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Items: 26

1.

HLA-B57 micropolymorphism defines the sequence and conformational breadth of the immunopeptidome.

Illing PT, Pymm P, Croft NP, Hilton HG, Jojic V, Han AS, Mendoza JL, Mifsud NA, Dudek NL, McCluskey J, Parham P, Rossjohn J, Vivian JP, Purcell AW.

Nat Commun. 2018 Nov 8;9(1):4693. doi: 10.1038/s41467-018-07109-w.

2.

Design of synthetic bacterial communities for predictable plant phenotypes.

Herrera Paredes S, Gao T, Law TF, Finkel OM, Mucyn T, Teixeira PJPL, Salas González I, Feltcher ME, Powers MJ, Shank EA, Jones CD, Jojic V, Dangl JL, Castrillo G.

PLoS Biol. 2018 Feb 20;16(2):e2003962. doi: 10.1371/journal.pbio.2003962. eCollection 2018 Feb.

3.

Tradict enables accurate prediction of eukaryotic transcriptional states from 100 marker genes.

Biswas S, Kerner K, Teixeira PJPL, Dangl JL, Jojic V, Wigge PA.

Nat Commun. 2017 May 5;8:15309. doi: 10.1038/ncomms15309.

4.

Phenetic and phylogenetic relationships among Aceria spp. (Acari: Eriophyoidea) inhabiting species within the family Brassicaceae in Serbia.

Živković Z, Vidović B, Jojić V, Cvrković T, Petanović R.

Exp Appl Acarol. 2017 Apr;71(4):329-343. doi: 10.1007/s10493-017-0128-8. Epub 2017 Apr 20.

PMID:
28429108
5.

Expression of specific inflammasome gene modules stratifies older individuals into two extreme clinical and immunological states.

Furman D, Chang J, Lartigue L, Bolen CR, Haddad F, Gaudilliere B, Ganio EA, Fragiadakis GK, Spitzer MH, Douchet I, Daburon S, Moreau JF, Nolan GP, Blanco P, Déchanet-Merville J, Dekker CL, Jojic V, Kuo CJ, Davis MM, Faustin B.

Nat Med. 2017 Feb;23(2):174-184. doi: 10.1038/nm.4267. Epub 2017 Jan 16.

6.

Learning Microbial Interaction Networks from Metagenomic Count Data.

Biswas S, Mcdonald M, Lundberg DS, Dangl JL, Jojic V.

J Comput Biol. 2016 Jun;23(6):526-35. doi: 10.1089/cmb.2016.0061.

PMID:
27267776
7.

Deconvolving molecular signatures of interactions between microbial colonies.

Harn YC, Powers MJ, Shank EA, Jojic V.

Bioinformatics. 2015 Jun 15;31(12):i142-50. doi: 10.1093/bioinformatics/btv251.

8.

Cytomegalovirus infection enhances the immune response to influenza.

Furman D, Jojic V, Sharma S, Shen-Orr SS, Angel CJ, Onengut-Gumuscu S, Kidd BA, Maecker HT, Concannon P, Dekker CL, Thomas PG, Davis MM.

Sci Transl Med. 2015 Apr 1;7(281):281ra43. doi: 10.1126/scitranslmed.aaa2293.

9.

Genetic and morphological variability of the European mudminnow Umbra krameri (Teleostei, Umbridae) in Serbia and in Bosnia and Herzegovina, a basis for future conservation activities.

Marić S, Snoj A, Sekulić N, Krpo-Ćetković J, Šanda R, Jojić V.

J Fish Biol. 2015 May;86(5):1534-48. doi: 10.1111/jfb.12657. Epub 2015 Mar 20.

PMID:
25801689
10.

Variation in the human immune system is largely driven by non-heritable influences.

Brodin P, Jojic V, Gao T, Bhattacharya S, Angel CJ, Furman D, Shen-Orr S, Dekker CL, Swan GE, Butte AJ, Maecker HT, Davis MM.

Cell. 2015 Jan 15;160(1-2):37-47. doi: 10.1016/j.cell.2014.12.020.

11.

Drug-induced mRNA signatures are enriched for the minority of genes that are highly heritable.

Gao T, Brodin P, Davis MM, Jojic V.

Pac Symp Biocomput. 2015:395-406.

12.

Geometric morphometric study of geographic and host-related variability in Aceria spp. (Acari: Eriophyoidea) inhabiting Cirsium spp. (Asteraceae).

Vidović B, Jojić V, Marić I, Marinković S, Hansen R, Petanović R.

Exp Appl Acarol. 2014 Nov;64(3):321-35. doi: 10.1007/s10493-014-9829-4. Epub 2014 Jun 19.

PMID:
24943490
13.

Robust multimodal dictionary learning.

Cao T, Jojic V, Modla S, Powell D, Czymmek K, Niethammer M.

Med Image Comput Comput Assist Interv. 2013;16(Pt 1):259-66.

14.

Systems analysis of sex differences reveals an immunosuppressive role for testosterone in the response to influenza vaccination.

Furman D, Hejblum BP, Simon N, Jojic V, Dekker CL, Thiébaut R, Tibshirani RJ, Davis MM.

