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Items: 1 to 50 of 135

1.

DPre: Computational identification of differentiation bias and genes underlying cell type conversions.

Steffens S, Fu X, He F, Li Y, Babarinde IA, Hutchins AP.

Bioinformatics. 2019 Oct 17. pii: btz789. doi: 10.1093/bioinformatics/btz789. [Epub ahead of print]

PMID:
31621827
2.

Pluripotency reprogramming by competent and incompetent POU factors uncovers temporal dependency for Oct4 and Sox2.

Malik V, Glaser LV, Zimmer D, Velychko S, Weng M, Holzner M, Arend M, Chen Y, Srivastava Y, Veerapandian V, Shah Z, Esteban MA, Wang H, Chen J, Schöler HR, Hutchins AP, Meijsing SH, Pott S, Jauch R.

Nat Commun. 2019 Aug 2;10(1):3477. doi: 10.1038/s41467-019-11054-7.

3.

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 Jul 26. doi: 10.1158/2159-8290.CD-18-1261. [Epub ahead of print]

PMID:
31350328
4.

Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts.

Babarinde IA, Li Y, Hutchins AP.

Comput Struct Biotechnol J. 2019 May 7;17:628-637. doi: 10.1016/j.csbj.2019.04.012. eCollection 2019. Review.

5.

An alternative CTCF isoform antagonizes canonical CTCF occupancy and changes chromatin architecture to promote apoptosis.

Li J, Huang K, Hu G, Babarinde IA, Li Y, Dong X, Chen YS, Shang L, Guo W, Wang J, Chen Z, Hutchins AP, Yang YG, Yao H.

Nat Commun. 2019 Apr 4;10(1):1535. doi: 10.1038/s41467-019-08949-w.

6.

Resolving Cell Fate Decisions during Somatic Cell Reprogramming by Single-Cell RNA-Seq.

Guo L, Lin L, Wang X, Gao M, Cao S, Mai Y, Wu F, Kuang J, Liu H, Yang J, Chu S, Song H, Li D, Liu Y, Wu K, Liu J, Wang J, Pan G, Hutchins AP, Liu J, Pei D, Chen J.

Mol Cell. 2019 Feb 21;73(4):815-829.e7. doi: 10.1016/j.molcel.2019.01.042. Epub 2019 Feb 13.

PMID:
30772174
7.

Transposable elements are regulated by context-specific patterns of chromatin marks in mouse embryonic stem cells.

He J, Fu X, Zhang M, He F, Li W, Abdul MM, Zhou J, Sun L, Chang C, Li Y, Liu H, Wu K, Babarinde IA, Zhuang Q, Loh YH, Chen J, Esteban MA, Hutchins AP.

Nat Commun. 2019 Jan 3;10(1):34. doi: 10.1038/s41467-018-08006-y.

8.

Sample Entropy of Speed Power Spectrum as a Measure of Laparoscopic Surgical Instrument Trajectory Smoothness.

Hutchins AR, Manson RJ, Zani S, Mann BP.

Conf Proc IEEE Eng Med Biol Soc. 2018 Jul;2018:5410-5413. doi: 10.1109/EMBC.2018.8513503.

PMID:
30441560
9.

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
10.

Objective Assessment of the Early Stages of the Learning Curve for the Senhance Surgical Robotic System.

Hutchins AR, Manson RJ, Lerebours R, Farjat AE, Cox ML, Mann BP, Zani S Jr.

J Surg Educ. 2019 Jan - Feb;76(1):201-214. doi: 10.1016/j.jsurg.2018.06.026. Epub 2018 Aug 8.

PMID:
30098933
11.

Publisher Correction: NCoR/SMRT co-repressors cooperate with c-MYC to create an epigenetic barrier to somatic cell reprogramming.

Zhuang Q, Li W, Benda C, Huang Z, Ahmed T, Liu P, Guo X, Ibañez DP, Luo Z, Zhang M, Abdul MM, Yang Z, Yang J, Huang Y, Zhang H, Huang D, Zhou J, Zhong X, Zhu X, Fu X, Fan W, Liu Y, Xu Y, Ward C, Khan MJ, Kanwal S, Mirza B, Tortorella MD, Tse HF, Chen J, Qin B, Bao X, Gao S, Hutchins AP, Esteban MA.

