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Items: 46

1.

Editorial: Methods and Applications of Computational Immunology.

Chain B, Greiff V, Textor J, Yaari G.

Front Immunol. 2019 Nov 29;10:2818. doi: 10.3389/fimmu.2019.02818. eCollection 2019. No abstract available.

2.

VDJbase: an adaptive immune receptor genotype and haplotype database.

Omer A, Shemesh O, Peres A, Polak P, Shepherd AJ, Watson CT, Boyd SD, Collins AM, Lees W, Yaari G.

Nucleic Acids Res. 2020 Jan 8;48(D1):D1051-D1056. doi: 10.1093/nar/gkz872.

3.

OGRDB: a reference database of inferred immune receptor genes.

Lees W, Busse CE, Corcoran M, Ohlin M, Scheepers C, Matsen FA, Yaari G, Watson CT; AIRR Community, Collins A, Shepherd AJ.

Nucleic Acids Res. 2020 Jan 8;48(D1):D964-D970. doi: 10.1093/nar/gkz822.

4.

Hepatitis C virus leaves an epigenetic signature post cure of infection by direct-acting antivirals.

Perez S, Kaspi A, Domovitz T, Davidovich A, Lavi-Itzkovitz A, Meirson T, Alison Holmes J, Dai CY, Huang CF, Chung RT, Nimer A, El-Osta A, Yaari G, Stemmer SM, Yu ML, Haviv I, Gal-Tanamy M.

PLoS Genet. 2019 Jun 19;15(6):e1008181. doi: 10.1371/journal.pgen.1008181. eCollection 2019 Jun.

5.

RAbHIT: R Antibody Haplotype Inference Tool.

Peres A, Gidoni M, Polak P, Yaari G.

Bioinformatics. 2019 Nov 1;35(22):4840-4842. doi: 10.1093/bioinformatics/btz481.

PMID:
31173062
6.

Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE).

Meng H, Yaari G, Bolen CR, Avey S, Kleinstein SH.

PLoS Comput Biol. 2019 Apr 2;15(4):e1006899. doi: 10.1371/journal.pcbi.1006899. eCollection 2019 Apr.

7.

Inferred Allelic Variants of Immunoglobulin Receptor Genes: A System for Their Evaluation, Documentation, and Naming.

Ohlin M, Scheepers C, Corcoran M, Lees WD, Busse CE, Bagnara D, Thörnqvist L, Bürckert JP, Jackson KJL, Ralph D, Schramm CA, Marthandan N, Breden F, Scott J, Matsen Iv FA, Greiff V, Yaari G, Kleinstein SH, Christley S, Sherkow JS, Kossida S, Lefranc MP, van Zelm MC, Watson CT, Collins AM.

Front Immunol. 2019 Mar 18;10:435. doi: 10.3389/fimmu.2019.00435. eCollection 2019. Review.

8.

BCR affinity differentially regulates colonization of the subepithelial dome and infiltration into germinal centers within Peyer's patches.

Biram A, Strömberg A, Winter E, Stoler-Barak L, Salomon R, Addadi Y, Dahan R, Yaari G, Bemark M, Shulman Z.

Nat Immunol. 2019 Apr;20(4):482-492. doi: 10.1038/s41590-019-0325-1. Epub 2019 Mar 4.

PMID:
30833793
9.

Identification of Subject-Specific Immunoglobulin Alleles From Expressed Repertoire Sequencing Data.

Gadala-Maria D, Gidoni M, Marquez S, Vander Heiden JA, Kos JT, Watson CT, O'Connor KC, Yaari G, Kleinstein SH.

Front Immunol. 2019 Feb 13;10:129. doi: 10.3389/fimmu.2019.00129. eCollection 2019.

10.

Mosaic deletion patterns of the human antibody heavy chain gene locus shown by Bayesian haplotyping.

Gidoni M, Snir O, Peres A, Polak P, Lindeman I, Mikocziova I, Sarna VK, Lundin KEA, Clouser C, Vigneault F, Collins AM, Sollid LM, Yaari G.

Nat Commun. 2019 Feb 7;10(1):628. doi: 10.1038/s41467-019-08489-3.

11.

Antibody Repertoire Analysis of Hepatitis C Virus Infections Identifies Immune Signatures Associated With Spontaneous Clearance.

