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All Publications
2010
- K.V. Pandit, D. Corcoran, H. Yousef, M. Yarlagadda, A. Tzouvelekis,
K.F. Gibson, K. Konishi, S.A. Yousem, M. Singh, D. Handley, T. Richards,
M. Selman, S.C. Watkins, A. Pardo, A. Ben-Yehudah, D. Bouros, O. Eickelberg,P. Ray, P.V. Benos, N. Kaminski,
"Inhibition and role of let-7d in idiopathic pulmonary fibrosis."
Am J Resp Crit Care Med, (2010) in press.
Abstract (PubMed) and pdf
PMID: 20395559
- N.A. Temiz, P.V. Benos, C.J. Camacho
"Electrostatic hot spot on DNA-binding domains mediates phosphate desolvation and the pre-organization of specificity determinant side chains."
Nucleic Acids Res., (2010) 38:2134-2144.
Abstract (PubMed) and pdf
PMID: 20047959
2009
- A.B. Tchagang, K.V. Bui, T. McGinnis, P.V. Benos,
"Extracting biologically significant patterns from short time series gene expression data."
BMC Bioinformatics, (2009) 10:255.
Abstract (PubMed) and pdf
PMID: 19695084
- D.L. Corcoran1, K.V. Pandit1, B. Gordon, A. Bhattacharjee, N. Kaminski†, P.V. Benos†
"Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data."
PLoS ONE, (2009) 4:e5279.
Abstract (PubMed) and pdf
PMID: 19390574
1 equal contribution, † corresponding authors
- R. Brower-Sinning, D.M. Carter, C.J. Crevar, E. Ghedin, T.M. Ross, P.V. Benos
"The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus."
Genome Biol, (2009) 10:R18.
Abstract (PubMed) and pdf
PMID: 19216739
- S. Kadri, V. Hinman, P.V. Benos
"HHMMiR: Efficient de novo prediction of microRNAs using hierarchical hidden Markov models."
BMC Bioinformatics (Proc APBC), (2009) 10(Suppl 1):S35.
Abstract (PubMed) and
pdf
PMID: 19208136
2008
- Y. Lu, S. Mahony, P.V. Benos, R. Rosenfeld, I. Simon, L. Breeden, Z. Bar-Joseph,
"Multiple evidence supporting cyclic assignments",
Genome Biol, (2008) 9:403.
[rebattle article on Jensen et al., Genome Biol (2008), 9:403]
Abstract (PubMed) and
pdf
PMID: 18598377
- A. Tchagang, P.V. Benos, A. Tewfik,
"Biological evaluation of biclustering algorithms using gene ontology and chip-chip data",
IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), (2008)
Las Vegas, NV, March 30 - April 4, 2008.
2007
- H. Feng, J.L. Taylor, P.V. Benos, R. Newton, K. Waddell, S.B. Lucas, Y. Chang, P.S. Moore
"Human transcriptome subtraction by using short sequence tags to search for tumor viruses in conjunctival carcinoma."
J Virol, (2007) 81:11332-11340.
Abstract (PubMed) and pdf
PMID: 17686852
- Y. Lu, S. Mahony, P.V. Benos, R. Rosenfeld, I. Simon, L.L. Breeden, Z. Bar-Joseph
"Combined analysis reveals a core set of cycling genes."
Genome Biol, (2007) 8:R146.
Abstract (PubMed) and pdf
PMID: 17650318
- S. Mahony, P.E. Auron and P.V. Benos
"Inferring protein-DNA dependencies using motif alignments and mutual information."
Bioinformatics (Proc ISMB), (2007) 23:i297-i304.
Abstract (PubMed) and pdf
PMID: 17646310
- S. Mahony, D.L. Corcoran, E. Feingold, P.V. Benos
"Regulatory conservation of protein coding and miRNA genes in vertebrates: lessons from the opossum genome."
Genome Biol, (2007) 8:R84.
Abstract (PubMed) and pdf
PMID: 17506886
- T.S. Mikkelsen(1), ..., P.V. Benos(18), ..., S. Mahony(37), ..., K. Lindblad-Toh(64)
"Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences."
