. Epub 2016 Sep 8.

Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0162173PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5015856PMC
August 2017

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

BMC Bioinformatics 2017 03 22;18(Suppl 4):159. Epub 2017 Mar 22.

Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, 32611-6125, USA.

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http://dx.doi.org/10.1186/s12859-017-1521-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5374696PMC
March 2017

Identification of large disjoint motifs in biological networks.

BMC Bioinformatics 2016 Oct 6;17(1):408. Epub 2016 Oct 6.

CISE Department, University of Florida, 432 Newell Dr, Gainesville, Florida, 32611, USA.

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http://dx.doi.org/10.1186/s12859-016-1271-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5053092PMC
October 2016

Identifying the topology of signaling networks from partial RNAi data.

BMC Syst Biol 2016 08 1;10 Suppl 2:53. Epub 2016 Aug 1.

Department of Computer & Information Science & Engineering, University of Florida, Gainesville, 32611, FL, USA.

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http://dx.doi.org/10.1186/s12918-016-0301-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4977480PMC
August 2016

Reachability Analysis in Probabilistic Biological Networks.

IEEE/ACM Trans Comput Biol Bioinform 2015 Jan-Feb;12(1):53-66

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http://dx.doi.org/10.1109/TCBB.2014.2343967DOI Listing
June 2016

Computing interaction probabilities in signaling networks.

EURASIP J Bioinform Syst Biol 2015 Dec 11;2015(1):10. Epub 2015 Nov 11.

Department of Computer & Information Science & Engineering, University of Florida, Gainesville, Florida, USA.

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http://dx.doi.org/10.1186/s13637-015-0031-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4642599PMC
December 2015

Indexing a protein-protein interaction network expedites network alignment.

BMC Bioinformatics 2015 Oct 9;16:326. Epub 2015 Oct 9.

Department of Computer & Information Science and Engineering, University of Florida, Gainesville FL, 32611, USA.

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http://dx.doi.org/10.1186/s12859-015-0756-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4600321PMC
October 2015

Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells.

Genome Res 2015 Aug 8;25(8):1091-103. Epub 2015 Jun 8.

Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295, USA; Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, Florida 32306, USA.

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http://dx.doi.org/10.1101/gr.187989.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4509994PMC
August 2015

Hierarchical decomposition of dynamically evolving regulatory networks.

BMC Bioinformatics 2015 May 15;16:161. Epub 2015 May 15.

Department of Computer and Information Science and Engineering, University of Florida, Gainesville, 32611, FL, USA.

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http://dx.doi.org/10.1186/s12859-015-0529-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4450841PMC
May 2015

Network-based Prediction of Cancer under Genetic Storm.

Cancer Inform 2014 15;13(Suppl 3):15-31. Epub 2014 Oct 15.

Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, USA.

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http://dx.doi.org/10.4137/CIN.S14025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4214593PMC
November 2014

A comparative encyclopedia of DNA elements in the mouse genome.

Authors:
Feng Yue Yong Cheng Alessandra Breschi Jeff Vierstra Weisheng Wu Tyrone Ryba Richard Sandstrom Zhihai Ma Carrie Davis Benjamin D Pope Yin Shen Dmitri D Pervouchine Sarah Djebali Robert E Thurman Rajinder Kaul Eric Rynes Anthony Kirilusha Georgi K Marinov Brian A Williams Diane Trout Henry Amrhein Katherine Fisher-Aylor Igor Antoshechkin Gilberto DeSalvo Lei-Hoon See Meagan Fastuca Jorg Drenkow Chris Zaleski Alex Dobin Pablo Prieto Julien Lagarde Giovanni Bussotti Andrea Tanzer Olgert Denas Kanwei Li M A Bender Miaohua Zhang Rachel Byron Mark T Groudine David McCleary Long Pham Zhen Ye Samantha Kuan Lee Edsall Yi-Chieh Wu Matthew D Rasmussen Mukul S Bansal Manolis Kellis Cheryl A Keller Christapher S Morrissey Tejaswini Mishra Deepti Jain Nergiz Dogan Robert S Harris Philip Cayting Trupti Kawli Alan P Boyle Ghia Euskirchen Anshul Kundaje Shin Lin Yiing Lin Camden Jansen Venkat S Malladi Melissa S Cline Drew T Erickson Vanessa M Kirkup Katrina Learned Cricket A Sloan Kate R Rosenbloom Beatriz Lacerda de Sousa Kathryn Beal Miguel Pignatelli Paul Flicek Jin Lian Tamer Kahveci Dongwon Lee W James Kent Miguel Ramalho Santos Javier Herrero Cedric Notredame Audra Johnson Shinny Vong Kristen Lee Daniel Bates Fidencio Neri Morgan Diegel Theresa Canfield Peter J Sabo Matthew S Wilken Thomas A Reh Erika Giste Anthony Shafer Tanya Kutyavin Eric Haugen Douglas Dunn Alex P Reynolds Shane Neph Richard Humbert R Scott Hansen Marella De Bruijn Licia Selleri Alexander Rudensky Steven Josefowicz Robert Samstein Evan E Eichler Stuart H Orkin Dana Levasseur Thalia Papayannopoulou Kai-Hsin Chang Arthur Skoultchi Srikanta Gosh Christine Disteche Piper Treuting Yanli Wang Mitchell J Weiss Gerd A Blobel Xiaoyi Cao Sheng Zhong Ting Wang Peter J Good Rebecca F Lowdon Leslie B Adams Xiao-Qiao Zhou Michael J Pazin Elise A Feingold Barbara Wold James Taylor Ali Mortazavi Sherman M Weissman John A Stamatoyannopoulos Michael P Snyder Roderic Guigo Thomas R Gingeras David M Gilbert Ross C Hardison Michael A Beer Bing Ren

