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Items: 29

1.

Network-based prediction of protein interactions.

Kovács IA, Luck K, Spirohn K, Wang Y, Pollis C, Schlabach S, Bian W, Kim DK, Kishore N, Hao T, Calderwood MA, Vidal M, Barabási AL.

Nat Commun. 2019 Mar 18;10(1):1240. doi: 10.1038/s41467-019-09177-y.

2.

APID database: redefining protein-protein interaction experimental evidences and binary interactomes.

Alonso-López D, Campos-Laborie FJ, Gutiérrez MA, Lambourne L, Calderwood MA, Vidal M, De Las Rivas J.

Database (Oxford). 2019 Jan 1;2019. doi: 10.1093/database/baz005.

3.

An inter-species protein-protein interaction network across vast evolutionary distance.

Zhong Q, Pevzner SJ, Hao T, Wang Y, Mosca R, Menche J, Taipale M, Taşan M, Fan C, Yang X, Haley P, Murray RR, Mer F, Gebreab F, Tam S, MacWilliams A, Dricot A, Reichert P, Santhanam B, Ghamsari L, Calderwood MA, Rolland T, Charloteaux B, Lindquist S, Barabási AL, Hill DE, Aloy P, Cusick ME, Xia Y, Roth FP, Vidal M.

Mol Syst Biol. 2016 Apr 22;12(4):865. doi: 10.15252/msb.20156484.

4.

Pooled-matrix protein interaction screens using Barcode Fusion Genetics.

Yachie N, Petsalaki E, Mellor JC, Weile J, Jacob Y, Verby M, Ozturk SB, Li S, Cote AG, Mosca R, Knapp JJ, Ko M, Yu A, Gebbia M, Sahni N, Yi S, Tyagi T, Sheykhkarimli D, Roth JF, Wong C, Musa L, Snider J, Liu YC, Yu H, Braun P, Stagljar I, Hao T, Calderwood MA, Pelletier L, Aloy P, Hill DE, Vidal M, Roth FP.

Mol Syst Biol. 2016 Apr 22;12(4):863. doi: 10.15252/msb.20156660.

5.

Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing.

Yang X, Coulombe-Huntington J, Kang S, Sheynkman GM, Hao T, Richardson A, Sun S, Yang F, Shen YA, Murray RR, Spirohn K, Begg BE, Duran-Frigola M, MacWilliams A, Pevzner SJ, Zhong Q, Trigg SA, Tam S, Ghamsari L, Sahni N, Yi S, Rodriguez MD, Balcha D, Tan G, Costanzo M, Andrews B, Boone C, Zhou XJ, Salehi-Ashtiani K, Charloteaux B, Chen AA, Calderwood MA, Aloy P, Roth FP, Hill DE, Iakoucheva LM, Xia Y, Vidal M.

Cell. 2016 Feb 11;164(4):805-17. doi: 10.1016/j.cell.2016.01.029.

6.

Widespread macromolecular interaction perturbations in human genetic disorders.

Sahni N, Yi S, Taipale M, Fuxman Bass JI, Coulombe-Huntington J, Yang F, Peng J, Weile J, Karras GI, Wang Y, Kovács IA, Kamburov A, Krykbaeva I, Lam MH, Tucker G, Khurana V, Sharma A, Liu YY, Yachie N, Zhong Q, Shen Y, Palagi A, San-Miguel A, Fan C, Balcha D, Dricot A, Jordan DM, Walsh JM, Shah AA, Yang X, Stoyanova AK, Leighton A, Calderwood MA, Jacob Y, Cusick ME, Salehi-Ashtiani K, Whitesell LJ, Sunyaev S, Berger B, Barabási AL, Charloteaux B, Hill DE, Hao T, Roth FP, Xia Y, Walhout AJM, Lindquist S, Vidal M.

Cell. 2015 Apr 23;161(3):647-660. doi: 10.1016/j.cell.2015.04.013.

7.

The EBNA3 family of Epstein-Barr virus nuclear proteins associates with the USP46/USP12 deubiquitination complexes to regulate lymphoblastoid cell line growth.

Ohashi M, Holthaus AM, Calderwood MA, Lai CY, Krastins B, Sarracino D, Johannsen E.

PLoS Pathog. 2015 Apr 9;11(4):e1004822. doi: 10.1371/journal.ppat.1004822. eCollection 2015 Apr.

8.

A proteome-scale map of the human interactome network.

