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Items: 1 to 50 of 386

1.

Optimization of the IPP-bypass mevalonate pathway and fed-batch fermentation for the production of isoprenol in Escherichia coli.

Kang A, Mendez-Perez D, Goh EB, Baidoo EEK, Benites VT, Beller HR, Keasling JD, Adams PD, Mukhopadhyay A, Lee TS.

Metab Eng. 2019 Sep 6;56:85-96. doi: 10.1016/j.ymben.2019.09.003. [Epub ahead of print]

PMID:
31499175
2.

Automated "Cells-To-Peptides" Sample Preparation Workflow for High-Throughput, Quantitative Proteomic Assays of Microbes.

Chen Y, Guenther JM, Gin JW, Chan LJG, Costello Z, Ogorzalek TL, Tran HM, Blake-Hedges JM, Keasling JD, Adams PD, García Martín H, Hillson NJ, Petzold CJ.

J Proteome Res. 2019 Aug 30. doi: 10.1021/acs.jproteome.9b00455. [Epub ahead of print]

PMID:
31436101
3.

PAK4 suppresses RELB to prevent senescence-like growth arrest in breast cancer.

Costa TDF, Zhuang T, Lorent J, Turco E, Olofsson H, Masia-Balague M, Zhao M, Rabieifar P, Robertson N, Kuiper R, Sjölund J, Spiess M, Hernández-Varas P, Rabenhorst U, Roswall P, Ma R, Gong X, Hartman J, Pietras K, Adams PD, Defilippi P, Strömblad S.

Nat Commun. 2019 Aug 9;10(1):3589. doi: 10.1038/s41467-019-11510-4.

4.

The role of TP53 in acute myeloid leukemia: Challenges and opportunities.

Barbosa K, Li S, Adams PD, Deshpande AJ.

Genes Chromosomes Cancer. 2019 Aug 8. doi: 10.1002/gcc.22796. [Epub ahead of print] Review.

PMID:
31393631
5.

Cryo_fit: Democratization of flexible fitting for cryo-EM.

Kim DN, Moriarty NW, Kirmizialtin S, Afonine PV, Poon B, Sobolev OV, Adams PD, Sanbonmatsu K.

J Struct Biol. 2019 Oct 1;208(1):1-6. doi: 10.1016/j.jsb.2019.05.012. Epub 2019 Jul 3.

PMID:
31279069
6.

Structural insights into dehydratase substrate selection for the borrelidin and fluvirucin polyketide synthases.

Barajas JF, McAndrew RP, Thompson MG, Backman TWH, Pang B, de Rond T, Pereira JH, Benites VT, Martín HG, Baidoo EEK, Hillson NJ, Adams PD, Keasling JD.

J Ind Microbiol Biotechnol. 2019 Aug;46(8):1225-1235. doi: 10.1007/s10295-019-02189-z. Epub 2019 May 21.

7.

Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Pseudomonas putida Lysine Metabolism.

Thompson MG, Blake-Hedges JM, Cruz-Morales P, Barajas JF, Curran SC, Eiben CB, Harris NC, Benites VT, Gin JW, Sharpless WA, Twigg FF, Skyrud W, Krishna RN, Pereira JH, Baidoo EEK, Petzold CJ, Adams PD, Arkin AP, Deutschbauer AM, Keasling JD.

MBio. 2019 May 7;10(3). pii: e02577-18. doi: 10.1128/mBio.02577-18.

8.

The HIRA histone chaperone complex subunit UBN1 harbors H3/H4- and DNA-binding activity.

Ricketts MD, Dasgupta N, Fan J, Han J, Gerace M, Tang Y, Black BE, Adams PD, Marmorstein R.

J Biol Chem. 2019 Jun 7;294(23):9239-9259. doi: 10.1074/jbc.RA119.007480. Epub 2019 Apr 30.

PMID:
31040182
9.

Notch Signaling Mediates Secondary Senescence.

Teo YV, Rattanavirotkul N, Olova N, Salzano A, Quintanilla A, Tarrats N, Kiourtis C, Müller M, Green AR, Adams PD, Acosta JC, Bird TG, Kirschner K, Neretti N, Chandra T.

Cell Rep. 2019 Apr 23;27(4):997-1007.e5. doi: 10.1016/j.celrep.2019.03.104.

10.

Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB).

