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Items: 39

1.

Persistent Gut Microbial Dysbiosis in Children with Acute Lymphoblastic Leukemia (ALL) During Chemotherapy.

Rajagopala SV, Singh H, Yu Y, Zabokrtsky KB, Torralba MG, Moncera KJ, Frank B, Pieper R, Sender L, Nelson KE.

Microb Ecol. 2019 Nov 21. doi: 10.1007/s00248-019-01448-x. [Epub ahead of print]

PMID:
31754744
2.

Nearly Complete Genome Sequences of 17 Enterovirus D68 Strains from Kansas City, Missouri, 2018.

Pakala SB, Tan Y, Hassan F, Mai A, Markowitz RH, Shilts MH, Rajagopala SV, Selvarangan R, Das SR.

Microbiol Resour Announc. 2019 Nov 7;8(45). pii: e00388-19. doi: 10.1128/MRA.00388-19.

3.

Publisher Correction: Toxoplasma Modulates Signature Pathways of Human Epilepsy, Neurodegeneration & Cancer.

Ngô HM, Zhou Y, Lorenzi H, Wang K, Kim TK, Zhou Y, El Bissati K, Mui E, Fraczek L, Rajagopala SV, Roberts CW, Henriquez FL, Montpetit A, Blackwell JM, Jamieson SE, Wheeler K, Begeman IJ, Naranjo-Galvis C, Alliey-Rodriguez N, Davis RG, Soroceanu L, Cobbs C, Steindler DA, Boyer K, Noble AG, Swisher CN, Heydemann PT, Rabiah P, Withers S, Soteropoulos P, Hood L, McLeod R.

Sci Rep. 2019 May 28;9(1):8110. doi: 10.1038/s41598-019-44545-0.

4.

The Salivary Microbiome Is Altered in Children With Eosinophilic Esophagitis and Correlates With Disease Activity.

Hiremath G, Shilts MH, Boone HH, Correa H, Acra S, Tovchigrechko A, Rajagopala SV, Das SR.

Clin Transl Gastroenterol. 2019 Jun;10(6):e00039. doi: 10.14309/ctg.0000000000000039.

5.

Cotton rat lung transcriptome reveals host immune response to Respiratory Syncytial Virus infection.

Rajagopala SV, Singh H, Patel MC, Wang W, Tan Y, Shilts MH, Hartert TV, Boukhvalova MS, Blanco JCG, Das SR.

Sci Rep. 2018 Jul 27;8(1):11318. doi: 10.1038/s41598-018-29374-x.

6.

Mechanisms of action of Coxiella burnetii effectors inferred from host-pathogen protein interactions.

Wallqvist A, Wang H, Zavaljevski N, Memišević V, Kwon K, Pieper R, Rajagopala SV, Reifman J.

PLoS One. 2017 Nov 27;12(11):e0188071. doi: 10.1371/journal.pone.0188071. eCollection 2017. Erratum in: PLoS One. 2018 Apr 20;13(4):e0196373.

7.

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.

8.

Toxoplasma Modulates Signature Pathways of Human Epilepsy, Neurodegeneration & Cancer.

Ngô HM, Zhou Y, Lorenzi H, Wang K, Kim TK, Zhou Y, El Bissati K, Mui E, Fraczek L, Rajagopala SV, Roberts CW, Henriquez FL, Montpetit A, Blackwell JM, Jamieson SE, Wheeler K, Begeman IJ, Naranjo-Galvis C, Alliey-Rodriguez N, Davis RG, Soroceanu L, Cobbs C, Steindler DA, Boyer K, Noble AG, Swisher CN, Heydemann PT, Rabiah P, Withers S, Soteropoulos P, Hood L, McLeod R.

Sci Rep. 2017 Sep 13;7(1):11496. doi: 10.1038/s41598-017-10675-6. Erratum in: Sci Rep. 2019 May 28;9(1):8110.

9.

Type 1 Diabetes: Urinary Proteomics and Protein Network Analysis Support Perturbation of Lysosomal Function.

