Publications/Publikationen

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[30] Silberberg SN, Taher L, Lindtner S, Sandberg M, Nord AS, Vogt D, Mckinsey GL, Hoch R, Pattabiraman K, Zhang D, Ferran JL, Rajkovic A, Golonzhka O, Kim C, Zeng H, Puelles L, Visel A, Rubenstein JLR. Subpallial Enhancer Transgenic Lines: a Data and Tool Resource to Study Transcriptional Regulation of GABAergic Cell Fate. Neuron (2016), 92(1), 59-74.
[29] Freiesleben S, Hecker M, Zettl UK, Fuellen G, Taher L. Analysis of microRNA and Gene Expression Profiles in Multiple Sclerosis: Integrating Interaction Data to Uncover Regulatory Mechanisms. Sci Rep. (2016), 6, 34512.
[28] Singh NK, Ernst M, Liebscher V, Fuellen G, Taher L. Revealing complex function, process and pathway interactions with high-throughput expression and biological annotation data. Mol Biosyst. (2016), 12(10):3196-208.
[27] TRIM32 modulates pluripotency entry and exit by directly regulating Oct4 stability. Bahnassawy L, Perumal TM, Gonzalez-Cano L, Hillje AL, Taher L, Makalowski W, Suzuki Y, Fuellen G, del Sol A, Schwamborn JC. Sci Rep. (2015) 5:13456.
[26] 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.
[25] 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.
[24] 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.
[23] 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.
[22] Taher, L., Pfeiffer, M. J., and Fuellen, G. Bioinformatics approaches to single-blastomere transcriptomics. Mol. Hum. Reprod. 21, 2 (Feb 2015), 115--125.
[21] 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.
[20] 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.
[19] 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.
[18] 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.
[17] 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.
[16] 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.
[15] 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.
[14] 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.
[13] Taher, L., Narlikar, L., and Ovcharenko, I. CLARE: Cracking the LAnguage of Regulatory Elements. Bioinformatics 28, 4 (Feb 2012), 581--583.
[12] 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.
[11] 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.
[10] 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.
[9] 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.
[8] 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.
[7] 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.
[6] 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.
[5] Casagranda, D., and Taher, L. Elementos bióticos, endemismo y parsimonia: Estudio de casos de distribuciones hipotéticas. Darwiniana 45, SUPPL. (2007), 37--39.
[4] 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.
[3] 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).
[2] 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.
[1] 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.