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Items: 1 to 50 of 98

1.

The sequencing and interpretation of the genome obtained from a Serbian individual.

Mohammed Ismail W, Pagel KA, Pejaver V, Zhang SV, Casasa S, Mort M, Cooper DN, Hahn MW, Radivojac P.

PLoS One. 2018 Dec 19;13(12):e0208901. doi: 10.1371/journal.pone.0208901. eCollection 2018.

2.

New Drosophila Long-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods.

Kacsoh BZ, Barton S, Jiang Y, Zhou N, Mooney SD, Friedberg I, Radivojac P, Greene CS, Bosco G.

G3 (Bethesda). 2019 Jan 9;9(1):251-267. doi: 10.1534/g3.118.200867.

3.

Target site specificity and in vivo complexity of the mammalian arginylome.

Wang J, Pejaver VR, Dann GP, Wolf MY, Kellis M, Huang Y, Garcia BA, Radivojac P, Kashina A.

Sci Rep. 2018 Nov 1;8(1):16177. doi: 10.1038/s41598-018-34639-6.

4.

Reproductive Longevity Predicts Mutation Rates in Primates.

Thomas GWC, Wang RJ, Puri A, Harris RA, Raveendran M, Hughes DST, Murali SC, Williams LE, Doddapaneni H, Muzny DM, Gibbs RA, Abee CR, Galinski MR, Worley KC, Rogers J, Radivojac P, Hahn MW.

Curr Biol. 2018 Oct 8;28(19):3193-3197.e5. doi: 10.1016/j.cub.2018.08.050. Epub 2018 Sep 27.

PMID:
30270182
5.

ISMB 2018 proceedings.

Bromberg Y, Radivojac P.

Bioinformatics. 2018 Jul 1;34(13):i2-i3. doi: 10.1093/bioinformatics/bty413. No abstract available.

6.

Enumerating consistent sub-graphs of directed acyclic graphs: an insight into biomedical ontologies.

Peng Y, Jiang Y, Radivojac P.

Bioinformatics. 2018 Jul 1;34(13):i313-i322. doi: 10.1093/bioinformatics/bty268.

7.

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.

8.

Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.

Daneshjou R, Wang Y, Bromberg Y, Bovo S, Martelli PL, Babbi G, Lena PD, Casadio R, Edwards M, Gifford D, Jones DT, Sundaram L, Bhat RR, Li X, Pal LR, Kundu K, Yin Y, Moult J, Jiang Y, Pejaver V, Pagel KA, Li B, Mooney SD, Radivojac P, Shah S, Carraro M, Gasparini A, Leonardi E, Giollo M, Ferrari C, Tosatto SCE, Bachar E, Azaria JR, Ofran Y, Unger R, Niroula A, Vihinen M, Chang B, Wang MH, Franke A, Petersen BS, Pirooznia M, Zandi P, McCombie R, Potash JB, Altman RB, Klein TE, Hoskins RA, Repo S, Brenner SE, Morgan AA.

Hum Mutat. 2017 Sep;38(9):1182-1192. doi: 10.1002/humu.23280. Epub 2017 Jul 7.

9.

Missense variant pathogenicity predictors generalize well across a range of function-specific prediction challenges.

Pejaver V, Mooney SD, Radivojac P.

Hum Mutat. 2017 Sep;38(9):1092-1108. doi: 10.1002/humu.23258. Epub 2017 Jun 12.

10.

COMPUTATIONAL APPROACHES TO UNDERSTANDING THE EVOLUTION OF MOLECULAR FUNCTION.

Bromberg Y, Hahn MW, Radivojac P.

Pac Symp Biocomput. 2017;22:1-2. doi: 10.1142/9789813207813_0001.

11.

Community-Wide Evaluation of Computational Function Prediction.

Friedberg I, Radivojac P.

Methods Mol Biol. 2017;1446:133-146.

PMID:
27812940
12.

REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants.