Adams PD, Afonine PV, Baskaran K, Berman HM, Berrisford J, Bricogne G, Brown DG, Burley SK, Chen M, Feng Z, Flensburg C, Gutmanas A, Hoch JC, Ikegawa Y, Kengaku Y, Krissinel E, Kurisu G, Liang Y, Liebschner D, Mak L, Markley JL, Moriarty NW, Murshudov GN, Noble M, Peisach E, Persikova I, Poon BK, Sobolev OV, Ulrich EL, Velankar S, Vonrhein C, Westbrook J, Wojdyr M, Yokochi M, Young JY.

Acta Crystallogr D Struct Biol. 2019 Apr 1;75(Pt 4):451-454. doi: 10.1107/S2059798319004522. Epub 2019 Apr 8. No abstract available.

PMID:
30988261
11.

Methyl ketone production by Pseudomonas putida is enhanced by plant-derived amino acids.

Dong J, Chen Y, Benites VT, Baidoo EEK, Petzold CJ, Beller HR, Eudes A, Scheller HV, Adams PD, Mukhopadhyay A, Simmons BA, Singer SW.

Biotechnol Bioeng. 2019 Aug;116(8):1909-1922. doi: 10.1002/bit.26995. Epub 2019 Apr 29.

PMID:
30982958
12.

A Multiscale Map of the Stem Cell State in Pancreatic Adenocarcinoma.

Lytle NK, Ferguson LP, Rajbhandari N, Gilroy K, Fox RG, Deshpande A, Schürch CM, Hamilton M, Robertson N, Lin W, Noel P, Wartenberg M, Zlobec I, Eichmann M, Galván JA, Karamitopoulou E, Gilderman T, Esparza LA, Shima Y, Spahn P, French R, Lewis NE, Fisch KM, Sasik R, Rosenthal SB, Kritzik M, Von Hoff D, Han H, Ideker T, Deshpande AJ, Lowy AM, Adams PD, Reya T.

Cell. 2019 Apr 18;177(3):572-586.e22. doi: 10.1016/j.cell.2019.03.010. Epub 2019 Apr 4.

PMID:
30955884
13.

The histone chaperone HIRA promotes the induction of host innate immune defences in response to HSV-1 infection.

McFarlane S, Orr A, Roberts APE, Conn KL, Iliev V, Loney C, da Silva Filipe A, Smollett K, Gu Q, Robertson N, Adams PD, Rai TS, Boutell C.

PLoS Pathog. 2019 Mar 22;15(3):e1007667. doi: 10.1371/journal.ppat.1007667. eCollection 2019 Mar.

14.

Histone Acetyltransferase p300 Induces De Novo Super-Enhancers to Drive Cellular Senescence.

Sen P, Lan Y, Li CY, Sidoli S, Donahue G, Dou Z, Frederick B, Chen Q, Luense LJ, Garcia BA, Dang W, Johnson FB, Adams PD, Schultz DC, Berger SL.

Mol Cell. 2019 Feb 21;73(4):684-698.e8. doi: 10.1016/j.molcel.2019.01.021. Epub 2019 Feb 14.

PMID:
30773298
15.

A rapid methods development workflow for high-throughput quantitative proteomic applications.

Chen Y, Vu J, Thompson MG, Sharpless WA, Chan LJG, Gin JW, Keasling JD, Adams PD, Petzold CJ.

PLoS One. 2019 Feb 14;14(2):e0211582. doi: 10.1371/journal.pone.0211582. eCollection 2019.

16.

Length-independent telomere damage drives post-mitotic cardiomyocyte senescence.

Anderson R, Lagnado A, Maggiorani D, Walaszczyk A, Dookun E, Chapman J, Birch J, Salmonowicz H, Ogrodnik M, Jurk D, Proctor C, Correia-Melo C, Victorelli S, Fielder E, Berlinguer-Palmini R, Owens A, Greaves LC, Kolsky KL, Parini A, Douin-Echinard V, LeBrasseur NK, Arthur HM, Tual-Chalot S, Schafer MJ, Roos CM, Miller JD, Robertson N, Mann J, Adams PD, Tchkonia T, Kirkland JL, Mialet-Perez J, Richardson GD, Passos JF.

EMBO J. 2019 Mar 1;38(5). pii: e100492. doi: 10.15252/embj.2018100492. Epub 2019 Feb 8.

17.

Modifiable Factors to Prevent Prolonged Length of Stay after Sleeve Gastrectomy.

Meneveau M, Mehaffey JH, Adams PD, Turrentine FE, Schirmer B, Hallowell PT.

Obes Surg. 2019 Jun;29(6):1751-1755. doi: 10.1007/s11695-019-03757-z.

PMID:
30715646
18.

Iron-sulfur clusters have no right angles.

Moriarty NW, Adams PD.

