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Items: 39

1.

Germinal center B cells selectively oxidize fatty acids for energy while conducting minimal glycolysis.

Weisel FJ, Mullett SJ, Elsner RA, Menk AV, Trivedi N, Luo W, Wikenheiser D, Hawse WF, Chikina M, Smita S, Conter LJ, Joachim SM, Wendell SG, Jurczak MJ, Winkler TH, Delgoffe GM, Shlomchik MJ.

Nat Immunol. 2020 Mar;21(3):331-342. doi: 10.1038/s41590-020-0598-4. Epub 2020 Feb 17.

PMID:
32066950
2.

Pan-mammalian analysis of molecular constraints underlying extended lifespan.

Kowalczyk A, Partha R, Clark NL, Chikina M.

Elife. 2020 Feb 11;9. pii: e51089. doi: 10.7554/eLife.51089.

3.

Causal network perturbations for instance-specific analysis of single cell and disease samples.

Buschur KL, Chikina M, Benos PV.

Bioinformatics. 2019 Dec 24. pii: btz949. doi: 10.1093/bioinformatics/btz949. [Epub ahead of print]

PMID:
31873725
4.

Liver Is a Generative Site for the B Cell Response to Ehrlichia muris.

Trivedi N, Weisel F, Smita S, Joachim S, Kader M, Radhakrishnan A, Clouser C, Rosenfeld AM, Chikina M, Vigneault F, Hershberg U, Ismail N, Shlomchik MJ.

Immunity. 2019 Dec 17;51(6):1088-1101.e5. doi: 10.1016/j.immuni.2019.10.004. Epub 2019 Nov 12.

PMID:
31732168
5.

Treg Cells Promote the SREBP1-Dependent Metabolic Fitness of Tumor-Promoting Macrophages via Repression of CD8+ T Cell-Derived Interferon-γ.

Liu C, Chikina M, Deshpande R, Menk AV, Wang T, Tabib T, Brunazzi EA, Vignali KM, Sun M, Stolz DB, Lafyatis RA, Chen W, Delgoffe GM, Workman CJ, Wendell SG, Vignali DAA.

Immunity. 2019 Aug 20;51(2):381-397.e6. doi: 10.1016/j.immuni.2019.06.017. Epub 2019 Jul 23.

PMID:
31350177
6.

Pathway-level information extractor (PLIER) for gene expression data.

Mao W, Zaslavsky E, Hartmann BM, Sealfon SC, Chikina M.

Nat Methods. 2019 Jul;16(7):607-610. doi: 10.1038/s41592-019-0456-1. Epub 2019 Jun 27.

PMID:
31249421
7.

RERconverge: an R package for associating evolutionary rates with convergent traits.

Kowalczyk A, Meyer WK, Partha R, Mao W, Clark NL, Chikina M.

Bioinformatics. 2019 Nov 1;35(22):4815-4817. doi: 10.1093/bioinformatics/btz468.

PMID:
31192356
8.

Robust Method for Detecting Convergent Shifts in Evolutionary Rates.

Partha R, Kowalczyk A, Clark NL, Chikina M.

Mol Biol Evol. 2019 Aug 1;36(8):1817-1830. doi: 10.1093/molbev/msz107.

PMID:
31077321
9.

Adaptive plasticity of IL-10+ and IL-35+ Treg cells cooperatively promotes tumor T cell exhaustion.

Sawant DV, Yano H, Chikina M, Zhang Q, Liao M, Liu C, Callahan DJ, Sun Z, Sun T, Tabib T, Pennathur A, Corry DB, Luketich JD, Lafyatis R, Chen W, Poholek AC, Bruno TC, Workman CJ, Vignali DAA.

Nat Immunol. 2019 Jun;20(6):724-735. doi: 10.1038/s41590-019-0346-9. Epub 2019 Apr 1.

10.

Evolutionary rate covariation analysis of E-cadherin identifies Raskol as a regulator of cell adhesion and actin dynamics in Drosophila.

Raza Q, Choi JY, Li Y, O'Dowd RM, Watkins SC, Chikina M, Hong Y, Clark NL, Kwiatkowski AV.

PLoS Genet. 2019 Feb 14;15(2):e1007720. doi: 10.1371/journal.pgen.1007720. eCollection 2019 Feb.

11.

Kidney-infiltrating T cells in murine lupus nephritis are metabolically and functionally exhausted.

Tilstra JS, Avery L, Menk AV, Gordon RA, Smita S, Kane LP, Chikina M, Delgoffe GM, Shlomchik MJ.

J Clin Invest. 2018 Nov 1;128(11):4884-4897. doi: 10.1172/JCI120859. Epub 2018 Sep 24.

12.

Ancient convergent losses of Paraoxonase 1 yield potential risks for modern marine mammals.

Meyer WK, Jamison J, Richter R, Woods SE, Partha R, Kowalczyk A, Kronk C, Chikina M, Bonde RK, Crocker DE, Gaspard J, Lanyon JM, Marsillach J, Furlong CE, Clark NL.

