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Items: 1 to 20 of 34

1.

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages.

Silva TC, Colaprico A, Olsen C, D'Angelo F, Bontempi G, Ceccarelli M, Noushmehr H.

Version 2. F1000Res. 2016 Jun 29 [revised 2016 Dec 1];5:1542. doi: 10.12688/f1000research.8923.2. eCollection 2016.

2.

Gene Evolutionary Trajectories and GC Patterns Driven by Recombination in Zea mays.

Sundararajan A, Dukowic-Schulze S, Kwicklis M, Engstrom K, Garcia N, Oviedo OJ, Ramaraj T, Gonzales MD, He Y, Wang M, Sun Q, Pillardy J, Kianian SF, Pawlowski WP, Chen C, Mudge J.

Front Plant Sci. 2016 Sep 22;7:1433. eCollection 2016.

3.

Prediction and Validation of Transcription Factors Modulating the Expression of Sestrin3 Gene Using an Integrated Computational and Experimental Approach.

Srivastava R, Zhang Y, Xiong X, Zhang X, Pan X, Dong XC, Liangpunsakul S, Janga SC.

PLoS One. 2016 Jul 28;11(7):e0160228. doi: 10.1371/journal.pone.0160228. eCollection 2016.

4.

Multi-reporter selection for the design of active and more specific zinc-finger nucleases for genome editing.

Oakes BL, Xia DF, Rowland EF, Xu DJ, Ankoudinova I, Borchardt JS, Zhang L, Li P, Miller JC, Rebar EJ, Noyes MB.

Nat Commun. 2016 Jan 7;7:10194. doi: 10.1038/ncomms10194.

5.

NeuroD1 reprograms chromatin and transcription factor landscapes to induce the neuronal program.

Pataskar A, Jung J, Smialowski P, Noack F, Calegari F, Straub T, Tiwari VK.

EMBO J. 2016 Jan 4;35(1):24-45. doi: 10.15252/embj.201591206. Epub 2015 Oct 29.

6.
7.

A Comprehensive Profile of ChIP-Seq-Based PU.1/Spi1 Target Genes in Microglia.

Satoh J, Asahina N, Kitano S, Kino Y.

Gene Regul Syst Bio. 2014 Dec 8;8:127-39. doi: 10.4137/GRSB.S19711. eCollection 2014.

8.

Next-generation sequencing of genomic DNA fragments bound to a transcription factor in vitro reveals its regulatory potential.

Kurihara Y, Makita Y, Kawashima M, Hamasaki H, Yamamoto YY, Matsui M.

Genes (Basel). 2014 Dec 19;5(4):1115-31. doi: 10.3390/genes5041115.

9.

Adaptation to environmental factors shapes the organization of regulatory regions in microbial communities.

Fernandez L, Mercader JM, Planas-Fèlix M, Torrents D.

BMC Genomics. 2014 Oct 8;15:877. doi: 10.1186/1471-2164-15-877.

10.

Novel DNA motif binding activity observed in vivo with an estrogen receptor α mutant mouse.

Hewitt SC, Li L, Grimm SA, Winuthayanon W, Hamilton KJ, Pockette B, Rubel CA, Pedersen LC, Fargo D, Lanz RB, DeMayo FJ, Schütz G, Korach KS.

Mol Endocrinol. 2014 Jun;28(6):899-911. doi: 10.1210/me.2014-1051. Epub 2014 Apr 8.

11.

Bidirectional promoters are the major source of gene activation-associated non-coding RNAs in mammals.

Uesaka M, Nishimura O, Go Y, Nakashima K, Agata K, Imamura T.

BMC Genomics. 2014 Jan 17;15:35. doi: 10.1186/1471-2164-15-35.

12.

T-KDE: a method for genome-wide identification of constitutive protein binding sites from multiple ChIP-seq data sets.

Li Y, Umbach DM, Li L.

BMC Genomics. 2014 Jan 15;15:27. doi: 10.1186/1471-2164-15-27.

13.

Diethylstilbestrol (DES)-stimulated hormonal toxicity is mediated by ERα alteration of target gene methylation patterns and epigenetic modifiers (DNMT3A, MBD2, and HDAC2) in the mouse seminal vesicle.

Li Y, Hamilton KJ, Lai AY, Burns KA, Li L, Wade PA, Korach KS.

Environ Health Perspect. 2014 Mar;122(3):262-8. doi: 10.1289/ehp.1307351. Epub 2013 Dec 6.

14.

Epigenomic enhancer annotation reveals a key role for NFIX in neural stem cell quiescence.

Martynoga B, Mateo JL, Zhou B, Andersen J, Achimastou A, Urbán N, van den Berg D, Georgopoulou D, Hadjur S, Wittbrodt J, Ettwiller L, Piper M, Gronostajski RM, Guillemot F.

Genes Dev. 2013 Aug 15;27(16):1769-86. doi: 10.1101/gad.216804.113.

15.

Characterization of constitutive CTCF/cohesin loci: a possible role in establishing topological domains in mammalian genomes.

Li Y, Huang W, Niu L, Umbach DM, Covo S, Li L.

BMC Genomics. 2013 Aug 14;14:553. doi: 10.1186/1471-2164-14-553.

16.

DNA methylation contributes to natural human variation.

Heyn H, Moran S, Hernando-Herraez I, Sayols S, Gomez A, Sandoval J, Monk D, Hata K, Marques-Bonet T, Wang L, Esteller M.

Genome Res. 2013 Sep;23(9):1363-72. doi: 10.1101/gr.154187.112. Epub 2013 Aug 1.

17.

PairMotif+: a fast and effective algorithm for de novo motif discovery in DNA sequences.

Yu Q, Huo H, Zhang Y, Guo H, Guo H.

Int J Biol Sci. 2013 Apr 29;9(4):412-24. doi: 10.7150/ijbs.5786. Print 2013.

18.

p53 Integrates host defense and cell fate during bacterial pneumonia.

Madenspacher JH, Azzam KM, Gowdy KM, Malcolm KC, Nick JA, Dixon D, Aloor JJ, Draper DW, Guardiola JJ, Shatz M, Menendez D, Lowe J, Lu J, Bushel P, Li L, Merrick BA, Resnick MA, Fessler MB.

J Exp Med. 2013 May 6;210(5):891-904. doi: 10.1084/jem.20121674. Epub 2013 Apr 29.

19.

Novel Foxo1-dependent transcriptional programs control T(reg) cell function.

Ouyang W, Liao W, Luo CT, Yin N, Huse M, Kim MV, Peng M, Chan P, Ma Q, Mo Y, Meijer D, Zhao K, Rudensky AY, Atwal G, Zhang MQ, Li MO.

Nature. 2012 Nov 22;491(7425):554-9. doi: 10.1038/nature11581. Epub 2012 Nov 7.

20.

Motif discovery and transcription factor binding sites before and after the next-generation sequencing era.

Zambelli F, Pesole G, Pavesi G.

Brief Bioinform. 2013 Mar;14(2):225-37. doi: 10.1093/bib/bbs016. Epub 2012 Apr 19.

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