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Items: 1 to 50 of 96

1.

Protein-protein interactions of human viruses.

Goodacre N, Devkota P, Bae E, Wuchty S, Uetz P.

Semin Cell Dev Biol. 2018 Jul 18. pii: S1084-9521(17)30499-8. doi: 10.1016/j.semcdb.2018.07.018. [Epub ahead of print] Review.

PMID:
30031213
2.

Making the Right Choice: Critical Parameters of the Y2H Systems.

Mehla J, Caufield JH, Uetz P.

Methods Mol Biol. 2018;1794:17-28. doi: 10.1007/978-1-4939-7871-7_2.

PMID:
29855948
3.

The original descriptions of reptiles and their subspecies.

Uetz P, Stylianou A.

Zootaxa. 2018 Jan 24;4375(2):257-264. doi: 10.11646/zootaxa.4375.2.5.

PMID:
29689772
4.

Proteome Data Improves Protein Function Prediction in the Interactome of Helicobacter pylori.

Wuchty S, Müller SA, Caufield JH, Häuser R, Aloy P, Kalkhof S, Uetz P.

Mol Cell Proteomics. 2018 May;17(5):961-973. doi: 10.1074/mcp.RA117.000474. Epub 2018 Feb 1.

PMID:
29414760
5.

The Nitrogen Regulatory PII Protein (GlnB) and N-Acetylglucosamine 6-Phosphate Epimerase (NanE) Allosterically Activate Glucosamine 6-Phosphate Deaminase (NagB) in Escherichia coli.

Rodionova IA, Goodacre N, Babu M, Emili A, Uetz P, Saier MH Jr.

J Bacteriol. 2018 Feb 7;200(5). pii: e00691-17. doi: 10.1128/JB.00691-17. Print 2018 Mar 1.

PMID:
29229699
6.

Author Correction: The global distribution of tetrapods reveals a need for targeted reptile conservation.

Roll U, Feldman A, Novosolov M, Allison A, Bauer AM, Bernard R, Böhm M, Castro-Herrera F, Chirio L, Collen B, Colli GR, Dabool L, Das I, Doan TM, Grismer LL, Hoogmoed M, Itescu Y, Kraus F, LeBreton M, Lewin A, Martins M, Maza E, Meirte D, Nagy ZT, Nogueira CC, Pauwels OSG, Pincheira-Donoso D, Powney GD, Sindaco R, Tallowin O, Torres-Carvajal O, Trape JF, Vidan E, Uetz P, Wagner P, Wang Y, Orme CDL, Grenyer R, Meiri S.

Nat Ecol Evol. 2018 Jan;2(1):193. doi: 10.1038/s41559-017-0399-9. No abstract available.

PMID:
29208994
7.

Virus-host protein-protein interactions of mycobacteriophage Giles.

Mehla J, Dedrick RM, Caufield JH, Wagemans J, Sakhawalkar N, Johnson A, Hatfull GF, Uetz P.

Sci Rep. 2017 Nov 28;7(1):16514. doi: 10.1038/s41598-017-16303-7.

8.

Global landscape of cell envelope protein complexes in Escherichia coli.

Babu M, Bundalovic-Torma C, Calmettes C, Phanse S, Zhang Q, Jiang Y, Minic Z, Kim S, Mehla J, Gagarinova A, Rodionova I, Kumar A, Guo H, Kagan O, Pogoutse O, Aoki H, Deineko V, Caufield JH, Holtzapple E, Zhang Z, Vastermark A, Pandya Y, Lai CC, El Bakkouri M, Hooda Y, Shah M, Burnside D, Hooshyar M, Vlasblom J, Rajagopala SV, Golshani A, Wuchty S, F Greenblatt J, Saier M, Uetz P, F Moraes T, Parkinson J, Emili A.

Nat Biotechnol. 2018 Jan;36(1):103-112. doi: 10.1038/nbt.4024. Epub 2017 Nov 27.

9.

Publisher Correction: The global distribution of tetrapods reveals a need for targeted reptile conservation.