Science. 2018 Aug 10;361(6402):591-594. doi: 10.1126/science.aap7714.

13.

Hepatocyte-Derived Lipocalin 2 Is a Potential Serum Biomarker Reflecting Tumor Burden in Hepatoblastoma.

Molina L, Bell D, Tao J, Preziosi M, Pradhan-Sundd T, Singh S, Poddar M, Luo J, Ranganathan S, Chikina M, Monga SP.

Am J Pathol. 2018 Aug;188(8):1895-1909. doi: 10.1016/j.ajpath.2018.05.006. Epub 2018 Jun 18.

14.

Coloc-stats: a unified web interface to perform colocalization analysis of genomic features.

Simovski B, Kanduri C, Gundersen S, Titov D, Domanska D, Bock C, Bossini-Castillo L, Chikina M, Favorov A, Layer RM, Mironov AA, Quinlan AR, Sheffield NC, Trynka G, Sandve GK.

Nucleic Acids Res. 2018 Jul 2;46(W1):W186-W193. doi: 10.1093/nar/gky474.

15.

Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling.

Partha R, Chauhan BK, Ferreira Z, Robinson JD, Lathrop K, Nischal KK, Chikina M, Clark NL.

Elife. 2017 Oct 16;6. pii: e25884. doi: 10.7554/eLife.25884.

16.

LAG3 limits regulatory T cell proliferation and function in autoimmune diabetes.

Zhang Q, Chikina M, Szymczak-Workman AL, Horne W, Kolls JK, Vignali KM, Normolle D, Bettini M, Workman CJ, Vignali DAA.

Sci Immunol. 2017 Mar 31;2(9). pii: eaah4569. doi: 10.1126/sciimmunol.aah4569.

17.

Differential requirements for myeloid leukemia IFN-γ conditioning determine graft-versus-leukemia resistance and sensitivity.

Matte-Martone C, Liu J, Zhou M, Chikina M, Green DR, Harty JT, Shlomchik WD.

J Clin Invest. 2017 Jun 30;127(7):2765-2776. doi: 10.1172/JCI85736. Epub 2017 Jun 12.

18.

Interferon-γ Drives Treg Fragility to Promote Anti-tumor Immunity.

Overacre-Delgoffe AE, Chikina M, Dadey RE, Yano H, Brunazzi EA, Shayan G, Horne W, Moskovitz JM, Kolls JK, Sander C, Shuai Y, Normolle DP, Kirkwood JM, Ferris RL, Delgoffe GM, Bruno TC, Workman CJ, Vignali DAA.

Cell. 2017 Jun 1;169(6):1130-1141.e11. doi: 10.1016/j.cell.2017.05.005. Epub 2017 May 25.

19.

Assessing significance in a Markov chain without mixing.

Chikina M, Frieze A, Pegden W.

Proc Natl Acad Sci U S A. 2017 Mar 14;114(11):2860-2864. doi: 10.1073/pnas.1617540114. Epub 2017 Feb 28.

20.

Wnt signaling regulates hepatobiliary repair following cholestatic liver injury in mice.

Okabe H, Yang J, Sylakowski K, Yovchev M, Miyagawa Y, Nagarajan S, Chikina M, Thompson M, Oertel M, Baba H, Monga SP, Nejak-Bowen KN.

Hepatology. 2016 Nov;64(5):1652-1666. doi: 10.1002/hep.28774. Epub 2016 Sep 26.

21.

Modeling a human hepatocellular carcinoma subset in mice through coexpression of met and point-mutant β-catenin.

Tao J, Xu E, Zhao Y, Singh S, Li X, Couchy G, Chen X, Zucman-Rossi J, Chikina M, Monga SP.

Hepatology. 2016 Nov;64(5):1587-1605. doi: 10.1002/hep.28601. Epub 2016 May 28.

22.

Characterization of Gonadotrope Secretoproteome Identifies Neurosecretory Protein VGF-derived Peptide Suppression of Follicle-stimulating Hormone Gene Expression.

Choi SG, Wang Q, Jia J, Chikina M, Pincas H, Dolios G, Sasaki K, Wang R, Minamino N, Salton SR, Sealfon SC.

J Biol Chem. 2016 Sep 30;291(40):21322-21334. Epub 2016 Jul 27.

23.

Hundreds of Genes Experienced Convergent Shifts in Selective Pressure in Marine Mammals.

Chikina M, Robinson JD, Clark NL.

Mol Biol Evol. 2016 Sep;33(9):2182-92. doi: 10.1093/molbev/msw112. Epub 2016 Jun 21.

24.

A Temporal Switch in the Germinal Center Determines Differential Output of Memory B and Plasma Cells.

Weisel FJ, Zuccarino-Catania GV, Chikina M, Shlomchik MJ.

Immunity. 2016 Jan 19;44(1):116-130. doi: 10.1016/j.immuni.2015.12.004. Epub 2016 Jan 12.

25.

A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes.

