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Items: 1 to 50 of 57

1.

SPRING: A next-generation compressor for FASTQ data.

Chandak S, Tatwawadi K, Ochoa I, Hernaez M, Weissman T.

Bioinformatics. 2018 Dec 7. doi: 10.1093/bioinformatics/bty1015. [Epub ahead of print]

PMID:
30535063
2.

Cell-type specific polysome profiling from mammalian tissues.

Seimetz J, Arif W, Bangru S, Hernaez M, Kalsotra A.

Methods. 2018 Nov 27. pii: S1046-2023(18)30226-3. doi: 10.1016/j.ymeth.2018.11.015. [Epub ahead of print]

PMID:
30500367
3.

Identification of the Missing Protein Hyaluronan Synthase 1 in Human Mesenchymal Stem Cells Derived from Adipose Tissue or Umbilical Cord.

Clemente LF, Hernáez ML, Ramos-Fernández A, Ligero G, Gil C, Corrales FJ, Marcilla M.

J Proteome Res. 2018 Jul 6. doi: 10.1021/acs.jproteome.8b00384. [Epub ahead of print]

PMID:
29974749
4.

Unraveling Gardnerella vaginalis Surface Proteins Using Cell Shaving Proteomics.

Marín E, Haesaert A, Padilla L, Adán J, Hernáez ML, Monteoliva L, Gil C.

Front Microbiol. 2018 May 15;9:975. doi: 10.3389/fmicb.2018.00975. eCollection 2018.

5.

SILAC-based phosphoproteomics reveals new PP2A-Cdc55-regulated processes in budding yeast.

Baro B, Játiva S, Calabria I, Vinaixa J, Bech-Serra JJ, de LaTorre C, Rodrigues J, Hernáez ML, Gil C, Barceló-Batllori S, Larsen MR, Queralt E.

Gigascience. 2018 May 1;7(5). doi: 10.1093/gigascience/giy047.

6.

FaStore: a space-saving solution for raw sequencing data.

Roguski L, Ochoa I, Hernaez M, Deorowicz S.

Bioinformatics. 2018 Aug 15;34(16):2748-2756. doi: 10.1093/bioinformatics/bty205.

PMID:
29617939
7.

Graphene Oxide in Lossy Mode Resonance-Based Optical Fiber Sensors for Ethanol Detection.

Hernaez M, Mayes AG, Melendi-Espina S.

Sensors (Basel). 2017 Dec 27;18(1). pii: E58. doi: 10.3390/s18010058.

8.

CALQ: compression of quality values of aligned sequencing data.

Voges J, Ostermann J, Hernaez M.

Bioinformatics. 2018 May 15;34(10):1650-1658. doi: 10.1093/bioinformatics/btx737.

PMID:
29186284
9.

QVZ: lossy compression of quality values.

Malysa G, Hernaez M, Ochoa I, Rao M, Ganesan K, Weissman T.

Bioinformatics. 2018 Jan 1;34(1):179. doi: 10.1093/bioinformatics/btx654. No abstract available.

10.

GeneComp, a new reference-based compressor for SAM files.

Long R, Hernaez M, Ochoa I, Weissman T.

Proc Data Compress Conf. 2017 Apr;2017:330-339. doi: 10.1109/DCC.2017.76. Epub 2017 May 11.

11.

Micro and Nanostructured Materials for the Development of Optical Fibre Sensors.

Elosua C, Arregui FJ, Villar ID, Ruiz-Zamarreño C, Corres JM, Bariain C, Goicoechea J, Hernaez M, Rivero PJ, Socorro AB, Urrutia A, Sanchez P, Zubiate P, Lopez-Torres D, Acha N, Ascorbe J, Ozcariz A, Matias IR.

Sensors (Basel). 2017 Oct 11;17(10). pii: E2312. doi: 10.3390/s17102312. Review.

12.

Optical Fibre Sensors Using Graphene-Based Materials: A Review.

Hernaez M, Zamarreño CR, Melendi-Espina S, Bird LR, Mayes AG, Arregui FJ.

