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Items: 40

1.

αKLOTHO and sTGFβR2 treatment counteract the osteoarthritic phenotype developed in a rat model.

Martinez-Redondo P, Guillen-Guillen I, Davidsohn N, Wang C, Prieto J, Kurita M, Hatanaka F, Zhong C, Hernandez-Benitez R, Hishida T, Lezaki T, Sakamoto A, Nemeth AN, Hishida Y, Esteban CR, Shojima K, Huang L, Shokhirev M, Nuñez-Delicado E, Campistol JM, Guillen-Vicente I, Rodriguez-Iñigo E, Lopez-Alcorocho JM, Guillen-Vicente M, Church G, Reddy P, Guillen-Garcia P, Liu GH, Belmonte JCI.

Protein Cell. 2020 Jan 16. doi: 10.1007/s13238-019-00685-7. [Epub ahead of print] No abstract available.

PMID:
31950348
2.

Accurate annotation of human protein-coding small open reading frames.

Martinez TF, Chu Q, Donaldson C, Tan D, Shokhirev MN, Saghatelian A.

Nat Chem Biol. 2019 Dec 9. doi: 10.1038/s41589-019-0425-0. [Epub ahead of print]

PMID:
31819274
3.

Elevating acetyl-CoA levels reduces aspects of brain aging.

Currais A, Huang L, Goldberg J, Petrascheck M, Ates G, Pinto-Duarte A, Shokhirev MN, Schubert D, Maher P.

Elife. 2019 Nov 19;8. pii: e47866. doi: 10.7554/eLife.47866.

4.

Dynamical Electrical Complexity Is Reduced during Neuronal Differentiation in Autism Spectrum Disorder.

Amatya DN, Linker SB, Mendes APD, Santos R, Erikson G, Shokhirev MN, Zhou Y, Sharpee T, Gage FH, Marchetto MC, Kim Y.

Stem Cell Reports. 2019 Sep 10;13(3):474-484. doi: 10.1016/j.stemcr.2019.08.001. Epub 2019 Aug 29.

5.

Revamping the evolutionary theories of aging.

Johnson AA, Shokhirev MN, Shoshitaishvili B.

Ageing Res Rev. 2019 Nov;55:100947. doi: 10.1016/j.arr.2019.100947. Epub 2019 Aug 23. Review.

6.

Heterozygous Mutations in SMARCA2 Reprogram the Enhancer Landscape by Global Retargeting of SMARCA4.

Gao F, Elliott NJ, Ho J, Sharp A, Shokhirev MN, Hargreaves DC.

Mol Cell. 2019 Sep 5;75(5):891-904.e7. doi: 10.1016/j.molcel.2019.06.024. Epub 2019 Jul 30.

PMID:
31375262
7.

The AMPK-Related Kinases SIK1 and SIK3 Mediate Key Tumor-Suppressive Effects of LKB1 in NSCLC.

Hollstein PE, Eichner LJ, Brun SN, Kamireddy A, Svensson RU, Vera LI, Ross DS, Rymoff TJ, Hutchins A, Galvez HM, Williams AE, Shokhirev MN, Screaton RA, Berdeaux R, Shaw RJ.

Cancer Discov. 2019 Nov;9(11):1606-1627. doi: 10.1158/2159-8290.CD-18-1261. Epub 2019 Jul 26.

PMID:
31350328
8.

CDK12 phosphorylates 4E-BP1 to enable mTORC1-dependent translation and mitotic genome stability.

Choi SH, Martinez TF, Kim S, Donaldson C, Shokhirev MN, Saghatelian A, Jones KA.

Genes Dev. 2019 Apr 1;33(7-8):418-435. doi: 10.1101/gad.322339.118. Epub 2019 Feb 28.

9.

Genetic Liver-Specific AMPK Activation Protects against Diet-Induced Obesity and NAFLD.

Garcia D, Hellberg K, Chaix A, Wallace M, Herzig S, Badur MG, Lin T, Shokhirev MN, Pinto AFM, Ross DS, Saghatelian A, Panda S, Dow LE, Metallo CM, Shaw RJ.

