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Items: 25

1.

Active Instrument Engagement Combined with a Real-Time Database Search for Improved Performance of Sample Multiplexing Workflows.

Erickson BK, Mintseris J, Schweppe DK, Navarrete-Perea J, Erickson AR, Nusinow DP, Paulo JA, Gygi SP.

J Proteome Res. 2019 Mar 1;18(3):1299-1306. doi: 10.1021/acs.jproteome.8b00899. Epub 2019 Feb 4.

PMID:
30658528
2.

The BioPlex Network: A Systematic Exploration of the Human Interactome.

Huttlin EL, Ting L, Bruckner RJ, Gebreab F, Gygi MP, Szpyt J, Tam S, Zarraga G, Colby G, Baltier K, Dong R, Guarani V, Vaites LP, Ordureau A, Rad R, Erickson BK, Wühr M, Chick J, Zhai B, Kolippakkam D, Mintseris J, Obar RA, Harris T, Artavanis-Tsakonas S, Sowa ME, De Camilli P, Paulo JA, Harper JW, Gygi SP.

Cell. 2015 Jul 16;162(2):425-440. doi: 10.1016/j.cell.2015.06.043.

3.

Transcription factor networks in Drosophila melanogaster.

Rhee DY, Cho DY, Zhai B, Slattery M, Ma L, Mintseris J, Wong CY, White KP, Celniker SE, Przytycka TM, Gygi SP, Obar RA, Artavanis-Tsakonas S.

Cell Rep. 2014 Sep 25;8(6):2031-2043. doi: 10.1016/j.celrep.2014.08.038. Epub 2014 Sep 18.

4.

Drosophila protein interaction map (DPiM): a paradigm for metazoan protein complex interactions.

Guruharsha KG, Obar RA, Mintseris J, Aishwarya K, Krishnan RT, Vijayraghavan K, Artavanis-Tsakonas S.

Fly (Austin). 2012 Oct-Dec;6(4):246-53. doi: 10.4161/fly.22108.

5.

Mycobacterium tuberculosis prokaryotic ubiquitin-like protein-deconjugating enzyme is an unusual aspartate amidase.

Burns KE, McAllister FE, Schwerdtfeger C, Mintseris J, Cerda-Maira F, Noens EE, Wilmanns M, Hubbard SR, Melandri F, Ovaa H, Gygi SP, Darwin KH.

J Biol Chem. 2012 Oct 26;287(44):37522-9. doi: 10.1074/jbc.M112.384784. Epub 2012 Aug 31.

6.

A protein complex network of Drosophila melanogaster.

Guruharsha KG, Rual JF, Zhai B, Mintseris J, Vaidya P, Vaidya N, Beekman C, Wong C, Rhee DY, Cenaj O, McKillip E, Shah S, Stapleton M, Wan KH, Yu C, Parsa B, Carlson JW, Chen X, Kapadia B, VijayRaghavan K, Gygi SP, Celniker SE, Obar RA, Artavanis-Tsakonas S.

Cell. 2011 Oct 28;147(3):690-703. doi: 10.1016/j.cell.2011.08.047.

7.

Photoreactive stapled BH3 peptides to dissect the BCL-2 family interactome.

Braun CR, Mintseris J, Gavathiotis E, Bird GH, Gygi SP, Walensky LD.

Chem Biol. 2010 Dec 22;17(12):1325-33. doi: 10.1016/j.chembiol.2010.09.015.

8.

Prokaryotic ubiquitin-like protein (Pup) proteome of Mycobacterium tuberculosis [corrected] .

Festa RA, McAllister F, Pearce MJ, Mintseris J, Burns KE, Gygi SP, Darwin KH.

PLoS One. 2010 Jan 6;5(1):e8589. doi: 10.1371/journal.pone.0008589. Erratum in: PLoS One. 2010;5(7) doi: 10.1371/annotation/bf95b2c0-4085-417b-a2b2-7a85ffe77a9e.

9.

Ubiquitin-like protein involved in the proteasome pathway of Mycobacterium tuberculosis.

Pearce MJ, Mintseris J, Ferreyra J, Gygi SP, Darwin KH.

Science. 2008 Nov 14;322(5904):1104-7. doi: 10.1126/science.1163885. Epub 2008 Oct 2.

10.

Protein-protein docking benchmark version 3.0.

Hwang H, Pierce B, Mintseris J, Janin J, Weng Z.

Proteins. 2008 Nov 15;73(3):705-9. doi: 10.1002/prot.22106.

11.

Phosphoproteome analysis of Drosophila melanogaster embryos.

Zhai B, Villén J, Beausoleil SA, Mintseris J, Gygi SP.

J Proteome Res. 2008 Apr;7(4):1675-82. doi: 10.1021/pr700696a. Epub 2008 Mar 8.

12.

Protein-protein docking: overview and performance analysis.

Wiehe K, Peterson MW, Pierce B, Mintseris J, Weng Z.

Methods Mol Biol. 2008;413:283-314.

PMID:
18075170
13.

The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI.

Wiehe K, Pierce B, Tong WW, Hwang H, Mintseris J, Weng Z.

Proteins. 2007 Dec 1;69(4):719-25.

PMID:
17803212
14.

Integrating statistical pair potentials into protein complex prediction.

Mintseris J, Pierce B, Wiehe K, Anderson R, Chen R, Weng Z.

Proteins. 2007 Nov 15;69(3):511-20.

PMID:
17623839
15.

Structural similarity enhances interaction propensity of proteins.

Lukatsky DB, Shakhnovich BE, Mintseris J, Shakhnovich EI.

J Mol Biol. 2007 Feb 2;365(5):1596-606. Epub 2006 Nov 10.

16.

Design of a combinatorial DNA microarray for protein-DNA interaction studies.

Mintseris J, Eisen MB.

BMC Bioinformatics. 2006 Oct 3;7:429.

17.

Structure, function, and evolution of transient and obligate protein-protein interactions.

Mintseris J, Weng Z.

Proc Natl Acad Sci U S A. 2005 Aug 2;102(31):10930-5. Epub 2005 Jul 25.

18.

Protein-Protein Docking Benchmark 2.0: an update.

Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z.

Proteins. 2005 Aug 1;60(2):214-6.

PMID:
15981264
19.

ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5.

Wiehe K, Pierce B, Mintseris J, Tong WW, Anderson R, Chen R, Weng Z.

Proteins. 2005 Aug 1;60(2):207-13.

PMID:
15981263
20.

Optimizing protein representations with information theory.

Mintseris J, Weng Z.

Genome Inform. 2004;15(1):160-9.

PMID:
15712119
21.

Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?

Caffrey DR, Somaroo S, Hughes JD, Mintseris J, Huang ES.

Protein Sci. 2004 Jan;13(1):190-202.

22.

Atomic contact vectors in protein-protein recognition.

Mintseris J, Weng Z.

Proteins. 2003 Nov 15;53(3):629-39.

PMID:
14579354
23.

A protein-protein docking benchmark.

Chen R, Mintseris J, Janin J, Weng Z.

Proteins. 2003 Jul 1;52(1):88-91.

PMID:
12784372
24.

ZDOCK predictions for the CAPRI challenge.

Chen R, Tong W, Mintseris J, Li L, Weng Z.

Proteins. 2003 Jul 1;52(1):68-73.

PMID:
12784369
25.

Predictome: a database of putative functional links between proteins.

Mellor JC, Yanai I, Clodfelter KH, Mintseris J, DeLisi C.

Nucleic Acids Res. 2002 Jan 1;30(1):306-9.

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