Sensors (Basel). 2017 Jan 14;17(1). pii: E155. doi: 10.3390/s17010155. Review.

13.

A multicentric study to evaluate the use of relative retention times in targeted proteomics.

Vialas V, Colomé-Calls N, Abian J, Aloria K, Alvarez-Llamas G, Antúnez O, Arizmendi JM, Azkargorta M, Barceló-Batllori S, Barderas MG, Blanco F, Casal JI, Casas V, de la Torre C, Chicano-Gálvez E, Elortza F, Espadas G, Estanyol JM, Fernandez-Irigoyen J, Fernandez-Puente P, Fidalgo MJ, Fuentes M, Gay M, Gil C, Hainard A, Hernaez ML, Ibarrola N, Kopylov AT, Lario A, Lopez JA, López-Lucendo M, Marcilla M, Marina-Ramírez A, Marko-Varga G, Martín L, Mora MI, Morato-López E, Muñoz J, Odena MA, de Oliveira E, Orera I, Ortea I, Pasquarello C, Ray KB, Rezeli M, Ruppen I, Sabidó E, Del Pino MMS, Sancho J, Santamaría E, Vazquez J, Vilaseca M, Vivanco F, Walters JJ, Zgoda VG, Corrales FJ, Canals F, Paradela A.

J Proteomics. 2017 Jan 30;152:138-149. doi: 10.1016/j.jprot.2016.10.014. Epub 2016 Oct 29.

PMID:
27989941
14.

GTRAC: fast retrieval from compressed collections of genomic variants.

Tatwawadi K, Hernaez M, Ochoa I, Weissman T.

Bioinformatics. 2016 Sep 1;32(17):i479-i486. doi: 10.1093/bioinformatics/btw437.

15.

CROMqs: an infinitesimal successive refinement lossy compressor for the quality scores.

Ochoa I, No A, Hernaez M, Weissman T.

Proc Inf Theory Workshop. 2016 Sep;2016:121-125. doi: 10.1109/ITW.2016.7606808. Epub 2016 Oct 27.

16.

Effect of lossy compression of quality scores on variant calling.

Ochoa I, Hernaez M, Goldfeder R, Weissman T, Ashley E.

Brief Bioinform. 2017 Mar 1;18(2):183-194. doi: 10.1093/bib/bbw011.

17.

Denoising of Quality Scores for Boosted Inference and Reduced Storage.

Ochoa I, Hernaez M, Goldfeder R, Weissman T, Ashley E.

Proc Data Compress Conf. 2016 Mar-Apr;2016:251-260. doi: 10.1109/DCC.2016.92. Epub 2016 Dec 19.

18.

A cluster-based approach to compression of Quality Scores.

Hernaez M, Ochoa I, Weissman T.

Proc Data Compress Conf. 2016 Mar-Apr;2016:261-270. doi: 10.1109/DCC.2016.49. Epub 2016 Dec 19.

19.

An Evaluation Framework for Lossy Compression of Genome Sequencing Quality Values.

Alberti C, Daniels N, Hernaez M, Voges J, Goldfeder RL, Hernandez-Lopez AA, Mattavelli M, Berger B.

Proc Data Compress Conf. 2016 Mar-Apr;2016:221-230. doi: 10.1109/DCC.2016.39. Epub 2016 Dec 19.

20.

Candida albicans Shaving to Profile Human Serum Proteins on Hyphal Surface.

Marín E, Parra-Giraldo CM, Hernández-Haro C, Hernáez ML, Nombela C, Monteoliva L, Gil C.

Front Microbiol. 2015 Dec 8;6:1343. doi: 10.3389/fmicb.2015.01343. eCollection 2015.

21.

Comment on: 'ERGC: an efficient referential genome compression algorithm'.

Deorowicz S, Grabowski S, Ochoa I, Hernaez M, Weissman T.

Bioinformatics. 2016 Apr 1;32(7):1115-7. doi: 10.1093/bioinformatics/btv704. Epub 2015 Nov 28.