Singh H, Yu Y, Suh MJ, Torralba MG, Stenzel RD, Tovchigrechko A, Thovarai V, Harkins DM, Rajagopala SV, Osborne W, Cogen FR, Kaplowitz PB, Nelson KE, Madupu R, Pieper R.

Theranostics. 2017 Jul 7;7(10):2704-2717. doi: 10.7150/thno.19679. eCollection 2017.

10.

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.

11.

The Human Microbiome and Cancer.

Rajagopala SV, Vashee S, Oldfield LM, Suzuki Y, Venter JC, Telenti A, Nelson KE.

Cancer Prev Res (Phila). 2017 Apr;10(4):226-234. doi: 10.1158/1940-6207.CAPR-16-0249. Epub 2017 Jan 17. Review.

12.

Enterovirus D-68 Infection, Prophylaxis, and Vaccination in a Novel Permissive Animal Model, the Cotton Rat (Sigmodon hispidus).

Patel MC, Wang W, Pletneva LM, Rajagopala SV, Tan Y, Hartert TV, Boukhvalova MS, Vogel SN, Das SR, Blanco JC.

PLoS One. 2016 Nov 4;11(11):e0166336. doi: 10.1371/journal.pone.0166336. eCollection 2016.

13.

Gastrointestinal microbial populations can distinguish pediatric and adolescent Acute Lymphoblastic Leukemia (ALL) at the time of disease diagnosis.

Rajagopala SV, Yooseph S, Harkins DM, Moncera KJ, Zabokrtsky KB, Torralba MG, Tovchigrechko A, Highlander SK, Pieper R, Sender L, Nelson KE.

BMC Genomics. 2016 Aug 15;17(1):635. doi: 10.1186/s12864-016-2965-y.

14.

Using host-pathogen protein interactions to identify and characterize Francisella tularensis virulence factors.

Wallqvist A, Memišević V, Zavaljevski N, Pieper R, Rajagopala SV, Kwon K, Yu C, Hoover TA, Reifman J.

BMC Genomics. 2015 Dec 29;16:1106. doi: 10.1186/s12864-015-2351-1.

15.

Mapping the Protein-Protein Interactome Networks Using Yeast Two-Hybrid Screens.

Rajagopala SV.

Adv Exp Med Biol. 2015;883:187-214. doi: 10.1007/978-3-319-23603-2_11. Review.

PMID:
26621469
16.

Mining host-pathogen protein interactions to characterize Burkholderia mallei infectivity mechanisms.

Memišević V, Zavaljevski N, Rajagopala SV, Kwon K, Pieper R, DeShazer D, Reifman J, Wallqvist A.

PLoS Comput Biol. 2015 Mar 4;11(3):e1004088. doi: 10.1371/journal.pcbi.1004088. eCollection 2015 Mar.

17.

Chromosome segregation proteins of Vibrio cholerae as transcription regulators.

Baek JH, Rajagopala SV, Chattoraj DK.

MBio. 2014 May 6;5(3):e01061-14. doi: 10.1128/mBio.01061-14.

18.

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.

19.

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.

20.

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.

21.

Novel Burkholderia mallei virulence factors linked to specific host-pathogen protein interactions.

Memisević V, Zavaljevski N, Pieper R, Rajagopala SV, Kwon K, Townsend K, Yu C, Yu X, DeShazer D, Reifman J, Wallqvist A.

Mol Cell Proteomics. 2013 Nov;12(11):3036-51. doi: 10.1074/mcp.M113.029041. Epub 2013 Jun 24.

22.

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.

23.

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
24.

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
25.

The protein interaction map of bacteriophage lambda.

Rajagopala SV, Casjens S, Uetz P.

BMC Microbiol. 2011 Sep 26;11:213. doi: 10.1186/1471-2180-11-213.

26.

Analysis of protein-protein interactions using high-throughput yeast two-hybrid screens.

Rajagopala SV, Uetz P.

Methods Mol Biol. 2011;781:1-29. doi: 10.1007/978-1-61779-276-2_1.

PMID:
21877274
27.

Exhaustive benchmarking of the yeast two-hybrid system.

Chen YC, Rajagopala SV, Stellberger T, Uetz P.