Nat Cell Biol. 2018 Oct;20(10):1227. doi: 10.1038/s41556-018-0128-x.

PMID:
29907862
12.

PCGF5 is required for neural differentiation of embryonic stem cells.

Yao M, Zhou X, Zhou J, Gong S, Hu G, Li J, Huang K, Lai P, Shi G, Hutchins AP, Sun H, Wang H, Yao H.

Nat Commun. 2018 May 15;9(1):1463. doi: 10.1038/s41467-018-03781-0.

13.

NCoR/SMRT co-repressors cooperate with c-MYC to create an epigenetic barrier to somatic cell reprogramming.

Zhuang Q, Li W, Benda C, Huang Z, Ahmed T, Liu P, Guo X, Ibañez DP, Luo Z, Zhang M, Abdul MM, Yang Z, Yang J, Huang Y, Zhang H, Huang D, Zhou J, Zhong X, Zhu X, Fu X, Fan W, Liu Y, Xu Y, Ward C, Khan MJ, Kanwal S, Mirza B, Tortorella MD, Tse HF, Chen J, Qin B, Bao X, Gao S, Hutchins AP, Esteban MA.

Nat Cell Biol. 2018 Apr;20(4):400-412. doi: 10.1038/s41556-018-0047-x. Epub 2018 Mar 12. Erratum in: Nat Cell Biol. 2018 Oct;20(10):1227.

PMID:
29531310
14.

Capturing the interactome of newly transcribed RNA.

Bao X, Guo X, Yin M, Tariq M, Lai Y, Kanwal S, Zhou J, Li N, Lv Y, Pulido-Quetglas C, Wang X, Ji L, Khan MJ, Zhu X, Luo Z, Shao C, Lim DH, Liu X, Li N, Wang W, He M, Liu YL, Ward C, Wang T, Zhang G, Wang D, Yang J, Chen Y, Zhang C, Jauch R, Yang YG, Wang Y, Qin B, Anko ML, Hutchins AP, Sun H, Wang H, Fu XD, Zhang B, Esteban MA.

Nat Methods. 2018 Mar;15(3):213-220. doi: 10.1038/nmeth.4595. Epub 2018 Feb 12.

15.

Genomic and molecular control of cell type and cell type conversions.

Fu X, He F, Li Y, Shahveranov A, Hutchins AP.

Cell Regen (Lond). 2017 Nov 22;6:1-7. doi: 10.1016/j.cr.2017.09.001. eCollection 2017 Dec. Review.

16.

Arizona Registered Dietitians Show Gaps in Knowledge of Bean Health Benefits.

Winham DM, Hutchins AM, Thompson SV, Dougherty MK.

Nutrients. 2018 Jan 8;10(1). pii: E52. doi: 10.3390/nu10010052.

17.

Chromatin Accessibility Dynamics during iPSC Reprogramming.

Li D, Liu J, Yang X, Zhou C, Guo J, Wu C, Qin Y, Guo L, He J, Yu S, Liu H, Wang X, Wu F, Kuang J, Hutchins AP, Chen J, Pei D.

Cell Stem Cell. 2017 Dec 7;21(6):819-833.e6. doi: 10.1016/j.stem.2017.10.012.

18.

Kdm2b Regulates Somatic Reprogramming through Variant PRC1 Complex-Dependent Function.

Zhou Z, Yang X, He J, Liu J, Wu F, Yu S, Liu Y, Lin R, Liu H, Cui Y, Zhou C, Wang X, Wu J, Cao S, Guo L, Lin L, Wang T, Peng X, Qiang B, Hutchins AP, Pei D, Chen J.

Cell Rep. 2017 Nov 21;21(8):2160-2170. doi: 10.1016/j.celrep.2017.10.091.

19.

Glycemic Response to Black Beans and Chickpeas as Part of a Rice Meal: A Randomized Cross-Over Trial.

Winham DM, Hutchins AM, Thompson SV.

Nutrients. 2017 Oct 4;9(10). pii: E1095. doi: 10.3390/nu9101095.

20.

Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences.

Andrabi M, Hutchins AP, Miranda-Saavedra D, Kono H, Nussinov R, Mizuguchi K, Ahmad S.

Sci Rep. 2017 Jun 22;7(1):4071. doi: 10.1038/s41598-017-03199-6.

21.