Nature, (2007) 447:167-177.
Abstract (PubMed) and pdf
PMID: 17495919
- S. Mahony, P.E. Auron, P.V. Benos
"DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies."
PLoS Comput Biol, (2007) 3:e61.
Abstract (PubMed) and pdf
PMID: 17397256
- (Web tool)
S. Mahony, P.V. Benos
"STAMP: a web tool for exploring DNA-binding motif similarities."
Nucl Acids Res, (2007) 35:W253-258.
Abstract (PubMed) and pdf
PMID: 17478497
2006
- S. Mahony, P.V. Benos, T.J. Smith, and A. Golden
"Self-Organizing Neural Networks to Support the Discovery of DNA-Binding Motifs."
Neural Networks, (2006) 19:950-962.
Abstract (PubMed) and pdf
PMID: 16839740
- K. Belov, J.E. Deakin, A.T. Papenfuss, M.L. Baker, S.D. Melman,
H.V. Siddle, N. Gouin, D.L. Goode, T.J. Sargeant, M.D. Robinson, M.J.
Wakefield, S. Mahony, J.G.R. Cross, P.V. Benos, P.B. Samollow, T.P. Speed, J.A.M. Graves, and R.D. Miller
"Reconstructing an Ancestral Mammalian Immune Supercomplex from a Marsupial MHC."
PLoS Biology, (2006) 4:e46.
Abstract (PubMed) and pdf
PMID: 16435885
2005
- K.R. Rogulski, D.E. Cohen, D.L. Corcoran, P.V. Benos and E.V. Prochownik
"Deregulation of common genes by c-Myc and its direct target, MT-MC1."
Proc Natl Acad Sci USA, (2005) 102:18968-18973.
Abstract (PubMed) and
pdf
PMID: 16365299
- S. Mahony, A. Golden, T.J. Smith and P.V. Benos
"Improved detection of DNA motifs using a self-organized clustering of familial binding profiles."
Bioinformatics (Proc ISMB), (2005) 21 Suppl:i283-i291.
Abstract (PubMed) and
pdf
PMID: 15961468
- D.L. Corcoran, E. Feingold, J. Dominick, M. Wright, J. Harnaha, M. Trucco, N. Giannoukakis and P.V. Benos
"Footer: a quantitative comparative genomics method for efficient recognition of cis-regulatory elements."
Genome Res, (2005) 15:840-847.
Abstract (PubMed) and pdf
PMID: 15930494
- (Web tool)
D.L. Corcoran, E. Feingold, and P.V. Benos
"FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting."
Nucl Acids Res, (2005) 33:W442-446.
Abstract (PubMed) and pdf
PMID: 15980508
- (Web tool)
C.T. Workman, Y. Yin, D.L. Corcoran, T. Ideker, G.D. Stormo and P.V. Benos
"EnoLOGOS: a versatile web tool for energy normalized sequence logos."
Nucl Acids Res, (2005) 33:W389-392.
Abstract (PubMed) and
pdf
PMID: 15980495
- (Web tool)
S. Ringquist, C. Pecoraro, C. Gilchrist, A. Styche, W. Rudert, P.V. Benos, and M. Trucco
"SOP3v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms."
Nucl Acids Res, (2005) 33:W548-552.
Abstract (PubMed) and pdf
PMID: 15980532
- A.M. Alexander, C. Pecoraro, A. Styche, W.A. Rudert, P.V. Benos, S. Ringquist, M. Trucco,
"SOP3: a web-based tool for selection of oligonucleotide primers for single nucleotide polymorphism analysis by Pyrosequencing",
Biotechniques, (2005) 38:87-94.
Abstract (PubMed)
pdf
PMID: 15679090
2004
- J.K. Vries, R. Munshi, D. Tobi, J. Klein-Seetharaman, P.V. Benos, I. Bahar,
"A sequence alignment-independent method for protein classification",
Appl Bioinformatics, (2004) 3:137-148.
