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Items: 23

1.

Evaluation of the secondary use of electronic health records to detect seasonal, holiday-related, and rare events related to traumatic injury and poisoning.

Bergquist T, Pejaver V, Hammarlund N, Mooney SD, Mooney SJ.

BMC Public Health. 2020 Jan 13;20(1):46. doi: 10.1186/s12889-020-8153-7.

2.

Assessment of predicted enzymatic activity of α-N-acetylglucosaminidase variants of unknown significance for CAGI 2016.

Clark WT, Kasak L, Bakolitsa C, Hu Z, Andreoletti G, Babbi G, Bromberg Y, Casadio R, Dunbrack R, Folkman L, Ford CT, Jones D, Katsonis P, Kundu K, Lichtarge O, Martelli PL, Mooney SD, Nodzak C, Pal LR, Radivojac P, Savojardo C, Shi X, Zhou Y, Uppal A, Xu Q, Yin Y, Pejaver V, Wang M, Wei L, Moult J, Yu GK, Brenner SE, LeBowitz JH.

Hum Mutat. 2019 Sep;40(9):1519-1529. doi: 10.1002/humu.23875.

PMID:
31342580
3.

Assessment of blind predictions of the clinical significance of BRCA1 and BRCA2 variants.

Cline MS, Babbi G, Bonache S, Cao Y, Casadio R, de la Cruz X, Díez O, Gutiérrez-Enríquez S, Katsonis P, Lai C, Lichtarge O, Martelli PL, Mishne G, Moles-Fernández A, Montalban G, Mooney SD, O'Conner R, Ootes L, Özkan S, Padilla N, Pagel KA, Pejaver V, Radivojac P, Riera C, Savojardo C, Shen Y, Sun Y, Topper S, Parsons MT, Spurdle AB, Goldgar DE; ENIGMA Consortium.

Hum Mutat. 2019 Sep;40(9):1546-1556. doi: 10.1002/humu.23861. Epub 2019 Aug 23.

PMID:
31294896
4.

Assessing the performance of in silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer.

Voskanian A, Katsonis P, Lichtarge O, Pejaver V, Radivojac P, Mooney SD, Capriotti E, Bromberg Y, Wang Y, Miller M, Martelli PL, Savojardo C, Babbi G, Casadio R, Cao Y, Sun Y, Shen Y, Garg A, Pal D, Yu Y, Huff CD, Tavtigian SV, Young E, Neuhausen SL, Ziv E, Pal LR, Andreoletti G, Brenner SE, Kann MG.

Hum Mutat. 2019 Sep;40(9):1612-1622. doi: 10.1002/humu.23849. Epub 2019 Aug 17.

PMID:
31241222
5.

Assessment of methods for predicting the effects of PTEN and TPMT protein variants.

Pejaver V, Babbi G, Casadio R, Folkman L, Katsonis P, Kundu K, Lichtarge O, Martelli PL, Miller M, Moult J, Pal LR, Savojardo C, Yin Y, Zhou Y, Radivojac P, Bromberg Y.

Hum Mutat. 2019 Sep;40(9):1495-1506. doi: 10.1002/humu.23838. Epub 2019 Jul 3.

PMID:
31184403
6.

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.

7.

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.

8.

Big Data in Public Health: Terminology, Machine Learning, and Privacy.

Mooney SJ, Pejaver V.

Annu Rev Public Health. 2018 Apr 1;39:95-112. doi: 10.1146/annurev-publhealth-040617-014208. Epub 2017 Dec 20. Review.

9.

Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework.

Glusman G, Rose PW, Prlić A, Dougherty J, Duarte JM, Hoffman AS, Barton GJ, Bendixen E, Bergquist T, Bock C, Brunk E, Buljan M, Burley SK, Cai B, Carter H, Gao J, Godzik A, Heuer M, Hicks M, Hrabe T, Karchin R, Leman JK, Lane L, Masica DL, Mooney SD, Moult J, Omenn GS, Pearl F, Pejaver V, Reynolds SM, Rokem A, Schwede T, Song S, Tilgner H, Valasatava Y, Zhang Y, Deutsch EW.

Genome Med. 2017 Dec 18;9(1):113. doi: 10.1186/s13073-017-0509-y. Review.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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
16.

Draft Genome Sequence of Caedibacter varicaedens, a Kappa Killer Endosymbiont Bacterium of the Ciliate Paramecium biaurelia.

