The Next Generation of Transcription Factor Binding Site Prediction
Author
Abstract
Suggested Citation
DOI: 10.1371/journal.pcbi.1003214
Download full text from publisher
References listed on IDEAS
- Martin C Frith & Neil F W Saunders & Bostjan Kobe & Timothy L Bailey, 2008. "Discovering Sequence Motifs with Arbitrary Insertions and Deletions," PLOS Computational Biology, Public Library of Science, vol. 4(5), pages 1-12, May.
- Liron Levkovitz & Nir Yosef & Marvin C Gershengorn & Eytan Ruppin & Roded Sharan & Yoram Oron, 2010. "A Novel HMM-Based Method for Detecting Enriched Transcription Factor Binding Sites Reveals RUNX3 as a Potential Target in Pancreatic Cancer Biology," PLOS ONE, Public Library of Science, vol. 5(12), pages 1-9, December.
- Barbara Felice & Claudia Cattoglio & Davide Cittaro & Anna Testa & Annarita Miccio & Giuliana Ferrari & Lucilla Luzi & Alessandra Recchia & Fulvio Mavilio, 2009. "Transcription Factor Binding Sites Are Genetic Determinants of Retroviral Integration in the Human Genome," PLOS ONE, Public Library of Science, vol. 4(2), pages 1-16, February.
- Elizabeth G Wilbanks & Marc T Facciotti, 2010. "Evaluation of Algorithm Performance in ChIP-Seq Peak Detection," PLOS ONE, Public Library of Science, vol. 5(7), pages 1-12, July.
- Eran Segal & Yvonne Fondufe-Mittendorf & Lingyi Chen & AnnChristine Thåström & Yair Field & Irene K. Moore & Ji-Ping Z. Wang & Jonathan Widom, 2006. "A genomic code for nucleosome positioning," Nature, Nature, vol. 442(7104), pages 772-778, August.
Citations
Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
Cited by:
- Saeed Omidi & Mihaela Zavolan & Mikhail Pachkov & Jeremie Breda & Severin Berger & Erik van Nimwegen, 2017. "Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors," PLOS Computational Biology, Public Library of Science, vol. 13(7), pages 1-22, July.
- Miaomiao Li & Tao Yao & Wanru Lin & Will E. Hinckley & Mary Galli & Wellington Muchero & Andrea Gallavotti & Jin-Gui Chen & Shao-shan Carol Huang, 2023. "Double DAP-seq uncovered synergistic DNA binding of interacting bZIP transcription factors," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
Most related items
These are the items that most often cite the same works as this one and are cited by the same works as this one.- Ji-Ping Wang & Yvonne Fondufe-Mittendorf & Liqun Xi & Guei-Feng Tsai & Eran Segal & Jonathan Widom, 2008. "Preferentially Quantized Linker DNA Lengths in Saccharomyces cerevisiae," PLOS Computational Biology, Public Library of Science, vol. 4(9), pages 1-10, September.
- Zing Tsung-Yeh Tsai & Shin-Han Shiu & Huai-Kuang Tsai, 2015. "Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast," PLOS Computational Biology, Public Library of Science, vol. 11(8), pages 1-22, August.
- Caiyan Jia & Matthew B Carson & Yang Wang & Youfang Lin & Hui Lu, 2014. "A New Exhaustive Method and Strategy for Finding Motifs in ChIP-Enriched Regions," PLOS ONE, Public Library of Science, vol. 9(1), pages 1-13, January.
- Segal Mark R, 2008. "Re-Cracking the Nucleosome Positioning Code," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 7(1), pages 1-24, April.
- Moser Carlee & Gupta Mayetri, 2012. "A Generalized Hidden Markov Model for Determining Sequence-based Predictors of Nucleosome Positioning," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(2), pages 1-23, January.
- Monica Naughtin & Zofia Haftek-Terreau & Johan Xavier & Sam Meyer & Maud Silvain & Yan Jaszczyszyn & Nicolas Levy & Vincent Miele & Mohamed Salah Benleulmi & Marc Ruff & Vincent Parissi & Cédric Vaill, 2015. "DNA Physical Properties and Nucleosome Positions Are Major Determinants of HIV-1 Integrase Selectivity," PLOS ONE, Public Library of Science, vol. 10(6), pages 1-28, June.
