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Items: 1 to 50 of 340

1.

A Theoretical Study on Trehalose + Water Mixtures for Dry Preservation Purposes.

Kumar A, Cincotti A, Aparicio S.

Molecules. 2020 Mar 21;25(6). pii: E1435. doi: 10.3390/molecules25061435.

2.

Theoretical Study on Deep Eutectic Solvents as Vehicles for the Delivery of Anesthetics.

Gutiérrez A, Atilhan M, Aparicio S.

J Phys Chem B. 2020 Mar 5;124(9):1794-1805. doi: 10.1021/acs.jpcb.9b11756. Epub 2020 Feb 24.

PMID:
32049519
3.

Eleven grand challenges in single-cell data science.

Lähnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Campbell KR, Beerenwinkel N, Mahfouz A, Pinello L, Skums P, Stamatakis A, Attolini CS, Aparicio S, Baaijens J, Balvert M, Barbanson B, Cappuccio A, Corleone G, Dutilh BE, Florescu M, Guryev V, Holmer R, Jahn K, Lobo TJ, Keizer EM, Khatri I, Kielbasa SM, Korbel JO, Kozlov AM, Kuo TH, Lelieveldt BPF, Mandoiu II, Marioni JC, Marschall T, Mölder F, Niknejad A, Raczkowski L, Reinders M, Ridder J, Saliba AE, Somarakis A, Stegle O, Theis FJ, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, Schönhuth A.

Genome Biol. 2020 Feb 7;21(1):31. doi: 10.1186/s13059-020-1926-6. Review.

4.

Improving membrane photobioreactor performance by reducing light path: operating conditions and key performance indicators.

González-Camejo J, Aparicio S, Jiménez-Benítez A, Pachés M, Ruano MV, Borrás L, Barat R, Seco A.

Water Res. 2020 Apr 1;172:115518. doi: 10.1016/j.watres.2020.115518. Epub 2020 Jan 21.

PMID:
31991292
5.

Deep Eutectic Solvent Reline at 2D Nanomaterial Interfaces.

Rozas S, Atilhan M, Aparicio S.

J Phys Chem B. 2020 Feb 20;124(7):1197-1206. doi: 10.1021/acs.jpcb.9b08873. Epub 2020 Feb 6.

PMID:
31983208
6.

Nitrite inhibition of microalgae induced by the competition between microalgae and nitrifying bacteria.

González-Camejo J, Montero P, Aparicio S, Ruano MV, Borrás L, Seco A, Barat R.

Water Res. 2020 Apr 1;172:115499. doi: 10.1016/j.watres.2020.115499. Epub 2020 Jan 14.

PMID:
31978839
7.

Identification of a selective DDX3X inhibitor with newly developed quantitative high-throughput RNA helicase assays.

Nakao S, Nogami M, Iwatani M, Imaeda T, Ito M, Tanaka T, Tawada M, Endo S, Cary DR, Ohori M, Imaeda Y, Kawamoto T, Aparicio S, Nakanishi A, Araki S.

Biochem Biophys Res Commun. 2020 Mar 12;523(3):795-801. doi: 10.1016/j.bbrc.2019.12.094. Epub 2020 Jan 15.

8.

Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing.

Laks E, McPherson A, Zahn H, Lai D, Steif A, Brimhall J, Biele J, Wang B, Masud T, Ting J, Grewal D, Nielsen C, Leung S, Bojilova V, Smith M, Golovko O, Poon S, Eirew P, Kabeer F, Ruiz de Algara T, Lee SR, Taghiyar MJ, Huebner C, Ngo J, Chan T, Vatrt-Watts S, Walters P, Abrar N, Chan S, Wiens M, Martin L, Scott RW, Underhill TM, Chavez E, Steidl C, Da Costa D, Ma Y, Coope RJN, Corbett R, Pleasance S, Moore R, Mungall AJ, Mar C, Cafferty F, Gelmon K, Chia S; CRUK IMAXT Grand Challenge Team, Marra MA, Hansen C, Shah SP, Aparicio S.