Abstract (PubMed)
PMID: 15693739
2002
- 13. D.G. Peters, X.C. Zhang, P.V. Benos, E. Heidrich-O’Hare, R.E. Ferrell,
"Genomic analysis of the immediate/early response to shear stress in human coronary artery endothelial cell",
Physiol Genomics, (2002) 12:25-33.
Abstract (PubMed) and
pdf
PMID: 12407183
- P.V. Benos, A.S. Lapedes and G.D. Stormo,
"Probabilistic code for DNA recognition by proteins of the EGR-family",
J. Mol. Biol., (2002) 323:701-727.
Abstract (PubMed) and pdf
PMID: 12419259
- P.V. Benos, M.L. Bulyk and G.D. Stormo,
"Additivity in protein-DNA interactions: how good an approximation is it?",
Nucleic Acids Res., (2002) 30:4442-445.
Abstract (PubMed) and pdf
PMID: 12384591
- P.V. Benos, A.S. Lapedes and G.D. Stormo,
"Is there a code for protein-DNA recognition? Probab(ilistical)ly...",
Bioessays, (2002) 24:466-475. (Review article)
Abstract (PubMed) and pdf
PMID: 12001270
- A. Peter, P. Schoettler, M. Werner, N. Beinert,
G. Dowe, P. Burkert, F. Mourkioti, L. Denzer, Y. He, P. Deak,
P.V. Benos, M.K. Gatt, L. Murphy, D. Harris,
B. Barrel, C. Ferraz, S. Vidal, C. Brun, J. Demaille, E. Cadieu,
S. Dreano, S. Gloux, V. Lelaure, S. Mottier, F. Galibert,
D. Borkova, B. Minana, F.C. Kafatos, S. Bolshakov, I. Siden-Kiamos,
G. Papagiannakis, L. Spanos, C. Louis, E. Madueno, B. de Pablos,
J. Modolell, A. Bucheton, D. Callister, L. Campbell, N.S. Henderson,
P.J. Mcmillan, C. Salles, E. Tait, P. Valenti, R.D.C. Saunders,
A. Billaud, L. Pachter, R. Klapper, W. Janning, D.M. Glover,
M. Ashburner, H.J. Bellen, H. Jaeckle, U. Schaefer,
"Mapping and identification of essential gene functions on the X chromosome of Drosophila",
EMBO Reports (2002) 3:34-38.
Abstract (PubMed) and
pdf
PMID: 11751581
2001
- P.V. Benos||, A.S. Lapedes, D.S. Fields, G.D. Stormo,
"SAMIE: Statistical Algorithm for Modeling Interaction Energies",
Pac. Symp. Biocomput. (2001) 6:115-126.
Abstract (PubMed) and
pdf
PMID: 11262933
- P.V. Benos, M.K. Gatt, L. Murphy, D. Harris, B.
Barrel, C. Ferraz, S. Vidal, C. Brun, J. Demaille, E. Cadieu, S.
Dreano, S. Gloux, V. Lelaure, S. Mottier, F. Galibert, D. Borkova, B.
Minana, F.C. Kafatos, S. Bolshakov, I. Siden-Kiamos, G. Papagiannakis,
L. Spanos, C. Louis, E. Madueno, B. de Pablos, J. Modolell, A. Peter,
P. Schoettler, M. Werner, F. Mourkioti, N. Beinert, G. Dowe, U.
Schaefer, H. Jaeckle, A. Bucheton, D. Callister, L. Campbell, N.S.
Henderson, P.J. Mcmillan, C. Salles, E. Tait, P. Valenti, R.D.C.
Saunders, A. Billaud, L. Pachter, D.M. Glover and M. Ashburner,
"From first base: The sequence of the tip of the X chromosome of D. melanogaster, a comparison of two sequencing strategies",
Genome Res, (2001) 11:710-730.
Abstract (PubMed) and
pdf (publisher).
PMID: 11337470
- S. Brogna*, P.V. Benos*, G. Gasperi, C. Savakis,
"The Drosophila alcohol dehydrogenase gene may have evolved independently of the functionally homologous medfly, olive fly and flesh fly genes",
Mol. Biol. Evol., (2001) 18:322-329.
Abstract (PubMed) and
pdf (publisher).