A sequential EMT-MET mechanism drives the differentiation of human embryonic stem cells towards hepatocytes.

Li Q, Hutchins AP, Chen Y, Li S, Shan Y, Liao B, Zheng D, Shi X, Li Y, Chan WY, Pan G, Wei S, Shu X, Pei D.

Nat Commun. 2017 May 3;8:15166. doi: 10.1038/ncomms15166.

22.

Models of global gene expression define major domains of cell type and tissue identity.

Hutchins AP, Yang Z, Li Y, He F, Fu X, Wang X, Li D, Liu K, He J, Wang Y, Chen J, Esteban MA, Pei D.

Nucleic Acids Res. 2017 Mar 17;45(5):2354-2367. doi: 10.1093/nar/gkx054.

23.

RNA Helicase DDX5 Inhibits Reprogramming to Pluripotency by miRNA-Based Repression of RYBP and its PRC1-Dependent and -Independent Functions.

Li H, Lai P, Jia J, Song Y, Xia Q, Huang K, He N, Ping W, Chen J, Yang Z, Li J, Yao M, Dong X, Zhao J, Hou C, Esteban MA, Gao S, Pei D, Hutchins AP, Yao H.

Cell Stem Cell. 2017 Apr 6;20(4):571. doi: 10.1016/j.stem.2017.03.014. No abstract available.

24.

The Impact of Virgin Coconut Oil and High-Oleic Safflower Oil on Body Composition, Lipids, and Inflammatory Markers in Postmenopausal Women.

Harris M, Hutchins A, Fryda L.

J Med Food. 2017 Apr;20(4):345-351. doi: 10.1089/jmf.2016.0114. Epub 2017 Mar 9.

PMID:
28277823
25.

Generation of Human Liver Chimeric Mice with Hepatocytes from Familial Hypercholesterolemia Induced Pluripotent Stem Cells.

Yang J, Wang Y, Zhou T, Wong LY, Tian XY, Hong X, Lai WH, Au KW, Wei R, Liu Y, Cheng LH, Liang G, Huang Z, Fan W, Zhao P, Wang X, Ibañez DP, Luo Z, Li Y, Zhong X, Chen S, Wang D, Li L, Lai L, Qin B, Bao X, Hutchins AP, Siu CW, Huang Y, Esteban MA, Tse HF.

Stem Cell Reports. 2017 Mar 14;8(3):605-618. doi: 10.1016/j.stemcr.2017.01.027. Epub 2017 Mar 2.

26.

RNA Helicase DDX5 Inhibits Reprogramming to Pluripotency by miRNA-Based Repression of RYBP and its PRC1-Dependent and -Independent Functions.

Li H, Lai P, Jia J, Song Y, Xia Q, Huang K, He N, Ping W, Chen J, Yang Z, Li J, Yao M, Dong X, Zhao J, Hou C, Esteban MA, Gao S, Pei D, Hutchins AP, Yao H.

Cell Stem Cell. 2017 Apr 6;20(4):462-477.e6. doi: 10.1016/j.stem.2016.12.002. Epub 2017 Jan 19. Erratum in: Cell Stem Cell. 2017 Apr 6;20(4):571.

27.

Generation and Analysis of GATA2w/eGFP Human ESCs Reveal ITGB3/CD61 as a Reliable Marker for Defining Hemogenic Endothelial Cells during Hematopoiesis.

Huang K, Gao J, Du J, Ma N, Zhu Y, Wu P, Zhang T, Wang W, Li Y, Chen Q, Hutchins AP, Yang Z, Zheng Y, Zhang J, Shan Y, Li X, Liao B, Liu J, Wang J, Liu B, Pan G.

Stem Cell Reports. 2016 Nov 8;7(5):854-868. doi: 10.1016/j.stemcr.2016.09.008. Epub 2016 Oct 13.

28.

Inhibition of acetyl-CoA carboxylase suppresses fatty acid synthesis and tumor growth of non-small-cell lung cancer in preclinical models.

Svensson RU, Parker SJ, Eichner LJ, Kolar MJ, Wallace M, Brun SN, Lombardo PS, Van Nostrand JL, Hutchins A, Vera L, Gerken L, Greenwood J, Bhat S, Harriman G, Westlin WF, Harwood HJ Jr, Saghatelian A, Kapeller R, Metallo CM, Shaw RJ.

