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Items: 1 to 50 of 71

1.

Millisecond dynamics of BTK reveal kinome-wide conformational plasticity within the apo kinase domain.

Sultan MM, Denny RA, Unwalla R, Lovering F, Pande VS.

Sci Rep. 2017 Nov 15;7(1):15604. doi: 10.1038/s41598-017-10697-0.

2.

Progress towards a public chemogenomic set for protein kinases and a call for contributions.

Drewry DH, Wells CI, Andrews DM, Angell R, Al-Ali H, Axtman AD, Capuzzi SJ, Elkins JM, Ettmayer P, Frederiksen M, Gileadi O, Gray N, Hooper A, Knapp S, Laufer S, Luecking U, Michaelides M, Müller S, Muratov E, Denny RA, Saikatendu KS, Treiber DK, Zuercher WJ, Willson TM.

PLoS One. 2017 Aug 2;12(8):e0181585. doi: 10.1371/journal.pone.0181585. eCollection 2017.

3.

Hybrid assembly with long and short reads improves discovery of gene family expansions.

Miller JR, Zhou P, Mudge J, Gurtowski J, Lee H, Ramaraj T, Walenz BP, Liu J, Stupar RM, Denny R, Song L, Singh N, Maron LG, McCouch SR, McCombie WR, Schatz MC, Tiffin P, Young ND, Silverstein KAT.

BMC Genomics. 2017 Jul 19;18(1):541. doi: 10.1186/s12864-017-3927-8.

4.

Segregation Lag in Polyploid Cells of the Pathogen Genus Borrelia: Implications for Antigenic Variation
.

Crowder CD, Denny RL, Barbour AG.

Yale J Biol Med. 2017 Jun 23;90(2):195-218. eCollection 2017 Jun.

5.

Markov modeling reveals novel intracellular modulation of the human TREK-2 selectivity filter.

Harrigan MP, McKiernan KA, Shanmugasundaram V, Denny RA, Pande VS.

Sci Rep. 2017 Apr 4;7(1):632. doi: 10.1038/s41598-017-00256-y.

6.

Structure-Based Design of Highly Selective Inhibitors of the CREB Binding Protein Bromodomain.

Denny RA, Flick AC, Coe J, Langille J, Basak A, Liu S, Stock I, Sahasrabudhe P, Bonin P, Hay DA, Brennan PE, Pletcher M, Jones LH, Chekler ELP.

J Med Chem. 2017 Jul 13;60(13):5349-5363. doi: 10.1021/acs.jmedchem.6b01839. Epub 2017 May 12.

PMID:
28375629
7.

Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes.

Zhou P, Silverstein KA, Ramaraj T, Guhlin J, Denny R, Liu J, Farmer AD, Steele KP, Stupar RM, Miller JR, Tiffin P, Mudge J, Young ND.

BMC Genomics. 2017 Mar 27;18(1):261. doi: 10.1186/s12864-017-3654-1.

8.

Validating Genome-Wide Association Candidates Controlling Quantitative Variation in Nodulation.

Curtin SJ, Tiffin P, Guhlin J, Trujillo DI, Burghart LT, Atkins P, Baltes NJ, Denny R, Voytas DF, Stupar RM, Young ND.

Plant Physiol. 2017 Feb;173(2):921-931. doi: 10.1104/pp.16.01923. Epub 2017 Jan 5.

9.
10.

Increasing the Endoplasmic Reticulum Pool of the F508del Allele of the Cystic Fibrosis Transmembrane Conductance Regulator Leads to Greater Folding Correction by Small Molecule Therapeutics.

Chung WJ, Goeckeler-Fried JL, Havasi V, Chiang A, Rowe SM, Plyler ZE, Hong JS, Mazur M, Piazza GA, Keeton AB, White EL, Rasmussen L, Weissman AM, Denny RA, Brodsky JL, Sorscher EJ.

PLoS One. 2016 Oct 12;11(10):e0163615. doi: 10.1371/journal.pone.0163615. eCollection 2016.

11.

Computational Modeling of β-Secretase 1 (BACE-1) Inhibitors Using Ligand Based Approaches.

Subramanian G, Ramsundar B, Pande V, Denny RA.

J Chem Inf Model. 2016 Oct 24;56(10):1936-1949. doi: 10.1021/acs.jcim.6b00290. Epub 2016 Oct 10.

PMID:
27689393
12.

