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2019

An integrated genome-wide multi-omics analysis of gene expression dynamics in the preimplantation mouse embryo

Israel, S., Ernst, M., Psathaki, O. E., Drexler, H. C. A., Casser, E., Suzuki, Y., Makalowski, W., Boiani, M., Fuellen, G. & Taher, L., 16 Sep 2019, In : Scientific reports. 9, 1, p. 13356

Research output: Contribution to journalArticleResearchpeer-review

Blastocyst
Genome
Gene Expression
Morula
Ribosomes

Evolutionary conserved networks of human height identify multiple Mendelian causes of short stature

Hauer, N. N., Popp, B., Taher, L., Vogl, C., Dhandapany, P. S., Büttner, C., Uebe, S., Sticht, H., Ferrazzi, F., Ekici, A. B., De Luca, A., Klinger, P., Kraus, C., Zweier, C., Wiesener, A., Jamra, R. A., Kunstmann, E., Rauch, A., Wieczorek, D., Jung, A-M. & 5 othersRohrer, T. R., Zenker, M., Doerr, H-G., Reis, A. & Thiel, C. T., Jul 2019, In : European Journal of Human Genetics . 27, 7, p. 1061-1071 11 p.

Research output: Contribution to journalArticleResearchpeer-review

Genes
Growth
Exome
Chondrocytes
Population
2018

A Dispensable Chromosome Is Required for Virulence in the Hemibiotrophic Plant Pathogen Colletotrichum higginsianum

Plaumann, P-L., Schmidpeter, J., Dahl, M., Taher, L. & Koch, C., 2018, In : Frontiers in Microbiology . 9, p. 1005

Research output: Contribution to journalArticleResearchpeer-review

Colletotrichum
Virulence
Chromosomes, Human, Pair 11
Hyphae
Chromosomes

Comparative High-Resolution Transcriptome Sequencing of Lymphoma Cell Lines and de novo Lymphomas Reveals Cell-Line-Specific Pathway Dysregulation

Taher, L., Beck, J., Liu, W., Roolf, C., Soller, J. T., Rütgen, B. C., Hammer, S. E., Chodisetti, M., Sender, S., Sterenczak, K. A., Fuellen, G., Junghanss, C., Brenig, B., Nolte, I., Schütz, E. & Murua Escobar, H., 19 Apr 2018, In : Scientific reports. 8, 1, p. 6279

Research output: Contribution to journalArticleResearchpeer-review

Transcriptome
Lymphoma
Cell Line
Lymphocytes
Canidae

Genomic analysis of transcriptional networks directing progression of cell states during MGE development

Sandberg, M., Taher, L., Hu, J., Black, B. L., Nord, A. S. & Rubenstein, J. L. R., 14 Sep 2018, In : Neural networks. 13, 1, p. 21

Research output: Contribution to journalArticleResearchpeer-review

Median Eminence
Transcription factors
Gene Regulatory Networks
Cells
Neurons

Identification of Prognostic Biomarkers by Combined mRNA and miRNA Expression Microarray Analysis in Pancreatic Cancer

Liu, B., Yang, H., Taher, L., Denz, A., Grützmann, R., Pilarsky, C. & Weber, G. F., Jun 2018, In : Translational Oncology. 11, 3, p. 700-714 15 p.

Research output: Contribution to journalArticleResearchpeer-review

Microarray Analysis
MicroRNAs
Pancreatic Neoplasms
Biomarkers
Messenger RNA

Pairs of Adjacent Conserved Noncoding Elements Separated by Conserved Genomic Distances Act as Cis-Regulatory Units

Li, L., Barth, N. K. H., Hirth, E. & Taher, L., 1 Sep 2018, In : Genome Biology and Evolution. 10, 9, p. 2535-2550 16 p.

Research output: Contribution to journalArticleResearchpeer-review

Inborn Genetic Diseases
Medical Genetics
Human Genome
Epigenomics
Genome
2016

Analysis of microRNA and Gene Expression Profiles in Multiple Sclerosis: Integrating Interaction Data to Uncover Regulatory Mechanisms

Freiesleben, S., Hecker, M., Zettl, U. K., Fuellen, G. & Taher, L., 3 Oct 2016, In : Scientific reports. 6, p. 34512

Research output: Contribution to journalArticleResearchpeer-review

MicroRNAs
Transcriptome
Multiple Sclerosis
Gene Expression
Hematologic Diseases

Revealing complex function, process and pathway interactions with high-throughput expression and biological annotation data

Singh, N. K., Ernst, M., Liebscher, V., Fuellen, G. & Taher, L., 20 Oct 2016, In : Molecular BioSystems. 12, 10, p. 3196-208 13 p.