- Wolfram Möbius & Ulrich Gerland, 2010. "Quantitative Test of the Barrier Nucleosome Model for Statistical Positioning of Nucleosomes Up- and Downstream of Transcription Start Sites," PLOS Computational Biology, Public Library of Science, vol. 6(8), pages 1-11, August.
- Weronika Sikora-Wohlfeld & Marit Ackermann & Eleni G Christodoulou & Kalaimathy Singaravelu & Andreas Beyer, 2013. "Assessing Computational Methods for Transcription Factor Target Gene Identification Based on ChIP-seq Data," PLOS Computational Biology, Public Library of Science, vol. 9(11), pages 1-11, November.
- Guo-Cheng Yuan & Jun S Liu, 2008. "Genomic Sequence Is Highly Predictive of Local Nucleosome Depletion," PLOS Computational Biology, Public Library of Science, vol. 4(1), pages 1-11, January.
- Yuzhuo Wang & Chengzhi Zhang & Kai Li, 2022. "A review on method entities in the academic literature: extraction, evaluation, and application," Scientometrics, Springer;Akadémiai Kiadó, vol. 127(5), pages 2479-2520, May.
- Leelavati Narlikar & Raluca Gordân & Alexander J Hartemink, 2007. "A Nucleosome-Guided Map of Transcription Factor Binding Sites in Yeast," PLOS Computational Biology, Public Library of Science, vol. 3(11), pages 1-10, November.
- Matti Annala & Kirsti Laurila & Harri Lähdesmäki & Matti Nykter, 2011. "A Linear Model for Transcription Factor Binding Affinity Prediction in Protein Binding Microarrays," PLOS ONE, Public Library of Science, vol. 6(5), pages 1-13, May.
- Daniel Ryan & Laura Jenniches & Sarah Reichardt & Lars Barquist & Alexander J. Westermann, 2020. "A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron," Nature Communications, Nature, vol. 11(1), pages 1-16, December.
- Wei Chen & Hao Lin & Peng-Mian Feng & Chen Ding & Yong-Chun Zuo & Kuo-Chen Chou, 2012. "iNuc-PhysChem: A Sequence-Based Predictor for Identifying Nucleosomes via Physicochemical Properties," PLOS ONE, Public Library of Science, vol. 7(10), pages 1-9, October.
- Timothy Bailey & Pawel Krajewski & Istvan Ladunga & Celine Lefebvre & Qunhua Li & Tao Liu & Pedro Madrigal & Cenny Taslim & Jie Zhang, 2013. "Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data," PLOS Computational Biology, Public Library of Science, vol. 9(11), pages 1-8, November.
- Dongjun Chung & Dan Park & Kevin Myers & Jeffrey Grass & Patricia Kiley & Robert Landick & Sündüz Keleş, 2013. "dPeak: High Resolution Identification of Transcription Factor Binding Sites from PET and SET ChIP-Seq Data," PLOS Computational Biology, Public Library of Science, vol. 9(10), pages 1-13, October.
- Joke J F A van Vugt & Martijn de Jager & Magdalena Murawska & Alexander Brehm & John van Noort & Colin Logie, 2009. "Multiple Aspects of ATP-Dependent Nucleosome Translocation by RSC and Mi-2 Are Directed by the Underlying DNA Sequence," PLOS ONE, Public Library of Science, vol. 4(7), pages 1-14, July.
- Miguel A Fortuna & Luis Zaman & Charles Ofria & Andreas Wagner, 2017. "The genotype-phenotype map of an evolving digital organism," PLOS Computational Biology, Public Library of Science, vol. 13(2), pages 1-20, February.
- Fang Liu & Eivind Tøstesen & Jostein K Sundet & Tor-Kristian Jenssen & Christoph Bock & Geir Ivar Jerstad & William G Thilly & Eivind Hovig, 2007. "The Human Genomic Melting Map," PLOS Computational Biology, Public Library of Science, vol. 3(5), pages 1-13, May.
- Harsh Nagpal & Ahmad Ali-Ahmad & Yasuhiro Hirano & Wei Cai & Mario Halic & Tatsuo Fukagawa & Nikolina Sekulić & Beat Fierz, 2023. "CENP-A and CENP-B collaborate to create an open centromeric chromatin state," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
Corrections
All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pcbi00:1003214. See general information about how to correct material in RePEc.
If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.
If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .
If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.
For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: ploscompbiol (email available below). General contact details of provider: https://journals.plos.org/ploscompbiol/ .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.