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Items: 29

1.

Corrigendum: A novel translational control mechanism involving RNA structures within coding sequences.

Jungfleisch J, Nedialkova DD, Dotu I, Sloan KE, Martinez-Bosch N, Brüning L, Raineri E, Navarro P, Bohnsack MT, Leidel SA, Díez J.

Genome Res. 2017 Apr;27(4):663. doi: 10.1101/gr.222133.117. No abstract available.

2.

Distinct Trends of DNA Methylation Patterning in the Innate and Adaptive Immune Systems.

Schuyler RP, Merkel A, Raineri E, Altucci L, Vellenga E, Martens JHA, Pourfarzad F, Kuijpers TW, Burden F, Farrow S, Downes K, Ouwehand WH, Clarke L, Datta A, Lowy E, Flicek P, Frontini M, Stunnenberg HG, Martín-Subero JI, Gut I, Heath S.

Cell Rep. 2016 Nov 15;17(8):2101-2111. doi: 10.1016/j.celrep.2016.10.054.

3.

Decoding the DNA Methylome of Mantle Cell Lymphoma in the Light of the Entire B Cell Lineage.

Queirós AC, Beekman R, Vilarrasa-Blasi R, Duran-Ferrer M, Clot G, Merkel A, Raineri E, Russiñol N, Castellano G, Beà S, Navarro A, Kulis M, Verdaguer-Dot N, Jares P, Enjuanes A, Calasanz MJ, Bergmann A, Vater I, Salaverría I, van de Werken HJG, Wilson WH, Datta A, Flicek P, Royo R, Martens J, Giné E, Lopez-Guillermo A, Stunnenberg HG, Klapper W, Pott C, Heath S, Gut IG, Siebert R, Campo E, Martín-Subero JI.

Cancer Cell. 2016 Nov 14;30(5):806-821. doi: 10.1016/j.ccell.2016.09.014.

4.

A novel translational control mechanism involving RNA structures within coding sequences.

Jungfleisch J, Nedialkova DD, Dotu I, Sloan KE, Martinez-Bosch N, Brüning L, Raineri E, Navarro P, Bohnsack MT, Leidel SA, Díez J.

Genome Res. 2017 Jan;27(1):95-106. doi: 10.1101/gr.209015.116. Epub 2016 Nov 7. Erratum in: Genome Res. 2017 Apr;27(4):663.

5.

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

Alioto TS, Buchhalter I, Derdak S, Hutter B, Eldridge MD, Hovig E, Heisler LE, Beck TA, Simpson JT, Tonon L, Sertier AS, Patch AM, Jäger N, Ginsbach P, Drews R, Paramasivam N, Kabbe R, Chotewutmontri S, Diessl N, Previti C, Schmidt S, Brors B, Feuerbach L, Heinold M, Gröbner S, Korshunov A, Tarpey PS, Butler AP, Hinton J, Jones D, Menzies A, Raine K, Shepherd R, Stebbings L, Teague JW, Ribeca P, Giner FC, Beltran S, Raineri E, Dabad M, Heath SC, Gut M, Denroche RE, Harding NJ, Yamaguchi TN, Fujimoto A, Nakagawa H, Quesada V, Valdés-Mas R, Nakken S, Vodák D, Bower L, Lynch AG, Anderson CL, Waddell N, Pearson JV, Grimmond SM, Peto M, Spellman P, He M, Kandoth C, Lee S, Zhang J, Létourneau L, Ma S, Seth S, Torrents D, Xi L, Wheeler DA, López-Otín C, Campo E, Campbell PJ, Boutros PC, Puente XS, Gerhard DS, Pfister SM, McPherson JD, Hudson TJ, Schlesner M, Lichter P, Eils R, Jones DT, Gut IG.

Nat Commun. 2015 Dec 9;6:10001. doi: 10.1038/ncomms10001.

6.

Whole-genome fingerprint of the DNA methylome during human B cell differentiation.

Kulis M, Merkel A, Heath S, Queirós AC, Schuyler RP, Castellano G, Beekman R, Raineri E, Esteve A, Clot G, Verdaguer-Dot N, Duran-Ferrer M, Russiñol N, Vilarrasa-Blasi R, Ecker S, Pancaldi V, Rico D, Agueda L, Blanc J, Richardson D, Clarke L, Datta A, Pascual M, Agirre X, Prosper F, Alignani D, Paiva B, Caron G, Fest T, Muench MO, Fomin ME, Lee ST, Wiemels JL, Valencia A, Gut M, Flicek P, Stunnenberg HG, Siebert R, Küppers R, Gut IG, Campo E, Martín-Subero JI.

