Publications

 All Journal Papers:

2016


Sun MGF*, Seo MH*, Nim S, Corbi-Verge C, Kim PM. Protein Engineering by highly parallel screening of computational designed variants. Science Advances. 20 Jul 2016: Vol. 2, no. 7, e1600692 [PDF] [News coverage]
Jeon J, Arnold R, Singh F, Teyra J, Braun T, Kim PM. PAT: predictor for structured units and its application for the optimization of target molecules for the generation of synthetic antibodies. BMC Bioinformatics. 2016 Apr 1;17:150. doi: 10.1186/s12859-016-1001-1. [PDF] [Webserver]
Corbi-Verge C, Kim PM. Motif mediated protein-protein interactions as drug targets. Cell Commun Signal. 2016 Mar 2;14:8. doi: 10.1186/s12964-016-0131-4.
Nim S*, Jeon JH*, Corbi-Verge C, Seo MH, Ivarsson Y, Tarasova N, Kim PM. Pooled screening for antiproliferative inhibitors of protein-protein interactions. Nature Chemical Biology 2016 Feb 22. doi 10.1038/nchembio.2026 [PDF]
Na H, Laver JD, Jeon J, Singh F, Ancevicius K, Fan Y, Cao WX, Nie K, Yang Z, Luo H, Wang M, Rissland O, Westwood JT, Kim PMSmibert CA, Lipshitz HD, Sidhu SS. A high-throughput pipeline for the production of synthetic antibodies for analysis of ribonucleoprotein complexes. RNA. 2016 Feb 4. [Epub ahead of print] PubMed PMID: 26847261

Garrido-Urbani S, Garg P, Ghossoub R, Arnold R, Lembo F, Sundell GN, Kim PM, Lopez M, Zimmermann P, Sidhu SS, Ivarsson Y. Proteomic peptide phage display uncovers novel interactions of the PDZ1-2 supramodule of syntenin. FEBS Lett. 2016 Jan;590(1):3-12. doi: 10.1002/1873-3468.12037

Witvliet D*, Strokach A*, Giraldo AF, Teyra J, Colak RA, Kim PM. ELASPIC web-server: proteome-wide structure based prediction of mutation effects on protein stability and binding affinity. Bioinformatics 2016 Jan 21. pii: btw031 [PDF] [Webserver]

Colak RA, Kim TH, Kazan H, Oh Y, Cruz M, Valladares A, Peralta J, Escobedo J, Parra E, Kim PM#, Goldenberg A#. JBASE: Joint Bayesian Analysis of Sub-phentoypes and Epistasis. Bioinformatics 2016 Jan 15;32(2):203-10. doi: 10.1093/bioinformatics/btv504 [PDF]

2015

Garton M,
Najafabadi HS, Schmitges FW, Radovani E, Hughes TR, Kim PM. Breaking the C2H2 recognition code enigma: a structural approach reveals the influence of neighbor context on DNA binding specificity. Nucleic Acids Res 2015 Oct 30;43(19):9147-57. doi: 10.1093/nar/gkv919 [PDF]


Hao Y*, Colak R*, Teyra J
*, Corbi-Verge C
Ignatschenko A, Hahne H, Wilhelm M, Kuster B, Braun P, Kaida D, Kislinger T, Kim PM. Semi-supervised Learning Predicts Approximately One Third of the Alternative Splicing Isoforms as Functional Proteins. Cell Reports 2015 Jul 14;12(2):183-9

Seo MH, Nim S, Jeon CJ, Kim PM. Large-scale interaction profiling of protein domains through proteomic peptide-phage display using custom peptidomes. Methods Mol Biol. (in press)

Najafabadi HS, Mnaimneh S, Schmitges FW, Garton M, Lam KN, Yang A, Albu M, Weirauch MT, Radovani E, Kim PM, Greenblatt J, Frey BJ, Hughes TR. C2H2 zinc finger proteins greatly expand the human regulatory lexicon. Nature Biotechnol. 2015 Feb 18.

2014

Berliner N*, Teyra J*, Colak R*, Garcia Lopez S, Kim PM
. Combining structural modeling with ensemble machine learning to accurately predict stability effects of mutations on protein stability and protein-protein interactions. PLoS ONE 2014 Sep 22;9(9):e107353.