Nature 2014 Nov;515(7527):355-64

Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1038/nature13992DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266106PMC
November 2014

Characterizing the topology of probabilistic biological networks.

IEEE/ACM Trans Comput Biol Bioinform 2013 Jul-Aug;10(4):970-83

University of Florida, Gainesville.

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https://www.computer.org/csdl/trans/tb/2013/04/ttb2013040970
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http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumbe
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http://dx.doi.org/10.1109/TCBB.2013.108DOI Listing
August 2014

Large scale analysis of signal reachability.

Bioinformatics 2014 Jun;30(12):i96-104

CISE Department, University of Florida, Gainesville, FL 32611, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu262DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058948PMC
June 2014

Probabilistic biological network alignment.

IEEE/ACM Trans Comput Biol Bioinform 2013 Jan-Feb;10(1):109-21

Department of Computer and Information Science and Engineering, University of Florida, PO Box 116120, E301 CSE Building, Gainesville, FL 32611-6120, USA.

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http://dx.doi.org/10.1109/TCBB.2012.142DOI Listing
January 2014

SSLPred: predicting synthetic sickness lethality.

Pac Symp Biocomput 2012 :7-18

CISE Department, University of Florida, Gainesville, FL 32611, USA.

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December 2013

From uncertain protein interaction networks to signaling pathways through intensive color coding.

Pac Symp Biocomput 2013 :111-22

CISE Department, University of Florida, Gainesville, FL 32611, USA.

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December 2013

Large-scale signaling network reconstruction.

IEEE/ACM Trans Comput Biol Bioinform 2012 Nov-Dec;9(6):1696-708

Department of Computer Engineering, Middle East Technical University, Ankara 06800, Turkey.

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http://dx.doi.org/10.1109/TCBB.2012.128DOI Listing
July 2013

Stability analysis of phylogenetic trees.

Bioinformatics 2013 Jan 18;29(2):166-74. Epub 2012 Nov 18.

Department of Computer and Information Science and Engineering, University of Florida, FL 32611, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts657DOI Listing
January 2013

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

BMC Bioinformatics 2012 Oct 3;13:256. Epub 2012 Oct 3.

Electrical and Computer Engineering, University of Florida, Gainesville, FL, USA.

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http://dx.doi.org/10.1186/1471-2105-13-256DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3543182PMC
October 2012

HIDEN: Hierarchical decomposition of regulatory networks.

BMC Bioinformatics 2012 Sep 28;13:250. Epub 2012 Sep 28.

Computer and Information Sciences and Engineering, University of Florida, Gainesville, FL 32611, USA.

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http://dx.doi.org/10.1186/1471-2105-13-250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3556311PMC
September 2012

Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks.

Genome Res 2012 Jul 28;22(7):1334-49. Epub 2012 Mar 28.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1101/gr.127191.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3396374PMC
July 2012

CMRF: analyzing differential gene regulation in two group perturbation experiments.

BMC Genomics 2012 Apr 12;13 Suppl 2:S2. Epub 2012 Apr 12.

Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32603, USA.

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http://dx.doi.org/10.1186/1471-2164-13-S2-S2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394417PMC
April 2012

Metabolic network alignment in large scale by network compression.

BMC Bioinformatics 2012 Mar 21;13 Suppl 3:S2. Epub 2012 Mar 21.

Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611, USA.

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http://dx.doi.org/10.1186/1471-2105-13-S3-S2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3402922PMC
March 2012

Topac: alignment of gene regulatory networks using topology-aware coloring.

J Bioinform Comput Biol 2012 Feb;10(1):1240001

Computer and Information Sciences and Engineering Department, University of Florida, Gainesville, FL, USA.

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http://dx.doi.org/10.1142/S021972001240001XDOI Listing
February 2012

Manipulating the steady state of metabolic pathways.

IEEE/ACM Trans Comput Biol Bioinform 2011 May-Jun;8(3):732-47

Department of Computer and Information Science and Engineering, University of Florida, CSE Building, Room E436, Gainesville, FL 32611-6125, USA.

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http://dx.doi.org/10.1109/TCBB.2010.41DOI Listing
August 2011

TRIAL: a tool for finding distant structural similarities.

IEEE/ACM Trans Comput Biol Bioinform 2011 May-Jun;8(3):819-31

Epic Systems Corporation, 221 S High Point Rd., Apt# 115, Madison, WI 53717, USA.