Eliyahu S, Sharabi O, Elmedvi S, Timor R, Davidovich A, Vigneault F, Clouser C, Hope R, Nimer A, Braun M, Weiss YY, Polak P, Yaari G, Gal-Tanamy M.

Front Immunol. 2018 Dec 21;9:3004. doi: 10.3389/fimmu.2018.03004. eCollection 2018.

12.

A primer set for comprehensive amplification of V-genes from rhesus macaque origin based on repertoire sequencing.

Rosenfeld R, Zvi A, Winter E, Hope R, Israeli O, Mazor O, Yaari G.

J Immunol Methods. 2019 Feb;465:67-71. doi: 10.1016/j.jim.2018.11.011. Epub 2018 Nov 22.

PMID:
30471299
13.

Questions of Stochasticity and Control in Immune Repertoires.

Yaari G, Flajnik M, Hershberg U.

Trends Immunol. 2018 Nov;39(11):859-861. doi: 10.1016/j.it.2018.09.001. Epub 2018 Sep 19. No abstract available.

PMID:
30243818
14.

Evidence for Sequential Performance Effects in Professional Darts.

Stins JF, Yaari G, Wijmer K, Burger JF, Beek PJ.

Front Psychol. 2018 Apr 26;9:591. doi: 10.3389/fpsyg.2018.00591. eCollection 2018.

15.

Fast Image-Guided Stratification Using Anti-Programmed Death Ligand 1 Gold Nanoparticles for Cancer Immunotherapy.

Meir R, Shamalov K, Sadan T, Motiei M, Yaari G, Cohen CJ, Popovtzer R.

ACS Nano. 2017 Nov 28;11(11):11127-11134. doi: 10.1021/acsnano.7b05299. Epub 2017 Oct 20.

PMID:
29028305
16.

Effects of correlations and fees in random multiplicative environments: Implications for portfolio management.

Alper O, Somekh-Baruch A, Pirvandy O, Schaps M, Yaari G.

Phys Rev E. 2017 Aug;96(2-1):022305. doi: 10.1103/PhysRevE.96.022305. Epub 2017 Aug 7.

PMID:
28950518
17.

Stereotyped antibody responses target posttranslationally modified gluten in celiac disease.

Snir O, Chen X, Gidoni M, du Pré MF, Zhao Y, Steinsbø Ø, Lundin KE, Yaari G, Sollid LM.

JCI Insight. 2017 Sep 7;2(17). pii: 93961. doi: 10.1172/jci.insight.93961. eCollection 2017 Sep 7.

18.

Branching morphology determines signal propagation dynamics in neurons.

Ofer N, Shefi O, Yaari G.

Sci Rep. 2017 Aug 21;7(1):8877. doi: 10.1038/s41598-017-09184-3.

19.

System-wide Analysis of the T Cell Response.

Covacu R, Philip H, Jaronen M, Almeida J, Kenison JE, Darko S, Chao CC, Yaari G, Louzoun Y, Carmel L, Douek DC, Efroni S, Quintana FJ.

Cell Rep. 2016 Mar 22;14(11):2733-44. doi: 10.1016/j.celrep.2016.02.056. Epub 2016 Mar 10.

20.

Quantification of read species behavior within whole genome sequencing of cancer genomes for the stratification and visualization of genomic variation.

Hibsh D, Buetow KH, Yaari G, Efroni S.

Nucleic Acids Res. 2016 May 19;44(9):e81. doi: 10.1093/nar/gkw031. Epub 2016 Jan 24.

21.

Practical guidelines for B-cell receptor repertoire sequencing analysis.

Yaari G, Kleinstein SH.

Genome Med. 2015 Nov 20;7:121. doi: 10.1186/s13073-015-0243-2. Review.

22.

The mutation patterns in B-cell immunoglobulin receptors reflect the influence of selection acting at multiple time-scales.

Yaari G, Benichou JI, Vander Heiden JA, Kleinstein SH, Louzoun Y.

Philos Trans R Soc Lond B Biol Sci. 2015 Sep 5;370(1676). pii: 20140242. doi: 10.1098/rstb.2014.0242.

23.

Responsive population dynamics and wide seeding into the duodenal lamina propria of transglutaminase-2-specific plasma cells in celiac disease.

