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Items: 45

1.

Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome.

Pagel KA, Antaki D, Lian A, Mort M, Cooper DN, Sebat J, Iakoucheva LM, Mooney SD, Radivojac P.

PLoS Comput Biol. 2019 Jun 14;15(6):e1007112. doi: 10.1371/journal.pcbi.1007112. eCollection 2019 Jun.

2.

Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder.

Gandal MJ, Zhang P, Hadjimichael E, Walker RL, Chen C, Liu S, Won H, van Bakel H, Varghese M, Wang Y, Shieh AW, Haney J, Parhami S, Belmont J, Kim M, Moran Losada P, Khan Z, Mleczko J, Xia Y, Dai R, Wang D, Yang YT, Xu M, Fish K, Hof PR, Warrell J, Fitzgerald D, White K, Jaffe AE; PsychENCODE Consortium, Peters MA, Gerstein M, Liu C, Iakoucheva LM, Pinto D, Geschwind DH.

Science. 2018 Dec 14;362(6420). pii: eaat8127. doi: 10.1126/science.aat8127.

3.

Paternally inherited cis-regulatory structural variants are associated with autism.

Brandler WM, Antaki D, Gujral M, Kleiber ML, Whitney J, Maile MS, Hong O, Chapman TR, Tan S, Tandon P, Pang T, Tang SC, Vaux KK, Yang Y, Harrington E, Juul S, Turner DJ, Thiruvahindrapuram B, Kaur G, Wang Z, Kingsmore SF, Gleeson JG, Bisson D, Kakaradov B, Telenti A, Venter JC, Corominas R, Toma C, Cormand B, Rueda I, Guijarro S, Messer KS, Nievergelt CM, Arranz MJ, Courchesne E, Pierce K, Muotri AR, Iakoucheva LM, Hervas A, Scherer SW, Corsello C, Sebat J.

Science. 2018 Apr 20;360(6386):327-331. doi: 10.1126/science.aan2261.

4.

When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants.

Pagel KA, Pejaver V, Lin GN, Nam HJ, Mort M, Cooper DN, Sebat J, Iakoucheva LM, Mooney SD, Radivojac P.

Bioinformatics. 2017 Jul 15;33(14):i389-i398. doi: 10.1093/bioinformatics/btx272.

5.

Comprehensive Analyses of Tissue-Specific Networks with Implications to Psychiatric Diseases.

Lin GN, Corominas R, Nam HJ, Urresti J, Iakoucheva LM.

Methods Mol Biol. 2017;1613:371-402. doi: 10.1007/978-1-4939-7027-8_15.

6.

Frequency and Complexity of De Novo Structural Mutation in Autism.

Brandler WM, Antaki D, Gujral M, Noor A, Rosanio G, Chapman TR, Barrera DJ, Lin GN, Malhotra D, Watts AC, Wong LC, Estabillo JA, Gadomski TE, Hong O, Fajardo KV, Bhandari A, Owen R, Baughn M, Yuan J, Solomon T, Moyzis AG, Maile MS, Sanders SJ, Reiner GE, Vaux KK, Strom CM, Zhang K, Muotri AR, Akshoomoff N, Leal SM, Pierce K, Courchesne E, Iakoucheva LM, Corsello C, Sebat J.

Am J Hum Genet. 2016 Apr 7;98(4):667-79. doi: 10.1016/j.ajhg.2016.02.018. Epub 2016 Mar 24.

7.

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.

8.

Spatiotemporal 16p11.2 protein network implicates cortical late mid-fetal brain development and KCTD13-Cul3-RhoA pathway in psychiatric diseases.

Lin GN, Corominas R, Lemmens I, Yang X, Tavernier J, Hill DE, Vidal M, Sebat J, Iakoucheva LM.

Neuron. 2015 Feb 18;85(4):742-54. doi: 10.1016/j.neuron.2015.01.010.

9.

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.

10.

Pathological unfoldomics of uncontrolled chaos: intrinsically disordered proteins and human diseases.

Uversky VN, Davé V, Iakoucheva LM, Malaney P, Metallo SJ, Pathak RR, Joerger AC.