Research output: Contribution to journalArticleResearchpeer-review

Biological Phenomena
Gene Expression
Gene Regulatory Networks
Liver
Cell Differentiation

Subpallial Enhancer Transgenic Lines: a Data and Tool Resource to Study Transcriptional Regulation of GABAergic Cell Fate

Silberberg, S. N., Taher, L., Lindtner, S., Sandberg, M., Nord, A. S., Vogt, D., Mckinsey, G. L., Hoch, R., Pattabiraman, K., Zhang, D., Ferran, J. L., Rajkovic, A., Golonzhka, O., Kim, C., Zeng, H., Puelles, L., Visel, A. & Rubenstein, J. L. R., 5 Oct 2016, In : Neuron. 92, 1, p. 59-74 16 p.

Research output: Contribution to journalArticleResearchpeer-review

Prosencephalon
Amygdala
Basal Ganglia
Transgenic Mice
Transcription Factors
2015

Bioinformatics approaches to single-blastomere transcriptomics

Taher, L., Pfeiffer, M. J. & Fuellen, G., Feb 2015, In : Molecular Human Reproduction. 21, 2, p. 115-25 11 p.

Research output: Contribution to journalArticleResearchpeer-review

Blastomeres
Computational Biology
Blastocyst
Gene Expression
Microfluidics

Chromatin decompaction by the nucleosomal binding protein HMGN5 impairs nuclear sturdiness

Furusawa, T., Rochman, M., Taher, L., Dimitriadis, E. K., Nagashima, K., Anderson, S. & Bustin, M., 22 Jan 2015, In : Nature Communications. 6, p. 6138

Research output: Contribution to journalArticleResearchpeer-review

HMGN Proteins
chromatin
Heterochromatin
Nuclear Lamina
Chromatin

Comparative computational analysis of pluripotency in human and mouse stem cells

Ernst, M., Abu Dawud, R., Kurtz, A., Schotta, G., Taher, L. & Fuellen, G., 21 Jan 2015, In : Scientific reports. 5, p. 7927

Research output: Contribution to journalArticleResearchpeer-review

Stem Cells
Molecular Sequence Annotation
Acetylation
Histones
DNA Damage

Differences in embryo quality are associated with differences in oocyte composition: a proteomic study in inbred mice

Pfeiffer, M. J., Taher, L., Drexler, H., Suzuki, Y., Makałowski, W., Schwarzer, C., Wang, B., Fuellen, G. & Boiani, M., Feb 2015, In : Proteomics. 15, 4, p. 675-87 13 p.

Research output: Contribution to journalArticleResearchpeer-review

Proteomics
Oocytes
Embryonic Structures
Inbred Strains Mice
Chemical analysis

Identification and computational analysis of gene regulatory elements

Taher, L., Narlikar, L. & Ovcharenko, I., 5 Jan 2015, In : Cold Spring Harbor Protocols. 2015, 1, p. pdb.top083642

Research output: Contribution to journalReview articleResearchpeer-review

Regulator Genes
Genome
Technology
Untranslated RNA
Human Genome

TRIM32 modulates pluripotency entry and exit by directly regulating Oct4 stability

Bahnassawy, L., Perumal, T. M., Gonzalez-Cano, L., Hillje, A-L., Taher, L., Makalowski, W., Suzuki, Y., Fuellen, G., del Sol, A. & Schwamborn, J. C., 26 Aug 2015, In : Scientific reports. 5, p. 13456

Research output: Contribution to journalArticleResearchpeer-review

Induced Pluripotent Stem Cells
Knockout Mice
Fibroblasts
Regenerative Medicine
Neural Stem Cells
2014

Transcriptional regulation of enhancers active in protodomains of the developing cerebral cortex

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. & Rubenstein, J. L. R., 4 Jun 2014, In : Neuron. 82, 5, p. 989-1003 15 p.

Research output: Contribution to journalArticleResearchpeer-review

Cerebral Cortex
Transcription Factors
Informatics
Brain Diseases
Transgenic Mice
2013

A high-resolution enhancer atlas of the developing telencephalon

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. & 5 othersKriegstein, A. R., Rubin, E. M., Ovcharenko, I., Pennacchio, L. A. & Rubenstein, J. L. R., 14 Feb 2013, In : Cell. 152, 4, p. 895-908 14 p.

Research output: Contribution to journalArticleResearchpeer-review

Telencephalon
Atlases
Genes
Prosencephalon
Regulator Genes

Identifying genes relevant to specific biological conditions in time course microarray experiments

Singh, N. K., Repsilber, D., Liebscher, V., Taher, L. & Fuellen, G., 2013, In : PLoS ONE. 8, 10, p. e76561

Research output: Contribution to journalArticleResearchpeer-review

Microarrays
selection methods
Genes
Signal-To-Noise Ratio
gene expression

Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model

Smith, R. P., Taher, L., Patwardhan, R. P., Kim, M. J., Inoue, F., Shendure, J., Ovcharenko, I. & Ahituv, N., Sep 2013, In : Nature genetics. 45, 9, p. 1021-1028 8 p.

