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Items: 36

1.

AIRR Community Standardized Representations for Annotated Immune Repertoires.

Vander Heiden JA, Marquez S, Marthandan N, Bukhari SAC, Busse CE, Corrie B, Hershberg U, Kleinstein SH, Matsen Iv FA, Ralph DK, Rosenfeld AM, Schramm CA; AIRR Community, Christley S, Laserson U.

Front Immunol. 2018 Sep 28;9:2206. doi: 10.3389/fimmu.2018.02206. eCollection 2018.

2.

ImmuneDB, a Novel Tool for the Analysis, Storage, and Dissemination of Immune Repertoire Sequencing Data.

Rosenfeld AM, Meng W, Luning Prak ET, Hershberg U.

Front Immunol. 2018 Sep 21;9:2107. doi: 10.3389/fimmu.2018.02107. eCollection 2018.

3.

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
4.

Human Lymph Nodes Maintain TCF-1hi Memory T Cells with High Functional Potential and Clonal Diversity throughout Life.

Miron M, Kumar BV, Meng W, Granot T, Carpenter DJ, Senda T, Chen D, Rosenfeld AM, Zhang B, Lerner H, Friedman AL, Hershberg U, Shen Y, Rahman A, Luning Prak ET, Farber DL.

J Immunol. 2018 Oct 1;201(7):2132-2140. doi: 10.4049/jimmunol.1800716. Epub 2018 Aug 15.

PMID:
30111633
5.

Computational Evaluation of B-Cell Clone Sizes in Bulk Populations.

Rosenfeld AM, Meng W, Chen DY, Zhang B, Granot T, Farber DL, Hershberg U, Luning Prak ET.

Front Immunol. 2018 Jun 29;9:1472. doi: 10.3389/fimmu.2018.01472. eCollection 2018.

6.

Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data.

Rubelt F, Busse CE, Bukhari SAC, Bürckert JP, Mariotti-Ferrandiz E, Cowell LG, Watson CT, Marthandan N, Faison WJ, Hershberg U, Laserson U, Corrie BD, Davis MM, Peters B, Lefranc MP, Scott JK, Breden F; AIRR Community, Luning Prak ET, Kleinstein SH.

Nat Immunol. 2017 Nov 16;18(12):1274-1278. doi: 10.1038/ni.3873. No abstract available.

7.

An atlas of B-cell clonal distribution in the human body.

Meng W, Zhang B, Schwartz GW, Rosenfeld AM, Ren D, Thome JJC, Carpenter DJ, Matsuoka N, Lerner H, Friedman AL, Granot T, Farber DL, Shlomchik MJ, Hershberg U, Luning Prak ET.

Nat Biotechnol. 2017 Sep;35(9):879-884. doi: 10.1038/nbt.3942. Epub 2017 Aug 21.

8.

Applying systems-level spectral imaging and analysis to reveal the organelle interactome.

Valm AM, Cohen S, Legant WR, Melunis J, Hershberg U, Wait E, Cohen AR, Davidson MW, Betzig E, Lippincott-Schwartz J.

Nature. 2017 Jun 1;546(7656):162-167. doi: 10.1038/nature22369. Epub 2017 May 24.

9.

VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements.

Toby IT, Levin MK, Salinas EA, Christley S, Bhattacharya S, Breden F, Buntzman A, Corrie B, Fonner J, Gupta NT, Hershberg U, Marthandan N, Rosenfeld A, Rounds W, Rubelt F, Scarborough W, Scott JK, Uduman M, Vander Heiden JA, Scheuermann RH, Monson N, Kleinstein SH, Cowell LG.

BMC Bioinformatics. 2016 Oct 6;17(Suppl 13):333.

10.

ImmuneDB: a system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data.

Rosenfeld AM, Meng W, Luning Prak ET, Hershberg U.

Bioinformatics. 2017 Jan 15;33(2):292-293. doi: 10.1093/bioinformatics/btw593. Epub 2016 Sep 11.

11.

Utilization of HIV-1 envelope V3 to identify X4- and R5-specific Tat and LTR sequence signatures.