An Alternative Approach to "Identification of Unknowns": Designing a Protocol to Verify the Identities of Nitrogen Fixing Bacteria.

Martinez-Vaz BM, Denny R, Young ND, Sadowsky MJ.

J Microbiol Biol Educ. 2015 Dec 1;16(2):247-53. doi: 10.1128/jmbe.v16i2.973. eCollection 2015 Dec.

13.

Transcriptional Profiling of a Selective CREB Binding Protein Bromodomain Inhibitor Highlights Therapeutic Opportunities.

Chekler EL, Pellegrino JA, Lanz TA, Denny RA, Flick AC, Coe J, Langille J, Basak A, Liu S, Stock IA, Sahasrabudhe P, Bonin PD, Lee K, Pletcher MT, Jones LH.

Chem Biol. 2015 Dec 17;22(12):1588-96. doi: 10.1016/j.chembiol.2015.10.013. Epub 2015 Dec 3.

14.

Fluorine in drug design: a case study with fluoroanisoles.

Xing L, Blakemore DC, Narayanan A, Unwalla R, Lovering F, Denny RA, Zhou H, Bunnage ME.

ChemMedChem. 2015 Apr;10(4):715-26. doi: 10.1002/cmdc.201402555. Epub 2015 Mar 6.

PMID:
25755132
15.

Candidate genes and genetic architecture of symbiotic and agronomic traits revealed by whole-genome, sequence-based association genetics in Medicago truncatula.

Stanton-Geddes J, Paape T, Epstein B, Briskine R, Yoder J, Mudge J, Bharti AK, Farmer AD, Zhou P, Denny R, May GD, Erlandson S, Yakub M, Sugawara M, Sadowsky MJ, Young ND, Tiffin P.

PLoS One. 2013 May 31;8(5):e65688. doi: 10.1371/journal.pone.0065688. Print 2013.

16.

Identification of ion series using ion mobility mass spectrometry: the example of alkyl-benzothiophene and alkyl-dibenzothiophene ions in diesel fuels.

Maire F, Neeson K, Denny R, McCullagh M, Lange C, Afonso C, Giusti P.

Anal Chem. 2013 Jun 4;85(11):5530-4. doi: 10.1021/ac400731d. Epub 2013 May 16.

PMID:
23638962
17.

Recent developments in targeting protein misfolding diseases.

Denny RA, Gavrin LK, Saiah E.

Bioorg Med Chem Lett. 2013 Apr 1;23(7):1935-44. doi: 10.1016/j.bmcl.2013.01.089. Epub 2013 Feb 4. Review.

18.

Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies.

Sugawara M, Epstein B, Badgley BD, Unno T, Xu L, Reese J, Gyaneshwar P, Denny R, Mudge J, Bharti AK, Farmer AD, May GD, Woodward JE, Médigue C, Vallenet D, Lajus A, Rouy Z, Martinez-Vaz B, Tiffin P, Young ND, Sadowsky MJ.

Genome Biol. 2013 Feb 20;14(2):R17. doi: 10.1186/gb-2013-14-2-r17.

19.

Small molecules that target protein misfolding.

Gavrin LK, Denny RA, Saiah E.

J Med Chem. 2012 Dec 27;55(24):10823-43. doi: 10.1021/jm301182j. Epub 2012 Nov 1.

PMID:
23075044
20.

A probabilistic framework for peptide and protein quantification from data-dependent and data-independent LC-MS proteomics experiments.

Richardson K, Denny R, Hughes C, Skilling J, Sikora J, Dadlez M, Manteca A, Jung HR, Jensen ON, Redeker V, Melki R, Langridge JI, Vissers JP.

OMICS. 2012 Sep;16(9):468-82. doi: 10.1089/omi.2012.0019. Epub 2012 Aug 7.

21.

Evolution of a complex disease resistance gene cluster in diploid Phaseolus and tetraploid Glycine.

Ashfield T, Egan AN, Pfeil BE, Chen NW, Podicheti R, Ratnaparkhe MB, Ameline-Torregrosa C, Denny R, Cannon S, Doyle JJ, Geffroy V, Roe BA, Saghai Maroof MA, Young ND, Innes RW.

Plant Physiol. 2012 May;159(1):336-54. doi: 10.1104/pp.112.195040. Epub 2012 Mar 28.

22.

The Medicago genome provides insight into the evolution of rhizobial symbioses.