Acta Crystallogr D Struct Biol. 2019 Jan 1;75(Pt 1):16-20. doi: 10.1107/S205979831801519X. Epub 2019 Jan 4.

19.

Intergenerational inheritance of high fat diet-induced cardiac lipotoxicity in Drosophila.

Guida MC, Birse RT, Dall'Agnese A, Toto PC, Diop SB, Mai A, Adams PD, Puri PL, Bodmer R.

Nat Commun. 2019 Jan 14;10(1):193. doi: 10.1038/s41467-018-08128-3.

20.

As time flies by: Investigating cardiac aging in the short-lived Drosophila model.

Blice-Baum AC, Guida MC, Hartley PS, Adams PD, Bodmer R, Cammarato A.

Biochim Biophys Acta Mol Basis Dis. 2019 Jul 1;1865(7):1831-1844. doi: 10.1016/j.bbadis.2018.11.010. Epub 2018 Nov 27. Review.

PMID:
30496794
21.

Structures of the intermediates of Kok's photosynthetic water oxidation clock.

Kern J, Chatterjee R, Young ID, Fuller FD, Lassalle L, Ibrahim M, Gul S, Fransson T, Brewster AS, Alonso-Mori R, Hussein R, Zhang M, Douthit L, de Lichtenberg C, Cheah MH, Shevela D, Wersig J, Seuffert I, Sokaras D, Pastor E, Weninger C, Kroll T, Sierra RG, Aller P, Butryn A, Orville AM, Liang M, Batyuk A, Koglin JE, Carbajo S, Boutet S, Moriarty NW, Holton JM, Dobbek H, Adams PD, Bergmann U, Sauter NK, Zouni A, Messinger J, Yano J, Yachandra VK.

Nature. 2018 Nov;563(7731):421-425. doi: 10.1038/s41586-018-0681-2. Epub 2018 Nov 7.

22.

Renewable production of high density jet fuel precursor sesquiterpenes from Escherichia coli.

Liu CL, Tian T, Alonso-Gutierrez J, Garabedian B, Wang S, Baidoo EEK, Benites V, Chen Y, Petzold CJ, Adams PD, Keasling JD, Tan T, Lee TS.

Biotechnol Biofuels. 2018 Oct 20;11:285. doi: 10.1186/s13068-018-1272-z. eCollection 2018.

23.

A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps.

Terwilliger TC, Adams PD, Afonine PV, Sobolev OV.

Nat Methods. 2018 Nov;15(11):905-908. doi: 10.1038/s41592-018-0173-1. Epub 2018 Oct 30.

24.

Author Correction: Jungle Express is a versatile repressor system for tight transcriptional control.

Ruegg TL, Pereira JH, Chen JC, DeGiovanni A, Novichkov P, Mutalik VK, Tomaleri GP, Singer SW, Hillson NJ, Simmons BA, Adams PD, Thelen MP.

Nat Commun. 2018 Oct 30;9(1):4596. doi: 10.1038/s41467-018-07111-2.

25.

Iron- and aluminium-induced depletion of molybdenum in acidic environments impedes the nitrogen cycle.

Ge X, Vaccaro BJ, Thorgersen MP, Poole FL 2nd, Majumder EL, Zane GM, De León KB, Lancaster WA, Moon JW, Paradis CJ, von Netzer F, Stahl DA, Adams PD, Arkin AP, Wall JD, Hazen TC, Adams MWW.

Environ Microbiol. 2019 Jan;21(1):152-163. doi: 10.1111/1462-2920.14435. Epub 2018 Nov 21.

PMID:
30289197
26.

Rapid characterization of the activities of lignin-modifying enzymes based on nanostructure-initiator mass spectrometry (NIMS).

Deng K, Zeng J, Cheng G, Gao J, Sale KL, Simmons BA, Singh AK, Adams PD, Northen TR.

Biotechnol Biofuels. 2018 Sep 27;11:266. doi: 10.1186/s13068-018-1261-2. eCollection 2018.

27.

Distribution of evaluation scores for the models submitted to the second cryo-EM model challenge.

Kryshtafovych A, Monastyrskyy B, Adams PD, Lawson CL, Chiu W.

Data Brief. 2018 Sep 8;20:1629-1638. doi: 10.1016/j.dib.2018.08.214. eCollection 2018 Oct.

28.

DNA Methylation Clocks in Aging: Categories, Causes, and Consequences.

Field AE, Robertson NA, Wang T, Havas A, Ideker T, Adams PD.

Mol Cell. 2018 Sep 20;71(6):882-895. doi: 10.1016/j.molcel.2018.08.008. Review.

29.