Nat Genet. 2015 Jul;47(7):746-56. doi: 10.1038/ng.3291. Epub 2015 Jun 8.

7.

Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers.

Agirre X, Castellano G, Pascual M, Heath S, Kulis M, Segura V, Bergmann A, Esteve A, Merkel A, Raineri E, Agueda L, Blanc J, Richardson D, Clarke L, Datta A, Russiñol N, Queirós AC, Beekman R, Rodríguez-Madoz JR, San José-Enériz E, Fang F, Gutiérrez NC, García-Verdugo JM, Robson MI, Schirmer EC, Guruceaga E, Martens JH, Gut M, Calasanz MJ, Flicek P, Siebert R, Campo E, Miguel JF, Melnick A, Stunnenberg HG, Gut IG, Prosper F, Martín-Subero JI.

Genome Res. 2015 Apr;25(4):478-87. doi: 10.1101/gr.180240.114. Epub 2015 Feb 2.

8.

A note on exact differences between beta distributions in genomic (Methylation) studies.

Raineri E, Dabad M, Heath S.

PLoS One. 2014 May 13;9(5):e97349. doi: 10.1371/journal.pone.0097349. eCollection 2014.

9.

The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild.

Prado-Martinez J, Hernando-Herraez I, Lorente-Galdos B, Dabad M, Ramirez O, Baeza-Delgado C, Morcillo-Suarez C, Alkan C, Hormozdiari F, Raineri E, Estellé J, Fernandez-Callejo M, Valles M, Ritscher L, Schöneberg T, de la Calle-Mustienes E, Casillas S, Rubio-Acero R, Melé M, Engelken J, Caceres M, Gomez-Skarmeta JL, Gut M, Bertranpetit J, Gut IG, Abello T, Eichler EE, Mingarro I, Lalueza-Fox C, Navarro A, Marques-Bonet T.

BMC Genomics. 2013 May 31;14:363. doi: 10.1186/1471-2164-14-363.

10.

Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs.

Esteve-Codina A, Paudel Y, Ferretti L, Raineri E, Megens HJ, Silió L, Rodríguez MC, Groenen MA, Ramos-Onsins SE, Pérez-Enciso M.

BMC Genomics. 2013 Mar 5;14:148. doi: 10.1186/1471-2164-14-148.

11.

SNP calling by sequencing pooled samples.

Raineri E, Ferretti L, Esteve-Codina A, Nevado B, Heath S, Pérez-Enciso M.

BMC Bioinformatics. 2012 Sep 20;13:239. doi: 10.1186/1471-2105-13-239.

12.

Modelling and simulating generic RNA-Seq experiments with the flux simulator.

Griebel T, Zacher B, Ribeca P, Raineri E, Lacroix V, Guigó R, Sammeth M.

Nucleic Acids Res. 2012 Nov 1;40(20):10073-83. doi: 10.1093/nar/gks666. Epub 2012 Sep 7.

13.

Neutrality tests for sequences with missing data.

Ferretti L, Raineri E, Ramos-Onsins S.

Genetics. 2012 Aug;191(4):1397-401. doi: 10.1534/genetics.112.139949. Epub 2012 Jun 1.

14.

Fast computation and applications of genome mappability.

Derrien T, Estellé J, Marco Sola S, Knowles DG, Raineri E, Guigó R, Ribeca P.

PLoS One. 2012;7(1):e30377. doi: 10.1371/journal.pone.0030377. Epub 2012 Jan 19.

15.

BlastR--fast and accurate database searches for non-coding RNAs.

Bussotti G, Raineri E, Erb I, Zytnicki M, Wilm A, Beaudoing E, Bucher P, Notredame C.

Nucleic Acids Res. 2011 Sep 1;39(16):6886-95. doi: 10.1093/nar/gkr335. Epub 2011 May 30.

16.

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.

Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg Le Ann, Bouffard P, Burt DW, Crasta O, Crooijmans RP, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, Dong JJ, Evans C, Frederickson KM, Flicek P, Florea L, Folkerts O, Groenen MA, Harkins TT, Herrero J, Hoffmann S, Megens HJ, Jiang A, de Jong P, Kaiser P, Kim H, Kim KW, Kim S, Langenberger D, Lee MK, Lee T, Mane S, Marcais G, Marz M, McElroy AP, Modise T, Nefedov M, Notredame C, Paton IR, Payne WS, Pertea G, Prickett D, Puiu D, Qioa D, Raineri E, Ruffier M, Salzberg SL, Schatz MC, Scheuring C, Schmidt CJ, Schroeder S, Searle SM, Smith EJ, Smith J, Sonstegard TS, Stadler PF, Tafer H, Tu ZJ, Van Tassell CP, Vilella AJ, Williams KP, Yorke JA, Zhang L, Zhang HB, Zhang X, Zhang Y, Reed KM.