Cell. 2019 Nov 14;179(5):1207-1221.e22. doi: 10.1016/j.cell.2019.10.026.

9.

Microwire-Based Sensor Array for Measuring Wheel Loads of Vehicles.

Olivera J, Aparicio S, Hernández MG, Zhukov A, Varga R, Campusano M, Echavarria E, Anaya Velayos JJ.

Sensors (Basel). 2019 Oct 26;19(21). pii: E4658. doi: 10.3390/s19214658.

10.

Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses.

O'Flanagan CH, Campbell KR, Zhang AW, Kabeer F, Lim JLP, Biele J, Eirew P, Lai D, McPherson A, Kong E, Bates C, Borkowski K, Wiens M, Hewitson B, Hopkins J, Pham J, Ceglia N, Moore R, Mungall AJ, McAlpine JN; CRUK IMAXT Grand Challenge Team, Shah SP, Aparicio S.

Genome Biol. 2019 Oct 17;20(1):210. doi: 10.1186/s13059-019-1830-0.

11.

A Multisensor System for the Characterization of the Field Pressure in Terrain. Accuracy, Response, and Adjustments.

Sicilia I, Aparicio S, Frutos B, Muñoz E, González M, Anaya JJ.

Sensors (Basel). 2019 Sep 12;19(18). pii: E3942. doi: 10.3390/s19183942.

12.

Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling.

Zhang AW, O'Flanagan C, Chavez EA, Lim JLP, Ceglia N, McPherson A, Wiens M, Walters P, Chan T, Hewitson B, Lai D, Mottok A, Sarkozy C, Chong L, Aoki T, Wang X, Weng AP, McAlpine JN, Aparicio S, Steidl C, Campbell KR, Shah SP.

Nat Methods. 2019 Oct;16(10):1007-1015. doi: 10.1038/s41592-019-0529-1. Epub 2019 Sep 9.

PMID:
31501550
13.

Quantum Chemistry Insight into the Interactions Between Deep Eutectic Solvents and SO2.

Atilhan M, Altamash T, Aparicio S.

Molecules. 2019 Aug 15;24(16). pii: E2963. doi: 10.3390/molecules24162963.

14.

Effect of ambient temperature variations on an indigenous microalgae-nitrifying bacteria culture dominated by Chlorella.

González-Camejo J, Aparicio S, Ruano MV, Borrás L, Barat R, Ferrer J.

Bioresour Technol. 2019 Oct;290:121788. doi: 10.1016/j.biortech.2019.121788. Epub 2019 Jul 11.

PMID:
31326649
15.

Design of arginine-based therapeutic deep eutectic solvents as drug solubilization vehicles for active pharmaceutical ingredients.

Gutiérrez A, Aparicio S, Atilhan M.

Phys Chem Chem Phys. 2019 May 28;21(20):10621-10634. doi: 10.1039/c9cp01408j. Epub 2019 May 13.

PMID:
31080981
16.

Pharmacological systems analysis defines EIF4A3 functions in cell-cycle and RNA stress granule formation.

Mazloomian A, Araki S, Ohori M, El-Naggar AM, Yap D, Bashashati A, Nakao S, Sorensen PH, Nakanishi A, Shah S, Aparicio S.

Commun Biol. 2019 May 3;2:165. doi: 10.1038/s42003-019-0391-9. eCollection 2019.

17.

Dynamics of breast-cancer relapse reveal late-recurring ER-positive genomic subgroups.

Rueda OM, Sammut SJ, Seoane JA, Chin SF, Caswell-Jin JL, Callari M, Batra R, Pereira B, Bruna A, Ali HR, Provenzano E, Liu B, Parisien M, Gillett C, McKinney S, Green AR, Murphy L, Purushotham A, Ellis IO, Pharoah PD, Rueda C, Aparicio S, Caldas C, Curtis C.

Nature. 2019 Mar;567(7748):399-404. doi: 10.1038/s41586-019-1007-8. Epub 2019 Mar 13.