New tools for the analysis and validation of cryo-EM maps and atomic models.

Afonine PV, Klaholz BP, Moriarty NW, Poon BK, Sobolev OV, Terwilliger TC, Adams PD, Urzhumtsev A.

Acta Crystallogr D Struct Biol. 2018 Sep 1;74(Pt 9):814-840. doi: 10.1107/S2059798318009324. Epub 2018 Sep 3.

30.

Jungle Express is a versatile repressor system for tight transcriptional control.

Ruegg TL, Pereira JH, Chen JC, DeGiovanni A, Novichkov P, Mutalik VK, Tomaleri GP, Singer SW, Hillson NJ, Simmons BA, Adams PD, Thelen MP.

Nat Commun. 2018 Sep 6;9(1):3617. doi: 10.1038/s41467-018-05857-3. Erratum in: Nat Commun. 2018 Oct 30;9(1):4596.

31.

A Role for p53 in the Adaptation to Glutamine Starvation through the Expression of SLC1A3.

Tajan M, Hock AK, Blagih J, Robertson NA, Labuschagne CF, Kruiswijk F, Humpton TJ, Adams PD, Vousden KH.

Cell Metab. 2018 Nov 6;28(5):721-736.e6. doi: 10.1016/j.cmet.2018.07.005. Epub 2018 Aug 16.

32.

Evaluation of models determined by neutron diffraction and proposed improvements to their validation and deposition.

Liebschner D, Afonine PV, Moriarty NW, Langan P, Adams PD.

Acta Crystallogr D Struct Biol. 2018 Aug 1;74(Pt 8):800-813. doi: 10.1107/S2059798318004588. Epub 2018 Jul 24. Review.

33.

Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge.

Terwilliger TC, Adams PD, Afonine PV, Sobolev OV.

J Struct Biol. 2018 Nov;204(2):338-343. doi: 10.1016/j.jsb.2018.07.016. Epub 2018 Jul 29.

34.

Evaluation system and web infrastructure for the second cryo-EM model challenge.

Kryshtafovych A, Adams PD, Lawson CL, Chiu W.

J Struct Biol. 2018 Oct;204(1):96-108. doi: 10.1016/j.jsb.2018.07.006. Epub 2018 Jul 12.

35.

Engineering glycoside hydrolase stability by the introduction of zinc binding.

Ellinghaus TL, Pereira JH, McAndrew RP, Welner DH, DeGiovanni AM, Guenther JM, Tran HM, Feldman T, Simmons BA, Sale KL, Adams PD.

Acta Crystallogr D Struct Biol. 2018 Jul 1;74(Pt 7):702-710. doi: 10.1107/S2059798318006678. Epub 2018 Jun 27.

36.

From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation.

Afonine PV, Adams PD, Urzhumtsev A.

Acta Crystallogr D Struct Biol. 2018 Jul 1;74(Pt 7):621-631. doi: 10.1107/S2059798318005764. Epub 2018 Jun 8.

37.

Automated map sharpening by maximization of detail and connectivity.

Terwilliger TC, Sobolev OV, Afonine PV, Adams PD.

Acta Crystallogr D Struct Biol. 2018 Jun 1;74(Pt 6):545-559. doi: 10.1107/S2059798318004655. Epub 2018 May 18.

38.

Real-space refinement in PHENIX for cryo-EM and crystallography.

Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD.

Acta Crystallogr D Struct Biol. 2018 Jun 1;74(Pt 6):531-544. doi: 10.1107/S2059798318006551. Epub 2018 May 30.

39.

Discovery of enzymes for toluene synthesis from anoxic microbial communities.

Beller HR, Rodrigues AV, Zargar K, Wu YW, Saini AK, Saville RM, Pereira JH, Adams PD, Tringe SG, Petzold CJ, Keasling JD.

Nat Chem Biol. 2018 May;14(5):451-457. doi: 10.1038/s41589-018-0017-4. Epub 2018 Mar 19.

40.

Integrated analysis of isopentenyl pyrophosphate (IPP) toxicity in isoprenoid-producing Escherichia coli.

George KW, Thompson MG, Kim J, Baidoo EEK, Wang G, Benites VT, Petzold CJ, Chan LJG, Yilmaz S, Turhanen P, Adams PD, Keasling JD, Lee TS.

Metab Eng. 2018 May;47:60-72. doi: 10.1016/j.ymben.2018.03.004. Epub 2018 Mar 9.

PMID:
29530749
41.

DiSCaMB: a software library for aspherical atom model X-ray scattering factor calculations with CPUs and GPUs.

