Results 41 to 50 of about 15,248,084 (403)

Base-resolution models of transcription factor binding reveal soft motif syntax

Nature Genetics, 2019
The arrangement (syntax) of transcription factor (TF) binding motifs is an important part of the cis-regulatory code, yet remains elusive. We introduce a deep learning model, BPNet, that uses DNA sequence to predict base-resolution chromatin ...
Žiga Avsec, Melanie Weilert, Avanti Shrikumar, S. Krueger, Amr M. Alexandari, Khyati Dalal, Robin Fropf, Charles E. McAnany, J. Gagneur, Anshul Kundaje, J. Zeitlinger   +10 more
semanticscholar   +1 more source

Stochastic model of transcription factor-regulated gene expression [PDF]

, 2006
We consider a stochastic model of transcription factor (TF)-regulated gene expression. The model describes two genes: Gene A and Gene B which synthesize the TFs and the target gene proteins respectively.
Alberts B, Bose I, Ferrer J, Fodde R, Ghosh B, Hume D A, Indrani Bose, Karmakar R, Kepler T B, Rajesh Karmakar, Santarosa M, Scott M   +11 more
core   +2 more sources

Benchmark and integration of resources for the estimation of human transcription factor activities

bioRxiv, 2018
Prediction of transcription factor (TF) activities from the gene expression of their targets (i.e. TF regulon) is becoming a widely-used approach to characterize the functional status of transcriptional regulatory circuits.
Luz Garcia-Alonso, Mahmoud M. Ibrahim, D. Turei, J. Sáez-Rodríguez   +3 more
semanticscholar   +1 more source

Transcription factor dynamics

Microbiology, 2008
Gene expression is a fundamental process that is highly conserved from humans to bacteria. The first step in gene expression, transcription, is performed by structurally conserved DNA-dependent RNA polymerases (RNAPs), which results in the synthesis of an RNA molecule from a DNA template.
Lewis, P. J., Doherty, G. P., Clarke, J.
openaire   +5 more sources

NTH201, a Novel Class II KNOTTED1-Like Protein, Facilitates the Cell-to-Cell Movement of Tobacco mosaic virus in Tobacco

Molecular Plant-Microbe Interactions, 2008
NTH201, a novel class II KNOTTED1-like protein gene, was cloned from tobacco (Nicotiana tabacum cv. Xanthi) and its role in Tobacco mosaic virus (TMV) infection was analyzed. Virus-induced gene silencing of NTH201 caused a delay in viral RNA accumulation
Atsushi Yoshii, Takumi Shimizu, Akiko Yoshida, Koji Hamada, Keitaro Sakurai, Yasuyuki Yamaji, Masashi Suzuki, Shigetou Namba, Tadaaki Hibi   +8 more
doaj   +1 more source

Predicting Transcription Factor Specificity with All-Atom Models [PDF]

, 2008
The binding of a transcription factor (TF) to a DNA operator site can initiate or repress the expression of a gene. Computational prediction of sites recognized by a TF has traditionally relied upon knowledge of several cognate sites, rather than an ab ...
Arvidson, Benos, Blattner, Djordjevic, Donald, Endres, Endres, Foat, Glasfeld, He, Humphrey, Ingraham, Kalodimos, Kazakov, Kinney, Kullback, Lafontaine, Leonid A. Mirny, Liu, Lu, MacKerell, Maerkl, Man, Mehran Kardar, Meng, Mironov, Morozov, Onufriev, Paillard, Paillard, Peter Virnau, Pérez, Sahand J. Rahi, Schumacher, von Hippel, Wang   +35 more
core   +3 more sources

Structural basis of TFIIH activation for nucleotide excision repair. [PDF]

, 2019
Nucleotide excision repair (NER) is the major DNA repair pathway that removes UV-induced and bulky DNA lesions. There is currently no structure of NER intermediates, which form around the large multisubunit transcription factor IIH (TFIIH).
Chernev, A., Cramer, P., Dienemann, C., Kokic, G., Tegunov, D., Urlaub, H.   +5 more
core   +2 more sources

A patient‐derived explant (PDE) model of hormone‐dependent cancer

Molecular Oncology, 2018
Breast and prostate cancer research to date has largely been predicated on the use of cell lines in vitro or in vivo. These limitations have led to the development of more clinically relevant models, such as organoids or murine xenografts that utilize ...
Margaret M. Centenera, Theresa E. Hickey, Shalini Jindal, Natalie K. Ryan, Preethi Ravindranathan, Hisham Mohammed, Jessica L. Robinson, Matthew J. Schiewer, Shihong Ma, Payal Kapur, Peter D. Sutherland, Clive E. Hoffmann, Claus G. Roehrborn, Leonard G. Gomella, Jason S. Carroll, Stephen N. Birrell, Karen E. Knudsen, Ganesh V. Raj, Lisa M. Butler, Wayne D. Tilley   +19 more
doaj   +1 more source

A transcription factor for cold sensation!

Molecular Pain, 2005
The ability to feel hot and cold is critical for animals and human beings to survive in the natural environment. Unlike other sensations, the physiology of cold sensation is mostly unknown.
Milbrandt Jeffrey, Qu Zhican, Kim Susan J, Zhuo Min   +3 more
doaj   +1 more source

One-two punch mechanism of gene repression: a fresh perspective on gene regulation. [PDF]

, 2017
Cellular differentiation depends on temporally controlled waves of gene activation and inactivation that ultimately transform one cell type into another.
Tresenrider, Amy, Ünal, Elçin
core   +1 more source