Cell Rep. 2019 Jan 2;26(1):192-208.e6. doi: 10.1016/j.celrep.2018.12.036.

10.

Predicting age from the transcriptome of human dermal fibroblasts.

Fleischer JG, Schulte R, Tsai HH, Tyagi S, Ibarra A, Shokhirev MN, Huang L, Hetzer MW, Navlakha S.

Genome Biol. 2018 Dec 20;19(1):221. doi: 10.1186/s13059-018-1599-6.

11.

A non-canonical BRD9-containing BAF chromatin remodeling complex regulates naive pluripotency in mouse embryonic stem cells.

Gatchalian J, Malik S, Ho J, Lee DS, Kelso TWR, Shokhirev MN, Dixon JR, Hargreaves DC.

Nat Commun. 2018 Dec 3;9(1):5139. doi: 10.1038/s41467-018-07528-9.

12.

Genetic Analysis Reveals AMPK Is Required to Support Tumor Growth in Murine Kras-Dependent Lung Cancer Models.

Eichner LJ, Brun SN, Herzig S, Young NP, Curtis SD, Shackelford DB, Shokhirev MN, Leblanc M, Vera LI, Hutchins A, Ross DS, Shaw RJ, Svensson RU.

Cell Metab. 2019 Feb 5;29(2):285-302.e7. doi: 10.1016/j.cmet.2018.10.005. Epub 2018 Nov 8.

PMID:
30415923
13.

In vivo reprogramming of wound-resident cells generates skin epithelial tissue.

Kurita M, Araoka T, Hishida T, O'Keefe DD, Takahashi Y, Sakamoto A, Sakurai M, Suzuki K, Wu J, Yamamoto M, Hernandez-Benitez R, Ocampo A, Reddy P, Shokhirev MN, Magistretti P, Núñez Delicado E, Eto H, Harii K, Izpisua Belmonte JC.

Nature. 2018 Sep;561(7722):243-247. doi: 10.1038/s41586-018-0477-4. Epub 2018 Sep 5.

PMID:
30185909
14.

Multicilin and activated E2f4 induce multiciliated cell differentiation in primary fibroblasts.

Kim S, Ma L, Shokhirev MN, Quigley I, Kintner C.

Sci Rep. 2018 Aug 17;8(1):12369. doi: 10.1038/s41598-018-30791-1.

15.

Cooperative Metabolic Adaptations in the Host Can Favor Asymptomatic Infection and Select for Attenuated Virulence in an Enteric Pathogen.

Sanchez KK, Chen GY, Schieber AMP, Redford SE, Shokhirev MN, Leblanc M, Lee YM, Ayres JS.

Cell. 2018 Sep 20;175(1):146-158.e15. doi: 10.1016/j.cell.2018.07.016. Epub 2018 Aug 9.

16.

BART: bioinformatics array research tool.

Amaral ML, Erikson GA, Shokhirev MN.

BMC Bioinformatics. 2018 Aug 8;19(1):296. doi: 10.1186/s12859-018-2308-x.

17.

Author Correction: A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development.

Xie M, Chen H, Huang L, O'Neil RC, Shokhirev MN, Ecker JR.

Nat Commun. 2018 May 22;9(1):2075. doi: 10.1038/s41467-018-04514-z.

18.

Efficient Generation of CA3 Neurons from Human Pluripotent Stem Cells Enables Modeling of Hippocampal Connectivity In Vitro.

Sarkar A, Mei A, Paquola ACM, Stern S, Bardy C, Klug JR, Kim S, Neshat N, Kim HJ, Ku M, Shokhirev MN, Adamowicz DH, Marchetto MC, Jappelli R, Erwin JA, Padmanabhan K, Shtrahman M, Jin X, Gage FH.

Cell Stem Cell. 2018 May 3;22(5):684-697.e9. doi: 10.1016/j.stem.2018.04.009.

19.