Nat Methods. 2010 Sep;7(9):667-8; author reply 668. doi: 10.1038/nmeth0910-667. No abstract available.

PMID:
20805792
28.

The Escherichia coli K-12 ORFeome: a resource for comparative molecular microbiology.

Rajagopala SV, Yamamoto N, Zweifel AE, Nakamichi T, Huang HK, Mendez-Rios JD, Franca-Koh J, Boorgula MP, Fujita K, Suzuki K, Hu JC, Wanner BL, Mori H, Uetz P.

BMC Genomics. 2010 Aug 11;11:470. doi: 10.1186/1471-2164-11-470.

29.

Benchmarking yeast two-hybrid systems using the interactions of bacterial motility proteins.

Rajagopala SV, Hughes KT, Uetz P.

Proteomics. 2009 Dec;9(23):5296-302. doi: 10.1002/pmic.200900282.

30.

Evolutionarily conserved herpesviral protein interaction networks.

Fossum E, Friedel CC, Rajagopala SV, Titz B, Baiker A, Schmidt T, Kraus T, Stellberger T, Rutenberg C, Suthram S, Bandyopadhyay S, Rose D, von Brunn A, Uhlmann M, Zeretzke C, Dong YA, Boulet H, Koegl M, Bailer SM, Koszinowski U, Ideker T, Uetz P, Zimmer R, Haas J.

PLoS Pathog. 2009 Sep;5(9):e1000570. doi: 10.1371/journal.ppat.1000570. Epub 2009 Sep 4.

31.

Analysis of protein-protein interactions using array-based yeast two-hybrid screens.

Rajagopala SV, Uetz P.

Methods Mol Biol. 2009;548:223-45. doi: 10.1007/978-1-59745-540-4_13.

PMID:
19521828
32.

MPI-LIT: a literature-curated dataset of microbial binary protein--protein interactions.

Rajagopala SV, Goll J, Gowda ND, Sunil KC, Titz B, Mukherjee A, Mary SS, Raviswaran N, Poojari CS, Ramachandra S, Shtivelband S, Blazie SM, Hofmann J, Uetz P.

Bioinformatics. 2008 Nov 15;24(22):2622-7. doi: 10.1093/bioinformatics/btn481. Epub 2008 Sep 11.

33.

MPIDB: the microbial protein interaction database.

Goll J, Rajagopala SV, Shiau SC, Wu H, Lamb BT, Uetz P.

Bioinformatics. 2008 Aug 1;24(15):1743-4. doi: 10.1093/bioinformatics/btn285. Epub 2008 Jun 13.

34.

The binary protein interactome of Treponema pallidum--the syphilis spirochete.

Titz B, Rajagopala SV, Goll J, Häuser R, McKevitt MT, Palzkill T, Uetz P.

PLoS One. 2008 May 28;3(5):e2292. doi: 10.1371/journal.pone.0002292.

35.

The protein network of bacterial motility.

Rajagopala SV, Titz B, Goll J, Parrish JR, Wohlbold K, McKevitt MT, Palzkill T, Mori H, Finley RL Jr, Uetz P.

Mol Syst Biol. 2007;3:128. Epub 2007 Jul 31.

36.

Novel conserved assembly factor of the bacterial flagellum.

Titz B, Rajagopala SV, Ester C, Häuser R, Uetz P.

J Bacteriol. 2006 Nov;188(21):7700-6. Epub 2006 Aug 25.

37.

Transcriptional activators in yeast.

Titz B, Thomas S, Rajagopala SV, Chiba T, Ito T, Uetz P.

Nucleic Acids Res. 2006 Feb 7;34(3):955-67. Print 2006.

38.

Herpesviral protein networks and their interaction with the human proteome.

Uetz P, Dong YA, Zeretzke C, Atzler C, Baiker A, Berger B, Rajagopala SV, Roupelieva M, Rose D, Fossum E, Haas J.

Science. 2006 Jan 13;311(5758):239-42. Epub 2005 Dec 8.

39.

From ORFeomes to protein interaction maps in viruses.

Uetz P, Rajagopala SV, Dong YA, Haas J.

Genome Res. 2004 Oct;14(10B):2029-33. Review.

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