The Genome Sequence of Drosophila melanogaster

…, L Bayraktaroglu, EM Beasley, KY Beeson, PV Benos… - Science, 2000 - science.org
The fly Drosophila melanogaster is one of the most intensively studied organisms in biology
and serves as a model system for the investigation of many developmental and cellular …

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

…, T Sharpe, ML Baker, MA Batzer, PV Benos… - Nature, 2007 - nature.com
We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis
domestica). As the first metatherian (‘marsupial’) species to be sequenced, the …

Mesenchymal glioma stem cells are maintained by activated glycolytic metabolism involving aldehyde dehydrogenase 1A3

…, S Luthra, UR Chandran, PV Benos… - Proceedings of the …, 2013 - National Acad Sciences
Tumor heterogeneity of high-grade glioma (HGG) is recognized by four clinically relevant
subtypes based on core gene signatures. However, molecular signaling in glioma stem cells (…

STAMP: a web tool for exploring DNA-binding motif similarities

S Mahony, PV Benos - Nucleic acids research, 2007 - academic.oup.com
STAMP is a newly developed web server that is designed to support the study of DNA-binding
motifs. STAMP may be used to query motifs against databases of known motifs; the …

Inhibition and role of let-7d in idiopathic pulmonary fibrosis

…, D Bouros, O Eickelberg, P Ray, PV Benos… - American journal of …, 2010 - atsjournals.org
Rationale: Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and usually lethal
fibrotic lung disease characterized by profound changes in epithelial cell phenotype and …

Proliferating SPP1/MERTK-expressing macrophages in idiopathic pulmonary fibrosis

…, K Gibson, W Chen, A Mora, PV Benos… - European …, 2019 - Eur Respiratory Soc
… Gibson reviewed clinical data; PV Benos supervised graphical modelling; W. Chen supervised
RNA-sequencing analysis; C. … Conflict of interest: PV Benos has nothing to disclose. …

Is there a code for protein–DNA recognition? Probab (ilistical) ly…

PV Benos, AS Lapedes, GD Stormo - Bioessays, 2002 - Wiley Online Library
… Equation 1 is a simplified version of the one presented in Benos et al.(16) in that it does
not include the relative frequencies of the different binding site types. However, these fre…

Additivity in protein–DNA interactions: how good an approximation is it?

PV Benos, ML Bulyk, GD Stormo - Nucleic acids research, 2002 - academic.oup.com
Man and Stormo and Bulyk et al. recently presented their results on the study of the DNA
binding affinity of proteins. In both of these studies the main conclusion is that the additivity …

[HTML][HTML] Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data

…, B Gordon, A Bhattacharjee, N Kaminski, PV Benos - PloS one, 2009 - journals.plos.org
Background MicroRNAs (miRNAs) are short, non-coding RNA regulators of protein coding
genes. miRNAs play a very important role in diverse biological processes and various …

[HTML][HTML] Myofibroblast transcriptome indicates SFRP2hi fibroblast progenitors in systemic sclerosis skin

…, R Behera, M Jia, M Bulik, DE Monier, PV Benos… - Nature …, 2021 - nature.com
Skin and lung fibrosis in systemic sclerosis (SSc) is driven by myofibroblasts, alpha-smooth
muscle actin expressing cells. The number of myofibroblasts in SSc skin correlates with the …