Young ND, Debellé F, Oldroyd GE, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KF, Gouzy J, Schoof H, Van de Peer Y, Proost S, Cook DR, Meyers BC, Spannagl M, Cheung F, De Mita S, Krishnakumar V, Gundlach H, Zhou S, Mudge J, Bharti AK, Murray JD, Naoumkina MA, Rosen B, Silverstein KA, Tang H, Rombauts S, Zhao PX, Zhou P, Barbe V, Bardou P, Bechner M, Bellec A, Berger A, Bergès H, Bidwell S, Bisseling T, Choisne N, Couloux A, Denny R, Deshpande S, Dai X, Doyle JJ, Dudez AM, Farmer AD, Fouteau S, Franken C, Gibelin C, Gish J, Goldstein S, González AJ, Green PJ, Hallab A, Hartog M, Hua A, Humphray SJ, Jeong DH, Jing Y, Jöcker A, Kenton SM, Kim DJ, Klee K, Lai H, Lang C, Lin S, Macmil SL, Magdelenat G, Matthews L, McCorrison J, Monaghan EL, Mun JH, Najar FZ, Nicholson C, Noirot C, O'Bleness M, Paule CR, Poulain J, Prion F, Qin B, Qu C, Retzel EF, Riddle C, Sallet E, Samain S, Samson N, Sanders I, Saurat O, Scarpelli C, Schiex T, Segurens B, Severin AJ, Sherrier DJ, Shi R, Sims S, Singer SR, Sinharoy S, Sterck L, Viollet A, Wang BB, Wang K, Wang M, Wang X, Warfsmann J, Weissenbach J, White DD, White JD, Wiley GB, Wincker P, Xing Y, Yang L, Yao Z, Ying F, Zhai J, Zhou L, Zuber A, Dénarié J, Dixon RA, May GD, Schwartz DC, Rogers J, Quétier F, Town CD, Roe BA.

Nature. 2011 Nov 16;480(7378):520-4. doi: 10.1038/nature10625.

23.

Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula.

Branca A, Paape TD, Zhou P, Briskine R, Farmer AD, Mudge J, Bharti AK, Woodward JE, May GD, Gentzbittel L, Ben C, Denny R, Sadowsky MJ, Ronfort J, Bataillon T, Young ND, Tiffin P.

Proc Natl Acad Sci U S A. 2011 Oct 18;108(42):E864-70. doi: 10.1073/pnas.1104032108. Epub 2011 Sep 26.

24.

Identification and SAR of a new series of thieno[3,2-d]pyrimidines as Tpl2 kinase inhibitors.

Ni Y, Gopalsamy A, Cole D, Hu Y, Denny R, Ipek M, Liu J, Lee J, Hall JP, Luong M, Telliez JB, Lin LL.

Bioorg Med Chem Lett. 2011 Oct 1;21(19):5952-6. doi: 10.1016/j.bmcl.2011.07.069. Epub 2011 Jul 26.

PMID:
21862328
25.

Discovery of indazoles as inhibitors of Tpl2 kinase.

Hu Y, Cole D, Denny RA, Anderson DR, Ipek M, Ni Y, Wang X, Thaisrivongs S, Chamberlain T, Hall JP, Liu J, Luong M, Lin LL, Telliez JB, Gopalsamy A.

Bioorg Med Chem Lett. 2011 Aug 15;21(16):4758-61. doi: 10.1016/j.bmcl.2011.06.065. Epub 2011 Jun 22.

PMID:
21742493
26.

A protein relational database and protein family knowledge bases to facilitate structure-based design analyses.

Mobilio D, Walker G, Brooijmans N, Nilakantan R, Denny RA, Dejoannis J, Feyfant E, Kowticwar RK, Mankala J, Palli S, Punyamantula S, Tatipally M, John RK, Humblet C.

Chem Biol Drug Des. 2010 Aug;76(2):142-53. doi: 10.1111/j.1747-0285.2010.00994.x.

PMID:
20629978
27.

Insights for predicting blood-brain barrier penetration of CNS targeted molecules using QSPR approaches.

Fan Y, Unwalla R, Denny RA, Di L, Kerns EH, Diller DJ, Humblet C.

J Chem Inf Model. 2010 Jun 28;50(6):1123-33. doi: 10.1021/ci900384c.

PMID:
20578728
28.

An enriched structural kinase database to enable kinome-wide structure-based analyses and drug discovery.

Brooijmans N, Chang YW, Mobilio D, Denny RA, Humblet C.

Protein Sci. 2010 Apr;19(4):763-74. doi: 10.1002/pro.355.