Aghaeepour N, Chattopadhyay P, Chikina M, Dhaene T, Van Gassen S, Kursa M, Lambrecht BN, Malek M, McLachlan GJ, Qian Y, Qiu P, Saeys Y, Stanton R, Tong D, Vens C, Walkowiak S, Wang K, Finak G, Gottardo R, Mosmann T, Nolan GP, Scheuermann RH, Brinkman RR.

Cytometry A. 2016 Jan;89(1):16-21. doi: 10.1002/cyto.a.22732. Epub 2015 Oct 8.

26.

Human Dendritic Cell Response Signatures Distinguish 1918, Pandemic, and Seasonal H1N1 Influenza Viruses.

Hartmann BM, Thakar J, Albrecht RA, Avey S, Zaslavsky E, Marjanovic N, Chikina M, Fribourg M, Hayot F, Schmolke M, Meng H, Wetmur J, García-Sastre A, Kleinstein SH, Sealfon SC.

J Virol. 2015 Oct;89(20):10190-205. doi: 10.1128/JVI.01523-15. Epub 2015 Jul 29.

27.

Low-variance RNAs identify Parkinson's disease molecular signature in blood.

Chikina MD, Gerald CP, Li X, Ge Y, Pincas H, Nair VD, Wong AK, Krishnan A, Troyanskaya OG, Raymond D, Saunders-Pullman R, Bressman SB, Yue Z, Sealfon SC.

Mov Disord. 2015 May;30(6):813-21. doi: 10.1002/mds.26205. Epub 2015 Mar 18.

28.

CellCODE: a robust latent variable approach to differential expression analysis for heterogeneous cell populations.

Chikina M, Zaslavsky E, Sealfon SC.

Bioinformatics. 2015 May 15;31(10):1584-91. doi: 10.1093/bioinformatics/btv015. Epub 2015 Jan 11.

29.

Hybrid Bayesian-rank integration approach improves the predictive power of genomic dataset aggregation.

Badgeley MA, Sealfon SC, Chikina MD.

Bioinformatics. 2015 Jan 15;31(2):209-15. doi: 10.1093/bioinformatics/btu518. Epub 2014 Sep 29.

30.

Increasing consistency of disease biomarker prediction across datasets.

Chikina MD, Sealfon SC.

PLoS One. 2014 Apr 16;9(4):e91272. doi: 10.1371/journal.pone.0091272. eCollection 2014.

31.

Homer1 alternative splicing is regulated by gonadotropin-releasing hormone and modulates gonadotropin gene expression.

Wang Q, Chikina MD, Pincas H, Sealfon SC.

Mol Cell Biol. 2014 May;34(10):1747-56. doi: 10.1128/MCB.01401-13. Epub 2014 Mar 3.

32.

β-catenin regulates GnRH-induced FSHβ gene expression.

Wang Q, Chikina M, Zaslavsky E, Pincas H, Sealfon SC.

Mol Endocrinol. 2013 Feb;27(2):224-37. doi: 10.1210/me.2012-1310. Epub 2012 Dec 4.

33.

Involvement of histone demethylase LSD1 in short-time-scale gene expression changes during cell cycle progression in embryonic stem cells.

Nair VD, Ge Y, Balasubramaniyan N, Kim J, Okawa Y, Chikina M, Troyanskaya O, Sealfon SC.

Mol Cell Biol. 2012 Dec;32(23):4861-76. doi: 10.1128/MCB.00816-12. Epub 2012 Oct 1.

34.

An effective statistical evaluation of ChIPseq dataset similarity.

Chikina MD, Troyanskaya OG.

Bioinformatics. 2012 Mar 1;28(5):607-13. doi: 10.1093/bioinformatics/bts009. Epub 2012 Jan 19.

35.

Misfolded proteins inhibit proliferation and promote stress-induced death in SV40-transformed mammalian cells.

Arslan MA, Chikina M, Csermely P, Soti C.

FASEB J. 2012 Feb;26(2):766-77. doi: 10.1096/fj.11-186197. Epub 2011 Nov 2.

PMID:
22049061
36.

Accurate quantification of functional analogy among close homologs.

Chikina MD, Troyanskaya OG.

PLoS Comput Biol. 2011 Feb 3;7(2):e1001074. doi: 10.1371/journal.pcbi.1001074.

37.

Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans.

Chikina MD, Huttenhower C, Murphy CT, Troyanskaya OG.

PLoS Comput Biol. 2009 Jun;5(6):e1000417. doi: 10.1371/journal.pcbi.1000417. Epub 2009 Jun 19.

38.

The Sleipnir library for computational functional genomics.

Huttenhower C, Schroeder M, Chikina MD, Troyanskaya OG.

Bioinformatics. 2008 Jul 1;24(13):1559-61. doi: 10.1093/bioinformatics/btn237. Epub 2008 May 21.

39.

Role of Domain IV/S4 outermost arginines in gating of T-type calcium channels.

Lam AD, Chikina MD, McNulty MM, Glaaser IW, Hanck DA.

Pflugers Arch. 2005 Nov;451(2):349-61. Epub 2005 Aug 26.

PMID:
16133267

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