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Items: 1 to 50 of 87

1.

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling.

Nir G, Farabella I, Pérez Estrada C, Ebeling CG, Beliveau BJ, Sasaki HM, Lee SD, Nguyen SC, McCole RB, Chattoraj S, Erceg J, AlHaj Abed J, Martins NMC, Nguyen HQ, Hannan MA, Russell S, Durand NC, Rao SSP, Kishi JY, Soler-Vila P, Di Pierro M, Onuchic JN, Callahan SP, Schreiner JM, Stuckey JA, Yin P, Aiden EL, Marti-Renom MA, Wu CT.

PLoS Genet. 2018 Dec 26;14(12):e1007872. doi: 10.1371/journal.pgen.1007872. eCollection 2018 Dec.

2.

Communicating Genome Architecture: Biovisualization of the Genome, from Data Analysis and Hypothesis Generation to Communication and Learning.

Goodstadt MN, Marti-Renom MA.

J Mol Biol. 2019 Mar 15;431(6):1071-1087. doi: 10.1016/j.jmb.2018.11.008. Epub 2018 Nov 10. Review.

PMID:
30419242
3.

Challenges and guidelines toward 4D nucleome data and model standards.

Marti-Renom MA, Almouzni G, Bickmore WA, Bystricky K, Cavalli G, Fraser P, Gasser SM, Giorgetti L, Heard E, Nicodemi M, Nollmann M, Orozco M, Pombo A, Torres-Padilla ME.

Nat Genet. 2018 Oct;50(10):1352-1358. doi: 10.1038/s41588-018-0236-3. Epub 2018 Sep 27. Review.

PMID:
30262815
4.

Promoter bivalency favors an open chromatin architecture in embryonic stem cells.

Mas G, Blanco E, Ballaré C, Sansó M, Spill YG, Hu D, Aoi Y, Le Dily F, Shilatifard A, Marti-Renom MA, Di Croce L.

Nat Genet. 2018 Oct;50(10):1452-1462. doi: 10.1038/s41588-018-0218-5. Epub 2018 Sep 17.

PMID:
30224650
5.

Lamin B1 mapping reveals the existence of dynamic and functional euchromatin lamin B1 domains.

Pascual-Reguant L, Blanco E, Galan S, Le Dily F, Cuartero Y, Serra-Bardenys G, Di Carlo V, Iturbide A, Cebrià-Costa JP, Nonell L, de Herreros AG, Di Croce L, Marti-Renom MA, Peiró S.

Nat Commun. 2018 Aug 24;9(1):3420. doi: 10.1038/s41467-018-05912-z.

6.

Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization.

Kojic A, Cuadrado A, De Koninck M, Giménez-Llorente D, Rodríguez-Corsino M, Gómez-López G, Le Dily F, Marti-Renom MA, Losada A.

Nat Struct Mol Biol. 2018 Jun;25(6):496-504. doi: 10.1038/s41594-018-0070-4. Epub 2018 Jun 4.

7.

The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia.

Beekman R, Chapaprieta V, Russiñol N, Vilarrasa-Blasi R, Verdaguer-Dot N, Martens JHA, Duran-Ferrer M, Kulis M, Serra F, Javierre BM, Wingett SW, Clot G, Queirós AC, Castellano G, Blanc J, Gut M, Merkel A, Heath S, Vlasova A, Ullrich S, Palumbo E, Enjuanes A, Martín-García D, Beà S, Pinyol M, Aymerich M, Royo R, Puiggros M, Torrents D, Datta A, Lowy E, Kostadima M, Roller M, Clarke L, Flicek P, Agirre X, Prosper F, Baumann T, Delgado J, López-Guillermo A, Fraser P, Yaspo ML, Guigó R, Siebert R, Martí-Renom MA, Puente XS, López-Otín C, Gut I, Stunnenberg HG, Campo E, Martin-Subero JI.

Nat Med. 2018 Jun;24(6):868-880. doi: 10.1038/s41591-018-0028-4. Epub 2018 May 21.

8.

OneD: increasing reproducibility of Hi-C samples with abnormal karyotypes.

Vidal E, le Dily F, Quilez J, Stadhouders R, Cuartero Y, Graf T, Marti-Renom MA, Beato M, Filion GJ.

Nucleic Acids Res. 2018 May 4;46(8):e49. doi: 10.1093/nar/gky064.

9.

Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming.

Stadhouders R, Vidal E, Serra F, Di Stefano B, Le Dily F, Quilez J, Gomez A, Collombet S, Berenguer C, Cuartero Y, Hecht J, Filion GJ, Beato M, Marti-Renom MA, Graf T.