Ioannidis NM, Rothstein JH, Pejaver V, Middha S, McDonnell SK, Baheti S, Musolf A, Li Q, Holzinger E, Karyadi D, Cannon-Albright LA, Teerlink CC, Stanford JL, Isaacs WB, Xu J, Cooney KA, Lange EM, Schleutker J, Carpten JD, Powell IJ, Cussenot O, Cancel-Tassin G, Giles GG, MacInnis RJ, Maier C, Hsieh CL, Wiklund F, Catalona WJ, Foulkes WD, Mandal D, Eeles RA, Kote-Jarai Z, Bustamante CD, Schaid DJ, Hastie T, Ostrander EA, Bailey-Wilson JE, Radivojac P, Thibodeau SN, Whittemore AS, Sieh W.

Am J Hum Genet. 2016 Oct 6;99(4):877-885. doi: 10.1016/j.ajhg.2016.08.016. Epub 2016 Sep 22.

13.

Impact of Amidination on Peptide Fragmentation and Identification in Shotgun Proteomics.

Li S, Dabir A, Misal SA, Tang H, Radivojac P, Reilly JP.

J Proteome Res. 2016 Oct 7;15(10):3656-3665. Epub 2016 Sep 27.

14.

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P.

Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6.

15.

The Loss and Gain of Functional Amino Acid Residues Is a Common Mechanism Causing Human Inherited Disease.

Lugo-Martinez J, Pejaver V, Pagel KA, Jain S, Mort M, Cooper DN, Mooney SD, Radivojac P.

PLoS Comput Biol. 2016 Aug 26;12(8):e1005091. doi: 10.1371/journal.pcbi.1005091. eCollection 2016 Aug.

16.

Physicochemical sequence characteristics that influence S-palmitoylation propensity.

Reddy KD, Malipeddi J, DeForte S, Pejaver V, Radivojac P, Uversky VN, Deschenes RJ.

J Biomol Struct Dyn. 2017 Aug;35(11):2337-2350. doi: 10.1080/07391102.2016.1217275. Epub 2016 Aug 7.

PMID:
27498722
17.

Protein function in precision medicine: deep understanding with machine learning.

Rost B, Radivojac P, Bromberg Y.

FEBS Lett. 2016 Aug;590(15):2327-41. doi: 10.1002/1873-3468.12307. Epub 2016 Aug 6. Review.

18.

Regulatory Single-Nucleotide Variant Predictor Increases Predictive Performance of Functional Regulatory Variants.

Peterson TA, Mort M, Cooper DN, Radivojac P, Kann MG, Mooney SD.

Hum Mutat. 2016 Nov;37(11):1137-1143. doi: 10.1002/humu.23049. Epub 2016 Aug 31.

19.

Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee).

Welch L, Brooksbank C, Schwartz R, Morgan SL, Gaeta B, Kilpatrick AM, Mietchen D, Moore BL, Mulder N, Pauley M, Pearson W, Radivojac P, Rosenberg N, Rosenwald A, Rustici G, Warnow T.

PLoS Comput Biol. 2016 May 13;12(5):e1004943. doi: 10.1371/journal.pcbi.1004943. eCollection 2016 May. No abstract available.

20.

XLSearch: a Probabilistic Database Search Algorithm for Identifying Cross-Linked Peptides.

Ji C, Li S, Reilly JP, Radivojac P, Tang H.

J Proteome Res. 2016 Jun 3;15(6):1830-41. doi: 10.1021/acs.jproteome.6b00004. Epub 2016 May 6.

21.

Examining the Influence of Phosphorylation on Peptide Ion Structure by Ion Mobility Spectrometry-Mass Spectrometry.

Glover MS, Dilger JM, Acton MD, Arnold RJ, Radivojac P, Clemmer DE.

J Am Soc Mass Spectrom. 2016 May;27(5):786-94. doi: 10.1007/s13361-016-1343-y. Epub 2016 Feb 9.

22.

Proteomic Evidence for In-Frame and Out-of-Frame Alternatively Spliced Isoforms in Human and Mouse.

Ramalho RF, Li S, Radivojac P, Hahn MW.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Jul-Aug;15(4):1284-1289. doi: 10.1109/TCBB.2015.2480068. Epub 2015 Sep 18.

PMID:
26394435
23.

Position of Proline Mediates the Reactivity of S-Palmitoylation.

Khanal N, Pejaver V, Li Z, Radivojac P, Clemmer DE, Mukhopadhyay S.

ACS Chem Biol. 2015 Nov 20;10(11):2529-36. doi: 10.1021/acschembio.5b00429. Epub 2015 Aug 19.