Di Niro R, Snir O, Kaukinen K, Yaari G, Lundin KE, Gupta NT, Kleinstein SH, Cols M, Cerutti A, Mäki M, Shlomchik MJ, Sollid LM.

Mucosal Immunol. 2016 Jan;9(1):254-64. doi: 10.1038/mi.2015.57. Epub 2015 Jul 8.

24.

Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data.

Gupta NT, Vander Heiden JA, Uduman M, Gadala-Maria D, Yaari G, Kleinstein SH.

Bioinformatics. 2015 Oct 15;31(20):3356-8. doi: 10.1093/bioinformatics/btv359. Epub 2015 Jun 10.

25.

Analysis of celiac disease autoreactive gut plasma cells and their corresponding memory compartment in peripheral blood using high-throughput sequencing.

Snir O, Mesin L, Gidoni M, Lundin KE, Yaari G, Sollid LM.

J Immunol. 2015 Jun 15;194(12):5703-12. doi: 10.4049/jimmunol.1402611. Epub 2015 May 13.

26.

Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles.

Gadala-Maria D, Yaari G, Uduman M, Kleinstein SH.

Proc Natl Acad Sci U S A. 2015 Feb 24;112(8):E862-70. doi: 10.1073/pnas.1417683112. Epub 2015 Feb 9.

27.

Species survival emerge from rare events of individual migration.

Zelnik YR, Solomon S, Yaari G.

Sci Rep. 2015 Jan 19;5:7877. doi: 10.1038/srep07877.

28.

B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes.

Stern JN, Yaari G, Vander Heiden JA, Church G, Donahue WF, Hintzen RQ, Huttner AJ, Laman JD, Nagra RM, Nylander A, Pitt D, Ramanan S, Siddiqui BA, Vigneault F, Kleinstein SH, Hafler DA, O'Connor KC.

Sci Transl Med. 2014 Aug 6;6(248):248ra107. doi: 10.1126/scitranslmed.3008879.

29.

Lessons from Google and Apple: creating an open workplace in an academic medical department to foster innovation and collaboration.

Ricciotti HA, Armstrong W, Yaari G, Campion S, Pollard M, Golen TH.

Acad Med. 2014 Sep;89(9):1235-8. doi: 10.1097/ACM.0000000000000364.

30.

High-resolution antibody dynamics of vaccine-induced immune responses.

Laserson U, Vigneault F, Gadala-Maria D, Yaari G, Uduman M, Vander Heiden JA, Kelton W, Taek Jung S, Liu Y, Laserson J, Chari R, Lee JH, Bachelet I, Hickey B, Lieberman-Aiden E, Hanczaruk B, Simen BB, Egholm M, Koller D, Georgiou G, Kleinstein SH, Church GM.

Proc Natl Acad Sci U S A. 2014 Apr 1;111(13):4928-33. doi: 10.1073/pnas.1323862111. Epub 2014 Mar 17.

31.

pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires.

Vander Heiden JA, Yaari G, Uduman M, Stern JN, O'Connor KC, Hafler DA, Vigneault F, Kleinstein SH.

Bioinformatics. 2014 Jul 1;30(13):1930-2. doi: 10.1093/bioinformatics/btu138. Epub 2014 Mar 10.

32.

Models of somatic hypermutation targeting and substitution based on synonymous mutations from high-throughput immunoglobulin sequencing data.

Yaari G, Vander Heiden JA, Uduman M, Gadala-Maria D, Gupta N, Stern JN, O'Connor KC, Hafler DA, Laserson U, Vigneault F, Kleinstein SH.

Front Immunol. 2013 Nov 15;4:358. doi: 10.3389/fimmu.2013.00358. eCollection 2013.

33.

The effects of somatic hypermutation on neutralization and binding in the PGT121 family of broadly neutralizing HIV antibodies.

Sok D, Laserson U, Laserson J, Liu Y, Vigneault F, Julien JP, Briney B, Ramos A, Saye KF, Le K, Mahan A, Wang S, Kardar M, Yaari G, Walker LM, Simen BB, St John EP, Chan-Hui PY, Swiderek K, Kleinstein SH, Alter G, Seaman MS, Chakraborty AK, Koller D, Wilson IA, Church GM, Burton DR, Poignard P.