(*) equal contribution
PMID: 11230533
2000
- M.D. Adams(1), ..., P.V. Benos(43), ..., J.C. Venter(195),
"The genome sequence of Drosophila melanogaster",
Science (2000) 287:2185-2195.
Abstract (PubMed) and
pdf (publisher).
PMID: 10731132
- P.V. Benos, M.K. Gatt, M. Ashburner, L. Murphy, D.
Harris, B. Barrel, C. Ferraz, S. Vidal, C. Brun, J. Demailles, E.
Cadieu, S. Dreano, S. Gloux, V. Lelaure, S. Mottier, F. Galibert, D.
Borkova, B. Minana, F.C. Kafatos, C. Louis, I. Siden-Kiamos, S.
Bolshakov, G. Papagiannakis, L. Spanos, S. Cox, E. Madueno, B. de
Pablos, J. Modolell, A. Peter, P. Schoettler, M. Werner, F. Mourkioti,
N. Beinert, G. Dowe, U. Schaefer, H. Jaeckle, A. Bucheton, D.
Callister, L. Campbell, N.S. Henderson, P.J. Mcmillan, C. Salles, E.
Tait, P. Valenti, R.D.C. Saunders and D.M. Glover,
"From DNA sequence to chromosome organisation: the tip of the X chromosome of D. melanogaster",
Science (2000) 287:2220-2222.
Abstract (PubMed) and
pdf (publisher).
PMID: 10731137
- P. Benos||, N. Tavernarakis, S.Brogna, G. Thireos, C. Savakis,
"Acquisition of a potential marker for insect transformation: isolation of a novel alcohol dehydrogenase gene from Bactrocera oleae by functional complementation in yeast",
Mol. Gen. Genet. (2000) 263:90-95.
Abstract (PubMed) and
pdf (publisher).
PMID: 10732677
1999
- R. Gessmann, P. Benos, H. Brueckner, M. Kokkinidis,
"The crystal structures of the synthetic C-terminal Octa- and Dodecapeptides of Trichovirin",
J Peptide Sci (1999) 5:83-95.
Abstract (PubMed) and
pdf
PMID: 10100124
1997
- P. Deak, M.M. Omar, R.D. Saunders, M. Pal,
O. Komonyi, J. Szidonya, P. Maroy, Y. Zhang, M. Ashburner,
P. Benos, C. Savakis, I. Siden-Kiamos,
C. Louis, V.N. Bolshakov, F.C. Kafatos, E. Madueno,
J. Modolell, D.M. Glover,
"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",
Genetics (1997) 147:1697-1722.
Abstract (PubMed) and
pdf
PMID: 9409831
- C. Louis, E. Madueno, J. Modolell, M.M. Omar,
G. Papagiannakis, R.D. Saunders, C. Savakis, I. Siden-Kiamos,
L. Spanos, P. Topalis, Y.Q. Zhang, M. Ashburner, P. Benos,
V.N. Bolshakov, P. Deak, D.M. Glover, S. Herrmann, F.C. Kafatos
"One-hundred and five new potential Drosophila melanogaster genes revealed through STS analysis",
Nucleic Acids Res (1997) 24:3437-3438.
Abstract (PubMed) and
pdf
PMID: 9305763
1996
- M. Tabler, P. Benos, M. Dörr,
"Representation of unique sequences in libraries of randomized nucleic acids",
Nucleic Acids Res (1996) 24:3437-3438.
Abstract (PubMed) and
pdf
PMID: 8811100
1995
- E. Madueno Amor, G. Papagiannakis, G. Rimington,
R.D.C. Saunders, C. Savakis, I. Siden-Kiamos, G. Skavdis, L. Spanos,
J. Trennear, P. Adam, M. Ashburner, P. Benos,
V. Bolshakov, D. Coulson, D.M. Glover, S. Herrmann, F.C. Kafatos,
C. Louis, T. Majerus, J. Modolell,
"A physical map of the X chromosome of Drosophila melanogaster: Cosmid contigs and sequence tagged sites",
Genetics (1995) 139:1631-1647.
Abstract (PubMed) and
pdf
PMID: 7789765
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