Chodkiewicz ML, Migacz S, Rudnicki W, Makal A, Kalinowski JA, Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Adams PD, Dominiak PM.

J Appl Crystallogr. 2018 Feb 1;51(Pt 1):193-199. doi: 10.1107/S1600576717015825. eCollection 2018 Feb 1.

42.

Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning.

He Z, Zhang P, Wu L, Rocha AM, Tu Q, Shi Z, Wu B, Qin Y, Wang J, Yan Q, Curtis D, Ning D, Van Nostrand JD, Wu L, Yang Y, Elias DA, Watson DB, Adams MWW, Fields MW, Alm EJ, Hazen TC, Adams PD, Arkin AP, Zhou J.

MBio. 2018 Feb 20;9(1). pii: e02435-17. doi: 10.1128/mBio.02435-17.

43.

Employing a biochemical protecting group for a sustainable indigo dyeing strategy.

Hsu TM, Welner DH, Russ ZN, Cervantes B, Prathuri RL, Adams PD, Dueber JE.

Nat Chem Biol. 2018 Mar;14(3):256-261. doi: 10.1038/nchembio.2552. Epub 2018 Jan 8.

44.

Expression of naturally ionic liquid-tolerant thermophilic cellulases in Aspergillus niger.

Amaike Campen S, Lynn J, Sibert SJ, Srikrishnan S, Phatale P, Feldman T, Guenther JM, Hiras J, Tran YTA, Singer SW, Adams PD, Sale KL, Simmons BA, Baker SE, Magnuson JK, Gladden JM.

PLoS One. 2017 Dec 27;12(12):e0189604. doi: 10.1371/journal.pone.0189604. eCollection 2017.

45.

Toward industrial production of isoprenoids in Escherichia coli: Lessons learned from CRISPR-Cas9 based optimization of a chromosomally integrated mevalonate pathway.

Alonso-Gutierrez J, Koma D, Hu Q, Yang Y, Chan LJG, Petzold CJ, Adams PD, Vickers CE, Nielsen LK, Keasling JD, Lee TS.

Biotechnol Bioeng. 2018 Apr;115(4):1000-1013. doi: 10.1002/bit.26530. Epub 2018 Feb 7.

46.

A bacterial pioneer produces cellulase complexes that persist through community succession.

Kolinko S, Wu YW, Tachea F, Denzel E, Hiras J, Gabriel R, Bäcker N, Chan LJG, Eichorst SA, Frey D, Chen Q, Azadi P, Adams PD, Pray TR, Tanjore D, Petzold CJ, Gladden JM, Simmons BA, Singer SW.

Nat Microbiol. 2018 Jan;3(1):99-107. doi: 10.1038/s41564-017-0052-z. Epub 2017 Nov 6.

47.

MolProbity: More and better reference data for improved all-atom structure validation.

Williams CJ, Headd JJ, Moriarty NW, Prisant MG, Videau LL, Deis LN, Verma V, Keedy DA, Hintze BJ, Chen VB, Jain S, Lewis SM, Arendall WB 3rd, Snoeyink J, Adams PD, Lovell SC, Richardson JS, Richardson DC.

Protein Sci. 2018 Jan;27(1):293-315. doi: 10.1002/pro.3330. Epub 2017 Nov 27.

48.

Berkeley Screen: a set of 96 solutions for general macromolecular crystallization.

Pereira JH, McAndrew RP, Tomaleri GP, Adams PD.

J Appl Crystallogr. 2017 Sep 5;50(Pt 5):1352-1358. doi: 10.1107/S1600576717011347. eCollection 2017 Oct 1.

49.

Histone chaperone HIRA deposits histone H3.3 onto foreign viral DNA and contributes to anti-viral intrinsic immunity.

Rai TS, Glass M, Cole JJ, Rather MI, Marsden M, Neilson M, Brock C, Humphreys IR, Everett RD, Adams PD.

Nucleic Acids Res. 2017 Nov 16;45(20):11673-11683. doi: 10.1093/nar/gkx771.

50.

Cytoplasmic chromatin triggers inflammation in senescence and cancer.

Dou Z, Ghosh K, Vizioli MG, Zhu J, Sen P, Wangensteen KJ, Simithy J, Lan Y, Lin Y, Zhou Z, Capell BC, Xu C, Xu M, Kieckhaefer JE, Jiang T, Shoshkes-Carmel M, Tanim KMAA, Barber GN, Seykora JT, Millar SE, Kaestner KH, Garcia BA, Adams PD, Berger SL.

Nature. 2017 Oct 19;550(7676):402-406. doi: 10.1038/nature24050. Epub 2017 Oct 4.

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