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Items: 1 to 20 of 54

1.

Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips.

Wear EE, Song J, Zynda GJ, LeBlanc C, Lee TJ, Mickelson-Young L, Concia L, Mulvaney P, Szymanski ES, Allen GC, Martienssen RA, Vaughn MW, Hanley-Bowdoin L, Thompson WF.

Plant Cell. 2017 Sep;29(9):2126-2149. doi: 10.1105/tpc.17.00037. Epub 2017 Aug 25.

2.

Whole-genome analysis of papillary kidney cancer finds significant noncoding alterations.

Li S, Shuch BM, Gerstein MB.

PLoS Genet. 2017 Mar 30;13(3):e1006685. doi: 10.1371/journal.pgen.1006685. eCollection 2017 Mar.

3.

Choosing panels of genomics assays using submodular optimization.

Wei K, Libbrecht MW, Bilmes JA, Noble WS.

Genome Biol. 2016 Nov 15;17(1):229.

4.

Maps of context-dependent putative regulatory regions and genomic signal interactions.

Diamanti K, Umer HM, Kruczyk M, Dąbrowski MJ, Cavalli M, Wadelius C, Komorowski J.

Nucleic Acids Res. 2016 Nov 2;44(19):9110-9120. Epub 2016 Sep 12.

5.

CHANGE POINT ANALYSIS OF HISTONE MODIFICATIONS REVEALS EPIGENETIC BLOCKS LINKING TO PHYSICAL DOMAINS.

Chen M, Lin H, Zhao H.

Ann Appl Stat. 2016 Mar;10(1):506-526. Epub 2016 Mar 25.

6.

Computing interaction probabilities in signaling networks.

Gabr H, Rivera-Mulia JC, Gilbert DM, Kahveci T.

EURASIP J Bioinform Syst Biol. 2015 Nov 11;2015(1):10. eCollection 2015 Dec.

7.

Simultaneous characterization of sense and antisense genomic processes by the double-stranded hidden Markov model.

Glas J, Dümcke S, Zacher B, Poron D, Gagneur J, Tresch A.

Nucleic Acids Res. 2016 Mar 18;44(5):e44. doi: 10.1093/nar/gkv1184. Epub 2015 Nov 17.

8.

De novo identification of replication-timing domains in the human genome by deep learning.

Liu F, Ren C, Li H, Zhou P, Bo X, Shu W.

Bioinformatics. 2016 Mar 1;32(5):641-9. doi: 10.1093/bioinformatics/btv643. Epub 2015 Nov 5.

9.

Analysis methods for studying the 3D architecture of the genome.

Ay F, Noble WS.

Genome Biol. 2015 Sep 2;16:183. doi: 10.1186/s13059-015-0745-7. Review.

10.

Differential DNA mismatch repair underlies mutation rate variation across the human genome.

Supek F, Lehner B.

Nature. 2015 May 7;521(7550):81-4. doi: 10.1038/nature14173. Epub 2015 Feb 23.

11.

Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression.

Libbrecht MW, Ay F, Hoffman MM, Gilbert DM, Bilmes JA, Noble WS.

Genome Res. 2015 Apr;25(4):544-57. doi: 10.1101/gr.184341.114. Epub 2015 Feb 12.

12.

Embryonic stem cell specific "master" replication origins at the heart of the loss of pluripotency.

Julienne H, Audit B, Arneodo A.

PLoS Comput Biol. 2015 Feb 6;11(2):e1003969. doi: 10.1371/journal.pcbi.1003969. eCollection 2015 Feb.

13.

Hypermutation in human cancer genomes: footprints and mechanisms.

Roberts SA, Gordenin DA.

Nat Rev Cancer. 2014 Dec;14(12):786-800. doi: 10.1038/nrc3816. Review. Erratum in: Nat Rev Cancer. 2015 Nov;15(11):694.

14.

Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle.

Zacher B, Lidschreiber M, Cramer P, Gagneur J, Tresch A.

Mol Syst Biol. 2014 Dec 19;10:768. doi: 10.15252/msb.20145654.

15.

A genome-wide map of adeno-associated virus-mediated human gene targeting.

Deyle DR, Hansen RS, Cornea AM, Li LB, Burt AA, Alexander IE, Sandstrom RS, Stamatoyannopoulos JA, Wei CL, Russell DW.

Nat Struct Mol Biol. 2014 Nov;21(11):969-75. doi: 10.1038/nsmb.2895. Epub 2014 Oct 5.

16.

Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7.

Ebert G, Steininger A, Weißmann R, Boldt V, Lind-Thomsen A, Grune J, Badelt S, Heßler M, Peiser M, Hitzler M, Jensen LR, Müller I, Hu H, Arndt PF, Kuss AW, Tebel K, Ullmann R.

BMC Genomics. 2014 Jun 29;15:537. doi: 10.1186/1471-2164-15-537.

17.

Cancer epigenetics: tumor heterogeneity, plasticity of stem-like states, and drug resistance.

Easwaran H, Tsai HC, Baylin SB.

Mol Cell. 2014 Jun 5;54(5):716-27. doi: 10.1016/j.molcel.2014.05.015. Review.

18.

The spatiotemporal program of DNA replication is associated with specific combinations of chromatin marks in human cells.

Picard F, Cadoret JC, Audit B, Arneodo A, Alberti A, Battail C, Duret L, Prioleau MN.

PLoS Genet. 2014 May 1;10(5):e1004282. doi: 10.1371/journal.pgen.1004282. eCollection 2014 May.

19.

Multiscale representation of genomic signals.

Knijnenburg TA, Ramsey SA, Berman BP, Kennedy KA, Smit AF, Wessels LF, Laird PW, Aderem A, Shmulevich I.

Nat Methods. 2014 Jun;11(6):689-94. doi: 10.1038/nmeth.2924. Epub 2014 Apr 13.

20.

Human genome replication proceeds through four chromatin states.

Julienne H, Zoufir A, Audit B, Arneodo A.

PLoS Comput Biol. 2013;9(10):e1003233. doi: 10.1371/journal.pcbi.1003233. Epub 2013 Oct 10.

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