Research output: Contribution to journalArticleResearchpeer-review

Organizational Models
Binding Sites
Transcription Factors
Cataloging
Gene Expression

Sequence signatures extracted from proximal promoters can be used to predict distal enhancers

Taher, L., Smith, R. P., Kim, M. J., Ahituv, N. & Ovcharenko, I., 2013, In : Genome biology. 14, 10, p. R117

Research output: Contribution to journalArticleResearchpeer-review

promoter regions
prediction
gene expression
gene
Genes

Sost and its paralog Sostdc1 coordinate digit number in a Gli3-dependent manner

Collette, N. M., Yee, C. S., Murugesh, D., Sebastian, A., Taher, L., Gale, N. W., Economides, A. N., Harland, R. M. & Loots, G. G., 1 Nov 2013, In : BMC Biology . 383, 1, p. 90-105 16 p.

Research output: Contribution to journalArticleResearchpeer-review

Ectoderm
mice
limbs (animal)
Extremities
Syndactyly
2012

A machine learning approach for identifying novel cell type-specific transcriptional regulators of myogenesis

Busser, B. W., Taher, L., Kim, Y., Tansey, T., Bloom, M. J., Ovcharenko, I. & Michelson, A. M., 2012, In : PLoS Genetics. 8, 3, p. e1002531

Research output: Contribution to journalArticleResearchpeer-review

Muscle Development
Binding Sites
Transcription Factors
Drosophila melanogaster
Muscle Cells

CLARE: Cracking the LAnguage of Regulatory Elements

Taher, L., Narlikar, L. & Ovcharenko, I., 15 Feb 2012, In : Bioinformatics. 28, 4, p. 581-3 3 p.

Research output: Contribution to journalArticleResearchpeer-review

Cracking
Language
Tissue
Gene Regulation
Predictive Model

Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control

Burzynski, G. M., Reed, X., Taher, L., Stine, Z. E., Matsui, T., Ovcharenko, I. & McCallion, A. S., Nov 2012, In : Genome research. 22, 11, p. 2278-89 12 p.

Research output: Contribution to journalArticleResearchpeer-review

Rhombencephalon
Zebrafish
Human Genome
Nervous System
Chromatin
2011

Effects of HMGN variants on the cellular transcription profile

Rochman, M., Taher, L., Kurahashi, T., Cherukuri, S., Uversky, V. N., Landsman, D., Ovcharenko, I. & Bustin, M., May 2011, In : Nucleic acids research. 39, 10, p. 4076-87 12 p.

Research output: Contribution to journalArticleResearchpeer-review

High Mobility Group Proteins
Nucleosomes
Intrinsically Disordered Proteins
Nuclear Proteins
Chromatin

Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes

Martin, D., Pantoja, C., Fernández Miñán, A., Valdes-Quezada, C., Moltó, E., Matesanz, F., Bogdanović, O., de la Calle-Mustienes, E., Domínguez, O., Taher, L., Furlan-Magaril, M., Alcina, A., Cañón, S., Fedetz, M., Blasco, M. A., Pereira, P. S., Ovcharenko, I., Recillas-Targa, F., Montoliu, L., Manzanares, M. & 4 othersGuigó, R., Serrano, M., Casares, F. & Gómez-Skarmeta, J. L., Jun 2011, In : Nature structural & molecular biology. 18, 6, p. 708-14 7 p.

Research output: Contribution to journalArticleResearchpeer-review

Vertebrates
Genome
Genes
Insulator Elements
Zinc Fingers

Genome-wide identification of conserved regulatory function in diverged sequences

Taher, L., McGaughey, D. M., Maragh, S., Aneas, I., Bessling, S. L., Miller, W., Nobrega, M. A., McCallion, A. S. & Ovcharenko, I., Jul 2011, In : Genome research. 21, 7, p. 1139-49 11 p.

Research output: Contribution to journalArticleResearchpeer-review

Transcription Factors
Binding Sites
Genome
Zebrafish
Regulator Genes

Global gene expression analysis of murine limb development

Taher, L., Collette, N. M., Murugesh, D., Maxwell, E., Ovcharenko, I. & Loots, G. G., 2011, In : PLoS ONE. 6, 12, p. e28358

Research output: Contribution to journalArticleResearchpeer-review

limbs (animal)
Gene expression
Extremities
Genes
Gene Expression
2010

The genome of the Western clawed frog Xenopus tropicalis

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. & 28 othersGrigoriev, 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. & Rokhsar, D. S., 30 Apr 2010, In : Science. 328, 5978, p. 633-6 4 p.

Research output: Contribution to journalArticleResearchpeer-review

Xenopus
Anura
Genome
DNA Transposable Elements
Chromosomes