22.

Quantitative differential proteomics of yeast extracellular matrix: there is more to it than meets the eye.

Faria-Oliveira F, Carvalho J, Ferreira C, Hernáez ML, Gil C, Lucas C.

BMC Microbiol. 2015 Nov 25;15:271. doi: 10.1186/s12866-015-0550-1.

23.

A comprehensive Candida albicans PeptideAtlas build enables deep proteome coverage.

Vialas V, Sun Z, Reales-Calderón JA, Hernáez ML, Casas V, Carrascal M, Abián J, Monteoliva L, Deutsch EW, Moritz RL, Gil C.

J Proteomics. 2016 Jan 10;131:122-130. doi: 10.1016/j.jprot.2015.10.019. Epub 2015 Oct 19.

24.

In Vitro Transcription/Translation System: A Versatile Tool in the Search for Missing Proteins.

Horvatovich P, Végvári Á, Saul J, Park JG, Qiu J, Syring M, Pirrotte P, Petritis K, Tegeler TJ, Aziz M, Fuentes M, Diez P, Gonzalez-Gonzalez M, Ibarrola N, Droste C, De Las Rivas J, Gil C, Clemente F, Hernaez ML, Corrales FJ, Nilsson CL, Berven FS, Bischoff R, Fehniger TE, LaBaer J, Marko-Varga G.

J Proteome Res. 2015 Sep 4;14(9):3441-51. doi: 10.1021/acs.jproteome.5b00486. Epub 2015 Jul 28.

PMID:
26155874
25.

Candida albicans cell shaving uncovers new proteins involved in cell wall integrity, yeast to hypha transition, stress response and host-pathogen interaction.

Gil-Bona A, Parra-Giraldo CM, Hernáez ML, Reales-Calderon JA, Solis NV, Filler SG, Monteoliva L, Gil C.

J Proteomics. 2015 Sep 8;127(Pt B):340-351. doi: 10.1016/j.jprot.2015.06.006. Epub 2015 Jun 15.

26.

QVZ: lossy compression of quality values.

Malysa G, Hernaez M, Ochoa I, Rao M, Ganesan K, Weissman T.

Bioinformatics. 2015 Oct 1;31(19):3122-9. doi: 10.1093/bioinformatics/btv330. Epub 2015 May 28. Erratum in: Bioinformatics. 2018 Jan 1;34(1):179.

27.

Aligned genomic data compression via improved modeling.

Ochoa I, Hernaez M, Weissman T.

J Bioinform Comput Biol. 2014 Dec;12(6):1442002. doi: 10.1142/S0219720014420025.

28.

iDoComp: a compression scheme for assembled genomes.

Ochoa I, Hernaez M, Weissman T.

Bioinformatics. 2015 Mar 1;31(5):626-33. doi: 10.1093/bioinformatics/btu698. Epub 2014 Oct 24.

29.

Methodologies to generate, extract, purify and fractionate yeast ECM for analytical use in proteomics and glycomics.

Faria-Oliveira F, Carvalho J, Belmiro CL, Martinez-Gomariz M, Hernaez ML, Pavão M, Gil C, Lucas C, Ferreira C.

BMC Microbiol. 2014 Oct 25;14:244. doi: 10.1186/s12866-014-0244-0.

30.

General statistical framework for quantitative proteomics by stable isotope labeling.

Navarro P, Trevisan-Herraz M, Bonzon-Kulichenko E, Núñez E, Martínez-Acedo P, Pérez-Hernández D, Jorge I, Mesa R, Calvo E, Carrascal M, Hernáez ML, García F, Bárcena JA, Ashman K, Abian J, Gil C, Redondo JM, Vázquez J.

J Proteome Res. 2014 Mar 7;13(3):1234-47. doi: 10.1021/pr4006958. Epub 2014 Feb 10.

PMID:
24512137
31.

Numerical assessment of the dispersion of overspilled sediment from a dredge barge and its sensitivity to various parameters.