29.

A structural informatics approach to mine kinase knowledge bases.

Brooijmans N, Mobilio D, Walker G, Nilakantan R, Denny RA, Feyfant E, Diller D, Bikker J, Humblet C.

Drug Discov Today. 2010 Mar;15(5-6):203-9. doi: 10.1016/j.drudis.2009.11.005. Epub 2009 Dec 3. Review.

PMID:
19948242
30.

Development of QSAR models for microsomal stability: identification of good and bad structural features for rat, human and mouse microsomal stability.

Hu Y, Unwalla R, Denny RA, Bikker J, Di L, Humblet C.

J Comput Aided Mol Des. 2010 Jan;24(1):23-35. doi: 10.1007/s10822-009-9309-9. Epub 2009 Nov 24.

PMID:
19937264
31.

Tetrahydrocarbazole-based serotonin reuptake inhibitor/dopamine D2 partial agonists for the potential treatment of schizophrenia.

Rotella DP, McFarlane GR, Greenfield A, Grosanu C, Robichaud AJ, Denny RA, Feenstra RW, Núñez-García S, Reinders JH, Neut Mv, McCreary A, Kruse CG, Sullivan K, Pruthi F, Lai M, Zhang J, Kowal DM, Carrick T, Grauer SM, Navarra RL, Graf R, Brennan J, Marquis KL, Pausch MH.

Bioorg Med Chem Lett. 2009 Oct 1;19(19):5552-5. doi: 10.1016/j.bmcl.2009.08.050. Epub 2009 Aug 15.

PMID:
19720528
32.

Replication of nonautonomous retroelements in soybean appears to be both recent and common.

Wawrzynski A, Ashfield T, Chen NW, Mammadov J, Nguyen A, Podicheti R, Cannon SB, Thareau V, Ameline-Torregrosa C, Cannon E, Chacko B, Couloux A, Dalwani A, Denny R, Deshpande S, Egan AN, Glover N, Howell S, Ilut D, Lai H, Del Campo SM, Metcalf M, O'Bleness M, Pfeil BE, Ratnaparkhe MB, Samain S, Sanders I, Ségurens B, Sévignac M, Sherman-Broyles S, Tucker DM, Yi J, Doyle JJ, Geffroy V, Roe BA, Maroof MA, Young ND, Innes RW.

Plant Physiol. 2008 Dec;148(4):1760-71. doi: 10.1104/pp.108.127910. Epub 2008 Oct 24.

33.

Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean.

Innes RW, Ameline-Torregrosa C, Ashfield T, Cannon E, Cannon SB, Chacko B, Chen NW, Couloux A, Dalwani A, Denny R, Deshpande S, Egan AN, Glover N, Hans CS, Howell S, Ilut D, Jackson S, Lai H, Mammadov J, Del Campo SM, Metcalf M, Nguyen A, O'Bleness M, Pfeil BE, Podicheti R, Ratnaparkhe MB, Samain S, Sanders I, Ségurens B, Sévignac M, Sherman-Broyles S, Thareau V, Tucker DM, Walling J, Wawrzynski A, Yi J, Doyle JJ, Geffroy V, Roe BA, Maroof MA, Young ND.

Plant Physiol. 2008 Dec;148(4):1740-59. doi: 10.1104/pp.108.127902. Epub 2008 Oct 8.

34.

ProbSeq--a fragmentation model for interpretation of electrospray tandem mass spectrometry data.

Skilling J, Denny R, Richardson K, Young P, McKenna T, Campuzano I, Ritchie M.

Comp Funct Genomics. 2004;5(1):61-8. doi: 10.1002/cfg.370.

35.

CONFIRM: connecting fragments found in receptor molecules.

Thompson DC, Denny RA, Nilakantan R, Humblet C, Joseph-McCarthy D, Feyfant E.

J Comput Aided Mol Des. 2008 Oct;22(10):761-72. doi: 10.1007/s10822-008-9221-8. Epub 2008 Jul 9.

PMID:
18612831
36.

Distribution of microsatellites in the genome of Medicago truncatula: a resource of genetic markers that integrate genetic and physical maps.

Mun JH, Kim DJ, Choi HK, Gish J, Debellé F, Mudge J, Denny R, Endré G, Saurat O, Dudez AM, Kiss GB, Roe B, Young ND, Cook DR.

Genetics. 2006 Apr;172(4):2541-55. Epub 2006 Feb 19.