Antell GC, Dampier W, Aiamkitsumrit B, Nonnemacher MR, Jacobson JM, Pirrone V, Zhong W, Kercher K, Passic S, Williams JW, Schwartz G, Hershberg U, Krebs FC, Wigdahl B.

Retrovirology. 2016 May 3;13(1):32. doi: 10.1186/s12977-016-0266-9.

12.

T Cell Receptor-induced Nuclear Factor κB (NF-κB) Signaling and Transcriptional Activation Are Regulated by STIM1- and Orai1-mediated Calcium Entry.

Liu X, Berry CT, Ruthel G, Madara JJ, MacGillivray K, Gray CM, Madge LA, McCorkell KA, Beiting DP, Hershberg U, May MJ, Freedman BD.

J Biol Chem. 2016 Apr 15;291(16):8440-52. doi: 10.1074/jbc.M115.713008. Epub 2016 Jan 29.

13.

Discrimination of germline V genes at different sequencing lengths and mutational burdens: A new tool for identifying and evaluating the reliability of V gene assignment.

Zhang B, Meng W, Prak ET, Hershberg U.

J Immunol Methods. 2015 Dec;427:105-16. doi: 10.1016/j.jim.2015.10.009. Epub 2015 Nov 1.

14.

Computational Image Analysis Reveals Intrinsic Multigenerational Differences between Anterior and Posterior Cerebral Cortex Neural Progenitor Cells.

Winter MR, Liu M, Monteleone D, Melunis J, Hershberg U, Goderie SK, Temple S, Cohen AR.

Stem Cell Reports. 2015 Oct 13;5(4):609-20. doi: 10.1016/j.stemcr.2015.08.002. Epub 2015 Sep 3.

15.

The analysis of clonal expansions in normal and autoimmune B cell repertoires.

Hershberg U, Luning Prak ET.

Philos Trans R Soc Lond B Biol Sci. 2015 Sep 5;370(1676). pii: 20140239. doi: 10.1098/rstb.2014.0239. Review.

16.

Prokaryotic nucleotide composition is shaped by both phylogeny and the environment.

Reichenberger ER, Rosen G, Hershberg U, Hershberg R.

Genome Biol Evol. 2015 Apr 9;7(5):1380-9. doi: 10.1093/gbe/evv063.

17.

B cell variable genes have evolved their codon usage to focus the targeted patterns of somatic mutation on the complementarity determining regions.

Saini J, Hershberg U.

Mol Immunol. 2015 May;65(1):157-67. doi: 10.1016/j.molimm.2015.01.001. Epub 2015 Feb 6.

18.

Ig gene analysis reveals altered selective pressures on Ig-producing cells in parotid glands of primary Sjögren's syndrome patients.

Hamza N, Hershberg U, Kallenberg CG, Vissink A, Spijkervet FK, Bootsma H, Kroese FG, Bos NA.

J Immunol. 2015 Jan 15;194(2):514-21. doi: 10.4049/jimmunol.1302644. Epub 2014 Dec 8.

19.

Viral CD8 T cell epitope nucleotide composition shows evidence of short- and long-term evolutionary strategies.

Maman Y, Hershberg U, Louzoun Y.

Immunogenetics. 2015 Jan;67(1):15-24. doi: 10.1007/s00251-014-0811-4. Epub 2014 Nov 8.

PMID:
25376343
20.

Lasting antibody responses are mediated by a combination of newly formed and established bone marrow plasma cells drawn from clonally distinct precursors.

Chernova I, Jones DD, Wilmore JR, Bortnick A, Yucel M, Hershberg U, Allman D.

J Immunol. 2014 Nov 15;193(10):4971-9. doi: 10.4049/jimmunol.1401264. Epub 2014 Oct 17.

21.

Trials and Tribulations with VH Replacement.

Meng W, Jayaraman S, Zhang B, Schwartz GW, Daber RD, Hershberg U, Garfall AL, Carlson CS, Luning Prak ET.

Front Immunol. 2014 Jan 30;5:10. doi: 10.3389/fimmu.2014.00010. eCollection 2014. Review.

22.

Persistence and selection of an expanded B-cell clone in the setting of rituximab therapy for Sjögren's syndrome.

