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Items: 1 to 50 of 79

1.

Translatome profiling of plum pox virus infected leaves in European plum reveals temporal and spatial coordination of defense responses in phloem tissues.

Collum TD, Stone AL, Sherman DJ, Rogers EE, Dardick C, Culver JN.

Mol Plant Microbe Interact. 2019 Jul 26. doi: 10.1094/MPMI-06-19-0152-FI. [Epub ahead of print]

PMID:
31347973
2.

Lipopolysaccharide is transported to the cell surface by a membrane-to-membrane protein bridge.

Sherman DJ, Xie R, Taylor RJ, George AH, Okuda S, Foster PJ, Needleman DJ, Kahne D.

Science. 2018 Feb 16;359(6377):798-801. doi: 10.1126/science.aar1886.

3.

The Antibiotic Novobiocin Binds and Activates the ATPase That Powers Lipopolysaccharide Transport.

May JM, Owens TW, Mandler MD, Simpson BW, Lazarus MB, Sherman DJ, Davis RM, Okuda S, Massefski W, Ruiz N, Kahne D.

J Am Chem Soc. 2017 Dec 6;139(48):17221-17224. doi: 10.1021/jacs.7b07736. Epub 2017 Nov 22.

4.

Many interspecific chromosomal introgressions are highly prevalent in Holarctic Saccharomyces uvarum strains found in human-related fermentations.

Albertin W, Chernova M, Durrens P, Guichoux E, Sherman DJ, Masneuf-Pomarede I, Marullo P.

Yeast. 2018 Jan;35(1):141-156. doi: 10.1002/yea.3248. Epub 2017 Nov 29.

5.

Genome Sequence of the Yeast Clavispora lusitaniae Type Strain CBS 6936.

Durrens P, Klopp C, Biteau N, Fitton-Ouhabi V, Dementhon K, Accoceberry I, Sherman DJ, Noël T.

Genome Announc. 2017 Aug 3;5(31). pii: e00724-17. doi: 10.1128/genomeA.00724-17.

6.

Host Adaptation of Soybean Dwarf Virus Following Serial Passages on Pea (Pisum sativum) and Soybean (Glycine max).

Tian B, Gildow FE, Stone AL, Sherman DJ, Damsteegt VD, Schneider WL.

Viruses. 2017 Jun 21;9(6). pii: E155. doi: 10.3390/v9060155.

7.

Lipopolysaccharide transport and assembly at the outer membrane: the PEZ model.

Okuda S, Sherman DJ, Silhavy TJ, Ruiz N, Kahne D.

Nat Rev Microbiol. 2016 Jun;14(6):337-45. doi: 10.1038/nrmicro.2016.25. Epub 2016 Mar 30. Review.

8.

Lipopolysaccharide transport to the cell surface: biosynthesis and extraction from the inner membrane.

Simpson BW, May JM, Sherman DJ, Kahne D, Ruiz N.

Philos Trans R Soc Lond B Biol Sci. 2015 Oct 5;370(1679). pii: 20150029. doi: 10.1098/rstb.2015.0029. Review.

9.

Lipopolysaccharide transport to the cell surface: periplasmic transport and assembly into the outer membrane.

May JM, Sherman DJ, Simpson BW, Ruiz N, Kahne D.

Philos Trans R Soc Lond B Biol Sci. 2015 Oct 5;370(1679). pii: 20150027. doi: 10.1098/rstb.2015.0027. Review.

10.

Phylogenomic Analysis of Oenococcus oeni Reveals Specific Domestication of Strains to Cider and Wines.

Campbell-Sills H, El Khoury M, Favier M, Romano A, Biasioli F, Spano G, Sherman DJ, Bouchez O, Coton E, Coton M, Okada S, Tanaka N, Dols-Lafargue M, Lucas PM.

Genome Biol Evol. 2015 May 14;7(6):1506-18. doi: 10.1093/gbe/evv084.

11.

Mimoza: web-based semantic zooming and navigation in metabolic networks.

