Publications/Publikationen

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[1] Ernst, M., Abu Dawud, R., Kurtz, A., Schotta, G., Taher, L., and Fuellen, G. Comparative computational analysis of pluripotency in human and mouse stem cells. Sci Rep 5 (2015), 7927.
[2] Furusawa, T., Rochman, M., Taher, L., Dimitriadis, E. K., Nagashima, K., Anderson, S., and Bustin, M. Chromatin decompaction by the nucleosomal binding protein HMGN5 impairs nuclear sturdiness. Nat Commun 6 (2015), 6138.
[3] Pfeiffer, M. J., Taher, L., Drexler, H., Suzuki, Y., Maka?owski, W., Schwarzer, C., Wang, B., Fuellen, G., and Boiani, M. Differences in embryo quality are associated with differences in oocyte composition: a proteomic study in inbred mice. Proteomics 15, 4 (Feb 2015), 675--687.
[4] Taher, L., Narlikar, L., and Ovcharenko, I. Identification and computational analysis of gene regulatory elements. Cold Spring Harb Protoc 2015, 1 (Jan 2015), pdb.top083642.
[5] Taher, L., Pfeiffer, M. J., and Fuellen, G. Bioinformatics approaches to single-blastomere transcriptomics. Mol. Hum. Reprod. 21, 2 (Feb 2015), 115--125.
[6] Pattabiraman, K., Golonzhka, O., Lindtner, S., Nord, A. S., Taher, L., Hoch, R., Silberberg, S. N., Zhang, D., Chen, B., Zeng, H., Pennacchio, L. A., Puelles, L., Visel, A., and Rubenstein, J. L. Transcriptional regulation of enhancers active in protodomains of the developing cerebral cortex. Neuron 82, 5 (Jun 2014), 989--1003.
[7] Collette, N. M., Yee, C. S., Murugesh, D., Sebastian, A., Taher, L., Gale, N. W., Economides, A. N., Harland, R. M., and Loots, G. G. Sost and its paralog Sostdc1 coordinate digit number in a Gli3-dependent manner. Dev. Biol. 383, 1 (Nov 2013), 90--105.
[8] Singh, N. K., Repsilber, D., Liebscher, V., Taher, L., and Fuellen, G. Identifying genes relevant to specific biological conditions in time course microarray experiments. PLoS ONE 8, 10 (2013), e76561.
[9] Smith, R. P., Taher, L., Patwardhan, R. P., Kim, M. J., Inoue, F., Shendure, J., Ovcharenko, I., and Ahituv, N. Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model. Nat. Genet. 45, 9 (Sep 2013), 1021--1028.
[10] Taher, L., Smith, R. P., Kim, M. J., Ahituv, N., and Ovcharenko, I. Sequence signatures extracted from proximal promoters can be used to predict distal enhancers. Genome Biol. 14, 10 (2013), R117.
[11] Visel, A., Taher, L., Girgis, H., May, D., Golonzhka, O., Hoch, R. V., McKinsey, G. L., Pattabiraman, K., Silberberg, S. N., Blow, M. J., Hansen, D. V., Nord, A. S., Akiyama, J. A., Holt, A., Hosseini, R., Phouanenavong, S., Plajzer-Frick, I., Shoukry, M., Afzal, V., Kaplan, T., Kriegstein, A. R., Rubin, E. M., Ovcharenko, I., Pennacchio, L. A., and Rubenstein, J. L. A high-resolution enhancer atlas of the developing telencephalon. Cell 152, 4 (Feb 2013), 895--908.
[12] Burzynski, G. M., Reed, X., Taher, L., Stine, Z. E., Matsui, T., Ovcharenko, I., and McCallion, A. S. Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control. Genome Res. 22, 11 (Nov 2012), 2278--2289.
[13] Busser, B. W., Taher, L., Kim, Y., Tansey, T., Bloom, M. J., Ovcharenko, I., and Michelson, A. M. A machine learning approach for identifying novel cell type-specific transcriptional regulators of myogenesis. PLoS Genet. 8, 3 (2012), e1002531.
[14] Taher, L., Narlikar, L., and Ovcharenko, I. CLARE: Cracking the LAnguage of Regulatory Elements. Bioinformatics 28, 4 (Feb 2012), 581--583.