Glioblastoma Model Using Human Cerebral Organoids.

Ogawa J, Pao GM, Shokhirev MN, Verma IM.

Cell Rep. 2018 Apr 24;23(4):1220-1229. doi: 10.1016/j.celrep.2018.03.105.

20.

A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development.

Xie M, Chen H, Huang L, O'Neil RC, Shokhirev MN, Ecker JR.

Nat Commun. 2018 Apr 23;9(1):1604. doi: 10.1038/s41467-018-03921-6. Erratum in: Nat Commun. 2018 May 22;9(1):2075.

21.

The influence of transcript assembly on the proteogenomics discovery of microproteins.

Ma J, Saghatelian A, Shokhirev MN.

PLoS One. 2018 Mar 27;13(3):e0194518. doi: 10.1371/journal.pone.0194518. eCollection 2018.

22.

Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors.

Konermann S, Lotfy P, Brideau NJ, Oki J, Shokhirev MN, Hsu PD.

Cell. 2018 Apr 19;173(3):665-676.e14. doi: 10.1016/j.cell.2018.02.033. Epub 2018 Mar 15.

23.

Deriving Quantitative Cell Biological Information from Dye-Dilution Lymphocyte Proliferation Experiments.

Roy K, Shokhirev MN, Mitchell S, Hoffmann A.

Methods Mol Biol. 2018;1707:81-94. doi: 10.1007/978-1-4939-7474-0_6. Review.

PMID:
29388101
24.

The Aging Astrocyte Transcriptome from Multiple Regions of the Mouse Brain.

Boisvert MM, Erikson GA, Shokhirev MN, Allen NJ.

Cell Rep. 2018 Jan 2;22(1):269-285. doi: 10.1016/j.celrep.2017.12.039.

25.

Reprogramming pancreatic stellate cells via p53 activation: A putative target for pancreatic cancer therapy.

Saison-Ridinger M, DelGiorno KE, Zhang T, Kraus A, French R, Jaquish D, Tsui C, Erikson G, Spike BT, Shokhirev MN, Liddle C, Yu RT, Downes M, Evans RM, Saghatelian A, Lowy AM, Wahl GM.

PLoS One. 2017 Dec 6;12(12):e0189051. doi: 10.1371/journal.pone.0189051. eCollection 2017.

26.

Chromatin accessibility underlies synthetic lethality of SWI/SNF subunits in ARID1A-mutant cancers.

Kelso TWR, Porter DK, Amaral ML, Shokhirev MN, Benner C, Hargreaves DC.

Elife. 2017 Oct 2;6. pii: e30506. doi: 10.7554/eLife.30506.

27.

Differentiation of Inflammation-Responsive Astrocytes from Glial Progenitors Generated from Human Induced Pluripotent Stem Cells.

Santos R, Vadodaria KC, Jaeger BN, Mei A, Lefcochilos-Fogelquist S, Mendes APD, Erikson G, Shokhirev M, Randolph-Moore L, Fredlender C, Dave S, Oefner R, Fitzpatrick C, Pena M, Barron JJ, Ku M, Denli AM, Kerman BE, Charnay P, Kelsoe JR, Marchetto MC, Gage FH.

Stem Cell Reports. 2017 Jun 6;8(6):1757-1769. doi: 10.1016/j.stemcr.2017.05.011.

28.

Integration of CpG-free DNA induces de novo methylation of CpG islands in pluripotent stem cells.

Takahashi Y, Wu J, Suzuki K, Martinez-Redondo P, Li M, Liao HK, Wu MZ, Hernández-Benítez R, Hishida T, Shokhirev MN, Esteban CR, Sancho-Martinez I, Belmonte JCI.

Science. 2017 May 5;356(6337):503-508. doi: 10.1126/science.aag3260.

29.

AMPK governs lineage specification through Tfeb-dependent regulation of lysosomes.

Young NP, Kamireddy A, Van Nostrand JL, Eichner LJ, Shokhirev MN, Dayn Y, Shaw RJ.