18.

clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers.

Campbell KR, Steif A, Laks E, Zahn H, Lai D, McPherson A, Farahani H, Kabeer F, O'Flanagan C, Biele J, Brimhall J, Wang B, Walters P; IMAXT Consortium, Bouchard-Côté A, Aparicio S, Shah SP.

Genome Biol. 2019 Mar 12;20(1):54. doi: 10.1186/s13059-019-1645-z.

19.

Resource recovery from sulphate-rich sewage through an innovative anaerobic-based water resource recovery facility (WRRF).

Seco A, Aparicio S, González-Camejo J, Jiménez-Benítez A, Mateo O, Mora JF, Noriega-Hevia G, Sanchis-Perucho P, Serna-García R, Zamorano-López N, Giménez JB, Ruiz-Martínez A, Aguado D, Barat R, Borrás L, Bouzas A, Martí N, Pachés M, Ribes J, Robles A, Ruano MV, Serralta J, Ferrer J.

Water Sci Technol. 2018 Dec;78(9):1925-1936. doi: 10.2166/wst.2018.492.

PMID:
30566096
20.

A theoretical study on lidocaine solubility in deep eutectic solvents.

Gutiérrez A, Atilhan M, Aparicio S.

Phys Chem Chem Phys. 2018 Nov 7;20(43):27464-27473. doi: 10.1039/c8cp05641b.

PMID:
30357182
21.

Theoretical Study on Molten Alkali Carbonate Interfaces.

Gutiérrez A, Garroni S, Souentie S, Cuesta-López S, Yakoumis I, Aparicio S.

Langmuir. 2018 Oct 30;34(43):13065-13076. doi: 10.1021/acs.langmuir.8b02907. Epub 2018 Oct 22.

PMID:
30296102
22.

Decoding Transcriptome Dynamics of Genome-Encoded Polyadenylation and Autoregulation with Small-Molecule Modulators of Alternative Polyadenylation.

Araki S, Nakayama Y, Sano O, Nakao S, Shimizu-Ogasawara M, Toyoshiba H, Nakanishi A, Aparicio S.

Cell Chem Biol. 2018 Dec 20;25(12):1470-1484.e5. doi: 10.1016/j.chembiol.2018.09.006. Epub 2018 Oct 4.

23.

Epigenetic Study in Parkinson's Disease: A Pilot Analysis of DNA Methylation in Candidate Genes in Brain.

Navarro-Sánchez L, Águeda-Gómez B, Aparicio S, Pérez-Tur J.

Cells. 2018 Sep 26;7(10). pii: E150. doi: 10.3390/cells7100150.

24.

High-Resolution Single-Cell DNA Methylation Measurements Reveal Epigenetically Distinct Hematopoietic Stem Cell Subpopulations.

Hui T, Cao Q, Wegrzyn-Woltosz J, O'Neill K, Hammond CA, Knapp DJHF, Laks E, Moksa M, Aparicio S, Eaves CJ, Karsan A, Hirst M.

Stem Cell Reports. 2018 Aug 14;11(2):578-592. doi: 10.1016/j.stemcr.2018.07.003. Epub 2018 Aug 2.

25.

Discovery of 3-Benzyl-1-( trans-4-((5-cyanopyridin-2-yl)amino)cyclohexyl)-1-arylurea Derivatives as Novel and Selective Cyclin-Dependent Kinase 12 (CDK12) Inhibitors.

Ito M, Tanaka T, Toita A, Uchiyama N, Kokubo H, Morishita N, Klein MG, Zou H, Murakami M, Kondo M, Sameshima T, Araki S, Endo S, Kawamoto T, Morin GB, Aparicio SA, Nakanishi A, Maezaki H, Imaeda Y.

J Med Chem. 2018 Sep 13;61(17):7710-7728. doi: 10.1021/acs.jmedchem.8b00683. Epub 2018 Aug 20.

PMID:
30067358
26.

Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer.