Nat Genet. 2018 Feb;50(2):238-249. doi: 10.1038/s41588-017-0030-7. Epub 2018 Jan 15.

10.

Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions.

Cattoni DI, Cardozo Gizzi AM, Georgieva M, Di Stefano M, Valeri A, Chamousset D, Houbron C, Déjardin S, Fiche JB, González I, Chang JM, Sexton T, Marti-Renom MA, Bantignies F, Cavalli G, Nollmann M.

Nat Commun. 2017 Nov 24;8(1):1753. doi: 10.1038/s41467-017-01962-x.

11.

Parallel sequencing lives, or what makes large sequencing projects successful.

Quilez J, Vidal E, Dily FL, Serra F, Cuartero Y, Stadhouders R, Graf T, Marti-Renom MA, Beato M, Filion G.

Gigascience. 2017 Nov 1;6(11):1-6. doi: 10.1093/gigascience/gix100.

12.

Challenges for visualizing three-dimensional data in genomic browsers.

Goodstadt M, Marti-Renom MA.

FEBS Lett. 2017 Sep;591(17):2505-2519. doi: 10.1002/1873-3468.12778. Epub 2017 Aug 24. Review.

13.

Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors.

Serra F, Baù D, Goodstadt M, Castillo D, Filion GJ, Marti-Renom MA.

PLoS Comput Biol. 2017 Jul 19;13(7):e1005665. doi: 10.1371/journal.pcbi.1005665. eCollection 2017 Jul.

14.

Rational design of non-resistant targeted cancer therapies.

Martínez-Jiménez F, Overington JP, Al-Lazikani B, Marti-Renom MA.

Sci Rep. 2017 Apr 24;7:46632. doi: 10.1038/srep46632.

15.

Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae.

Trussart M, Yus E, Martinez S, Baù D, Tahara YO, Pengo T, Widjaja M, Kretschmer S, Swoger J, Djordjevic S, Turnbull L, Whitchurch C, Miyata M, Marti-Renom MA, Lluch-Senar M, Serrano L.

Nat Commun. 2017 Mar 8;8:14665. doi: 10.1038/ncomms14665.

16.

Should network biology be used for drug discovery?

Martínez-Jiménez F, Marti-Renom MA.

Expert Opin Drug Discov. 2016 Dec;11(12):1135-1137. Epub 2016 Sep 23. No abstract available.

PMID:
27635856
17.

Biological insertion of computationally designed short transmembrane segments.

Baeza-Delgado C, von Heijne G, Marti-Renom MA, Mingarro I.

Sci Rep. 2016 Mar 18;6:23397. doi: 10.1038/srep23397.

18.

Chromatin and RNA Maps Reveal Regulatory Long Noncoding RNAs in Mouse.

Bogu GK, Vizán P, Stanton LW, Beato M, Di Croce L, Marti-Renom MA.

Mol Cell Biol. 2015 Dec 28;36(5):809-19. doi: 10.1128/MCB.00955-15.

19.

The Conformation of Yeast Chromosome III Is Mating Type Dependent and Controlled by the Recombination Enhancer.

Belton JM, Lajoie BR, Audibert S, Cantaloube S, Lassadi I, Goiffon I, Baù D, Marti-Renom MA, Bystricky K, Dekker J.

Cell Rep. 2015 Dec 1;13(9):1855-67. doi: 10.1016/j.celrep.2015.10.063. Epub 2015 Nov 19.

20.

Release of 50 new, drug-like compounds and their computational target predictions for open source anti-tubercular drug discovery.

Rebollo-Lopez MJ, Lelièvre J, Alvarez-Gomez D, Castro-Pichel J, Martínez-Jiménez F, Papadatos G, Kumar V, Colmenarejo G, Mugumbate G, Hurle M, Barroso V, Young RJ, Martinez-Hoyos M, González del Río R, Bates RH, Lopez-Roman EM, Mendoza-Losana A, Brown JR, Alvarez-Ruiz E, Marti-Renom MA, Overington JP, Cammack N, Ballell L, Barros-Aguire D.

PLoS One. 2015 Dec 7;10(12):e0142293. doi: 10.1371/journal.pone.0142293. eCollection 2015.

21.

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop.

Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CA, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD.

Structure. 2015 Jul 7;23(7):1156-67. doi: 10.1016/j.str.2015.05.013. Epub 2015 Jun 18.

22.

On the demultiplexing of chromosome capture conformation data.

Junier I, Spill YG, Marti-Renom MA, Beato M, le Dily F.

FEBS Lett. 2015 Oct 7;589(20 Pt A):3005-13. doi: 10.1016/j.febslet.2015.05.049. Epub 2015 Jun 6. Review.