Mestres M, Sierra JP, Mösso C, Sánchez-Arcilla A, Hernáez M, Morales J.

Mar Pollut Bull. 2014 Feb 15;79(1-2):225-35. doi: 10.1016/j.marpolbul.2013.12.009. Epub 2013 Dec 21.

PMID:
24365453
32.

Comparative study of layer-by-layer deposition techniques for poly(sodium phosphate) and poly(allylamine hydrochloride).

Elosua C, Lopez-Torres D, Hernaez M, Matias IR, Arregui FJ.

Nanoscale Res Lett. 2013 Dec 20;8(1):539. doi: 10.1186/1556-276X-8-539.

33.

Dual Regulation of the mitotic exit network (MEN) by PP2A-Cdc55 phosphatase.

Baro B, Rodriguez-Rodriguez JA, Calabria I, Hernáez ML, Gil C, Queralt E.

PLoS Genet. 2013;9(12):e1003966. doi: 10.1371/journal.pgen.1003966. Epub 2013 Dec 5.

34.

Surfing transcriptomic landscapes. A step beyond the annotation of chromosome 16 proteome.

Segura V, Medina-Aunon JA, Mora MI, Martínez-Bartolomé S, Abian J, Aloria K, Antúnez O, Arizmendi JM, Azkargorta M, Barceló-Batllori S, Beaskoetxea J, Bech-Serra JJ, Blanco F, Monteiro MB, Cáceres D, Canals F, Carrascal M, Casal JI, Clemente F, Colomé N, Dasilva N, Díaz P, Elortza F, Fernández-Puente P, Fuentes M, Gallardo O, Gharbi SI, Gil C, González-Tejedo C, Hernáez ML, Lombardía M, Lopez-Lucendo M, Marcilla M, Mato JM, Mendes M, Oliveira E, Orera I, Pascual-Montano A, Prieto G, Ruiz-Romero C, Sánchez del Pino MM, Tabas-Madrid D, Valero ML, Vialas V, Villanueva J, Albar JP, Corrales FJ.

J Proteome Res. 2014 Jan 3;13(1):158-72. doi: 10.1021/pr400721r. Epub 2013 Nov 5.

PMID:
24138474
35.

Guidelines for reporting quantitative mass spectrometry based experiments in proteomics.

Martínez-Bartolomé S, Deutsch EW, Binz PA, Jones AR, Eisenacher M, Mayer G, Campos A, Canals F, Bech-Serra JJ, Carrascal M, Gay M, Paradela A, Navajas R, Marcilla M, Hernáez ML, Gutiérrez-Blázquez MD, Velarde LF, Aloria K, Beaskoetxea J, Medina-Aunon JA, Albar JP.

J Proteomics. 2013 Dec 16;95:84-8. doi: 10.1016/j.jprot.2013.02.026. Epub 2013 Mar 14.

PMID:
23500130
36.

Phosphoproteomic analysis of protein kinase C signaling in Saccharomyces cerevisiae reveals Slt2 mitogen-activated protein kinase (MAPK)-dependent phosphorylation of eisosome core components.

Mascaraque V, Hernáez ML, Jiménez-Sánchez M, Hansen R, Gil C, Martín H, Cid VJ, Molina M.

Mol Cell Proteomics. 2013 Mar;12(3):557-74. doi: 10.1074/mcp.M112.020438. Epub 2012 Dec 9.

37.

Design rules for lossy mode resonance based sensors.

Del Villar I, Hernaez M, Zamarreño CR, Sánchez P, Fernández-Valdivielso C, Arregui FJ, Matias IR.

Appl Opt. 2012 Jul 1;51(19):4298-307. doi: 10.1364/AO.51.004298.

PMID:
22772101
38.

Differential carbonylation of cytoskeletal proteins in blood group O erythrocytes: potential role in protection against severe malaria.

Méndez D, Hernáez ML, Kamali AN, Diez A, Puyet A, Bautista JM.

