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List of works by Panayiotis V Benos

A sequence alignment-independent method for protein classification

scientific article

Acquisition of a potential marker for insect transformation: isolation of a novel alcohol dehydrogenase gene from Bactrocera oleae by functional complementation in yeast

scientific article published in February 2000

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

scientific article

Aldosterone regulates microRNAs in the cortical collecting duct to alter sodium transport.

scientific article

Combined analysis reveals a core set of cycling genes

scientific article published on January 2007

ComiR: Combinatorial microRNA target prediction tool

scientific article published on 22 May 2013

DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies

scientific article

Deregulation of common genes by c-Myc and its direct target, MT-MC1.

scholarly article

Expression of regulatory platelet microRNAs in patients with sickle cell disease

scientific article

Extracting biologically significant patterns from short time series gene expression data

scientific article published on 20 August 2009

FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting

scientific article

Feasibility of lung cancer prediction from low-dose CT scan and smoking factors using causal models

scientific article published on 12 March 2019

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

scientific article

Finding subtypes of transcription factor motif pairs with distinct regulatory roles ⬇️

scientific article

Footer: a quantitative comparative genomics method for efficient recognition of cis-regulatory elements

scientific article published on June 2005

From first base: the sequence of the tip of the X chromosome of Drosophila melanogaster, a comparison of two sequencing strategies

scientific article

Gene expression profiling distinguishes proneural glioma stem cells from mesenchymal glioma stem cells

scientific article published in September 2015

Genomic analysis of immediate/early response to shear stress in human coronary artery endothelial cells

scientific article published on 26 December 2002

HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models

scientific article

High throughput determination of TGFβ1/SMAD3 targets in A549 lung epithelial cells

scientific article

Human transcriptome subtraction by using short sequence tags to search for tumor viruses in conjunctival carcinoma

scientific article

Improved detection of DNA motifs using a self-organized clustering of familial binding profiles

scientific article published in June 2005

Inferring protein-DNA dependencies using motif alignments and mutual information.

scientific article published on July 2007

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

scientific article

Is there a code for protein-DNA recognition? Probab(ilistical)ly. . .

scientific article published in May 2002

Large scale comparison of innate responses to viral and bacterial pathogens in mouse and macaque

scientific article

Mapping and identification of essential gene functions on the X chromosome of Drosophila

scientific article

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

scientific article published on 6 May 2013

Myofibroblast transcriptome indicates SFRP2<sup>hi</sup> fibroblast progenitors in systemic sclerosis skin

scientific article published on 19 July 2021

Novel modeling of combinatorial miRNA targeting identifies SNP with potential role in bone density

scientific article

One-hundred and five new potential Drosophila melanogaster genes revealed through STS analysis

scientific article published in August 1997

Overexpression of microRNA-1 promotes cardiomyocyte commitment from human cardiovascular progenitors via suppressing WNT and FGF signaling pathways

scientific journal article

P-Element Insertion Alleles of Essential Genes on the Third Chromosome of Drosophila melanogaster Correlation of Physical and Cytogenetic Maps in Chromosomal Region 86E-87F ⬇️

scientific article published on December 1, 1997

PARP1 rs1805407 Increases Sensitivity to PARP1 Inhibitors in Cancer Cells Suggesting an Improved Therapeutic Strategy

scientific article published on 01 March 2019

Probabilistic code for DNA recognition by proteins of the EGR family

scientific article published in November 2002

Profibrotic role of miR-154 in pulmonary fibrosis

scientific article published on 4 October 2012

RNA deep sequencing reveals differential microRNA expression during development of sea urchin and sea star

scientific article (publication date: 2011)

Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex

scientific article published in March 2006

Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome

scientific article

Representation of unique sequences in libraries of randomized nucleic acids

scientific article published on September 1996

SAMIE: statistical algorithm for modeling interaction energies.

scientific article

SOP3: a web-based tool for selection of oligonucleotide primers for single nucleotide polymorphism analysis by Pyrosequencing

scientific article published in January 2005

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

scientific article published on 3 May 2007

Self-organizing neural networks to support the discovery of DNA-binding motifs.

scientific article published on 12 July 2006

Spectral clustering strategies for heterogeneous disease expression data

scientific article

The center for causal discovery of biomedical knowledge from big data

scientific article

The crystal structures of the synthetic C-terminal octa- and dodecapeptides of trichovirin

scientific article published in February 1999

The crystal structures of the synthetic C-terminal octa- and dodecapeptides of trichovirin

scientific article published on 01 February 1999

The genome sequence of Drosophila melanogaster

scientific article

The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus

scientific article published on 12 February 2009

To bind or not to bind--FoxA1 determines estrogen receptor action in breast cancer progression

scientific article

Topographic heterogeneity of lung microbiota in end-stage idiopathic pulmonary fibrosis: the Microbiome in Lung Explants-2 (MiLEs-2) study

scientific article published on 02 December 2020

Web-based identification of evolutionary conserved DNA cis-regulatory elements

scientific article published in January 2007

Web-based primer design software for genome-scale genotyping by pyrosequencing

scientific article published in January 2007

enoLOGOS: a versatile web tool for energy normalized sequence logos

scientific article

mirConnX: condition-specific mRNA-microRNA network integrator

scientific article

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