Roll U, Feldman A, Novosolov M, Allison A, Bauer AM, Bernard R, Böhm M, Castro-Herrera F, Chirio L, Collen B, Colli GR, Dabool L, Das I, Doan TM, Grismer LL, Hoogmoed M, Itescu Y, Kraus F, LeBreton M, Lewin A, Martins M, Maza E, Meirte D, Nagy ZT, de C Nogueira C, Pauwels OSG, Pincheira-Donoso D, Powney GD, Sindaco R, Tallowin OJS, Torres-Carvajal O, Trape JF, Vidan E, Uetz P, Wagner P, Wang Y, Orme CDL, Grenyer R, Meiri S.

Nat Ecol Evol. 2017 Nov;1(11):1785. doi: 10.1038/s41559-017-0380-7.

PMID:
29046563
10.

The global distribution of tetrapods reveals a need for targeted reptile conservation.

Roll U, Feldman A, Novosolov M, Allison A, Bauer AM, Bernard R, Böhm M, Castro-Herrera F, Chirio L, Collen B, Colli GR, Dabool L, Das I, Doan TM, Grismer LL, Hoogmoed M, Itescu Y, Kraus F, LeBreton M, Lewin A, Martins M, Maza E, Meirte D, Nagy ZT, de C Nogueira C, Pauwels OSG, Pincheira-Donoso D, Powney GD, Sindaco R, Tallowin OJS, Torres-Carvajal O, Trape JF, Vidan E, Uetz P, Wagner P, Wang Y, Orme CDL, Grenyer R, Meiri S.

Nat Ecol Evol. 2017 Nov;1(11):1677-1682. doi: 10.1038/s41559-017-0332-2. Epub 2017 Oct 9. Erratum in: Nat Ecol Evol. 2017 Dec 5;:.

PMID:
28993667
11.

Bam35 tectivirus intraviral interaction map unveils new function and localization of phage ORFan proteins.

Berjón-Otero M, Lechuga A, Mehla J, Uetz P, Salas M, Redrejo-Rodríguez M.

J Virol. 2017 Jul 26. pii: JVI.00870-17. doi: 10.1128/JVI.00870-17. [Epub ahead of print]

12.

The Protein Interactome of Streptococcus pneumoniae and Bacterial Meta-interactomes Improve Function Predictions.

Wuchty S, Rajagopala SV, Blazie SM, Parrish JR, Khuri S, Finley RL Jr, Uetz P.

mSystems. 2017 Jun 6;2(3). pii: e00019-17. doi: 10.1128/mSystems.00019-17. eCollection 2017 May-Jun.

13.

The phosphocarrier protein HPr of the bacterial phosphotransferase system globally regulates energy metabolism by directly interacting with multiple enzymes in Escherichia coli.

Rodionova IA, Zhang Z, Mehla J, Goodacre N, Babu M, Emili A, Uetz P, Saier MH Jr.

J Biol Chem. 2017 Aug 25;292(34):14250-14257. doi: 10.1074/jbc.M117.795294. Epub 2017 Jun 20.

PMID:
28634232
14.

Molecular taxonomy: Species disconnected from DNA sequences.

Uetz P, Garg A.

Nature. 2017 May 24;545(7655):412. doi: 10.1038/545412c. No abstract available.

PMID:
28541320
15.

Bacterial protein meta-interactomes predict cross-species interactions and protein function.

Caufield JH, Wimble C, Shary S, Wuchty S, Uetz P.

BMC Bioinformatics. 2017 Mar 16;18(1):171. doi: 10.1186/s12859-017-1585-0.

16.

A Comparison of Two-Hybrid Approaches for Detecting Protein-Protein Interactions.

Mehla J, Caufield JH, Sakhawalkar N, Uetz P.

Methods Enzymol. 2017;586:333-358. doi: 10.1016/bs.mie.2016.10.020. Epub 2017 Jan 5.

17.

Local Action with Global Impact: Highly Similar Infection Patterns of Human Viruses and Bacteriophages.

Mariano R, Khuri S, Uetz P, Wuchty S.

mSystems. 2016 Mar 8;1(2). pii: e00030-15. eCollection 2016 Mar-Apr.

18.

The interactome of Streptococcus pneumoniae and its bacteriophages show highly specific patterns of interactions among bacteria and their phages.

