Volume 23; Issue 1

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Genome Research
Volume 23; Issue 1

Genome Research

Volume 23; Issue 1

1

P-value-based regulatory motif discovery using positional weight matrices

Hartmann, H., Guthohrlein, E. W., Siebert, M., Luehr, S., Soding, J.

Journal:

Genome Research

Year:

2013

Language:

english

File:

PDF, 1.78 MB

english, 2013

2

Small noncoding differentially methylated copy-number variants, including lncRNA genes, cause a lethal lung developmental disorder

Szafranski, P., Dharmadhikari, A. V., Brosens, E., Gurha, P., Kolodziejska, K. E., Zhishuo, O., Dittwald, P., Majewski, T., Mohan, K. N., Chen, B., Person, R. E., Tibboel, D., de Klein, A., Pinner, J.

Journal:

Genome Research

Year:

2013

Language:

english

File:

PDF, 864 KB

english, 2013

3

Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases

Schadt, E. E., Banerjee, O., Fang, G., Feng, Z., Wong, W. H., Zhang, X., Kislyuk, A., Clark, T. A., Luong, K., Keren-Paz, A., Chess, A., Kumar, V., Chen-Plotkin, A., Sondheimer, N., Korlach, J., Kasar

Journal:

Genome Research

Year:

2013

Language:

english

File:

PDF, 1.44 MB

english, 2013

4

Efficient targeted mutagenesis in the monarch butterfly using zinc-finger nucleases

Merlin, C., Beaver, L. E., Taylor, O. R., Wolfe, S. A., Reppert, S. M.

Journal:

Genome Research

Year:

2013

Language:

english

File:

PDF, 1.01 MB

english, 2013

5

RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development

Tan, M. H., Au, K. F., Yablonovitch, A. L., Wills, A. E., Chuang, J., Baker, J. C., Wong, W. H., Li, J. B.

Journal:

Genome Research

Year:

2013

Language:

english

File:

PDF, 1.39 MB

english, 2013

6

Genome-wide mapping of human DNA-replication origins: Levels of transcription at ORC1 sites regulate origin selection and replication timing

Dellino, G. I., Cittaro, D., Piccioni, R., Luzi, L., Banfi, S., Segalla, S., Cesaroni, M., Mendoza-Maldonado, R., Giacca, M., Pelicci, P. G.

Journal:

Genome Research

Year:

2013

Language:

english

File:

PDF, 1.21 MB

english, 2013

7

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

Batut, P., Dobin, A., Plessy, C., Carninci, P., Gingeras, T. R.

Journal:

Genome Research

Year:

2013

Language:

english

File:

PDF, 1.63 MB

english, 2013

8

Sequencing the unsequenceable: Expanded CGG-repeat alleles of the fragile X gene

Loomis, E. W., Eid, J. S., Peluso, P., Yin, J., Hickey, L., Rank, D., McCalmon, S., Hagerman, R. J., Tassone, F., Hagerman, P. J.

Journal:

Genome Research

Year:

2013

Language:

english

File:

PDF, 1.47 MB

english, 2013

9

Birth and expression evolution of mammalian microRNA genes

Meunier, J., Lemoine, F., Soumillon, M., Liechti, A., Weier, M., Guschanski, K., Hu, H., Khaitovich, P., Kaessmann, H.

Journal:

Genome Research

Year:

2013

Language:

english

File:

PDF, 1.08 MB

english, 2013

10

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

Sharon, I., Morowitz, M. J., Thomas, B. C., Costello, E. K., Relman, D. A., Banfield, J. F.

Journal:

Genome Research

Year:

2013

Language:

english

File:

PDF, 1.26 MB

english, 2013

11

Haplotype-based profiling of subtle allelic imbalance with SNP arrays

Vattathil, S., Scheet, P.

Journal:

Genome Research

Year:

2013

Language:

english

File:

PDF, 922 KB

english, 2013

12

SOAPindel: Efficient identification of indels from short paired reads

Li, S., Li, R., Li, H., Lu, J., Li, Y., Bolund, L., Schierup, M. H., Wang, J.

Journal:

Genome Research

Year:

2013

Language:

english

File:

PDF, 878 KB

english, 2013

13

Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana

Nolte, V., Pandey, R. V., Kofler, R., Schlotterer, C.

Journal:

Genome Research

Year:

2013

Language:

english

File:

PDF, 1.79 MB

english, 2013

14

Evolutionary dynamism of the primate LRRC37 gene family

Giannuzzi, G., Siswara, P., Malig, M., Marques-Bonet, T., Mullikin, J. C., Ventura, M., Eichler, E. E.

Journal:

Genome Research

Year:

2013

Language:

english

File:

PDF, 1.76 MB

english, 2013

15

GATA3 acts upstream of FOXA1 in mediating ESR1 binding by shaping enhancer accessibility

Theodorou, V., Stark, R., Menon, S., Carroll, J. S.

Journal:

Genome Research

Year:

2013

Language:

english

File:

PDF, 2.23 MB

english, 2013

16

Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictions

Naval-Sanchez, M., Potier, D., Haagen, L., Sanchez, M., Munck, S., Van de Sande, B., Casares, F., Christiaens, V., Aerts, S.

Journal:

Genome Research

Year:

2013

Language:

english

File:

PDF, 2.43 MB

english, 2013

17

Genotype calling and haplotyping in parent-offspring trios

Chen, W., Li, B., Zeng, Z., Sanna, S., Sidore, C., Busonero, F., Kang, H. M., Li, Y., Abecasis, G. R.

Journal:

Genome Research

Year:

2013

Language:

english

File:

PDF, 534 KB

english, 2013

18

A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence

Hu, T. T., Eisen, M. B., Thornton, K. R., Andolfatto, P.

Journal:

Genome Research

Year:

2013

Language:

english

File:

PDF, 19.23 MB

english, 2013

19

Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting

Arnold, P., Scholer, A., Pachkov, M., Balwierz, P. J., Jorgensen, H., Stadler, M. B., van Nimwegen, E., Schubeler, D.

Journal:

Genome Research

Year:

2013

Language:

english

File:

PDF, 1.08 MB

english, 2013