23.

Restraint-based three-dimensional modeling of genomes and genomic domains.

Serra F, Di Stefano M, Spill YG, Cuartero Y, Goodstadt M, Baù D, Marti-Renom MA.

FEBS Lett. 2015 Oct 7;589(20 Pt A):2987-95. doi: 10.1016/j.febslet.2015.05.012. Epub 2015 May 14. Review.

24.

Ligand-target prediction by structural network biology using nAnnoLyze.

Martínez-Jiménez F, Marti-Renom MA.

PLoS Comput Biol. 2015 Mar 27;11(3):e1004157. doi: 10.1371/journal.pcbi.1004157. eCollection 2015 Mar.

25.

Assessing the limits of restraint-based 3D modeling of genomes and genomic domains.

Trussart M, Serra F, Baù D, Junier I, Serrano L, Marti-Renom MA.

Nucleic Acids Res. 2015 Apr 20;43(7):3465-77. doi: 10.1093/nar/gkv221. Epub 2015 Mar 23.

26.

Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation.

Le Dily F, Baù D, Pohl A, Vicent GP, Serra F, Soronellas D, Castellano G, Wright RH, Ballare C, Filion G, Marti-Renom MA, Beato M.

Genes Dev. 2014 Oct 1;28(19):2151-62. doi: 10.1101/gad.241422.114.

27.

Target prediction for an open access set of compounds active against Mycobacterium tuberculosis.

Martínez-Jiménez F, Papadatos G, Yang L, Wallace IM, Kumar V, Pieper U, Sali A, Brown JR, Overington JP, Marti-Renom MA.

PLoS Comput Biol. 2013;9(10):e1003253. doi: 10.1371/journal.pcbi.1003253. Epub 2013 Oct 3.

28.

Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis.

Köser CU, Bryant JM, Becq J, Török ME, Ellington MJ, Marti-Renom MA, Carmichael AJ, Parkhill J, Smith GP, Peacock SJ.

N Engl J Med. 2013 Jul 18;369(3):290-2. doi: 10.1056/NEJMc1215305. No abstract available.

29.

A novel family of soluble minimal scaffolds provides structural insight into the catalytic domains of integral membrane metallopeptidases.

López-Pelegrín M, Cerdà-Costa N, Martínez-Jiménez F, Cintas-Pedrola A, Canals A, Peinado JR, Marti-Renom MA, López-Otín C, Arolas JL, Gomis-Rüth FX.

J Biol Chem. 2013 Jul 19;288(29):21279-94. doi: 10.1074/jbc.M113.476580. Epub 2013 Jun 3.

30.

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.

Dekker J, Marti-Renom MA, Mirny LA.

Nat Rev Genet. 2013 Jun;14(6):390-403. doi: 10.1038/nrg3454. Epub 2013 May 9. Review.

31.

Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package.

Kemena C, Bussotti G, Capriotti E, Marti-Renom MA, Notredame C.

Bioinformatics. 2013 May 1;29(9):1112-9. doi: 10.1093/bioinformatics/btt096. Epub 2013 Feb 28.

PMID:
23449094
32.

Polar/Ionizable residues in transmembrane segments: effects on helix-helix packing.

Bañó-Polo M, Baeza-Delgado C, Orzáez M, Marti-Renom MA, Abad C, Mingarro I.

PLoS One. 2012;7(9):e44263. doi: 10.1371/journal.pone.0044263. Epub 2012 Sep 12.

33.

Structure-based statistical analysis of transmembrane helices.

Baeza-Delgado C, Marti-Renom MA, Mingarro I.

Eur Biophys J. 2013 Mar;42(2-3):199-207. doi: 10.1007/s00249-012-0813-9. Epub 2012 May 16.

PMID:
22588483
34.

Genome structure determination via 3C-based data integration by the Integrative Modeling Platform.

Baù D, Marti-Renom MA.

Methods. 2012 Nov;58(3):300-6. doi: 10.1016/j.ymeth.2012.04.004. Epub 2012 Apr 13. Review.

PMID:
22522224
35.

The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation.

Umbarger MA, Toro E, Wright MA, Porreca GJ, Baù D, Hong SH, Fero MJ, Zhu LJ, Marti-Renom MA, McAdams HH, Shapiro L, Dekker J, Church GM.

Mol Cell. 2011 Oct 21;44(2):252-64. doi: 10.1016/j.molcel.2011.09.010.

36.

Impact of Fgd1 and ddn diversity in Mycobacterium tuberculosis complex on in vitro susceptibility to PA-824.

Feuerriegel S, Köser CU, Baù D, Rüsch-Gerdes S, Summers DK, Archer JA, Marti-Renom MA, Niemann S.