Mariano R, Wuchty S, Vizoso-Pinto MG, Häuser R, Uetz P.

Sci Rep. 2016 Apr 22;6:24597. doi: 10.1038/srep24597.

19.

Predicting nsSNPs that Disrupt Protein-Protein Interactions Using Docking.

Goodacre N, Edwards N, Danielsen M, Uetz P, Wu C.

IEEE/ACM Trans Comput Biol Bioinform. 2017 Sep-Oct;14(5):1082-1093. doi: 10.1109/TCBB.2016.2520931. Epub 2016 Jan 22.

PMID:
26812731
20.

The Hepatitis E virus intraviral interactome.

Osterman A, Stellberger T, Gebhardt A, Kurz M, Friedel CC, Uetz P, Nitschko H, Baiker A, Vizoso-Pinto MG.

Sci Rep. 2015 Oct 14;5:13872. doi: 10.1038/srep13872.

21.

The Protein Interactome of Mycobacteriophage Giles Predicts Functions for Unknown Proteins.

Mehla J, Dedrick RM, Caufield JH, Siefring R, Mair M, Johnson A, Hatfull GF, Uetz P.

J Bacteriol. 2015 Aug 1;197(15):2508-16. doi: 10.1128/JB.00164-15. Epub 2015 May 18.

22.

Stable isotope labeling by amino acids in cell culture based proteomics reveals differences in protein abundances between spiral and coccoid forms of the gastric pathogen Helicobacter pylori.

Müller SA, Pernitzsch SR, Haange SB, Uetz P, von Bergen M, Sharma CM, Kalkhof S.

J Proteomics. 2015 Aug 3;126:34-45. doi: 10.1016/j.jprot.2015.05.011. Epub 2015 May 12.

PMID:
25979772
23.

The yeast two-hybrid system: a tool for mapping protein-protein interactions.

Mehla J, Caufield JH, Uetz P.

Cold Spring Harb Protoc. 2015 May 1;2015(5):425-30. doi: 10.1101/pdb.top083345.

PMID:
25934943
24.

Mapping protein-protein interactions using yeast two-hybrid assays.

Mehla J, Caufield JH, Uetz P.

Cold Spring Harb Protoc. 2015 May 1;2015(5):442-52. doi: 10.1101/pdb.prot086157.

PMID:
25934935
25.

Protein complexes in bacteria.

Caufield JH, Abreu M, Wimble C, Uetz P.

PLoS Comput Biol. 2015 Feb 27;11(2):e1004107. doi: 10.1371/journal.pcbi.1004107. eCollection 2015 Feb.

26.

The EHEC-host interactome reveals novel targets for the translocated intimin receptor.

Blasche S, Arens S, Ceol A, Siszler G, Schmidt MA, Häuser R, Schwarz F, Wuchty S, Aloy P, Uetz P, Stradal T, Koegl M.

Sci Rep. 2014 Dec 18;4:7531. doi: 10.1038/srep07531.

27.

An ontology for microbial phenotypes.

Chibucos MC, Zweifel AE, Herrera JC, Meza W, Eslamfam S, Uetz P, Siegele DA, Hu JC, Giglio MG.

BMC Microbiol. 2014 Nov 30;14:294. doi: 10.1186/s12866-014-0294-3.

28.

Protein-protein Interaction Networks of E. coli and S. cerevisiae are similar.

Wuchty S, Uetz P.

Sci Rep. 2014 Nov 28;4:7187. doi: 10.1038/srep07187.

29.

Functional elucidation of antibacterial phage ORFans targeting Pseudomonas aeruginosa.

Wagemans J, Blasdel BG, Van den Bossche A, Uytterhoeven B, De Smet J, Paeshuyse J, Cenens W, Aertsen A, Uetz P, Delattre AS, Ceyssens PJ, Lavigne R.

Cell Microbiol. 2014 Dec;16(12):1822-35. doi: 10.1111/cmi.12330. Epub 2014 Aug 26.

PMID:
25059764
30.

A second-generation protein-protein interaction network of Helicobacter pylori.

Häuser R, Ceol A, Rajagopala SV, Mosca R, Siszler G, Wermke N, Sikorski P, Schwarz F, Schick M, Wuchty S, Aloy P, Uetz P.