Jeon J, Nim S, Teyra J, Datti A, Wrana JL, Sidhu SS, Moffat J, Kim PM. Integrated prediction and in vivo validation of novel cancer drug targets. Genome Medicine 2014 Jul 30;6(7):57

Babu M*, Arnold R*, Bundalovic-Torma C, Gagarinova A, Wong KS, Phanse S, Kumar A, Wagih O, Krunal L, Samanfar B, Stewart G, Graham C, Aoki H, Brown E, Golshani A, Kim P, Moreno-Hagelsieb G, Greenblatt J, Houry WA, Parkinson J, Emili A. Quantitative genome-wiede genetic interaction screens reveal the global functional organization of soluble protein complexes in Escherichia coli. PLoS Genetics 2014 Feb 20;10(2):e1004120

van der Lee R, Buljan M, Daughdrill G, Dunker K, Fuxreiter M, Gough J, Gsponer J, Jones D, Kim PM, Kriwacki R, Lang B, Pappu R, Tompa P, Uversky V, Wright P, Babu MM. Classification of Intrinsically Disordered Regions and Proteins. Chemical Reviews  2014 Jul 9;114(13):6589-631.

Abu-Odeh M, Bar-Mag T, Huang H, Kim T, Salah Z, Abdeen SK, Sudol M, Reichmann D, Sidhu S, Kim PM, Aqeilan RI. Characterizing WW Domain Interactions of Tumor Suppressor WWOX Reveals its Association with Multiprotein Networks. J Biol Chem. 2014 Mar 28;289(13):8865-80

Ivarsson Y, Arnold R, McLaughlin M, Nim S, Joshi R, Ray D, Liu B, Teyra J, Pawson T, Moffat J, Li S, Sidhu SS, Kim PM. Proteomic peptide phage display: large scale interaction profiling using  human and viral phage peptidomes. Proc Natl Acad Sci. 2014 Feb 18;111(7):2542-7

Chen C, Ha BH, Thévenin AF, Lou HJ, Zhang R, Yip KY, Peterson JR, Gerstein M, Kim PM, Filippakopoulos P, Knapp S, Boggon TJ, Turk BE. Identification of a major determinant for serine-threonine kinase phosphoacceptor specificity. Mol Cell. 2014 Jan 9;53(1):140-7

2013

Vizeacoumar FJ*, Arnold R*, Vizeacoumar FS, Chandrashekhar M, Buzina A, Young JT, Kwan JH, Sayad A, Mero P, Lawo S, Tanaka H, Brown KR, Baryshnikova A, Mak AB, Fedyshyn Y, Wang Y, Brito GC, Kasimer D, Makhnevych T, Ketela T, Datti A, Babu M, Emili A, Pelletier L, Wrana J, Wainberg Z, Kim PM, Rottapel R, O'Brien CA, Andrews B, Boone C, Moffat J. A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. Mol Syst Biol. 2013 Oct 8;9:696

Teyra J, Kim PM. Interpreting protein networks with three-dimensional structures. Nat Methods. 2013 Jan;10(1):43-4.

Colak R*, Kim T*, Michaut M, Sun MFG, Irimia M, Bellay J, Myers CL, Blencowe BJ, Kim PM. Distinct types of disorder in the human proteome: functional implications for alternative splicing. PLoS Comp Biol  2013 Apr;9(4):e1003030

Barbosa-Morais NL, Irimia M, Pan Q, Xiong HY, Gueroussov S, Lee LJ, Slobodeniuc V, Kutter C, Watt S, Colak R, Kim T, Misquitta-Ali CM, Wilson MD, Kim PM, Odom DT, Frey BJ, Blencowe BJ. The evolutionary landscape of alternative splicing in vertebrate species. Science. 2012 Dec 21;338(6114):1587-93

2012


Arnold R, Boonen K, Sun MG, Kim PM. Computational analysis of interactomes: Current and future perspectives for bioinformatics approaches to model the host-pathogen interaction space. Methods. 2012 Jun 28.

Ellis JD*, Barrios-Rodiles M*, Colak R*, Irimia M, Kim T, Calarco JA, Wang X, Pan Q, O'Hanlon D, Kim PM#, Wrana JL#, Blencowe BJ#. Tissue-specific alternative splicing remodels protein-protein interaction networks. Mol Cell. 2012 Jun 29;46(6):884-92.

Teyra J, Sidhu SS, Kim PM. Elucidation of the binding preferences of peptide recognition modules: SH3 and PDZ domains. FEBS Lett. 2012 Aug 14;586(17):2631-7. Epub 2012 Jun 9.

Hooda Y, Kim PM. Computational structural analysis of protein interactions and networks. Proteomics. 2012 May;12(10):1697-705. doi:10.1002/pmic.201100597.