Hershberg U, Meng W, Zhang B, Haff N, St Clair EW, Cohen PL, McNair PD, Li L, Levesque MC, Luning Prak ET.

Arthritis Res Ther. 2014 Feb 11;16(1):R51. doi: 10.1186/ar4481.

23.

Local BLyS production by T follicular cells mediates retention of high affinity B cells during affinity maturation.

Goenka R, Matthews AH, Zhang B, O'Neill PJ, Scholz JL, Migone TS, Leonard WJ, Stohl W, Hershberg U, Cancro MP.

J Exp Med. 2014 Jan 13;211(1):45-56. doi: 10.1084/jem.20130505. Epub 2013 Dec 23.

24.

Germline Amino Acid Diversity in B Cell Receptors is a Good Predictor of Somatic Selection Pressures.

Schwartz GW, Hershberg U.

Front Immunol. 2013 Nov 8;4:357. doi: 10.3389/fimmu.2013.00357. eCollection 2013.

25.

Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection.

Zaslavsky E, Nudelman G, Marquez S, Hershberg U, Hartmann BM, Thakar J, Sealfon SC, Kleinstein SH.

BMC Bioinformatics. 2013;14 Suppl 6:S1. doi: 10.1186/1471-2105-14-S6-S1. Epub 2013 Apr 17.

26.

Conserved variation: identifying patterns of stability and variability in BCR and TCR V genes with different diversity and richness metrics.

Schwartz GW, Hershberg U.

Phys Biol. 2013 Jun;10(3):035005. doi: 10.1088/1478-3975/10/3/035005. Epub 2013 Jun 4.

PMID:
23735612
27.

Establishing a relationship between bacteria in the human gut and complex regional pain syndrome.

Reichenberger ER, Alexander GM, Perreault MJ, Russell JA, Schwartzman RJ, Hershberg U, Rosen G.

Brain Behav Immun. 2013 Mar;29:62-9. doi: 10.1016/j.bbi.2012.12.005. Epub 2012 Dec 20.

PMID:
23261776
28.

Biomedical model fitting and error analysis.

Costa KD, Kleinstein SH, Hershberg U.

Sci Signal. 2011 Sep 20;4(192):tr9. doi: 10.1126/scisignal.2001983.

29.

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.

30.

Antiviral response dictated by choreographed cascade of transcription factors.

Zaslavsky E, Hershberg U, Seto J, Pham AM, Marquez S, Duke JL, Wetmur JG, Tenoever BR, Sealfon SC, Kleinstein SH.

J Immunol. 2010 Mar 15;184(6):2908-17. doi: 10.4049/jimmunol.0903453. Epub 2010 Feb 17.

31.

Taking advantage: high-affinity B cells in the germinal center have lower death rates, but similar rates of division, compared to low-affinity cells.

Anderson SM, Khalil A, Uduman M, Hershberg U, Louzoun Y, Haberman AM, Kleinstein SH, Shlomchik MJ.

J Immunol. 2009 Dec 1;183(11):7314-25. doi: 10.4049/jimmunol.0902452. Epub 2009 Nov 16.

32.

T cell-independent and toll-like receptor-dependent antigen-driven activation of autoreactive B cells.

Herlands RA, Christensen SR, Sweet RA, Hershberg U, Shlomchik MJ.

Immunity. 2008 Aug 15;29(2):249-60. doi: 10.1016/j.immuni.2008.06.009.

33.

Improved methods for detecting selection by mutation analysis of Ig V region sequences.

Hershberg U, Uduman M, Shlomchik MJ, Kleinstein SH.

Int Immunol. 2008 May;20(5):683-94. doi: 10.1093/intimm/dxn026. Epub 2008 Apr 7.

PMID:
18397909
34.
35.

Differences in potential for amino acid change after mutation reveals distinct strategies for kappa and lambda light-chain variation.

Hershberg U, Shlomchik MJ.

Proc Natl Acad Sci U S A. 2006 Oct 24;103(43):15963-8. Epub 2006 Oct 12.

36.

Antigen-receptor degeneracy and immunological paradigms.

Cohen IR, Hershberg U, Solomon S.

Mol Immunol. 2004 Feb;40(14-15):993-6. Review.

PMID:
15036901

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