Mol Cell Proteomics. 2014 May;13(5):1318-29. doi: 10.1074/mcp.O113.033571. Epub 2014 Mar 13.

31.

The binary protein-protein interaction landscape of Escherichia coli.

Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Häuser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P.

Nat Biotechnol. 2014 Mar;32(3):285-290. doi: 10.1038/nbt.2831. Epub 2014 Feb 23.

32.

Toward more transparent and reproducible omics studies through a common metadata checklist and data publications.

Kolker E, Özdemir V, Martens L, Hancock W, Anderson G, Anderson N, Aynacioglu S, Baranova A, Campagna SR, Chen R, Choiniere J, Dearth SP, Feng WC, Ferguson L, Fox G, Frishman D, Grossman R, Heath A, Higdon R, Hutz MH, Janko I, Jiang L, Joshi S, Kel A, Kemnitz JW, Kohane IS, Kolker N, Lancet D, Lee E, Li W, Lisitsa A, Llerena A, Macnealy-Koch C, Marshall JC, Masuzzo P, May A, Mias G, Monroe M, Montague E, Mooney S, Nesvizhskii A, Noronha S, Omenn G, Rajasimha H, Ramamoorthy P, Sheehan J, Smarr L, Smith CV, Smith T, Snyder M, Rapole S, Srivastava S, Stanberry L, Stewart E, Toppo S, Uetz P, Verheggen K, Voy BH, Warnich L, Wilhelm SW, Yandl G.

OMICS. 2014 Jan;18(1):10-4. doi: 10.1089/omi.2013.0149.

33.

Protein domains of unknown function are essential in bacteria.

Goodacre NF, Gerloff DL, Uetz P.

MBio. 2013 Dec 31;5(1):e00744-13. doi: 10.1128/mBio.00744-13.

34.

The Burmese python genome reveals the molecular basis for extreme adaptation in snakes.

Castoe TA, de Koning AP, Hall KT, Card DC, Schield DR, Fujita MK, Ruggiero RP, Degner JF, Daza JM, Gu W, Reyes-Velasco J, Shaney KJ, Castoe JM, Fox SE, Poole AW, Polanco D, Dobry J, Vandewege MW, Li Q, Schott RK, Kapusta A, Minx P, Feschotte C, Uetz P, Ray DA, Hoffmann FG, Bogden R, Smith EN, Chang BS, Vonk FJ, Casewell NR, Henkel CV, Richardson MK, Mackessy SP, Bronikowski AM, Yandell M, Warren WC, Secor SM, Pollock DD.

Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20645-50. doi: 10.1073/pnas.1314475110. Epub 2013 Dec 2. Erratum in: Proc Natl Acad Sci U S A. 2013 Dec 17;110(51). doi:10.1073/pnas.1324133111. Bronikowsi, Anne M [corrected to Bronikowski, Anne M]. Proc Natl Acad Sci U S A. 2014 Feb 25;111(8):3194.

35.

Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications.

Kolker E, Özdemir V, Martens L, Hancock W, Anderson G, Anderson N, Aynacioglu S, Baranova A, Campagna SR, Chen R, Choiniere J, Dearth SP, Feng WC, Ferguson L, Fox G, Frishman D, Grossman R, Heath A, Higdon R, Hutz MH, Janko I, Jiang L, Joshi S, Kel A, Kemnitz JW, Kohane IS, Kolker N, Lancet D, Lee E, Li W, Lisitsa A, Llerena A, MacNealy-Koch C, Marshall JC, Masuzzo P, May A, Mias G, Monroe M, Montague E, Mooney S, Nesvizhskii A, Noronha S, Omenn G, Rajasimha H, Ramamoorthy P, Sheehan J, Smarr L, Smith CV, Smith T, Snyder M, Rapole S, Srivastava S, Stanberry L, Stewart E, Toppo S, Uetz P, Verheggen K, Voy BH, Warnich L, Wilhelm SW, Yandl G.

Big Data. 2013 Dec;1(4):196-201. doi: 10.1089/big.2013.0039.

PMID:
27447251
36.

The protein interaction network of bacteriophage lambda with its host, Escherichia coli.