Zhukova A, Sherman DJ.

BMC Syst Biol. 2015 Feb 26;9:10. doi: 10.1186/s12918-015-0151-5.

12.

Pantograph: A template-based method for genome-scale metabolic model reconstruction.

Loira N, Zhukova A, Sherman DJ.

J Bioinform Comput Biol. 2015 Apr;13(2):1550006. doi: 10.1142/S0219720015500067. Epub 2015 Jan 8.

PMID:
25572717
13.

Diversity and variability of NOD-like receptors in fungi.

Dyrka W, Lamacchia M, Durrens P, Kobe B, Daskalov A, Paoletti M, Sherman DJ, Saupe SJ.

Genome Biol Evol. 2014 Nov 13;6(12):3137-58. doi: 10.1093/gbe/evu251.

14.

Draft Genome Sequence of Rhodosporidium toruloides CECT1137, an Oleaginous Yeast of Biotechnological Interest.

Morin N, Calcas X, Devillers H, Durrens P, Sherman DJ, Nicaud JM, Neuvéglise C.

Genome Announc. 2014 Jul 10;2(4). pii: e00641-14. doi: 10.1128/genomeA.00641-14.

15.

Modeling acclimatization by hybrid systems: condition changes alter biological system behavior models.

Assar R, Montecino MA, Maass A, Sherman DJ.

Biosystems. 2014 Jul;121:43-53. doi: 10.1016/j.biosystems.2014.05.007. Epub 2014 Jun 2.

PMID:
24892552
16.

A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum.

Almeida P, Gonçalves C, Teixeira S, Libkind D, Bontrager M, Masneuf-Pomarède I, Albertin W, Durrens P, Sherman DJ, Marullo P, Hittinger CT, Gonçalves P, Sampaio JP.

Nat Commun. 2014 Jun 2;5:4044. doi: 10.1038/ncomms5044.

17.

The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest.

Kunze G, Gaillardin C, Czernicka M, Durrens P, Martin T, Böer E, Gabaldón T, Cruz JA, Talla E, Marck C, Goffeau A, Barbe V, Baret P, Baronian K, Beier S, Bleykasten C, Bode R, Casaregola S, Despons L, Fairhead C, Giersberg M, Gierski PP, Hähnel U, Hartmann A, Jankowska D, Jubin C, Jung P, Lafontaine I, Leh-Louis V, Lemaire M, Marcet-Houben M, Mascher M, Morel G, Richard GF, Riechen J, Sacerdot C, Sarkar A, Savel G, Schacherer J, Sherman DJ, Stein N, Straub ML, Thierry A, Trautwein-Schult A, Vacherie B, Westhof E, Worch S, Dujon B, Souciet JL, Wincker P, Scholz U, Neuvéglise C.

Biotechnol Biofuels. 2014 Apr 24;7:66. doi: 10.1186/1754-6834-7-66. eCollection 2014.

18.

Knowledge-based generalization of metabolic models.

Zhukova A, Sherman DJ.

J Comput Biol. 2014 Jul;21(7):534-47. doi: 10.1089/cmb.2013.0143. Epub 2014 Apr 25.

19.

Knowledge-based generalization of metabolic networks: a practical study.

Zhukova A, Sherman DJ.

J Bioinform Comput Biol. 2014 Apr;12(2):1441001. doi: 10.1142/S0219720014410017. Epub 2014 Mar 6.

PMID:
24712528
20.

Decoupling catalytic activity from biological function of the ATPase that powers lipopolysaccharide transport.

Sherman DJ, Lazarus MB, Murphy L, Liu C, Walker S, Ruiz N, Kahne D.

Proc Natl Acad Sci U S A. 2014 Apr 1;111(13):4982-7. doi: 10.1073/pnas.1323516111. Epub 2014 Mar 17.

21.

QTL dissection of Lag phase in wine fermentation reveals a new translocation responsible for Saccharomyces cerevisiae adaptation to sulfite.