Antimicrob Agents Chemother. 2011 Dec;55(12):5718-22. doi: 10.1128/AAC.05500-11. Epub 2011 Sep 19.

37.

Bridging the resolution gap in structural modeling of 3D genome organization.

Marti-Renom MA, Mirny LA.

PLoS Comput Biol. 2011 Jul;7(7):e1002125. doi: 10.1371/journal.pcbi.1002125. Epub 2011 Jul 14. Review.

38.

Membrane protein integration into the endoplasmic reticulum.

Martínez-Gil L, Saurí A, Marti-Renom MA, Mingarro I.

FEBS J. 2011 Oct;278(20):3846-58. doi: 10.1111/j.1742-4658.2011.08185.x. Epub 2011 Jun 13. Review.

39.

Chromatin globules: a common motif of higher order chromosome structure?

Sanyal A, Baù D, Martí-Renom MA, Dekker J.

Curr Opin Cell Biol. 2011 Jun;23(3):325-31. doi: 10.1016/j.ceb.2011.03.009. Epub 2011 Apr 12. Review.

40.

All-atom knowledge-based potential for RNA structure prediction and assessment.

Capriotti E, Norambuena T, Marti-Renom MA, Melo F.

Bioinformatics. 2011 Apr 15;27(8):1086-93. doi: 10.1093/bioinformatics/btr093. Epub 2011 Feb 23.

PMID:
21349865
41.

Structure determination of genomic domains by satisfaction of spatial restraints.

Baù D, Marti-Renom MA.

Chromosome Res. 2011 Jan;19(1):25-35. doi: 10.1007/s10577-010-9167-2. Review.

PMID:
21190133
42.

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules.

Baù D, Sanyal A, Lajoie BR, Capriotti E, Byron M, Lawrence JB, Dekker J, Marti-Renom MA.

Nat Struct Mol Biol. 2011 Jan;18(1):107-14. doi: 10.1038/nsmb.1936. Epub 2010 Dec 5.

43.

N-glycosylation efficiency is determined by the distance to the C-terminus and the amino acid preceding an Asn-Ser-Thr sequon.

Bañó-Polo M, Baldin F, Tamborero S, Marti-Renom MA, Mingarro I.

Protein Sci. 2011 Jan;20(1):179-86. doi: 10.1002/pro.551.

44.

Quantifying the relationship between sequence and three-dimensional structure conservation in RNA.

Capriotti E, Marti-Renom MA.

BMC Bioinformatics. 2010 Jun 15;11:322. doi: 10.1186/1471-2105-11-322.

45.

Alignment of multiple protein structures based on sequence and structure features.

Madhusudhan MS, Webb BM, Marti-Renom MA, Eswar N, Sali A.

Protein Eng Des Sel. 2009 Sep;22(9):569-74. doi: 10.1093/protein/gzp040. Epub 2009 Jul 8.

46.

SARA: a server for function annotation of RNA structures.

Capriotti E, Marti-Renom MA.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W260-5. doi: 10.1093/nar/gkp433. Epub 2009 May 29.

47.

A kernel for open source drug discovery in tropical diseases.

Ortí L, Carbajo RJ, Pieper U, Eswar N, Maurer SM, Rai AK, Taylor G, Todd MH, Pineda-Lucena A, Sali A, Marti-Renom MA.

PLoS Negl Trop Dis. 2009;3(4):e418. doi: 10.1371/journal.pntd.0000418. Epub 2009 Apr 21.

48.

ModLink+: improving fold recognition by using protein-protein interactions.

Fornes O, Aragues R, Espadaler J, Marti-Renom MA, Sali A, Oliva B.

Bioinformatics. 2009 Jun 15;25(12):1506-12. doi: 10.1093/bioinformatics/btp238. Epub 2009 Apr 8.

49.

A kernel for the Tropical Disease Initiative.

Ortí L, Carbajo RJ, Pieper U, Eswar N, Maurer SM, Rai AK, Taylor G, Todd MH, Pineda-Lucena A, Sali A, Marti-Renom MA.

Nat Biotechnol. 2009 Apr;27(4):320-1. doi: 10.1038/nbt0409-320. No abstract available.

50.

MODBASE, a database of annotated comparative protein structure models and associated resources.

Pieper U, Eswar N, Webb BM, Eramian D, Kelly L, Barkan DT, Carter H, Mankoo P, Karchin R, Marti-Renom MA, Davis FP, Sali A.

Nucleic Acids Res. 2009 Jan;37(Database issue):D347-54. doi: 10.1093/nar/gkn791. Epub 2008 Oct 23.

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