Proc Natl Acad Sci U S A. 2014 Jan 14;111(2):869-74. doi: 10.1073/pnas.1321060111. Epub 2013 Dec 23.

15.

Identification of transcriptional regulators in the mouse immune system.

Jojic V, Shay T, Sylvia K, Zuk O, Sun X, Kang J, Regev A, Koller D; Immunological Genome Project Consortium, Best AJ, Knell J, Goldrath A, Joic V, Koller D, Shay T, Regev A, Cohen N, Brennan P, Brenner M, Kim F, Rao TN, Wagers A, Heng T, Ericson J, Rothamel K, Ortiz-Lopez A, Mathis D, Benoist C, Bezman NA, Sun JC, Min-Oo G, Kim CC, Lanier LL, Miller J, Brown B, Merad M, Gautier EL, Jakubzick C, Randolph GJ, Monach P, Blair DA, Dustin ML, Shinton SA, Hardy RR, Laidlaw D, Collins J, Gazit R, Rossi DJ, Malhotra N, Sylvia K, Kang J, Kreslavsky T, Fletcher A, Elpek K, Bellemarte-Pelletier A, Malhotra D, Turley S.

Nat Immunol. 2013 Jun;14(6):633-43. doi: 10.1038/ni.2587. Epub 2013 Apr 28.

16.

Apoptosis and other immune biomarkers predict influenza vaccine responsiveness.

Furman D, Jojic V, Kidd B, Shen-Orr S, Price J, Jarrell J, Tse T, Huang H, Lund P, Maecker HT, Utz PJ, Dekker CL, Koller D, Davis MM.

Mol Syst Biol. 2013 Apr 16;9:659. doi: 10.1038/msb.2013.15. Erratum in: Mol Syst Biol. 2013;9:680. Mol Syst Biol. 2014;10:750.

17.

AMP: Assembly Matching Pursuit.

Biswas S, Jojic V.

Pac Symp Biocomput. 2013:175-87.

18.

Conservation and divergence in the transcriptional programs of the human and mouse immune systems.

Shay T, Jojic V, Zuk O, Rothamel K, Puyraimond-Zemmour D, Feng T, Wakamatsu E, Benoist C, Koller D, Regev A; ImmGen Consortium.

Proc Natl Acad Sci U S A. 2013 Feb 19;110(8):2946-51. doi: 10.1073/pnas.1222738110. Epub 2013 Feb 4.

19.

Two-module organization of the mandible in the yellow-necked mouse: a comparison between two different morphometric approaches.

Jojić V, Blagojević J, Vujošević M.

J Evol Biol. 2012 Dec;25(12):2489-500. doi: 10.1111/j.1420-9101.2012.02612.x. Epub 2012 Sep 19.

20.

Deciphering the transcriptional network of the dendritic cell lineage.

Miller JC, Brown BD, Shay T, Gautier EL, Jojic V, Cohain A, Pandey G, Leboeuf M, Elpek KG, Helft J, Hashimoto D, Chow A, Price J, Greter M, Bogunovic M, Bellemare-Pelletier A, Frenette PS, Randolph GJ, Turley SJ, Merad M; Immunological Genome Consortium.

Nat Immunol. 2012 Sep;13(9):888-99. doi: 10.1038/ni.2370. Epub 2012 Jul 15.

21.

Genovo: de novo assembly for metagenomes.

Laserson J, Jojic V, Koller D.

J Comput Biol. 2011 Mar;18(3):429-43. doi: 10.1089/cmb.2010.0244.

PMID:
21385045
22.

Comparison of immunogen designs that optimize peptide coverage: reply to Fischer et al.

Nickle DC, Jojic N, Heckerman D, Jojic V, Kirovski D, Rolland M, Kosakovsky Pond S, Mullins JI.

PLoS Comput Biol. 2008 Jan;4(1):e25. doi: 10.1371/journal.pcbi.0040025. No abstract available. Erratum in: PLoS Comput Biol. 2008 Mar;4(3). doi: 10.1371/annotation/da2fae86-8f92-4d32-aefe-a30a1de7a8f8.

23.

Population sequencing using short reads: HIV as a case study.

Jojic V, Hertz T, Jojic N.

Pac Symp Biocomput. 2008:114-25.

24.

Recognition of HIV-1 peptides by host CTL is related to HIV-1 similarity to human proteins.

Rolland M, Nickle DC, Deng W, Frahm N, Brander C, Learn GH, Heckerman D, Jojic N, Jojic V, Walker BD, Mullins JI.

PLoS One. 2007 Sep 5;2(9):e823.

25.

Efficient approximations for learning phylogenetic HMM models from data.

Jojic V, Jojic N, Meek C, Geiger D, Siepel A, Haussler D, Heckerman D.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i161-8.

PMID:
15262795
26.

A panoramic view of yeast noncoding RNA processing.

Peng WT, Robinson MD, Mnaimneh S, Krogan NJ, Cagney G, Morris Q, Davierwala AP, Grigull J, Yang X, Zhang W, Mitsakakis N, Ryan OW, Datta N, Jojic V, Pal C, Canadien V, Richards D, Beattie B, Wu LF, Altschuler SJ, Roweis S, Frey BJ, Emili A, Greenblatt JF, Hughes TR.

Cell. 2003 Jun 27;113(7):919-33.

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