PLoS Pathog. 2013;9(11):e1003754. doi: 10.1371/journal.ppat.1003754. Epub 2013 Nov 21. Erratum in: PLoS Pathog. 2013 Dec;9(12). doi:10.1371/annotation/f1f8c791-61e9-45c6-a455-92c6dadf9f06. Kleinstein, Stephen H [corrected to Kleinstein, Steven H].

34.

The immune cell infiltrate populating meningiomas is composed of mature, antigen-experienced T and B cells.

Fang L, Lowther DE, Meizlish ML, Anderson RC, Bruce JN, Devine L, Huttner AJ, Kleinstein SH, Lee JY, Stern JN, Yaari G, Lovato L, Cronk KM, O'Connor KC.

Neuro Oncol. 2013 Nov;15(11):1479-90. doi: 10.1093/neuonc/not110. Epub 2013 Aug 26.

35.

Protein array-based profiling of CSF identifies RBPJ as an autoantigen in multiple sclerosis.

Querol L, Clark PL, Bailey MA, Cotsapas C, Cross AH, Hafler DA, Kleinstein SH, Lee JY, Yaari G, Willis SN, O'Connor KC.

Neurology. 2013 Sep 10;81(11):956-63. doi: 10.1212/WNL.0b013e3182a43b48. Epub 2013 Aug 6.

36.

Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations.

Yaari G, Bolen CR, Thakar J, Kleinstein SH.

Nucleic Acids Res. 2013 Oct;41(18):e170. doi: 10.1093/nar/gkt660. Epub 2013 Aug 5.

37.

Multiple transcription factor binding sites predict AID targeting in non-Ig genes.

Duke JL, Liu M, Yaari G, Khalil AM, Tomayko MM, Shlomchik MJ, Schatz DG, Kleinstein SH.

J Immunol. 2013 Apr 15;190(8):3878-88. doi: 10.4049/jimmunol.1202547. Epub 2013 Mar 20.

38.

Consistent scaling of persistence time in metapopulations.

Yaari G, Ben-Zion Y, Shnerb NM, Vasseur DA.

Ecology. 2012 May;93(5):1214-27.

PMID:
22764507
39.

Quantifying selection in high-throughput Immunoglobulin sequencing data sets.

Yaari G, Uduman M, Kleinstein SH.

Nucleic Acids Res. 2012 Sep 1;40(17):e134. Epub 2012 May 27.

40.

"Hot hand" on strike: bowling data indicates correlation to recent past results, not causality.

Yaari G, David G.

PLoS One. 2012;7(1):e30112. doi: 10.1371/journal.pone.0030112. Epub 2012 Jan 12.

41.

The hot (invisible?) hand: can time sequence patterns of success/failure in sports be modeled as repeated random independent trials?

Yaari G, Eisenmann S.

PLoS One. 2011;6(10):e24532. doi: 10.1371/journal.pone.0024532. Epub 2011 Oct 5.

42.

Detecting selection in immunoglobulin sequences.

Uduman M, Yaari G, Hershberg U, Stern JA, Shlomchik MJ, Kleinstein SH.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W499-504. doi: 10.1093/nar/gkr413. Epub 2011 Jun 10.

43.

Germinal center B cell and T follicular helper cell development initiates in the interfollicular zone.

Kerfoot SM, Yaari G, Patel JR, Johnson KL, Gonzalez DG, Kleinstein SH, Haberman AM.

Immunity. 2011 Jun 24;34(6):947-60. doi: 10.1016/j.immuni.2011.03.024.

44.

Optimizing metapopulation sustainability through a checkerboard strategy.

Zion YB, Yaari G, Shnerb NM.

PLoS Comput Biol. 2010 Jan 22;6(1):e1000643. doi: 10.1371/journal.pcbi.1000643.

45.

In-medium isovector piN amplitude from low-energy pion scattering.

Friedman E, Bauer M, Breitschopf J, Clement H, Denz H, Doroshkevich E, Erhardt A, Hofman GJ, Meier R, Wagner GJ, Yaari G.

Phys Rev Lett. 2004 Sep 17;93(12):122302. Epub 2004 Sep 16.

PMID:
15447255
46.

Mother and caregiver representations of toddlers in a kibbutz setting.

Ben-Aaron M, Eshel Y, Yaari G.

Br J Med Psychol. 1999 Jun;72 ( Pt 2):189-201.

PMID:
10397424

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