Zhang AW, McPherson A, Milne K, Kroeger DR, Hamilton PT, Miranda A, Funnell T, Little N, de Souza CPE, Laan S, LeDoux S, Cochrane DR, Lim JLP, Yang W, Roth A, Smith MA, Ho J, Tse K, Zeng T, Shlafman I, Mayo MR, Moore R, Failmezger H, Heindl A, Wang YK, Bashashati A, Grewal DS, Brown SD, Lai D, Wan ANC, Nielsen CB, Huebner C, Tessier-Cloutier B, Anglesio MS, Bouchard-Côté A, Yuan Y, Wasserman WW, Gilks CB, Karnezis AN, Aparicio S, McAlpine JN, Huntsman DG, Holt RA, Nelson BH, Shah SP.

Cell. 2018 Jun 14;173(7):1755-1769.e22. doi: 10.1016/j.cell.2018.03.073. Epub 2018 May 10.

27.

Homologous recombination deficiency and host anti-tumor immunity in triple-negative breast cancer.

Telli ML, Stover DG, Loi S, Aparicio S, Carey LA, Domchek SM, Newman L, Sledge GW, Winer EP.

Breast Cancer Res Treat. 2018 Aug;171(1):21-31. doi: 10.1007/s10549-018-4807-x. Epub 2018 May 7. Review.

PMID:
29736741
28.

A theoretical study on mixtures of amino acid-based ionic liquids.

Herrera C, Atilhan M, Aparicio S.

Phys Chem Chem Phys. 2018 Apr 18;20(15):10213-10223. doi: 10.1039/c7cp08533h.

PMID:
29594303
29.

Nutritional patterns associated with the maintenance of neurocognitive functions and the risk of dementia and Alzheimer's disease: A focus on human studies.

Pistollato F, Iglesias RC, Ruiz R, Aparicio S, Crespo J, Lopez LD, Manna PP, Giampieri F, Battino M.

Pharmacol Res. 2018 May;131:32-43. doi: 10.1016/j.phrs.2018.03.012. Epub 2018 Mar 16. Review.

PMID:
29555333
30.

Associations between genomic stratification of breast cancer and centrally reviewed tumour pathology in the METABRIC cohort.

Mukherjee A, Russell R, Chin SF, Liu B, Rueda OM, Ali HR, Turashvili G, Mahler-Araujo B, Ellis IO, Aparicio S, Caldas C, Provenzano E.

NPJ Breast Cancer. 2018 Mar 7;4:5. doi: 10.1038/s41523-018-0056-8. eCollection 2018.

31.

Molecular Modeling Analysis of CO2 Absorption by Glymes.

Gutiérrez A, Atilhan M, Aparicio S.

J Phys Chem B. 2018 Feb 15;122(6):1948-1957. doi: 10.1021/acs.jpcb.7b10276. Epub 2018 Feb 6.

PMID:
29377697
32.

Are by-products from beeswax recycling process a new promising source of bioactive compounds with biomedical properties?

Giampieri F, Quiles JL, Orantes-Bermejo FJ, Gasparrini M, Forbes-Hernandez TY, Sánchez-González C, Llopis J, Rivas-García L, Afrin S, Varela-López A, Cianciosi D, Reboredo-Rodriguez P, Fernández-Piñar CT, Iglesias RC, Ruiz R, Aparicio S, Crespo J, Dzul Lopez L, Xiao J, Battino M.

Food Chem Toxicol. 2018 Feb;112:126-133. doi: 10.1016/j.fct.2017.12.041. Epub 2017 Dec 25.

PMID:
29284135
33.

Wannier-Mott Excitons in Nanoscale Molecular Ices.

Chen YJ, Muñoz Caro GM, Aparicio S, Jiménez-Escobar A, Lasne J, Rosu-Finsen A, McCoustra MRS, Cassidy AM, Field D.

Phys Rev Lett. 2017 Oct 13;119(15):157703. doi: 10.1103/PhysRevLett.119.157703. Epub 2017 Oct 13.

PMID:
29077429
34.