Nat Med. 2016 Oct;22(10):1108-1119. doi: 10.1038/nm.4181. Epub 2016 Sep 19.

29.

The cancer-associated CTCFL/BORIS protein targets multiple classes of genomic repeats, with a distinct binding and functional preference for humanoid-specific SVA transposable elements.

Pugacheva EM, Teplyakov E, Wu Q, Li J, Chen C, Meng C, Liu J, Robinson S, Loukinov D, Boukaba A, Hutchins AP, Lobanenkov V, Strunnikov A.

Epigenetics Chromatin. 2016 Aug 31;9(1):35. doi: 10.1186/s13072-016-0084-2. eCollection 2016.

30.

Transcriptional Intricacies of Stem Cells.

Hutchins AP, Robson P.

Cell Syst. 2015 Aug 26;1(2):100-1. doi: 10.1016/j.cels.2015.08.007. Epub 2015 Aug 26.

31.

Remission for Loss of Odontogenic Potential in a New Micromilieu In Vitro.

Zheng Y, Cai J, Hutchins AP, Jia L, Liu P, Yang D, Chen S, Ge L, Pei D, Wei S.

PLoS One. 2016 Apr 6;11(4):e0152893. doi: 10.1371/journal.pone.0152893. eCollection 2016.

32.

TGFβ signaling regulates the choice between pluripotent and neural fates during reprogramming of human urine derived cells.

Wang L, Li X, Huang W, Zhou T, Wang H, Lin A, Hutchins AP, Su Z, Chen Q, Pei D, Pan G.

Sci Rep. 2016 Mar 3;6:22484. doi: 10.1038/srep22484.

33.

Transcriptional Control of Somatic Cell Reprogramming.

Xu Y, Zhang M, Li W, Zhu X, Bao X, Qin B, Hutchins AP, Esteban MA.

Trends Cell Biol. 2016 Apr;26(4):272-288. doi: 10.1016/j.tcb.2015.12.003. Epub 2016 Jan 15. Review.

PMID:
26776886
34.

Transient Activation of Mitoflashes Modulates Nanog at the Early Phase of Somatic Cell Reprogramming.

Ying Z, Chen K, Zheng L, Wu Y, Li L, Wang R, Long Q, Yang L, Guo J, Yao D, Li Y, Bao F, Xiang G, Liu J, Huang Q, Wu Z, Hutchins AP, Pei D, Liu X.

Cell Metab. 2016 Jan 12;23(1):220-6. doi: 10.1016/j.cmet.2015.10.002. Epub 2015 Nov 5.

35.
36.

Corrigendum: The oncogene c-Jun impedes somatic cell reprogramming.

Liu J, Han Q, Peng T, Peng M, Wei B, Li D, Wang X, Yu S, Yang J, Cao S, Huang K, Hutchins AP, Liu H, Kuang J, Zhou Z, Chen J, Wu H, Guo L, Chen Y, Chen Y, Li X, Wu H, Liao B, He W, Song H, Yao H, Pan G, Chen J, Pei D.

Nat Cell Biol. 2015 Sep;17(9):1228. doi: 10.1038/ncb3235. No abstract available.

PMID:
26316456
37.

The oncogene c-Jun impedes somatic cell reprogramming.

Liu J, Han Q, Peng T, Peng M, Wei B, Li D, Wang X, Yu S, Yang J, Cao S, Huang K, Hutchins AP, Liu H, Kuang J, Zhou Z, Chen J, Wu H, Guo L, Chen Y, Chen Y, Li X, Wu H, Liao B, He W, Song H, Yao H, Pan G, Chen J, Pei D.

Nat Cell Biol. 2015 Jul;17(7):856-67. doi: 10.1038/ncb3193. Epub 2015 Jun 22. Erratum in: Nat Cell Biol. 2015 Sep;17(9):1228.

PMID:
26098572
38.

A Drosophila-centric view of protein tyrosine phosphatases.

Hatzihristidis T, Desai N, Hutchins AP, Meng TC, Tremblay ML, Miranda-Saavedra D.

FEBS Lett. 2015 Apr 13;589(9):951-66. doi: 10.1016/j.febslet.2015.03.005. Epub 2015 Mar 13. Review.

39.
40.

The p53-induced lincRNA-p21 derails somatic cell reprogramming by sustaining H3K9me3 and CpG methylation at pluripotency gene promoters.