Bellay J, Michaut M, Kim TH, Han S, Colak R, Myers CL, Kim PM. An Omics Perspective on Protein Disorder. Molecular Biosystems 2012 Jan 1;8(1): 185-93

Sun MFG*, Sikora M*, Costanzo M, Boone C, Kim PM. Network Evolution: Rewiring and Signatures of Conservation in Signaling. PLoS Comp. Biol. (in press)

2011

Sun MFG, Kim PM. Evolution of Biological Networks. Genome Biology 2011 Dec 28;12(12):235 [PDF]

Kim TH, Tyndel M, Bader GD, Gfeller D#, Kim PM#. MUSI: An integrated system to identify multiple specificity in large peptide or nucleotide data sets. Nucleic Acids Research 2011 Dec 30

Yip KY*, Utz L*, Sitwell S, Turk BE, Gerstein MB#, Kim PM#. Identification of Specificity Determining Residues in Peptide Recognition Domains using an Information Theoretic Approach Applied to Large-Scale Binding Maps. BMC Biology 2011, 9:53

Gfeller D, Ernst A, Verschueren E, Vanhee P, Dar N, Serrano L, Sidhu SS, Bader GD#, Kim PM#. Uncovering Multiple Specificity in Protein Recognition Modules. Nature/EMBO Mol. Syst. Biol. 2011 Apr 26;7:484 

Bellay J, Atluri G, Sing TL, Toufighi K, Costanzo M, Ribeiro PS, Pandey G, Baller J, Vandersluis B, Michaut M, Han S, Kim P, Brown GW, Andrews BJ, Boone C,  Kumar V, Myers CL. Putting genetic interactions in context through a global modular decomposition. Genome Res. 2011 Aug;21(8):1375-87.

Fasolo J, Sboner A, Sun MGF, Yu H, Chen R, Sharon D, Kim PM, Gerstein M, Snyder M. Diverse Protein Kinase Interactions Identified by Protein Microarrays Reveals Novel Connections Between Cellular Processes. Genes Dev 2011 Apr 1;25(7):767-78

Bellay J*, Han S*, Michaut M*, Kim T, Costanzo M, Andrews BJ, Boone C, Bader GD, Myers CL#, Kim PM#. Bringing order to disorder: genomic analysis uncovers three distinct forms of protein disorder. Genome Biol. 2011, 12:R14 [PDF]

Shou C, Bhardwaj N, Lam HYK, Yan KK, Kim PM, Snyder M, Gerstein MB. Evolution of Biological Networks in Eukaryotes. PLoS Comp. Biol. 2011 Jan 6;7(1):e1001050

2010

Bhardwaj N, Kim PM#, Gerstein MB. Rewiring of transcriptional regulatory networks: Hierarchy, rather than connectivity, better reflects the importance of regulators. Science Signal. 3, ra79 (2010) [#joint corresponding author] [PDF]

Ernst A, Gfeller D, Kan Z, Seshagiri S, Kim PM, Bader GD, Sidhu SS. Coevolution of PDZ domain-ligand interactions analyzed by high-throughput phage display and deep sequencing. Mol Biosyst. 2010 Aug 11

Lam HY*, Kim PM*, Mok J, Tonikian R, Sidhu SS, Turk BE, Snyder M, Gerstein MB. MOTIPS: automated motif analysis for predicting targets of modular protein domains. BMC Bioinformatics 2010 May 11;11:243

Mok J, Kim PM, Lam HYK, Piccirillo S, Zhou X, Jeschke GR, Sheridan DL, Parker SA, Desai V, Jwa M, Cameroni E, Niu H, Good M, Remenyi A, Ma JLN, Sheu YJ, Sassi HE, Sopko R, Chan CSM, De Virgilio C, Hollingsworth NM, Lim WA, Stern DF, Stillman B, Andrews BJ, Gerstein MB, Snyder M, Turk B. Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation motifs. Sci. Signaling (2010) Feb 16;3(109):ra12

Han SJ, Kim PM. Chaperonin activity modulates codon adaptation. Mol. Syst. Biol. (2010);6:342. Epub 2010 Jan 19

Costanzo M*, Baryshnikova A*, Bellay J, Kim Y, Spear ED, Sevier SD, Ding H, Koh JLY, Toufighi K, Mostafavi S, Prinz J, St. Onge R, Vandersluis B, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Li ZY, Liang W, Marback M, Paw J, San Luis BJ, Shuteriqi E, Hin A, Tong AHY, van Dyk N, Wallace IM, Whitney JA, Weirauch MT, Zhong G, Zhu H, Houry W, Brudno M, Ragibizadeh S, Papp B, Roth FP, Giaever G, Nislow C, Troyanskaya OG, Bussey H, Bader GD, Gingras AC, Morris QD , Kim PM, Kaiser CK, Myers CM, Andrews B, Boone C. The Genetic Landscape of the Cell. Science (2010) Jan 22;327(5964):425-31