Engineered in-vitro cell line mixtures and robust evaluation of computational methods for clonal decomposition and longitudinal dynamics in cancer.

Farahani H, de Souza CPE, Billings R, Yap D, Shumansky K, Wan A, Lai D, Mes-Masson AM, Aparicio S, P Shah S.

Sci Rep. 2017 Oct 18;7(1):13467. doi: 10.1038/s41598-017-13338-8.

35.

The use of natural compounds for the targeting and chemoprevention of ovarian cancer.

Pistollato F, Calderón Iglesias R, Ruiz R, Aparicio S, Crespo J, Dzul Lopez L, Giampieri F, Battino M.

Cancer Lett. 2017 Dec 28;411:191-200. doi: 10.1016/j.canlet.2017.09.050. Epub 2017 Oct 7.

PMID:
29017913
36.

Correction to: ReMixT: clone-specific genomic structure estimation in cancer.

McPherson AW, Roth A, Ha G, Chauve C, Steif A, de Souza CPE, Eirew P, Bouchard-Côté A, Aparicio S, Sahinalp SC, Shah SP.

Genome Biol. 2017 Oct 6;18(1):188. doi: 10.1186/s13059-017-1327-7. No abstract available.

37.

Chronic Silymarin, Quercetin and Naringenin Treatments Increase Monoamines Synthesis and Hippocampal Sirt1 Levels Improving Cognition in Aged Rats.

Sarubbo F, Ramis MR, Kienzer C, Aparicio S, Esteban S, Miralles A, Moranta D.

J Neuroimmune Pharmacol. 2018 Mar;13(1):24-38. doi: 10.1007/s11481-017-9759-0. Epub 2017 Aug 14.

PMID:
28808887
38.

ReMixT: clone-specific genomic structure estimation in cancer.

McPherson AW, Roth A, Ha G, Chauve C, Steif A, de Souza CPE, Eirew P, Bouchard-Côté A, Aparicio S, Sahinalp SC, Shah SP.

Genome Biol. 2017 Jul 27;18(1):140. doi: 10.1186/s13059-017-1267-2. Erratum in: Genome Biol. 2017 Oct 6;18(1):188.

39.

Insights into Glycol Ether-Alkanol Mixtures from a Combined Experimental and Theoretical Approach.

Alcalde R, Gutiérrez A, Atilhan M, Trenzado JL, Aparicio S.

J Phys Chem B. 2017 Jun 8;121(22):5601-5612. doi: 10.1021/acs.jpcb.7b03598. Epub 2017 May 26.

PMID:
28520432
40.

Elucidating the Properties of Graphene-Deep Eutectic Solvents Interface.

Atilhan M, Costa LT, Aparicio S.

Langmuir. 2017 May 30;33(21):5154-5165. doi: 10.1021/acs.langmuir.7b00767. Epub 2017 May 16.

PMID:
28485942
41.

Impact of serum HER2, TIMP-1, and CAIX on outcome for HER2+ metastatic breast cancer patients: CCTG MA.31 (lapatinib vs. trastuzumab).

Ho D, Huang J, Chapman JW, Leitzel K, Ali SM, Shepherd L, Parulekar WR, Ellis CE, Crescnzo RJ, Zhu L, Virk S, Nomikos D, Aparicio S, Gelmon KA, Carney WP, Lipton A.

Breast Cancer Res Treat. 2017 Aug;164(3):571-580. doi: 10.1007/s10549-017-4273-x. Epub 2017 May 8.

PMID:
28484925
42.

Discovery and Characterization of a Eukaryotic Initiation Factor 4A-3-Selective Inhibitor That Suppresses Nonsense-Mediated mRNA Decay.

Iwatani-Yoshihara M, Ito M, Ishibashi Y, Oki H, Tanaka T, Morishita D, Ito T, Kimura H, Imaeda Y, Aparicio S, Nakanishi A, Kawamoto T.

ACS Chem Biol. 2017 Jul 21;12(7):1760-1768. doi: 10.1021/acschembio.7b00041. Epub 2017 May 10.