Zimmer A, Durand C, Loira N, Durrens P, Sherman DJ, Marullo P.

PLoS One. 2014 Jan 28;9(1):e86298. doi: 10.1371/journal.pone.0086298. eCollection 2014.

22.

Validation of inhibitors of an ABC transporter required to transport lipopolysaccharide to the cell surface in Escherichia coli.

Sherman DJ, Okuda S, Denny WA, Kahne D.

Bioorg Med Chem. 2013 Aug 15;21(16):4846-51. doi: 10.1016/j.bmc.2013.04.020. Epub 2013 Apr 18.

23.

A previously undescribed potyvirus isolated and characterized from arborescent Brugmansia.

Damsteegt VD, Stone AL, Smith OP, McDaniel L, Sherman DJ, Dardick C, Hammond J, Jordan R, Schneider WL.

Arch Virol. 2013 Jun;158(6):1235-44. doi: 10.1007/s00705-012-1600-8. Epub 2013 Feb 5.

PMID:
23381392
24.

A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica.

Loira N, Dulermo T, Nicaud JM, Sherman DJ.

BMC Syst Biol. 2012 May 4;6:35. doi: 10.1186/1752-0509-6-35.

25.

Pichia sorbitophila, an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization.

Louis VL, Despons L, Friedrich A, Martin T, Durrens P, Casarégola S, Neuvéglise C, Fairhead C, Marck C, Cruz JA, Straub ML, Kugler V, Sacerdot C, Uzunov Z, Thierry A, Weiss S, Bleykasten C, De Montigny J, Jacques N, Jung P, Lemaire M, Mallet S, Morel G, Richard GF, Sarkar A, Savel G, Schacherer J, Seret ML, Talla E, Samson G, Jubin C, Poulain J, Vacherie B, Barbe V, Pelletier E, Sherman DJ, Westhof E, Weissenbach J, Baret PV, Wincker P, Gaillardin C, Dujon B, Souciet JL.

G3 (Bethesda). 2012 Feb;2(2):299-311. doi: 10.1534/g3.111.000745. Epub 2012 Feb 1.

26.

Reusing and composing models of cell fate regulation of human bone precursor cells.

Assar R, Leisewitz AV, Garcia A, Inestrosa NC, Montecino MA, Sherman DJ.

Biosystems. 2012 Apr-Jun;108(1-3):63-72. doi: 10.1016/j.biosystems.2012.01.008. Epub 2012 Jan 27.

PMID:
22309764
27.

The Génolevures database.

Martin T, Sherman DJ, Durrens P.

C R Biol. 2011 Aug-Sep;334(8-9):585-9. doi: 10.1016/j.crvi.2011.05.004. Epub 2011 Jun 30. Review.

PMID:
21819938
28.

Acquisition and Transmissibility of U.S. Soybean dwarf virus Isolates by the Soybean Aphid, Aphis glycines.

Damsteegt VD, Stone AL, Kuhlmann M, Gildow FE, Domier LL, Sherman DJ, Tian B, Schneider WL.

Plant Dis. 2011 Aug;95(8):945-950. doi: 10.1094/PDIS-10-10-0726.

PMID:
30732111
29.

Molecular, ultrastructural, and biological characterization of Pennsylvania isolates of Plum pox virus.

Schneider WL, Damsteegt VD, Gildow FE, Stone AL, Sherman DJ, Levy LE, Mavrodieva V, Richwine N, Welliver R, Luster DG.

Phytopathology. 2011 May;101(5):627-36. doi: 10.1094/PHYTO-09-10-0256.

30.

Molecular analysis of soybean dwarf virus isolates in the eastern United States confirms the presence of both D and Y strains and provides evidence of mixed infections and recombination.

Schneider WL, Damsteegt VD, Stone AL, Kuhlmann M, Bunyard BA, Sherman DJ, Graves MV, Smythers G, Smith OP, Hatziloukas E.

Virology. 2011 Mar 30;412(1):46-54. doi: 10.1016/j.virol.2011.01.001. Epub 2011 Jan 21.

