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Chikina Lab


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, Vgnali DAA.

Immunity (July 2019) Show Abstract

RERconverge: an R package for associating evolutionary rates with convergent traits. Kowalczyk A, Meyer WK, Partha R, Mao W, Clark NL, Chikina M.

Bioinformatics (in press) Show Abstract

Robust method for detecting convergent shifts in evolutionary rates. Kowalczyk A, Partha R, Clark NL, Chikina M.

MBE (in press) Show Abstract

Pathway-Level Information ExtractoR (PLIER): a generative model for gene expression data Mao, Weiguang, Boris Hartmann, Elena Zaslavsky, Stuart Sealfon, Chikina, Maria

Nature Methods. July 2019 Show Abstract

Cancer control is a key functionality underlying evolution of extended lifespan in mammals Kowalczyk A, Partha R, Clark NL, Chikina M.

bioRxiv Show Abstract

DataRemix: a universal data transformation for optimal inference from gene expression datasets. Mao W, Hausler R, Chikina M.

bioRxiv Show Abstract

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 genetics 2019 Feb 14;15(2):e1007720 Show Abstract

Adaptive plasticity of IL-10+ and IL-35+ T reg 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. ... Vignali DA

Nature Immunology (April 2019) Show Abstract

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

The Journal of clinical investigation. 2018 Sep 24;128(11). Show Abstract

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 361.6402 (2018): 591-594 Show Abstract

Modeling Enhancer-Promoter Interactions with Attention-Based Neural Networks Mao, Weiguang, Kostka, Dennis, Chikina, Maria

bioRxiv Show Abstract

Differential requirements for myeloid leukemia IFN-gamma 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 Show Abstract

Interferon-gamma 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 Show Abstract

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: 2/9/eaah4569. doi: Show Abstract

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: Show Abstract

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. Show Abstract

Modeling a human hepatocellular carcinoma subset in mice through coexpression of met and point-mutant beta-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. Show Abstract

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. doi: 10.1074/jbc.M116.740365. Epub Show Abstract

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 Show Abstract

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 Show Abstract

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. Show Abstract

The center for causal discovery of biomedical knowledge from big data. Cooper GF, Bahar I, Becich MJ, Benos PV, Berg J, Espino JU, Glymour C, Jacobson RC, Kienholz M, Lee AV, Lu X, Scheines R

J Am Med Inform Assoc. 2015 Nov;22(6):1132-6. doi: 10.1093/jamia/ocv059. Epub Show Abstract

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, Garcia-Sastre A, Kleinstein SH, Sealfon SC

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

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. Show Abstract

Low-variance RNAs identify Parkinson's disease molecular signature in blood. Chikina M, 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. Show Abstract

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. Show Abstract

Homer1 alternative splicing is regulated by gonadotropin-releasing hormone and modulates gonadotropin gene expression. Wang Q, Chikina M, Pincas H, Sealfon SC

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

Increasing consistency of disease biomarker prediction across datasets. Chikina M, Sealfon SC

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

Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge. Tarca AL, Lauria M, Unger M, Bilal E, Boue S, Kumar Dey K, Hoeng J, Koeppl H, Martin F, Meyer P, Nandy P, Norel R, Peitsch M, Rice JJ, Romero R, Stolovitzky G, Talikka M, Xiang Y, Zechner C

Bioinformatics. 2013 Nov 15;29(22):2892-9. doi: 10.1093/bioinformatics/btt492. Show Abstract

Critical assessment of automated flow cytometry data analysis techniques. Aghaeepour N, Finak G, Hoos H, Mosmann TR, Brinkman R, Gottardo R, Scheuermann RH

Nat Methods. 2013 Mar;10(3):228-38. doi: 10.1038/nmeth.2365. Epub 2013 Feb 10. Show Abstract

beta-catenin regulates GnRH-induced FSHbeta 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 Show Abstract

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 Show Abstract

An effective statistical evaluation of ChIPseq dataset similarity. Chikina M, Troyanskaya OG

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

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. Show Abstract

Accurate quantification of functional analogy among close homologs. Chikina M, Troyanskaya OG

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

Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans. Chikina M, Huttenhower C, Murphy CT, Troyanskaya OG

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

The Sleipnir library for computational functional genomics. Huttenhower C, Schroeder M, Chikina M, Troyanskaya OG

Bioinformatics. 2008 Jul 1;24(13):1559-61. doi: 10.1093/bioinformatics/btn237. Show Abstract

Role of Domain IV/S4 outermost arginines in gating of T-type calcium channels. Lam AD, Chikina M, McNulty MM, Glaaser IW, Hanck DA

Pflugers Arch. 2005 Nov;451(2):349-61. doi: 10.1007/s00424-005-1407-5. Epub 2005 Show Abstract