PMID:
28440616
43.

Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes.

Wang YK, Bashashati A, Anglesio MS, Cochrane DR, Grewal DS, Ha G, McPherson A, Horlings HM, Senz J, Prentice LM, Karnezis AN, Lai D, Aniba MR, Zhang AW, Shumansky K, Siu C, Wan A, McConechy MK, Li-Chang H, Tone A, Provencher D, de Ladurantaye M, Fleury H, Okamoto A, Yanagida S, Yanaihara N, Saito M, Mungall AJ, Moore R, Marra MA, Gilks CB, Mes-Masson AM, McAlpine JN, Aparicio S, Huntsman DG, Shah SP.

Nat Genet. 2017 Jun;49(6):856-865. doi: 10.1038/ng.3849. Epub 2017 Apr 24.

PMID:
28436987
44.

Discovery of Novel 1,4-Diacylpiperazines as Selective and Cell-Active eIF4A3 Inhibitors.

Ito M, Tanaka T, Cary DR, Iwatani-Yoshihara M, Kamada Y, Kawamoto T, Aparicio S, Nakanishi A, Imaeda Y.

J Med Chem. 2017 Apr 27;60(8):3335-3351. doi: 10.1021/acs.jmedchem.6b01904. Epub 2017 Apr 11.

PMID:
28358513
45.

CDK12 regulates alternative last exon mRNA splicing and promotes breast cancer cell invasion.

Tien JF, Mazloomian A, Cheng SG, Hughes CS, Chow CCT, Canapi LT, Oloumi A, Trigo-Gonzalez G, Bashashati A, Xu J, Chang VC, Shah SP, Aparicio S, Morin GB.

Nucleic Acids Res. 2017 Jun 20;45(11):6698-6716. doi: 10.1093/nar/gkx187.

46.

Atrophin controls developmental signaling pathways via interactions with Trithorax-like.

Yeung K, Boija A, Karlsson E, Holmqvist PH, Tsatskis Y, Nisoli I, Yap D, Lorzadeh A, Moksa M, Hirst M, Aparicio S, Fanto M, Stenberg P, Mannervik M, McNeill H.

Elife. 2017 Mar 22;6. pii: e23084. doi: 10.7554/eLife.23084.

47.

Local environment structure and dynamics of CO2 in the 1-ethyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide and related ionic liquids.

Lourenço TC, Aparicio S, Costa GC, Costa LT.

J Chem Phys. 2017 Mar 14;146(10):104502. doi: 10.1063/1.4977786.

PMID:
28298100
48.

Discovery of selective ATP-competitive eIF4A3 inhibitors.

Ito M, Iwatani M, Kamada Y, Sogabe S, Nakao S, Tanaka T, Kawamoto T, Aparicio S, Nakanishi A, Imaeda Y.

Bioorg Med Chem. 2017 Apr 1;25(7):2200-2209. doi: 10.1016/j.bmc.2017.02.035. Epub 2017 Feb 20.

PMID:
28283335
49.

ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data.

Salehi S, Steif A, Roth A, Aparicio S, Bouchard-Côté A, Shah SP.

Genome Biol. 2017 Mar 1;18(1):44. doi: 10.1186/s13059-017-1169-3.

50.

CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor.

Funnell T, Tasaki S, Oloumi A, Araki S, Kong E, Yap D, Nakayama Y, Hughes CS, Cheng SG, Tozaki H, Iwatani M, Sasaki S, Ohashi T, Miyazaki T, Morishita N, Morishita D, Ogasawara-Shimizu M, Ohori M, Nakao S, Karashima M, Sano M, Murai A, Nomura T, Uchiyama N, Kawamoto T, Hara R, Nakanishi O, Shumansky K, Rosner J, Wan A, McKinney S, Morin GB, Nakanishi A, Shah S, Toyoshiba H, Aparicio S.

Nat Commun. 2017 Feb 23;8(1):7. doi: 10.1038/s41467-016-0008-7.

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