Chem Rev. 2014 Jul 9;114(13):6844-79. doi: 10.1021/cr400713r. Epub 2014 May 15. Review. No abstract available.

11.

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.

12.

Predicted disorder-to-order transition mutations in IκBα disrupt function.

Dembinski H, Wismer K, Balasubramaniam D, Gonzalez HA, Alverdi V, Iakoucheva LM, Komives EA.

Phys Chem Chem Phys. 2014 Apr 14;16(14):6480-5. doi: 10.1039/c3cp54427c. Epub 2014 Mar 6.

13.

Whole-genome sequencing in autism identifies hot spots for de novo germline mutation.

Michaelson JJ, Shi Y, Gujral M, Zheng H, Malhotra D, Jin X, Jian M, Liu G, Greer D, Bhandari A, Wu W, Corominas R, Peoples A, Koren A, Gore A, Kang S, Lin GN, Estabillo J, Gadomski T, Singh B, Zhang K, Akshoomoff N, Corsello C, McCarroll S, Iakoucheva LM, Li Y, Wang J, Sebat J.

Cell. 2012 Dec 21;151(7):1431-42. doi: 10.1016/j.cell.2012.11.019.

14.

Disease-associated mutations disrupt functionally important regions of intrinsic protein disorder.

Vacic V, Markwick PR, Oldfield CJ, Zhao X, Haynes C, Uversky VN, Iakoucheva LM.

PLoS Comput Biol. 2012;8(10):e1002709. doi: 10.1371/journal.pcbi.1002709. Epub 2012 Oct 4.

15.

Disease mutations in disordered regions--exception to the rule?

Vacic V, Iakoucheva LM.

Mol Biosyst. 2012 Jan;8(1):27-32. doi: 10.1039/c1mb05251a. Epub 2011 Nov 14. Review.

16.

Duplications of the neuropeptide receptor gene VIPR2 confer significant risk for schizophrenia.

Vacic V, McCarthy S, Malhotra D, Murray F, Chou HH, Peoples A, Makarov V, Yoon S, Bhandari A, Corominas R, Iakoucheva LM, Krastoshevsky O, Krause V, Larach-Walters V, Welsh DK, Craig D, Kelsoe JR, Gershon ES, Leal SM, Dell Aquila M, Morris DW, Gill M, Corvin A, Insel PA, McClellan J, King MC, Karayiorgou M, Levy DL, DeLisi LE, Sebat J.

Nature. 2011 Mar 24;471(7339):499-503. doi: 10.1038/nature09884. Epub 2011 Feb 23. Erratum in: Nature. 2011 Jun 2;474(7349):114.

17.

Mapping copy number variation by population-scale genome sequencing.

Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO; 1000 Genomes Project.

Nature. 2011 Feb 3;470(7332):59-65. doi: 10.1038/nature09708.

18.

Graphlet kernels for prediction of functional residues in protein structures.

Vacic V, Iakoucheva LM, Lonardi S, Radivojac P.

J Comput Biol. 2010 Jan;17(1):55-72. doi: 10.1089/cmb.2009.0029.

19.

Loss of post-translational modification sites in disease.

Li S, Iakoucheva LM, Mooney SD, Radivojac P.

Pac Symp Biocomput. 2010:337-47.

20.

Microduplications of 16p11.2 are associated with schizophrenia.

McCarthy SE, Makarov V, Kirov G, Addington AM, McClellan J, Yoon S, Perkins DO, Dickel DE, Kusenda M, Krastoshevsky O, Krause V, Kumar RA, Grozeva D, Malhotra D, Walsh T, Zackai EH, Kaplan P, Ganesh J, Krantz ID, Spinner NB, Roccanova P, Bhandari A, Pavon K, Lakshmi B, Leotta A, Kendall J, Lee YH, Vacic V, Gary S, Iakoucheva LM, Crow TJ, Christian SL, Lieberman JA, Stroup TS, Lehtimäki T, Puura K, Haldeman-Englert C, Pearl J, Goodell M, Willour VL, Derosse P, Steele J, Kassem L, Wolff J, Chitkara N, McMahon FJ, Malhotra AK, Potash JB, Schulze TG, Nöthen MM, Cichon S, Rietschel M, Leibenluft E, Kustanovich V, Lajonchere CM, Sutcliffe JS, Skuse D, Gill M, Gallagher L, Mendell NR; Wellcome Trust Case Control Consortium, Craddock N, Owen MJ, O'Donovan MC, Shaikh TH, Susser E, Delisi LE, Sullivan PF, Deutsch CK, Rapoport J, Levy DL, King MC, Sebat J.