37.

Simultaneous qualitative and quantitative analysis of the Escherichia coli proteome: a sweet tale.

Silva JC, Denny R, Dorschel C, Gorenstein MV, Li GZ, Richardson K, Wall D, Geromanos SJ.

Mol Cell Proteomics. 2006 Apr;5(4):589-607. Epub 2006 Jan 5.

38.

Chronic rejection and its multifactorial causes.

Denny RR, Rana A.

Curr Surg. 2005 May-Jun;62(3):294-9. No abstract available.

PMID:
15890211
39.

Graft and quality of life outcomes in older recipients of a kidney transplant.

Humar A, Denny R, Matas AJ, Najarian JS.

Exp Clin Transplant. 2003 Dec;1(2):69-72.

40.

Quantitative proteomic analysis by accurate mass retention time pairs.

Silva JC, Denny R, Dorschel CA, Gorenstein M, Kass IJ, Li GZ, McKenna T, Nold MJ, Richardson K, Young P, Geromanos S.

Anal Chem. 2005 Apr 1;77(7):2187-200.

PMID:
15801753
41.

Soybean bacterial artificial chromosome contigs anchored with RFLPs: insights into genome duplication and gene clustering.

Mudge J, Huihuang Y, Denny RL, Howe DK, Danesh D, Marek LF, Retzel E, Shoemaker RC, Young ND.

Genome. 2004 Apr;47(2):361-72.

PMID:
15060589
42.

Evolution and microsynteny of the apyrase gene family in three legume genomes.

Cannon SB, McCombie WR, Sato S, Tabata S, Denny R, Palmer L, Katari M, Young ND, Stacey G.

Mol Genet Genomics. 2003 Dec;270(4):347-61. Epub 2003 Nov 4.

PMID:
14598165
43.

Trap models and slow dynamics in supercooled liquids.

Denny RA, Reichman DR, Bouchaud JP.

Phys Rev Lett. 2003 Jan 17;90(2):025503. Epub 2003 Jan 17.

PMID:
12570556
44.

Comparative genomic analysis of sequences sampled from a small region on soybean (Glycine max) molecular linkage group G.

Foster-Hartnett D, Mudge J, Larsen D, Danesh D, Yan H, Denny R, Peñuela S, Young ND.

Genome. 2002 Aug;45(4):634-45.

PMID:
12175066
45.

Are wound complications after a kidney transplant more common with modern immunosuppression?

Humar A, Ramcharan T, Denny R, Gillingham KJ, Payne WD, Matas AJ.

Transplantation. 2001 Dec 27;72(12):1920-3.

PMID:
11773889
46.

Soybean genomic survey: BAC-end sequences near RFLP and SSR markers.

Marek LF, Mudge J, Darnielle L, Grant D, Hanson N, Paz M, Huihuang Y, Denny R, Larson K, Foster-Hartnett D, Cooper A, Danesh D, Larsen D, Schmidt T, Staggs R, Crow JA, Retzel E, Young ND, Shoemaker RC.

Genome. 2001 Aug;44(4):572-81.

PMID:
11550890
47.

Laparoscopic simultaneous nephrectomy and distal pancreatectomy from a live donor.

Gruessner RW, Kandaswamy R, Denny R.

J Am Coll Surg. 2001 Sep;193(3):333-7. No abstract available.

PMID:
11548807
48.

Mode-coupling theory of the fifth-order Raman spectrum of an atomic liquid.

Denny RA, Reichman DR.

Phys Rev E Stat Nonlin Soft Matter Phys. 2001 Jun;63(6 Pt 2):065101. Epub 2001 May 10.

PMID:
11415156
49.

Lack of cross-species transmission of porcine endogenous retrovirus infection to nonhuman primate recipients of porcine cells, tissues, or organs.

Switzer WM, Michler RE, Shanmugam V, Matthews A, Hussain AI, Wright A, Sandstrom P, Chapman LE, Weber C, Safley S, Denny RR, Navarro A, Evans V, Norin AJ, Kwiatkowski P, Heneine W.

Transplantation. 2001 Apr 15;71(7):959-65.

PMID:
11349732
50.

Differential regulation of a family of apyrase genes from Medicago truncatula.

Cohn JR, Uhm T, Ramu S, Nam YW, Kim DJ, Penmetsa RV, Wood TC, Denny RL, Young ND, Cook DR, Stacey G.

Plant Physiol. 2001 Apr;125(4):2104-19.

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