Source: https://www.csb.pitt.edu/Faculty/benos/?page_id=1219
Timestamp: 2019-04-23 10:23:25+00:00

Document:
Proc Machine Learning Research (2018) 92:48-65.
S. Kadri, V. Hinman, P.V. Benos, “RNA deep sequencing reveals differential microRNA expression during development of sea urchin and sea star”, PLoS One, (2011), 6:e29217. PMID: 22216218.
G. Zinman, R. Brower-Sinning, C.H. Emeche, J. Ernst, G.T. Huang, S. Mahony, A.J. Myers, D.M. O’Dee, J. L. Flynn, G.J. Nau, T.M. Ross, R.D. Salter, P.V. Benos, Z. Bar-Joseph, P.A. Morel, “Large scale comparison of innate responses to viral and bacterial pathogens in mouse and macaque”, PLoS One (2011) 6:e22401. PMID: 21789257.
Y. Zhang, D. Handley, T. Kaplan, H. Yu, A.S. Bais, T. Richards, K.V. Pandit, P.V. Benos, N. Friedman, O. Eickelberg, N. Kaminski, “High throughput determination of TGFβ1/SMAD3 targets in A549 lung epithelial cells”, PLoS One (2011) 6:e20319. PMID: 21625455.
(Web tool) G.T. Huang, C. Athanassiou, P.V. Benos, “mirConnX: Condition-specific mRNA-microRNA network integrator”, Nucleic Acids Research (2011) 39:W416-423.PMID: 21558324.
A.S. Bais, N. Kaminski, P.V. Benos, “Finding subtypes of transcription factor motif pairs with distinct regulatory roles”, Nucleic Acids Research (2011), 39:e76. PMID: 21486752.
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-7din idiopathic pulmonary fibrosis”, Am J Respir Crit Care Med. (2010) 182:220-229. PMID: 20395557.
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 Research (2010) 38:2134-2144. PMID: 20047959.
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.
D.L. Corcoran†, K.V. Pandit†, 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. PMID: 19390574.
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 Biology (2009), 10:R18. PMID: 19216739.
S. Kadri, V. Hinman, P.V. Benos, “HHMMiR: Efficient de novo prediction of microRNAs using hierarchical hidden Markov models”, BMC Bioinformatics (2009) 10(Supl 1):S35. (Proc APBC 2009) PMID: 19208136.
Y. Lu, S. Mahony, P.V. Benos, R. Rosenfeld, I. Simon, L. Breeden, Z. Bar-Joseph, “Multiple evidence supporting cyclic assignments”, Genome Biology (2008),9:403 [rebattle article on Jensen et al., “Circular reasoning rather than cyclic expression”, Genome Biol (2008),9:403]. PMID: 18598377.
H. Feng, J.L. Taylor, P.V. Benos, R. Newton, R. Downing, K. Waddell, Y. Chang, P.S. Moore, “Subtraction of the human transcriptome to search for human tumor viruses”, J Virology (2007) 81:11332-11340. PMID: 17686852.
Y. Lu, S. Mahony, P.V. Benos, R. Rosenfeld, I. Simon, L. Breeden, Z. Bar-Joseph, “Combined analysis reveals a core set of cycling genes”, Genome Biology (2007) 8:R146. PMID: 17650318.
S. Mahony, P.E. Auron and P.V. Benos “Inferring protein-DNA dependencies using motif alignments and mutual information.” Bioinformatics (2007) 23:i297-i304. (Proc ISMB 2007) 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 Biology (2007) 8:R84. PMID: 17506886.
T.S. Mikkelsen (1), …, P.V. Benos(18), …, K. Lindblad-Toh (61), “Genome of the marsupial Monodelphis domesticareveals lineage-specific innovation in coding and non-coding sequences”, Nature (2007) 447:167-177. PMID: 17495919.
(Web tool) S. Mahony, P.V. Benos, “STAMP: a web tool for exploring DNA-binding motif similarities”, Nucleic Acids Research (2007) 35:W253-258. PMID: 17478497.
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. PMID: 17397256.
S. Mahony, P.V. Benos, T.J. Smith, A. Golden, “Self-organizing neural networks to support the discovery of DNA-binding motifs”, Neural Networks (2006) 19:950-962. 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, R.D. Miller, “Reconstructing an Ancestral Mammalian Immune Supercomplex from a Marsupial Major Histocompatibility Complex”, PLoS Biology (2006) 4:e46. PMID: 16435885.
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. 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 (2005) 21 Suppl:i283-i291. (Proc ISMB 2005) PMID: 15961468.
(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.” Nucleic Acids Research (2005) 33:W548-552. PMID: 15980532.
(Web tool) D.L. Corcoran, E. Feingold, and P.V. Benos “FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting.” Nucleic Acids Research (2005) 33:W442-446. 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.” Nucleic Acids Research, (2005) 33:W389-392. PMID: 15980495.
D.L. Corcoran, E. Feingold, J. Dominick, M. Wright, J. Harnaha, M. Trucco, N. Giannoukakis, P.V. Benos, “FOOTER: a quantitative comparative genomics method for efficient recognition of cis-regulatory elements”, Genome Research (2005) 15:840-847.PMID: 15930494.
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. PMID: 15679090.
J.K. Vries, R. Munshi, D. Tobi, J. Klein-Seetharaman, P.V. Benos, I. Bahar, “A sequence alignment-independent method for protein classification”, Applied Bioinformatics (2004) 3:137-148. PMID: 15693739.
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.PMID: 12407183.
P.V. Benos, A.S. Lapedes, G.D. Stormo, “Is there a code for protein-DNA recognition? Probab(ilistical)ly…”, Bioessays (2002) 24:466-475. (Review) PMID: 12001270.
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. PMID: 11262933.
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. PMID: 11751581.
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, M. Ashburner, “From first base: The sequence of the tip of the X chromosome of D. melanogaster, a comparison of two sequencing strategies”, Genome Research (2001) 11:710-730. PMID: 11337470.
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. PMID: 10731137.
M. Adams(1), …, P.V. Benos(43), …, C. Venter(195), “The genome sequence of Drosophila melanogaster“, Science (2000) 287:2185-2195. PMID: 10731132.
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”, Molecular Biology Evolution, (2001) 18:322-329. PMID: 11230533.
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 fromBactrocera oleae by functional complementation in yeast”, Molecular General Genetics (2000) 263:90-95. PMID: 10732677.
R. Gessmann, P. Benos, H. Brueckner, M. Kokkinidis, “The crystal structures of the synthetic C-terminal Octa- and Dodecapeptides of Trichovirin”, J. Peptide Science (1999) 5:83-95. PMID: 10100124.
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. 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 melanogastergenes revealed through STS analysis”, Gene (1997) 195:187-193. PMID: 9305763.
M. Tabler, P. Benos, M. Doerr, “Representation of unique sequences in libraries of randomized nucleic acids”, Nucleic Acids Research (1996) 24:3437-3438. PMID: 8811100.
E. Madueno Amor, G. Papagiannakis, G. Rimmington, 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. PMID: 7789765.

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