Nat Genet. 2009 Nov;41(11):1223-7. doi: 10.1038/ng.474. Epub 2009 Oct 25.

21.

Identification, analysis, and prediction of protein ubiquitination sites.

Radivojac P, Vacic V, Haynes C, Cocklin RR, Mohan A, Heyen JW, Goebl MG, Iakoucheva LM.

Proteins. 2010 Feb 1;78(2):365-80. doi: 10.1002/prot.22555.

22.

Unfoldomics of human diseases: linking protein intrinsic disorder with diseases.

Uversky VN, Oldfield CJ, Midic U, Xie H, Xue B, Vucetic S, Iakoucheva LM, Obradovic Z, Dunker AK.

BMC Genomics. 2009 Jul 7;10 Suppl 1:S7. doi: 10.1186/1471-2164-10-S1-S7.

23.

A protein domain-based interactome network for C. elegans early embryogenesis.

Boxem M, Maliga Z, Klitgord N, Li N, Lemmens I, Mana M, de Lichtervelde L, Mul JD, van de Peut D, Devos M, Simonis N, Yildirim MA, Cokol M, Kao HL, de Smet AS, Wang H, Schlaitz AL, Hao T, Milstein S, Fan C, Tipsword M, Drew K, Galli M, Rhrissorrakrai K, Drechsel D, Koller D, Roth FP, Iakoucheva LM, Dunker AK, Bonneau R, Gunsalus KC, Hill DE, Piano F, Tavernier J, van den Heuvel S, Hyman AA, Vidal M.

Cell. 2008 Aug 8;134(3):534-45. doi: 10.1016/j.cell.2008.07.009. Erratum in: Cell. 2012 Dec 21;151(7):1633.

24.

Prediction of intrinsic disorder and its use in functional proteomics.

Uversky VN, Radivojac P, Iakoucheva LM, Obradovic Z, Dunker AK.

Methods Mol Biol. 2007;408:69-92.

PMID:
18314578
25.

RNA association or phosphorylation of the RS domain prevents aggregation of RS domain-containing proteins.

Nikolakaki E, Drosou V, Sanidas I, Peidis P, Papamarcaki T, Iakoucheva LM, Giannakouros T.

Biochim Biophys Acta. 2008 Feb;1780(2):214-25. Epub 2007 Nov 1.

PMID:
18022399
26.

Functional anthology of intrinsic disorder. 3. Ligands, post-translational modifications, and diseases associated with intrinsically disordered proteins.

Xie H, Vucetic S, Iakoucheva LM, Oldfield CJ, Dunker AK, Obradovic Z, Uversky VN.

J Proteome Res. 2007 May;6(5):1917-32. Epub 2007 Mar 29.

27.

Functional anthology of intrinsic disorder. 2. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions.

Vucetic S, Xie H, Iakoucheva LM, Oldfield CJ, Dunker AK, Obradovic Z, Uversky VN.

J Proteome Res. 2007 May;6(5):1899-916. Epub 2007 Mar 29.

28.

Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions.

Xie H, Vucetic S, Iakoucheva LM, Oldfield CJ, Dunker AK, Uversky VN, Obradovic Z.

J Proteome Res. 2007 May;6(5):1882-98. Epub 2007 Mar 29.

29.

Intrinsic disorder and functional proteomics.

Radivojac P, Iakoucheva LM, Oldfield CJ, Obradovic Z, Uversky VN, Dunker AK.

Biophys J. 2007 Mar 1;92(5):1439-56. Epub 2006 Dec 8. Review.

30.

Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes.

Haynes C, Oldfield CJ, Ji F, Klitgord N, Cusick ME, Radivojac P, Uversky VN, Vidal M, Iakoucheva LM.