Blasche S, Wuchty S, Rajagopala SV, Uetz P.

J Virol. 2013 Dec;87(23):12745-55. doi: 10.1128/JVI.02495-13. Epub 2013 Sep 18.

37.

A decadal view of biodiversity informatics: challenges and priorities.

Hardisty A, Roberts D; Biodiversity Informatics Community, Addink W, Aelterman B, Agosti D, Amaral-Zettler L, Ariño AH, Arvanitidis C, Backeljau T, Bailly N, Belbin L, Berendsohn W, Bertrand N, Caithness N, Campbell D, Cochrane G, Conruyt N, Culham A, Damgaard C, Davies N, Fady B, Faulwetter S, Feest A, Field D, Garnier E, Geser G, Gilbert J, Grosche, Grosser D, Hardisty A, Herbinet B, Hobern D, Jones A, de Jong Y, King D, Knapp S, Koivula H, Los W, Meyer C, Morris RA, Morrison N, Morse D, Obst M, Pafilis E, Page LM, Page R, Pape T, Parr C, Paton A, Patterson D, Paymal E, Penev L, Pollet M, Pyle R, von Raab-Straube E, Robert V, Roberts D, Robertson T, Rovellotti O, Saarenmaa H, Schalk P, Schaminee J, Schofield P, Sier A, Sierra S, Smith V, van Spronsen E, Thornton-Wood S, van Tienderen P, van Tol J, Tuama ÉÓ, Uetz P, Vaas L, Vignes Lebbe R, Vision T, Vu D, De Wever A, White R, Willis K, Young F.

BMC Ecol. 2013 Apr 15;13:16. doi: 10.1186/1472-6785-13-16. Review.

38.

Global taxonomic diversity of living reptiles.

Pincheira-Donoso D, Bauer AM, Meiri S, Uetz P.

PLoS One. 2013;8(3):e59741. doi: 10.1371/journal.pone.0059741. Epub 2013 Mar 27.

39.

The E. coli effector protein NleF is a caspase inhibitor.

Blasche S, Mörtl M, Steuber H, Siszler G, Nisa S, Schwarz F, Lavrik I, Gronewold TM, Maskos K, Donnenberg MS, Ullmann D, Uetz P, Kögl M.

PLoS One. 2013;8(3):e58937. doi: 10.1371/journal.pone.0058937. Epub 2013 Mar 14.

40.

Editorial for "The Yeast two-hybrid system".

Uetz P.

Methods. 2012 Dec;58(4):315-6. doi: 10.1016/j.ymeth.2013.01.001. No abstract available.

PMID:
23317557
41.

A comparison and optimization of yeast two-hybrid systems.

Caufield JH, Sakhawalkar N, Uetz P.

Methods. 2012 Dec;58(4):317-24. doi: 10.1016/j.ymeth.2012.12.001. Epub 2012 Dec 8.

42.

The magnitude of global marine species diversity.

Appeltans W, Ahyong ST, Anderson G, Angel MV, Artois T, Bailly N, Bamber R, Barber A, Bartsch I, Berta A, Błażewicz-Paszkowycz M, Bock P, Boxshall G, Boyko CB, Brandão SN, Bray RA, Bruce NL, Cairns SD, Chan TY, Cheng L, Collins AG, Cribb T, Curini-Galletti M, Dahdouh-Guebas F, Davie PJ, Dawson MN, De Clerck O, Decock W, De Grave S, de Voogd NJ, Domning DP, Emig CC, Erséus C, Eschmeyer W, Fauchald K, Fautin DG, Feist SW, Fransen CH, Furuya H, Garcia-Alvarez O, Gerken S, Gibson D, Gittenberger A, Gofas S, Gómez-Daglio L, Gordon DP, Guiry MD, Hernandez F, Hoeksema BW, Hopcroft RR, Jaume D, Kirk P, Koedam N, Koenemann S, Kolb JB, Kristensen RM, Kroh A, Lambert G, Lazarus DB, Lemaitre R, Longshaw M, Lowry J, Macpherson E, Madin LP, Mah C, Mapstone G, McLaughlin PA, Mees J, Meland K, Messing CG, Mills CE, Molodtsova TN, Mooi R, Neuhaus B, Ng PK, Nielsen C, Norenburg J, Opresko DM, Osawa M, Paulay G, Perrin W, Pilger JF, Poore GC, Pugh P, Read GB, Reimer JD, Rius M, Rocha RM, Saiz-Salinas JI, Scarabino V, Schierwater B, Schmidt-Rhaesa A, Schnabel KE, Schotte M, Schuchert P, Schwabe E, Segers H, Self-Sullivan C, Shenkar N, Siegel V, Sterrer W, Stöhr S, Swalla B, Tasker ML, Thuesen EV, Timm T, Todaro MA, Turon X, Tyler S, Uetz P, van der Land J, Vanhoorne B, van Ofwegen LP, van Soest RW, Vanaverbeke J, Walker-Smith G, Walter TC, Warren A, Williams GC, Wilson SP, Costello MJ.