Rolland T, Taşan M, Charloteaux B, Pevzner SJ, Zhong Q, Sahni N, Yi S, Lemmens I, Fontanillo C, Mosca R, Kamburov A, Ghiassian SD, Yang X, Ghamsari L, Balcha D, Begg BE, Braun P, Brehme M, Broly MP, Carvunis AR, Convery-Zupan D, Corominas R, Coulombe-Huntington J, Dann E, Dreze M, Dricot A, Fan C, Franzosa E, Gebreab F, Gutierrez BJ, Hardy MF, Jin M, Kang S, Kiros R, Lin GN, Luck K, MacWilliams A, Menche J, Murray RR, Palagi A, Poulin MM, Rambout X, Rasla J, Reichert P, Romero V, Ruyssinck E, Sahalie JM, Scholz A, Shah AA, Sharma A, Shen Y, Spirohn K, Tam S, Tejeda AO, Trigg SA, Twizere JC, Vega K, Walsh J, Cusick ME, Xia Y, Barabási AL, Iakoucheva LM, Aloy P, De Las Rivas J, Tavernier J, Calderwood MA, Hill DE, Hao T, Roth FP, Vidal M.

Cell. 2014 Nov 20;159(5):1212-1226. doi: 10.1016/j.cell.2014.10.050.

9.

Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism.

Corominas R, Yang X, Lin GN, Kang S, Shen Y, Ghamsari L, Broly M, Rodriguez M, Tam S, Trigg SA, Fan C, Yi S, Tasan M, Lemmens I, Kuang X, Zhao N, Malhotra D, Michaelson JJ, Vacic V, Calderwood MA, Roth FP, Tavernier J, Horvath S, Salehi-Ashtiani K, Korkin D, Sebat J, Hill DE, Hao T, Vidal M, Iakoucheva LM.

Nat Commun. 2014 Apr 11;5:3650. doi: 10.1038/ncomms4650.

10.

An RS motif within the Epstein-Barr virus BLRF2 tegument protein is phosphorylated by SRPK2 and is important for viral replication.

Duarte M, Wang L, Calderwood MA, Adelmant G, Ohashi M, Roecklein-Canfield J, Marto JA, Hill DE, Deng H, Johannsen E.

PLoS One. 2013;8(1):e53512. doi: 10.1371/journal.pone.0053512. Epub 2013 Jan 9.

11.

Identification of FAM111A as an SV40 host range restriction and adenovirus helper factor.

Fine DA, Rozenblatt-Rosen O, Padi M, Korkhin A, James RL, Adelmant G, Yoon R, Guo L, Berrios C, Zhang Y, Calderwood MA, Velmurgan S, Cheng J, Marto JA, Hill DE, Cusick ME, Vidal M, Florens L, Washburn MP, Litovchick L, DeCaprio JA.

PLoS Pathog. 2012;8(10):e1002949. doi: 10.1371/journal.ppat.1002949. Epub 2012 Oct 18.

12.

Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins.

Rozenblatt-Rosen O, Deo RC, Padi M, Adelmant G, Calderwood MA, Rolland T, Grace M, Dricot A, Askenazi M, Tavares M, Pevzner SJ, Abderazzaq F, Byrdsong D, Carvunis AR, Chen AA, Cheng J, Correll M, Duarte M, Fan C, Feltkamp MC, Ficarro SB, Franchi R, Garg BK, Gulbahce N, Hao T, Holthaus AM, James R, Korkhin A, Litovchick L, Mar JC, Pak TR, Rabello S, Rubio R, Shen Y, Singh S, Spangle JM, Tasan M, Wanamaker S, Webber JT, Roecklein-Canfield J, Johannsen E, Barabási AL, Beroukhim R, Kieff E, Cusick ME, Hill DE, Münger K, Marto JA, Quackenbush J, Roth FP, DeCaprio JA, Vidal M.

Nature. 2012 Jul 26;487(7408):491-5. doi: 10.1038/nature11288.

13.

Viral perturbations of host networks reflect disease etiology.

Gulbahce N, Yan H, Dricot A, Padi M, Byrdsong D, Franchi R, Lee DS, Rozenblatt-Rosen O, Mar JC, Calderwood MA, Baldwin A, Zhao B, Santhanam B, Braun P, Simonis N, Huh KW, Hellner K, Grace M, Chen A, Rubio R, Marto JA, Christakis NA, Kieff E, Roth FP, Roecklein-Canfield J, Decaprio JA, Cusick ME, Quackenbush J, Hill DE, Münger K, Vidal M, Barabási AL.

PLoS Comput Biol. 2012;8(6):e1002531. doi: 10.1371/journal.pcbi.1002531. Epub 2012 Jun 28.

14.

Proto-genes and de novo gene birth.

Carvunis AR, Rolland T, Wapinski I, Calderwood MA, Yildirim MA, Simonis N, Charloteaux B, Hidalgo CA, Barbette J, Santhanam B, Brar GA, Weissman JS, Regev A, Thierry-Mieg N, Cusick ME, Vidal M.