31.

A differential cell capture assay for evaluating antibody interactions with cell surface targets.

Sherman DJ, Kenanova VE, Lepin EJ, McCabe KE, Kamei K, Ohashi M, Wang S, Tseng HR, Wu AM, Behrenbruch CP.

Anal Biochem. 2010 Jun 15;401(2):173-81. doi: 10.1016/j.ab.2010.02.015. Epub 2010 Feb 21.

32.

Three-dimensional nanostructured substrates toward efficient capture of circulating tumor cells.

Wang S, Wang H, Jiao J, Chen KJ, Owens GE, Kamei K, Sun J, Sherman DJ, Behrenbruch CP, Wu H, Tseng HR.

Angew Chem Int Ed Engl. 2009;48(47):8970-3. doi: 10.1002/anie.200901668. No abstract available.

33.

Mining the semantics of genome super-blocks to infer ancestral architectures.

Jean G, Sherman DJ, Nikolski M.

J Comput Biol. 2009 Sep;16(9):1267-84. doi: 10.1089/cmb.2008.0046.

PMID:
19772437
34.

A community standard format for the representation of protein affinity reagents.

Gloriam DE, Orchard S, Bertinetti D, Björling E, Bongcam-Rudloff E, Borrebaeck CA, Bourbeillon J, Bradbury AR, de Daruvar A, Dübel S, Frank R, Gibson TJ, Gold L, Haslam N, Herberg FW, Hiltke T, Hoheisel JD, Kerrien S, Koegl M, Konthur Z, Korn B, Landegren U, Montecchi-Palazzi L, Palcy S, Rodriguez H, Schweinsberg S, Sievert V, Stoevesandt O, Taussig MJ, Ueffing M, Uhlén M, van der Maarel S, Wingren C, Woollard P, Sherman DJ, Hermjakob H.

Mol Cell Proteomics. 2010 Jan;9(1):1-10. doi: 10.1074/mcp.M900185-MCP200. Epub 2009 Aug 11.

35.

Unusual composition of a yeast chromosome arm is associated with its delayed replication.

Payen C, Fischer G, Marck C, Proux C, Sherman DJ, Coppée JY, Johnston M, Dujon B, Neuvéglise C.

Genome Res. 2009 Oct;19(10):1710-21. doi: 10.1101/gr.090605.108. Epub 2009 Jul 10.

36.

Comparative genomics of protoploid Saccharomycetaceae.

Génolevures Consortium, Souciet JL, Dujon B, Gaillardin C, Johnston M, Baret PV, Cliften P, Sherman DJ, Weissenbach J, Westhof E, Wincker P, Jubin C, Poulain J, Barbe V, Ségurens B, Artiguenave F, Anthouard V, Vacherie B, Val ME, Fulton RS, Minx P, Wilson R, Durrens P, Jean G, Marck C, Martin T, Nikolski M, Rolland T, Seret ML, Casarégola S, Despons L, Fairhead C, Fischer G, Lafontaine I, Leh V, Lemaire M, de Montigny J, Neuvéglise C, Thierry A, Blanc-Lenfle I, Bleykasten C, Diffels J, Fritsch E, Frangeul L, Goëffon A, Jauniaux N, Kachouri-Lafond R, Payen C, Potier S, Pribylova L, Ozanne C, Richard GF, Sacerdot C, Straub ML, Talla E.

Genome Res. 2009 Oct;19(10):1696-709. doi: 10.1101/gr.091546.109. Epub 2009 Jun 12.

37.

Minimum information requirements: neither bandits in the Attic nor bats in the belfry.

Sherman DJ.

N Biotechnol. 2009 Apr;25(4):173-4. doi: 10.1016/j.nbt.2008.12.002. Epub 2008 Dec 30.

PMID:
19185067
38.

Génolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes.

Sherman DJ, Martin T, Nikolski M, Cayla C, Souciet JL, Durrens P; Génolevures Consortium.