PLoS Biol. 2010 Sep 7;8(9). pii: e1000475. doi: 10.1371/journal.pbio.1000475.

17.

Rotation of antimicrobial therapy in the intensive care unit: impact on incidence of ventilator-associated pneumonia caused by antibiotic-resistant Gram-negative bacteria.

Raineri E, Crema L, Dal Zoppo S, Acquarolo A, Pan A, Carnevale G, Albertario F, Candiani A.

Eur J Clin Microbiol Infect Dis. 2010 Aug;29(8):1015-24. doi: 10.1007/s10096-010-0964-5. Epub 2010 Jun 4.

PMID:
20524138
18.

A more precise characterization of chaperonin substrates.

Raineri E, Ribeca P, Serrano L, Maier T.

Bioinformatics. 2010 Jul 15;26(14):1685-9. doi: 10.1093/bioinformatics/btq287. Epub 2010 Jun 2.

PMID:
20519287
19.

Impact of genome reduction on bacterial metabolism and its regulation.

Yus E, Maier T, Michalodimitrakis K, van Noort V, Yamada T, Chen WH, Wodke JA, Güell M, Martínez S, Bourgeois R, Kühner S, Raineri E, Letunic I, Kalinina OV, Rode M, Herrmann R, Gutiérrez-Gallego R, Russell RB, Gavin AC, Bork P, Serrano L.

Science. 2009 Nov 27;326(5957):1263-8. doi: 10.1126/science.1177263.

20.

[Noise-induced hearing loss: are health service surveillance programs always effective?].

Perbellini L, Veronese N, Raineri E, Rava M, Riolfi A.

Med Lav. 2009;100 Suppl 1:20-3. Italian.

PMID:
19848096
21.

Faster exact Markovian probability functions for motif occurrences: a DFA-only approach.

Ribeca P, Raineri E.

Bioinformatics. 2008 Dec 15;24(24):2839-48. doi: 10.1093/bioinformatics/btn525. Epub 2008 Oct 9.

PMID:
18845582
22.

Role of the infectious diseases specialist consultant on the appropriateness of antimicrobial therapy prescription in an intensive care unit.

Raineri E, Pan A, Mondello P, Acquarolo A, Candiani A, Crema L.

Am J Infect Control. 2008 May;36(4):283-90. doi: 10.1016/j.ajic.2007.06.009.

PMID:
18455049
23.

Evolvability and hierarchy in rewired bacterial gene networks.

Isalan M, Lemerle C, Michalodimitrakis K, Horn C, Beltrao P, Raineri E, Garriga-Canut M, Serrano L.

Nature. 2008 Apr 17;452(7189):840-5. doi: 10.1038/nature06847.

24.

Meticillin-resistant Staphylococcus aureus control in an intensive care unit: a 10 year analysis.

Raineri E, Crema L, De Silvestri A, Acquarolo A, Albertario F, Carnevale G, Latronico N, Petrosillo N, Tinelli C, Zoncada A, Pan A.

J Hosp Infect. 2007 Dec;67(4):308-15. Epub 2007 Oct 22.

PMID:
17945395
25.

Non-AIDS-related Kaposi sarcoma tissues do not contain DNA sequences of HHV-6, HHV-7, Epstein-Barr virus, cytomegalovirus and HSV.

Drago F, Raineri E, Rebora A.

Acta Derm Venereol. 1998 Nov;78(6):485. No abstract available.

PMID:
9833064
26.

Blood acetone concentration in "normal people" and in exposed workers 16 h after the end of the workshift.

Wang G, Maranelli G, Perbellini L, Raineri E, Brugnone F.

Int Arch Occup Environ Health. 1994;65(5):285-9.

PMID:
8175181
27.

Blood styrene concentrations in a "normal" population and in exposed workers 16 hours after the end of the workshift.

Brugnone F, Perbellini L, Wang GZ, Maranelli G, Raineri E, De Rosa E, Saletti C, Soave C, Romeo L.

Int Arch Occup Environ Health. 1993;65(2):125-30.

PMID:
8253510
28.

[Nevanide in female climacteric].

RAINERI E.

Dia Med. 1953 Mar 30;25(13):310-2. Undetermined Language. No abstract available.

PMID:
13043489
29.

[Treatment of femal climacteric with nevanide].

RAINERI E.

Rass Medica. 1952 Apr;29(4):60-2. Undetermined Language. No abstract available.

PMID:
12994053

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