Nature. 2012 Jul 19;487(7407):370-4. doi: 10.1038/nature11184.

15.

Genome-wide analysis of Epstein-Barr virus Rta DNA binding.

Heilmann AM, Calderwood MA, Portal D, Lu Y, Johannsen E.

J Virol. 2012 May;86(9):5151-64. doi: 10.1128/JVI.06760-11. Epub 2012 Feb 29.

16.

EBV nuclear antigen EBNALP dismisses transcription repressors NCoR and RBPJ from enhancers and EBNA2 increases NCoR-deficient RBPJ DNA binding.

Portal D, Zhao B, Calderwood MA, Sommermann T, Johannsen E, Kieff E.

Proc Natl Acad Sci U S A. 2011 May 10;108(19):7808-13. doi: 10.1073/pnas.1104991108. Epub 2011 Apr 25.

17.

Epstein-Barr virus nuclear protein 3C binds to the N-terminal (NTD) and beta trefoil domains (BTD) of RBP/CSL; only the NTD interaction is essential for lymphoblastoid cell growth.

Calderwood MA, Lee S, Holthaus AM, Blacklow SC, Kieff E, Johannsen E.

Virology. 2011 May 25;414(1):19-25. doi: 10.1016/j.virol.2011.02.018. Epub 2011 Mar 26.

18.

Epstein-Barr virus LF2 protein regulates viral replication by altering Rta subcellular localization.

Heilmann AM, Calderwood MA, Johannsen E.

J Virol. 2010 Oct;84(19):9920-31. doi: 10.1128/JVI.00573-10. Epub 2010 Jul 14.

19.

Epstein-Barr virus nuclear protein 3C domains necessary for lymphoblastoid cell growth: interaction with RBP-Jkappa regulates TCL1.

Lee S, Sakakibara S, Maruo S, Zhao B, Calderwood MA, Holthaus AM, Lai CY, Takada K, Kieff E, Johannsen E.

J Virol. 2009 Dec;83(23):12368-77. doi: 10.1128/JVI.01403-09. Epub 2009 Sep 23.

20.

The Epstein-Barr virus LF2 protein inhibits viral replication.

Calderwood MA, Holthaus AM, Johannsen E.

J Virol. 2008 Sep;82(17):8509-19. doi: 10.1128/JVI.00315-08. Epub 2008 Jun 18.

21.

Epstein-Barr virus and virus human protein interaction maps.

Calderwood MA, Venkatesan K, Xing L, Chase MR, Vazquez A, Holthaus AM, Ewence AE, Li N, Hirozane-Kishikawa T, Hill DE, Vidal M, Kieff E, Johannsen E.

Proc Natl Acad Sci U S A. 2007 May 1;104(18):7606-11. Epub 2007 Apr 19.

22.

Development of herpesvirus-based episomally maintained gene delivery vectors.

Calderwood MA, White RE, Whitehouse A.

Expert Opin Biol Ther. 2004 Apr;4(4):493-505. Review.

PMID:
15102599
23.

The herpesvirus saimiri ORF73 gene product interacts with host-cell mitotic chromosomes and self-associates via its C terminus.

Calderwood MA, Hall KT, Matthews DA, Whitehouse A.

J Gen Virol. 2004 Jan;85(Pt 1):147-53.

PMID:
14718629
25.

The Herpesvirus Saimiri open reading frame 73 gene product interacts with the cellular protein p32.

Hall KT, Giles MS, Calderwood MA, Goodwin DJ, Matthews DA, Whitehouse A.

J Virol. 2002 Nov;76(22):11612-22.

26.

Characterization of the herpesvirus saimiri ORF73 gene product.

Hall KT, Giles MS, Goodwin DJ, Calderwood MA, Markham AF, Whitehouse A.

J Gen Virol. 2000 Nov;81(Pt 11):2653-8.

PMID:
11038376
27.

The carboxy terminus of the herpesvirus saimiri ORF 57 gene contains domains that are required for transactivation and transrepression.

Goodwin DJ, Hall KT, Giles MS, Calderwood MA, Markham AF, Whitehouse A.

J Gen Virol. 2000 Sep;81(Pt 9):2253-65.

PMID:
10950983
28.

Specific oncolytic activity of herpesvirus saimiri in pancreatic cancer cells.

Stevenson AJ, Giles MS, Hall KT, Goodwin DJ, Calderwood MA, Markham AF, Whitehouse A.

Br J Cancer. 2000 Aug;83(3):329-32.

29.

Analysis of gene expression in a human cell line stably transduced with herpesvirus saimiri.

Hall KT, Giles MS, Goodwin DJ, Calderwood MA, Carr IM, Stevenson AJ, Markham AF, Whitehouse A.

J Virol. 2000 Aug;74(16):7331-7.

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