Infect Genet Evol. 2012 Dec;12(8):1780-7. doi: 10.1016/j.meegid.2012.06.013. Epub 2012 Jul 4.

PMID:
22771625
39.

Optical fiber refractometers based on indium tin oxide coatings fabricated by sputtering.

Lopez S, del Villar I, Ruiz Zamarreño C, Hernaez M, Arregui FJ, Matias IR.

Opt Lett. 2012 Jan 1;37(1):28-30. doi: 10.1364/OL.37.000028.

PMID:
22212780
40.

Quantitative proteome and acidic subproteome profiling of Candida albicans yeast-to-hypha transition.

Monteoliva L, Martinez-Lopez R, Pitarch A, Hernaez ML, Serna A, Nombela C, Albar JP, Gil C.

J Proteome Res. 2011 Feb 4;10(2):502-17. doi: 10.1021/pr100710g. Epub 2010 Dec 31.

PMID:
21133346
41.

Resonances in coated long period fiber gratings and cladding removed multimode optical fibers: a comparative study.

Del Villar I, Zamarreño CR, Hernaez M, Arregui FJ, Matias IR.

Opt Express. 2010 Sep 13;18(19):20183-9. doi: 10.1364/OE.18.020183.

PMID:
20940909
42.

Combined proteomic approaches for the identification of specific amino acid residues modified by 4-hydroxy-2-nonenal under physiological conditions.

Mendez D, Hernaez ML, Diez A, Puyet A, Bautista JM.

J Proteome Res. 2010 Nov 5;9(11):5770-81. doi: 10.1021/pr100555v. Epub 2010 Oct 8.

PMID:
20818828
43.

Optical fiber refractometers based on lossy mode resonances supported by TiO2 coatings.

Hernáez M, Del Villar I, Zamarreño CR, Arregui FJ, Matias IR.

Appl Opt. 2010 Jul 10;49(20):3980-5. doi: 10.1364/AO.49.003980.

PMID:
20648176
44.

Gel and gel-free proteomics to identify Saccharomyces cerevisiae cell surface proteins.

Insenser MR, Hernáez ML, Nombela C, Molina M, Molero G, Gil C.

J Proteomics. 2010 Apr 18;73(6):1183-95. doi: 10.1016/j.jprot.2010.02.005. Epub 2010 Feb 20.

PMID:
20176154
45.

Identification of Candida albicans exposed surface proteins in vivo by a rapid proteomic approach.

Hernáez ML, Ximénez-Embún P, Martínez-Gomariz M, Gutiérrez-Blázquez MD, Nombela C, Gil C.

J Proteomics. 2010 May 7;73(7):1404-9. doi: 10.1016/j.jprot.2010.02.008. Epub 2010 Feb 16.

PMID:
20167299
46.

Tetralin-induced and ThnR-regulated aldehyde dehydrogenase and beta-oxidation genes in Sphingomonas macrogolitabida strain TFA.

López-Sánchez A, Floriano B, Andújar E, Hernáez MJ, Santero E.

Appl Environ Microbiol. 2010 Jan;76(1):110-8. doi: 10.1128/AEM.01846-09. Epub 2009 Nov 6.

47.

Proteomic analysis by two-dimensional differential gel electrophoresis (2D DIGE) of a high-pressure effect in Bacillus cereus.

Martínez-Gomariz M, Hernáez ML, Gutiérrez D, Ximénez-Embún P, Préstamo G.

J Agric Food Chem. 2009 May 13;57(9):3543-9. doi: 10.1021/jf803272a.

PMID:
19338277
48.

[Molecular and genetic aspects of resistance to azoles in Candida albicans].

Hernáez ML, Pla J, Nombela C.

Rev Iberoam Micol. 1997 Dec;14(4):150-4. Spanish.

49.
50.

Identification of a hydratase and a class II aldolase involved in biodegradation of the organic solvent tetralin.

Hernáez MJ, Floriano B, Ríos JJ, Santero E.

Appl Environ Microbiol. 2002 Oct;68(10):4841-6.

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