Suzuki H, Dapper AL, Jackson CE, Lee H, Pejaver V, Doak TG, Lynch M, Preer JR Jr.

Genome Announc. 2015 Nov 5;3(6). pii: e01310-15. doi: 10.1128/genomeA.01310-15.

17.

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
18.

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.

19.

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.

20.

Patterning the cone mosaic array in zebrafish retina requires specification of ultraviolet-sensitive cones.

Raymond PA, Colvin SM, Jabeen Z, Nagashima M, Barthel LK, Hadidjojo J, Popova L, Pejaver VR, Lubensky DK.

PLoS One. 2014 Jan 21;9(1):e85325. doi: 10.1371/journal.pone.0085325. eCollection 2014.

21.

GeneclusterViz: a tool for conserved gene cluster visualization, exploration and analysis.

Pejaver VR, An J, Rhee S, Bhan A, Choi JH, Liu B, Lee H, Brown PJ, Kysela D, Brun YV, Kim S.

Bioinformatics. 2012 Jun 1;28(11):1527-9. doi: 10.1093/bioinformatics/bts177. Epub 2012 Apr 11.

22.

Gene Cluster Profile Vectors: a method to infer functionally related gene sets by grouping proximity-based gene clusters.

Pejaver VR, Kim S.

BMC Genomics. 2011;12 Suppl 2:S2. doi: 10.1186/1471-2164-12-S2-S2. Epub 2011 Jul 27.

23.

Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.

Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK; Nasonia Genome Working Group, Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Beukeboom LW, Desplan C, Elsik CG, Grimmelikhuijzen CJ, Kitts P, Lynch JA, Murphy T, Oliveira DC, Smith CD, van de Zande L, Worley KC, Zdobnov EM, Aerts M, Albert S, Anaya VH, Anzola JM, Barchuk AR, Behura SK, Bera AN, Berenbaum MR, Bertossa RC, Bitondi MM, Bordenstein SR, Bork P, Bornberg-Bauer E, Brunain M, Cazzamali G, Chaboub L, Chacko J, Chavez D, Childers CP, Choi JH, Clark ME, Claudianos C, Clinton RA, Cree AG, Cristino AS, Dang PM, Darby AC, de Graaf DC, Devreese B, Dinh HH, Edwards R, Elango N, Elhaik E, Ermolaeva O, Evans JD, Foret S, Fowler GR, Gerlach D, Gibson JD, Gilbert DG, Graur D, Gründer S, Hagen DE, Han Y, Hauser F, Hultmark D, Hunter HC 4th, Hurst GD, Jhangian SN, Jiang H, Johnson RM, Jones AK, Junier T, Kadowaki T, Kamping A, Kapustin Y, Kechavarzi B, Kim J, Kim J, Kiryutin B, Koevoets T, Kovar CL, Kriventseva EV, Kucharski R, Lee H, Lee SL, Lees K, Lewis LR, Loehlin DW, Logsdon JM Jr, Lopez JA, Lozado RJ, Maglott D, Maleszka R, Mayampurath A, Mazur DJ, McClure MA, Moore AD, Morgan MB, Muller J, Munoz-Torres MC, Muzny DM, Nazareth LV, Neupert S, Nguyen NB, Nunes FM, Oakeshott JG, Okwuonu GO, Pannebakker BA, Pejaver VR, Peng Z, Pratt SC, Predel R, Pu LL, Ranson H, Raychoudhury R, Rechtsteiner A, Reese JT, Reid JG, Riddle M, Robertson HM, Romero-Severson J, Rosenberg M, Sackton TB, Sattelle DB, Schlüns H, Schmitt T, Schneider M, Schüler A, Schurko AM, Shuker DM, Simões ZL, Sinha S, Smith Z, Solovyev V, Souvorov A, Springauf A, Stafflinger E, Stage DE, Stanke M, Tanaka Y, Telschow A, Trent C, Vattathil S, Verhulst EC, Viljakainen L, Wanner KW, Waterhouse RM, Whitfield JB, Wilkes TE, Williamson M, Willis JH, Wolschin F, Wyder S, Yamada T, Yi SV, Zecher CN, Zhang L, Gibbs RA.

Science. 2010 Jan 15;327(5963):343-8. doi: 10.1126/science.1178028. Erratum in: Science. 2010 Mar 26;327(5973):1577.

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