[15] Rochman, M., Taher, L., Kurahashi, T., Cherukuri, S., Uversky, V. N., Landsman, D., Ovcharenko, I., and Bustin, M. Effects of HMGN variants on the cellular transcription profile. Nucleic Acids Res. 39, 10 (May 2011), 4076--4087.
[16] Martin, D., Pantoja, C., Fernandez Minan, A., Valdes-Quezada, C., Molto, E., Matesanz, F., Bogdanovi?, O., de la Calle-Mustienes, E., Dominguez, O., Taher, L., Furlan-Magaril, M., Alcina, A., Canon, S., Fedetz, M., Blasco, M. A., Pereira, P. S., Ovcharenko, I., Recillas-Targa, F., Montoliu, L., Manzanares, M., Guigo, R., Serrano, M., Casares, F., and Gomez-Skarmeta, J. L. Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes. Nat. Struct. Mol. Biol. 18, 6 (Jun 2011), 708--714.
[17] Taher, L., Collette, N. M., Murugesh, D., Maxwell, E., Ovcharenko, I., and Loots, G. G. Global gene expression analysis of murine limb development. PLoS ONE 6, 12 (2011), e28358.
[18] Taher, L., McGaughey, D. M., Maragh, S., Aneas, I., Bessling, S. L., Miller, W., Nobrega, M. A., McCallion, A. S., and Ovcharenko, I. Genome-wide identification of conserved regulatory function in diverged sequences. Genome Res. 21, 7 (Jul 2011), 1139--1149.
[19] Hellsten, U., Harland, R. M., Gilchrist, M. J., Hendrix, D., Jurka, J., Kapitonov, V., Ovcharenko, I., Putnam, N. H., Shu, S., Taher, L., Blitz, I. L., Blumberg, B., Dichmann, D. S., Dubchak, I., Amaya, E., Detter, J. C., Fletcher, R., Gerhard, D. S., Goodstein, D., Graves, T., Grigoriev, I. V., Grimwood, J., Kawashima, T., Lindquist, E., Lucas, S. M., Mead, P. E., Mitros, T., Ogino, H., Ohta, Y., Poliakov, A. V., Pollet, N., Robert, J., Salamov, A., Sater, A. K., Schmutz, J., Terry, A., Vize, P. D., Warren, W. C., Wells, D., Wills, A., Wilson, R. K., Zimmerman, L. B., Zorn, A. M., Grainger, R., Grammer, T., Khokha, M. K., Richardson, P. M., and Rokhsar, D. S. The genome of the Western clawed frog Xenopus tropicalis. Science 328, 5978 (Apr 2010), 633--636.
[20] Casagranda, M. D., Arias, J. S., Goloboff, P. A., Szumik, C. A., Taher, L. M., Escalante, T., and Morrone, J. J. Proximity, interpenetration, and sympatry networks: a reply to Dos Santos et al. Syst. Biol. 58, 2 (Apr 2009), 271--276.
[21] Taher, L., and Ovcharenko, I. Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements. Bioinformatics 25, 5 (Mar 2009), 578--584.
[22] Casagranda, D., and Taher, L. Elementos bióticos, endemismo y parsimonia: Estudio de casos de distribuciones hipotéticas. Darwiniana 45, SUPPL. (2007), 37--39.
[23] Szumik, C., Nomdedeu, S., Panizza, A., Aagesen, L., Casagranda, D., Navarro, F., Gómez, J., Sandoval, M., Baldo, D., San Blas, G., Taher, L., Goloboff, P., Lizarralde, M., and Zuloaga, F. Biogeografía del norte argentino (paralelos 21 a 32): Primer ensayo utilizando vertebrados, insectos y plantas. Darwiniana 45, SUPPL. (2007), 49--51.
[24] Taher, L., Meinicke, P., and Morgenstern, B. On splice site prediction using weight array models: A comparison of smoothing techniques. Journal of Physics: Conference Series 90, 1 (2007).
[25] Taher, L., Rinner, O., Garg, S., Sczyrba, A., and Morgenstern, B. AGenDA: gene prediction by cross-species sequence comparison. Nucleic Acids Res. 32, Web Server issue (Jul 2004), W305--308.
[26] Taher, L., Rinner, O., Garg, S., Sczyrba, A., Brudno, M., Batzoglou, S., and Morgenstern, B. AGenDA: homology-based gene prediction. Bioinformatics 19, 12 (Aug 2003), 1575--1577.