PLoS Comput Biol. 2006 Aug 4;2(8):e100. Epub 2006 Jun 23.

31.

Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments.

Vacic V, Iakoucheva LM, Radivojac P.

Bioinformatics. 2006 Jun 15;22(12):1536-7. Epub 2006 Apr 21.

PMID:
16632492
32.

Serine/arginine-rich splicing factors belong to a class of intrinsically disordered proteins.

Haynes C, Iakoucheva LM.

Nucleic Acids Res. 2006 Jan 10;34(1):305-12. Print 2006.

33.

Flexible nets. The roles of intrinsic disorder in protein interaction networks.

Dunker AK, Cortese MS, Romero P, Iakoucheva LM, Uversky VN.

FEBS J. 2005 Oct;272(20):5129-48. Review.

34.

Combining prediction, computation and experiment for the characterization of protein disorder.

Bracken C, Iakoucheva LM, Romero PR, Dunker AK.

Curr Opin Struct Biol. 2004 Oct;14(5):570-6.

PMID:
15465317
35.

DisProt: a database of protein disorder.

Vucetic S, Obradovic Z, Vacic V, Radivojac P, Peng K, Iakoucheva LM, Cortese MS, Lawson JD, Brown CJ, Sikes JG, Newton CD, Dunker AK.

Bioinformatics. 2005 Jan 1;21(1):137-40. Epub 2004 Aug 13.

PMID:
15310560
36.

The importance of intrinsic disorder for protein phosphorylation.

Iakoucheva LM, Radivojac P, Brown CJ, O'Connor TR, Sikes JG, Obradovic Z, Dunker AK.

Nucleic Acids Res. 2004 Feb 11;32(3):1037-49. Print 2004.

37.

Order, disorder, and flexibility: prediction from protein sequence.

Iakoucheva LM, Dunker AK.

Structure. 2003 Nov;11(11):1316-7.

38.

Intrinsic disorder in cell-signaling and cancer-associated proteins.

Iakoucheva LM, Brown CJ, Lawson JD, Obradović Z, Dunker AK.

J Mol Biol. 2002 Oct 25;323(3):573-84.

PMID:
12381310
39.

Intrinsic disorder and protein function.

Dunker AK, Brown CJ, Lawson JD, Iakoucheva LM, Obradović Z.

Biochemistry. 2002 May 28;41(21):6573-82. No abstract available.

PMID:
12022860
40.

Equilibrium and stop-flow kinetic studies of fluorescently labeled DNA substrates with DNA repair proteins XPA and replication protein A.

Iakoucheva LM, Walker RK, van Houten B, Ackerman EJ.

Biochemistry. 2002 Jan 8;41(1):131-43.

PMID:
11772010
41.

Single-molecule conformational dynamics of fluctuating noncovalent DNA-protein interactions in DNA damage recognition.

Lu HP, Iakoucheva LM, Ackerman EJ.

J Am Chem Soc. 2001 Sep 19;123(37):9184-5. No abstract available.

PMID:
11552836
42.

Aberrant mobility phenomena of the DNA repair protein XPA.

Iakoucheva LM, Kimzey AL, Masselon CD, Smith RD, Dunker AK, Ackerman EJ.

Protein Sci. 2001 Jul;10(7):1353-62.

43.

Identification of intrinsic order and disorder in the DNA repair protein XPA.

Iakoucheva LM, Kimzey AL, Masselon CD, Bruce JE, Garner EC, Brown CJ, Dunker AK, Smith RD, Ackerman EJ.

Protein Sci. 2001 Mar;10(3):560-71.

44.

Nucleotide excision repair in oocyte nuclear extracts from Xenopus laevis.

Ackerman EJ, Iakoucheva LM.

Methods. 2000 Oct;22(2):188-93.

PMID:
11020334
45.

Extended X-ray absorption fine structure evidence for a single metal binding domain in Xenopus laevis nucleotide excision repair protein XPA.

Buchko GW, Iakoucheva LM, Kennedy MA, Ackerman EJ, Hess NJ.

Biochem Biophys Res Commun. 1999 Jan 8;254(1):109-13.

PMID:
9920741

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