Nucleic Acids Res. 2009 Jan;37(Database issue):D550-4. doi: 10.1093/nar/gkn859. Epub 2008 Nov 16.

39.

Exploratory simulation of cell ageing using hierarchical models.

Cvijovic M, Soueidan H, Sherman DJ, Klipp E, Nikolski M.

Genome Inform. 2008;21:114-25.

PMID:
19425152
40.

Adaptation of plum pox virus to a herbaceous host (Pisum sativum) following serial passages.

Wallis CM, Stone AL, Sherman DJ, Damsteegt VD, Gildow FE, Schneider WL.

J Gen Virol. 2007 Oct;88(Pt 10):2839-45.

PMID:
17872538
41.
42.

Family relationships: should consensus reign?--consensus clustering for protein families.

Nikolski M, Sherman DJ.

Bioinformatics. 2007 Jan 15;23(2):e71-6. Erratum in: Bioinformatics. 2009 Sep 1;25(17):2294.

PMID:
17237108
43.

ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome.

Taussig MJ, Stoevesandt O, Borrebaeck CA, Bradbury AR, Cahill D, Cambillau C, de Daruvar A, Dübel S, Eichler J, Frank R, Gibson TJ, Gloriam D, Gold L, Herberg FW, Hermjakob H, Hoheisel JD, Joos TO, Kallioniemi O, Koegl M, Konthur Z, Korn B, Kremmer E, Krobitsch S, Landegren U, van der Maarel S, McCafferty J, Muyldermans S, Nygren PA, Palcy S, Plückthun A, Polic B, Przybylski M, Saviranta P, Sawyer A, Sherman DJ, Skerra A, Templin M, Ueffing M, Uhlén M.

Nat Methods. 2007 Jan;4(1):13-7. Erratum in: Nat Methods. 2007 Feb;4(2):187. Koegll, Manfred [corrected to Koegl, Manfred].

PMID:
17195019
44.

Antibiotic treatment of intra-amniotic infection with Ureaplasma urealyticum. A case report and literature review.

Smorgick N, Frenkel E, Zaidenstein R, Lazarovitch T, Sherman DJ.

Fetal Diagn Ther. 2007;22(2):90-3. Epub 2006 Nov 27. Review.

PMID:
17135751
45.

Analysis of genetic bottlenecks during horizontal transmission of Cucumber mosaic virus.

Ali A, Li H, Schneider WL, Sherman DJ, Gray S, Smith D, Roossinck MJ.

J Virol. 2006 Sep;80(17):8345-50.

46.

A systematic nomenclature of chromosomal elements for hemiascomycete yeasts.

Durrens P, Sherman DJ.

Yeast. 2005 Apr 15;22(5):337-42.

47.

Congenital hypofibrinogenemia in pregnancy: report of two cases and review of the literature.

Frenkel E, Duksin C, Herman A, Sherman DJ.

Obstet Gynecol Surv. 2004 Nov;59(11):775-9. Review.

PMID:
15502629
48.

Specific detection and quantification of Plum pox virus by real-time fluorescent reverse transcription-PCR.

Schneider WL, Sherman DJ, Stone AL, Damsteegt VD, Frederick RD.

J Virol Methods. 2004 Sep 1;120(1):97-105.

PMID:
15234814
49.

The lateral recumbent head-down position decreases the incidence of epidural venous puncture during catheter insertion in obese parturients.

Bahar M, Chanimov M, Cohen ML, Friedland M, Shul I, Gofman V, Gershfeld S, Geller R, Sherman DJ.

Can J Anaesth. 2004 Jun-Jul;51(6):577-80.

PMID:
15197121
50.

The onset of p53-dependent apoptosis plays a role in terminal differentiation of human normoblasts.

Peller S, Frenkel J, Lapidot T, Kahn J, Rahimi-Levene N, Yona R, Nissim L, Goldfinger N, Sherman DJ, Rotter V.

Oncogene. 2003 Jul 24;22(30):4648-55.

PMID:
12879009

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