2009

Lam HYK*, Mu XJ*, Tanzer A, Stuetz A, Snyder M, Kim PM, Korbel JO, Gerstein MB. BreakSeq: Mining a breakpoint library rapidly identifies structural variants in personal genomes and reveals biases in their formation. Nature Biotech. (2010) Jan;28(1):47-55. Epub 2009 Dec 27

Tonikian R*, Xin X*, Toret CP*, Gfeller D, Landgraf C, Panni S, Paoluzi S, Castagnoli L, Currell B, Seshagiri S, Yu H, Winsor B, Vidal M, Gerstein MB, Bader GD, Volkmer R#, Cesareni G#, Drubin DG#, Kim PM#, Sidhu SS#,Boone C#. Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins. PLoS Biol. 2009 Oct;7(10):e1000218 [#joint corresponding author]] [PDF]

Yip KY, Kim PM, McDermott D, Gerstein MB. Multi-level Learning: Improving the Prediction of Protein, Domain and Residue Interactions by Allowing Information Flow between Levels. BMC Bioinformatics 2009 Aug 5;10:241 [PDF]

Alexander RP, Kim PM, Emonet T, Gerstein MB. Understanding modularity in molecular networks requires dynamics. Science Signal. 2009 Jul 28;2(81):pe44 [PDF]

2008

Kim PM*, Lam HY*, Urban AE, Korbel JO, Affourtit J, Grubert F, Chen X, Weissman S, Snyder M, Gerstein MB. Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history. Genome Res. 2008 18(12):1865-74 [PDF]

Hasin Y, Olender T, Khen M, Gonzaga-Jauregui C, Kim PM, Urban AE, Snyder M, Gerstein MB, Lancet D, Korbel JO. High-resolution copy-number variation map reflects human olfactory receptor diversity and evolution. PLoS Genetics 2008 4(11):e1000249 [PDF]

Korbel JO*, Kim PM*, Chen X, Urban AE, Weissman S, Snyder M, Gerstein MB. The current excitement about copy-number variation: how it relates to gene duplications and protein families. Curr. Op. Struct. Biol. 18(3):366-74 [*joint first author] [PDF]

Kim PM*, Sboner A*, Xia Y, Gerstein M. The role of disorder in interaction networks: a structural analysis. Nature Mol. Syst. Biol. 2008 4:179 [*joint first author] [PDF]

Yip KY, Patel P, Kim PM, Engelman DM, McDermott D, Gerstein M. An integrated system for studying residue coevolution in proteins. Bioinformatics 2008 24: 290-292 [PDF]

2007

Kim PM*, Korbel JO*, Gerstein MB. Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context.  PNAS 2007 104:20274-9 [*joint first author] [PDF] [Supplement Website]

Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L, Taillon BE, Chen Z, Tanzer A, Saunders AC, Chi J, Yang F, Carter NP, Hurles ME, Weissman SM, Harkins TT, Gerstein MB, Egholm M, Snyder M. Paired-end mapping reveals extensive structural variation in the human genome. Science 2007 318: 420-6 [PDF]

Lu LJ, Sboner A, Huang YJ, Lu HX, Gianoulis TA, Yip KY, Kim PM, Montelione GT, Gerstein MB. Comparing classical pathways and modern networks: towards the development of an edge ontology.  Trends in Biochemical Science 2007 32(7):320-31 [PDF]

Yu H*, Kim PM*, Sprecher E, Trifonov V, Gerstein M. The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comp. Biol. 2007 3(4):e59  [*joint first author] [PDF]

2006

Kim PM, Lu LJ, Xia Y, Gerstein MB. Relating three-dimensional structures to protein networks provides evolutionary insights. Science 2006 314: 1938-41. [PDF] [Supplement Website]

Yip KY, Yu H, Kim PM, Schultz M, Gerstein M. The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks. Bioinformatics 2006 22: 2968-70 [PDF] [Webserver]

pre 2006

Kim PM (2003) “Understanding Subsystems in Biology through Dimensionality Reduction, Graph Partitioning and Analytical Modeling”, Ph.D. Thesis, Massachusetts Institute of Technology

Kim PM, Tidor B. Limitations of Quantitative Gene Regulation Models: A Case Study. Genome Res 2003 13: 2391-2395 [PDF]

Kim PM, Tidor B. Subsystem Identification through Dimensionality Reduction of Large-scale Gene Expression Data. Genome Res 2003 13:1706-1718 [PDF]


Comments