Genes Dev. 2016 Mar 1;30(5):535-52. doi: 10.1101/gad.274142.115.

30.

A multi-scale approach reveals that NF-κB cRel enforces a B-cell decision to divide.

Shokhirev MN, Almaden J, Davis-Turak J, Birnbaum HA, Russell TM, Vargas JA, Hoffmann A.

Mol Syst Biol. 2015 Feb 13;11(1):783. doi: 10.15252/msb.20145554.

31.

Considering the kinetics of mRNA synthesis in the analysis of the genome and epigenome reveals determinants of co-transcriptional splicing.

Davis-Turak JC, Allison K, Shokhirev MN, Ponomarenko P, Tsimring LS, Glass CK, Johnson TL, Hoffmann A.

Nucleic Acids Res. 2015 Jan;43(2):699-707. doi: 10.1093/nar/gku1338. Epub 2014 Dec 24.

32.

A pathway switch directs BAFF signaling to distinct NFκB transcription factors in maturing and proliferating B cells.

Almaden JV, Tsui R, Liu YC, Birnbaum H, Shokhirev MN, Ngo KA, Davis-Turak JC, Otero D, Basak S, Rickert RC, Hoffmann A.

Cell Rep. 2014 Dec 24;9(6):2098-111. doi: 10.1016/j.celrep.2014.11.024. Epub 2014 Dec 11.

33.

IκBε is a key regulator of B cell expansion by providing negative feedback on cRel and RelA in a stimulus-specific manner.

Alves BN, Tsui R, Almaden J, Shokhirev MN, Davis-Turak J, Fujimoto J, Birnbaum H, Ponomarenko J, Hoffmann A.

J Immunol. 2014 Apr 1;192(7):3121-32. doi: 10.4049/jimmunol.1302351. Epub 2014 Mar 3.

34.

Effects of extrinsic mortality on the evolution of aging: a stochastic modeling approach.

Shokhirev MN, Johnson AA.

PLoS One. 2014 Jan 21;9(1):e86602. doi: 10.1371/journal.pone.0086602. eCollection 2014.

35.

FlowMax: A Computational Tool for Maximum Likelihood Deconvolution of CFSE Time Courses.

Shokhirev MN, Hoffmann A.

PLoS One. 2013 Jun 27;8(6):e67620. doi: 10.1371/journal.pone.0067620. Print 2013.

36.

Paternal RLIM/Rnf12 is a survival factor for milk-producing alveolar cells.

Jiao B, Ma H, Shokhirev MN, Drung A, Yang Q, Shin J, Lu S, Byron M, Kalantry S, Mercurio AM, Lawrence JB, Hoffmann A, Bach I.

Cell. 2012 Apr 27;149(3):630-41. doi: 10.1016/j.cell.2012.02.056.

37.

Biased coarse-grained molecular dynamics simulation approach for flexible fitting of X-ray structure into cryo electron microscopy maps.

Grubisic I, Shokhirev MN, Orzechowski M, Miyashita O, Tama F.

J Struct Biol. 2010 Jan;169(1):95-105. doi: 10.1016/j.jsb.2009.09.010. Epub 2009 Oct 2.

PMID:
19800974
38.

Effect of mutation of carboxyl side-chain amino acids near the heme on the midpoint potentials and ligand binding constants of nitrophorin 2 and its NO, histamine, and imidazole complexes.

Berry RE, Shokhirev MN, Ho AY, Yang F, Shokhireva TK, Zhang H, Weichsel A, Montfort WR, Walker FA.

J Am Chem Soc. 2009 Feb 18;131(6):2313-27. doi: 10.1021/ja808105d.

39.
40.

Effect of the N-terminus on heme cavity structure, ligand equilibrium, rate constants, and reduction potentials of nitrophorin 2 from Rhodnius prolixus.

Berry RE, Shokhireva TKh, Filippov I, Shokhirev MN, Zhang H, Walker FA.

Biochemistry. 2007 Jun 12;46(23):6830-43. Epub 2007 May 17.

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