PMID:
26255674
24.

Penultimate proline in neuropeptides.

Glover MS, Bellinger EP, Radivojac P, Clemmer DE.

Anal Chem. 2015 Aug 18;87(16):8466-72. doi: 10.1021/acs.analchem.5b01889. Epub 2015 Jul 29.

PMID:
26192015
25.

Intrinsic Size Parameters for Palmitoylated and Carboxyamidomethylated Peptides.

Li Z, Dilger JM, Pejaver V, Smiley D, Arnold RJ, Mooney SD, Mukhopadhyay S, Radivojac P, Clemmer DE.

Int J Mass Spectrom. 2014 Jul 15;368:6-14.

26.

Ten simple rules for a community computational challenge.

Friedberg I, Wass MN, Mooney SD, Radivojac P.

PLoS Comput Biol. 2015 Apr 23;11(4):e1004150. doi: 10.1371/journal.pcbi.1004150. eCollection 2015 Apr. No abstract available.

27.

Training the next generation of quantitative biologists in the era of big data.

Pattin KA, Greene AC, Altman RB, Cohen KB, Wethington E, Görg C, Hunter LE, Muse SV, Radivojac P, Moore JH.

Pac Symp Biocomput. 2015:488-92.

28.

On the split personality of penultimate proline.

Glover MS, Shi L, Fuller DR, Arnold RJ, Radivojac P, Clemmer DE.

J Am Soc Mass Spectrom. 2015 Mar;26(3):444-52. doi: 10.1007/s13361-014-1049-y. Epub 2014 Dec 12.

29.

Global human frequencies of predicted nuclear pathogenic variants and the role played by protein hydrophobicity in pathogenicity potential.

Pereira L, Soares P, Triska P, Rito T, van der Waerden A, Li B, Radivojac P, Samuels DC.

Sci Rep. 2014 Nov 21;4:7155. doi: 10.1038/srep07155.

30.

The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective.

Jiang Y, Clark WT, Friedberg I, Radivojac P.

Bioinformatics. 2014 Sep 1;30(17):i609-16. doi: 10.1093/bioinformatics/btu472.

31.

The structural and functional signatures of proteins that undergo multiple events of post-translational modification.

Pejaver V, Hsu WL, Xin F, Dunker AK, Uversky VN, Radivojac P.

Protein Sci. 2014 Aug;23(8):1077-93. doi: 10.1002/pro.2494. Epub 2014 Jun 11.

32.

Bioinformatics curriculum guidelines: toward a definition of core competencies.

Welch L, Lewitter F, Schwartz R, Brooksbank C, Radivojac P, Gaeta B, Schneider MV.

PLoS Comput Biol. 2014 Mar 6;10(3):e1003496. doi: 10.1371/journal.pcbi.1003496. eCollection 2014 Mar. No abstract available.

33.

The automated function prediction SIG looks back at 2013 and prepares for 2014.

Wass MN, Mooney SD, Linial M, Radivojac P, Friedberg I.

Bioinformatics. 2014 Jul 15;30(14):2091-2. doi: 10.1093/bioinformatics/btu117. Epub 2014 Mar 3. No abstract available.

34.

MutPred Splice: machine learning-based prediction of exonic variants that disrupt splicing.

Mort M, Sterne-Weiler T, Li B, Ball EV, Cooper DN, Radivojac P, Sanford JR, Mooney SD.

Genome Biol. 2014 Jan 13;15(1):R19. doi: 10.1186/gb-2014-15-1-r19.

35.
36.

ISCB computational biology Wikipedia competition.

Bateman A, Kelso J, Mietchen D, Macintyre G, Di Domenico T, Abeel T, Logan DW, Radivojac P, Rost B.

PLoS Comput Biol. 2013;9(9):e1003242. doi: 10.1371/journal.pcbi.1003242. Epub 2013 Sep 19. No abstract available.

37.

Information-theoretic evaluation of predicted ontological annotations.

Clark WT, Radivojac P.

Bioinformatics. 2013 Jul 1;29(13):i53-61. doi: 10.1093/bioinformatics/btt228.

38.