Curr Biol. 2012 Dec 4;22(23):2189-202. doi: 10.1016/j.cub.2012.09.036. Epub 2012 Nov 15.

43.

Studying protein complexes by the yeast two-hybrid system.

Rajagopala SV, Sikorski P, Caufield JH, Tovchigrechko A, Uetz P.

Methods. 2012 Dec;58(4):392-9. doi: 10.1016/j.ymeth.2012.07.015. Epub 2012 Jul 24.

44.

RsfA (YbeB) proteins are conserved ribosomal silencing factors.

Häuser R, Pech M, Kijek J, Yamamoto H, Titz B, Naeve F, Tovchigrechko A, Yamamoto K, Szaflarski W, Takeuchi N, Stellberger T, Diefenbacher ME, Nierhaus KH, Uetz P.

PLoS Genet. 2012;8(7):e1002815. doi: 10.1371/journal.pgen.1002815. Epub 2012 Jul 19.

45.

Bacteriophage protein-protein interactions.

Häuser R, Blasche S, Dokland T, Haggård-Ljungquist E, von Brunn A, Salas M, Casjens S, Molineux I, Uetz P.

Adv Virus Res. 2012;83:219-98. doi: 10.1016/B978-0-12-394438-2.00006-2. Review.

46.

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium.

Orchard S, Kerrien S, Abbani S, Aranda B, Bhate J, Bidwell S, Bridge A, Briganti L, Brinkman FS, Cesareni G, Chatr-aryamontri A, Chautard E, Chen C, Dumousseau M, Goll J, Hancock RE, Hannick LI, Jurisica I, Khadake J, Lynn DJ, Mahadevan U, Perfetto L, Raghunath A, Ricard-Blum S, Roechert B, Salwinski L, Stümpflen V, Tyers M, Uetz P, Xenarios I, Hermjakob H.

Nat Methods. 2012 Apr;9(4):345-50. doi: 10.1038/nmeth.1931. Erratum in: Nat Methods. 2012 Jun;9(6):626. Brinkman, Fiona [corrected to Brinkman, Fiona S L]; Hancock, Robert [corrected to Hancock, Robert E W].

47.

Array-based yeast two-hybrid screens: a practical guide.

Häuser R, Stellberger T, Rajagopala SV, Uetz P.

Methods Mol Biol. 2012;812:21-38. doi: 10.1007/978-1-61779-455-1_2.

PMID:
22218852
48.

Matrix-based yeast two-hybrid screen strategies and comparison of systems.

Häuser R, Stellberger T, Rajagopala SV, Uetz P.

Methods Mol Biol. 2012;812:1-20. doi: 10.1007/978-1-61779-455-1_1.

PMID:
22218851
49.

Yeast two-hybrid screens: improvement of array-based screening results by N- and C-terminally tagged fusion proteins.

Stellberger T, Häuser R, Uetz P, Brunn Av.

Methods Mol Biol. 2012;815:277-88. doi: 10.1007/978-1-61779-424-7_21.

PMID:
22130999
50.

Marine reptiles.

Rasmussen AR, Murphy JC, Ompi M, Gibbons JW, Uetz P.

PLoS One. 2011;6(11):e27373. doi: 10.1371/journal.pone.0027373. Epub 2011 Nov 8. Review. No abstract available.

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