Bao X, Wu H, Zhu X, Guo X, Hutchins AP, Luo Z, Song H, Chen Y, Lai K, Yin M, Xu L, Zhou L, Chen J, Wang D, Qin B, Frampton J, Tse HF, Pei D, Wang H, Zhang B, Esteban MA.

Cell Res. 2015 Jan;25(1):80-92. doi: 10.1038/cr.2014.165. Epub 2014 Dec 16.

41.

glbase: a framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data.

Hutchins AP, Jauch R, Dyla M, Miranda-Saavedra D.

Cell Regen (Lond). 2014 Jan 24;3(1):1. doi: 10.1186/2045-9769-3-1. eCollection 2014.

42.

Transcriptional pause release is a rate-limiting step for somatic cell reprogramming.

Liu L, Xu Y, He M, Zhang M, Cui F, Lu L, Yao M, Tian W, Benda C, Zhuang Q, Huang Z, Li W, Li X, Zhao P, Fan W, Luo Z, Li Y, Wu Y, Hutchins AP, Wang D, Tse HF, Schambach A, Frampton J, Qin B, Bao X, Yao H, Zhang B, Sun H, Pei D, Wang H, Wang J, Esteban MA.

Cell Stem Cell. 2014 Nov 6;15(5):574-88. doi: 10.1016/j.stem.2014.09.018. Epub 2014 Oct 9.

43.

Depletion of Rictor, an essential protein component of mTORC2, decreases male lifespan.

Lamming DW, Mihaylova MM, Katajisto P, Baar EL, Yilmaz OH, Hutchins A, Gultekin Y, Gaither R, Sabatini DM.

Aging Cell. 2014 Oct;13(5):911-7. doi: 10.1111/acel.12256. Epub 2014 Jul 25.

44.

Regional status assessment of stony corals in the US Virgin Islands.

Fisher WS, Fore LS, Oliver LM, Lobue C, Quarles R, Campbell J, Harris P, Hemmer B, Vickery S, Parsons M, Hutchins A, Bernier K, Rodriguez D, Bradley P.

Environ Monit Assess. 2014 Nov;186(11):7165-81. doi: 10.1007/s10661-014-3918-z. Epub 2014 Jul 23.

PMID:
25052328
45.

Where cell fate conversions meet Chinese philosophy.

Zheng H, Hutchins AP, Pan G, Li Y, Pei D, Pei G.

Cell Res. 2014 Oct;24(10):1162-3. doi: 10.1038/cr.2014.93. Epub 2014 Jul 15.

46.

Protein tyrosine phosphatase 1B is a regulator of the interleukin-10-induced transcriptional program in macrophages.

Pike KA, Hutchins AP, Vinette V, Théberge JF, Sabbagh L, Tremblay ML, Miranda-Saavedra D.

Sci Signal. 2014 May 6;7(324):ra43. doi: 10.1126/scisignal.2005020.

PMID:
24803538
47.

Estimation of bottle filling counts for conventional pharmaceutical tablets and capsules.

Mullarney MP, Hutchins A, Taylor G.

Drug Dev Ind Pharm. 2015 Apr;41(4):670-3. doi: 10.3109/03639045.2014.893354. Epub 2014 Mar 5.

PMID:
24592891
48.

Evaluation of automated and manual DNA purification methods for detecting Ricinus communis DNA during ricin investigations.

Hutchins AS, Astwood MJ, Saah JR, Michel PA, Newton BR, Dauphin LA.

Forensic Sci Int. 2014 Mar;236:10-5. doi: 10.1016/j.forsciint.2013.12.011. Epub 2013 Dec 21.

PMID:
24529769
49.

Genomic and computational approaches to dissect the mechanisms of STAT3's universal and cell type-specific functions.

Hutchins AP, Diez D, Miranda-Saavedra D.

JAKSTAT. 2013 Oct 1;2(4):e25097. doi: 10.4161/jkst.25097. Epub 2013 May 20. Review.

50.

Systematic identification of transcriptional regulatory modules from protein-protein interaction networks.

Diez D, Hutchins AP, Miranda-Saavedra D.

Nucleic Acids Res. 2014 Jan;42(1):e6. doi: 10.1093/nar/gkt913. Epub 2013 Oct 16.

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