Quantitative measurement of phosphoproteome response to osmotic stress in arabidopsis based on Library-Assisted eXtracted Ion Chromatogram (LAXIC).

Xue L, Wang P, Wang L, Renzi E, Radivojac P, Tang H, Arnold R, Zhu JK, Tao WA.

Mol Cell Proteomics. 2013 Aug;12(8):2354-69. doi: 10.1074/mcp.O113.027284. Epub 2013 May 8.

39.

Evaluating purifying selection in the mitochondrial DNA of various mammalian species.

Soares P, Abrantes D, Rito T, Thomson N, Radivojac P, Li B, Macaulay V, Samuels DC, Pereira L.

PLoS One. 2013;8(3):e58993. doi: 10.1371/journal.pone.0058993. Epub 2013 Mar 22.

40.

A large-scale evaluation of computational protein function prediction.

Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Törönen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kaßner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Björne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Škunca N, Supek F, Bošnjak M, Panov P, Džeroski S, Šmuc T, Kourmpetis YA, van Dijk AD, ter Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I.

Nat Methods. 2013 Mar;10(3):221-7. doi: 10.1038/nmeth.2340. Epub 2013 Jan 27.

41.

Extending the coverage of spectral libraries: a neighbor-based approach to predicting intensities of peptide fragmentation spectra.

Ji C, Arnold RJ, Sokoloski KJ, Hardy RW, Tang H, Radivojac P.

Proteomics. 2013 Mar;13(5):756-65. doi: 10.1002/pmic.201100670. Epub 2013 Feb 4.

42.

Computational approaches to protein inference in shotgun proteomics.

Li YF, Radivojac P.

BMC Bioinformatics. 2012;13 Suppl 16:S4. doi: 10.1186/1471-2105-13-S16-S4. Epub 2012 Nov 5. Review.

43.

Calibration of multiple in silico tools for predicting pathogenicity of mismatch repair gene missense substitutions.

Thompson BA, Greenblatt MS, Vallee MP, Herkert JC, Tessereau C, Young EL, Adzhubey IA, Li B, Bell R, Feng B, Mooney SD, Radivojac P, Sunyaev SR, Frebourg T, Hofstra RM, Sijmons RH, Boucher K, Thomas A, Goldgar DE, Spurdle AB, Tavtigian SV.

Hum Mutat. 2013 Jan;34(1):255-65. doi: 10.1002/humu.22214. Epub 2012 Oct 22.

44.

Post-translational modifications induce significant yet not extreme changes to protein structure.

Xin F, Radivojac P.

Bioinformatics. 2012 Nov 15;28(22):2905-13. doi: 10.1093/bioinformatics/bts541. Epub 2012 Sep 4.

PMID:
22947645
45.

Allosteric post-translational modification codes.

Nussinov R, Tsai CJ, Xin F, Radivojac P.

Trends Biochem Sci. 2012 Oct;37(10):447-55. doi: 10.1016/j.tibs.2012.07.001. Epub 2012 Aug 8. Review.

PMID:
22884395
46.

An integrated regulatory network reveals pervasive cross-regulation among transcription and splicing factors.

Kosti I, Radivojac P, Mandel-Gutfreund Y.

PLoS Comput Biol. 2012;8(7):e1002603. doi: 10.1371/journal.pcbi.1002603. Epub 2012 Jul 26.

47.

Protein identification problem from a Bayesian point of view.

Li YF, Arnold RJ, Radivojac P, Tang H.

Stat Interface. 2012 Jan 1;5(1):21-37.

48.

Investigation of VUV Photodissociation Propensities Using Peptide Libraries.

Liu X, Li YF, Bohrer BC, Arnold RJ, Radivojac P, Tang H, Reilly JP.

Int J Mass Spectrom. 2011 Dec 1;308(2-3):142-154.

49.

Prediction of functional regulatory SNPs in monogenic and complex disease.

Zhao Y, Clark WT, Mort M, Cooper DN, Radivojac P, Mooney SD.

Hum Mutat. 2011 Oct;32(10):1183-90. doi: 10.1002/humu.21559. Epub 2011 Sep 9.

50.

Computational methods for identification of functional residues in protein structures.

Xin F, Radivojac P.

Curr Protein Pept Sci. 2011 Sep;12(6):456-69. Review.

PMID:
21787297

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