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http://dx.doi.org/10.1109/TCBB.2009.28DOI Listing
August 2011

Pathway-BasedFeature Selection Algorithm for Cancer Microarray Data.

Adv Bioinformatics 2009 3:532989. Epub 2010 Mar 3.

Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611, USA.

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http://dx.doi.org/10.1155/2009/532989DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2831238PMC
July 2011

RINQ: Reference-based Indexing for Network Queries.

Bioinformatics 2011 Jul;27(13):i149-58

Computer and Information Sciences and Engineering Department, University of Florida, Gainesville, FL 32611, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117351PMC
July 2011

A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification.

EMBO J 2011 Mar 1;30(5):882-93. Epub 2011 Feb 1.

Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA.

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http://dx.doi.org/10.1038/emboj.2010.363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3049207PMC
March 2011

SubMAP: aligning metabolic pathways with subnetwork mappings.

J Comput Biol 2011 Mar;18(3):219-35

Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, USA.

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http://dx.doi.org/10.1089/cmb.2010.0280DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3123932PMC
March 2011

GBA manager: an online tool for querying low-complexity regions in proteins.

J Comput Biol 2010 Jan;17(1):73-7

Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, USA.

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http://dx.doi.org/10.1089/cmb.2009.0006DOI Listing
January 2010

Scalable steady state analysis of Boolean biological regulatory networks.

PLoS One 2009 Dec 1;4(12):e7992. Epub 2009 Dec 1.

Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007992PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779454PMC
December 2009

Inferring progression models for CGH data.

Bioinformatics 2009 Sep 15;25(17):2208-15. Epub 2009 Jun 15.

Computer and Information Science and Engineering, University of Florida, Gainesville, FL, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp365DOI Listing
September 2009

Consistent alignment of metabolic pathways without abstraction.

Comput Syst Bioinformatics Conf 2008 ;7:237-48

Department of Computer Science and Engineering, University of Florida, Gainesville, FL 32611, USA.

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August 2009

A fast and accurate algorithm for comparative analysis of metabolic pathways.

J Bioinform Comput Biol 2009 Jun;7(3):389-428

Department of Computer Science and Engineering, University of Florida, Gainesville, FL 32611, USA.

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June 2009

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

Int J Data Min Bioinform 2009 ;3(2):124-44

Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611, USA.

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June 2009

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

Bioinformatics 2008 Jul;24(13):i86-95

Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn145DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718623PMC
July 2008

Mining metabolic networks for optimal drug targets.

Pac Symp Biocomput 2008 :291-302

Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611, USA.

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March 2008

A novel genome-scale repeat finder geared towards transposons.

Bioinformatics 2008 Feb 18;24(4):468-76. Epub 2007 Dec 18.

CISE Department, University of Florida, Gainesville, FL 32611, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm613DOI Listing
February 2008

An iterative algorithm for metabolic network-based drug target identification.

Pac Symp Biocomput 2007 :88-99

Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611, USA.

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December 2007

Markers improve clustering of CGH data.

Bioinformatics 2007 Feb 6;23(4):450-7. Epub 2006 Dec 6.

Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btl624DOI Listing
February 2007

A new approach for alignment of multiple proteins.

Pac Symp Biocomput 2006 :339-50

Department of Computer and Information Sciences and Engineering, University of Florida, Gainesville, FL 32611, USA.

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January 2007

QOMA: quasi-optimal multiple alignment of protein sequences.

Bioinformatics 2007 Jan 22;23(2):162-8. Epub 2006 Nov 22.

Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl590DOI Listing
January 2007

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

Bioinformatics 2006 Dec 2;22(24):2980-7. Epub 2006 Oct 2.

Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/btl495DOI Listing
December 2006

Towards index-based similarity search for protein structure databases.

Proc IEEE Comput Soc Bioinform Conf 2003 ;2:148-58

Department of Computer Science, University of California, Santa Barbara, 93106, USA.

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August 2006

Distance-based clustering of CGH data.

Bioinformatics 2006 Aug 16;22(16):1971-8. Epub 2006 May 16.

Computer and Information Science and Engineering, University of Florida Gainesville, FL 32611, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl185DOI Listing
August 2006

PSI: indexing protein structures for fast similarity search.

Bioinformatics 2003 ;19 Suppl 1:i81-3

Department of Computer Science University of California, Santa Barbara, CA 93106, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg1009DOI Listing
October 2004

Speeding up whole-genome alignment by indexing frequency vectors.

Bioinformatics 2004 Sep 8;20(13):2122-34. Epub 2004 Apr 8.

Department of Computer Science, University of California, Santa Barbara, Santa Barbara, CA 93106-5110, USA.

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http://dx.doi.org/10.1093/bioinformatics/bth212DOI Listing
September 2004

Index-based similarity search for protein structure databases.

J Bioinform Comput Biol 2004 Mar;2(1):99-126

Department of Computer Science, University of California, Santa Barbara, CA 93106, USA.

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March 2004

MAP: searching large genome databases.

Pac Symp Biocomput 2003 :303-14

Department of Computer Science, University of California, Santa Barbara, CA 93106, USA.

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August 2003