Search Results - "Siegel, T"

Smoother: on-the-fly processing of interactome data using prefix sums by Schmidt, Markus R, Barcons-Simon, Anna, Rabuffo, Claudia, Siegel, T Nicolai

“…Abstract Nucleic acid interactome data, such as chromosome conformation capture data and RNA–DNA interactome data, are currently analyzed via pipelines that…”
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Strand-specific RNA-Seq reveals widespread and developmentally regulated transcription of natural antisense transcripts in Plasmodium falciparum by Siegel, T Nicolai, Hon, Chung-Chau, Zhang, Qinfeng, Lopez-Rubio, Jose-Juan, Scheidig-Benatar, Christine, Martins, Rafael M, Sismeiro, Odile, Coppée, Jean-Yves, Scherf, Artur

“…Advances in high-throughput sequencing have led to the discovery of widespread transcription of natural antisense transcripts (NATs) in a large number of…”
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Efficient and specific oligo-based depletion of rRNA by Kraus, Amelie J., Brink, Benedikt G., Siegel, T. Nicolai

“…In most organisms, ribosomal RNA (rRNA) contributes to >85% of total RNA. Thus, to obtain useful information from RNA-sequencing (RNA-seq) analyses at…”
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Novel insights into RNP granules by employing the trypanosome's microtubule skeleton as a molecular sieve by Fritz, Melanie, Vanselow, Jens, Sauer, Nadja, Lamer, Stephanie, Goos, Carina, Siegel, T Nicolai, Subota, Ines, Schlosser, Andreas, Carrington, Mark, Kramer, Susanne

“…RNP granules are ribonucleoprotein assemblies that regulate the post-transcriptional fate of mRNAs in all eukaryotes. Their exact function remains poorly…”
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Distinct roles for H4 and H2A.Z acetylation in RNA transcription in African trypanosomes by Kraus, Amelie J., Vanselow, Jens T., Lamer, Stephanie, Brink, Benedikt G., Schlosser, Andreas, Siegel, T. Nicolai

“…Despite histone H2A variants and acetylation of histones occurring in almost every eukaryotic organism, it has been difficult to establish direct functional…”
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Negative regulation of the interferon response by an interferon-induced long non-coding RNA by Kambara, Hiroto, Niazi, Farshad, Kostadinova, Lenche, Moonka, Dilip K, Siegel, Christopher T, Post, Anthony B, Carnero, Elena, Barriocanal, Marina, Fortes, Puri, Anthony, Donald D, Valadkhan, Saba

“…Long non-coding RNAs (lncRNAs) play critical roles in diverse cellular processes; however, their involvement in many critical aspects of the immune response…”
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GT‐rich promoters can drive RNA pol II transcription and deposition of H2A.Z in African trypanosomes by Wedel, Carolin, Förstner, Konrad U, Derr, Ramona, Siegel, T Nicolai

“…Genome‐wide transcription studies are revealing an increasing number of “dispersed promoters” that, unlike “focused promoters”, lack well‐conserved sequence…”
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Histone H3 Variant Regulates RNA Polymerase II Transcription Termination and Dual Strand Transcription of siRNA Loci in Trypanosoma brucei by Reynolds, David, Hofmeister, Brigitte T, Cliffe, Laura, Alabady, Magdy, Siegel, T Nicolai, Schmitz, Robert J, Sabatini, Robert

“…Base J, β-D-glucosyl-hydroxymethyluracil, is a chromatin modification of thymine in the nuclear DNA of flagellated protozoa of the order Kinetoplastida. In…”
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Genome organization and DNA accessibility control antigenic variation in trypanosomes by Müller, Laura S. M., Cosentino, Raúl O., Förstner, Konrad U., Guizetti, Julien, Wedel, Carolin, Kaplan, Noam, Janzen, Christian J., Arampatzi, Panagiota, Vogel, Jörg, Steinbiss, Sascha, Otto, Thomas D., Saliba, Antoine-Emmanuel, Sebra, Robert P., Siegel, T. Nicolai

“…Many evolutionarily distant pathogenic organisms have evolved similar survival strategies to evade the immune responses of their hosts. These include antigenic…”
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Comparative ribosome profiling uncovers a dominant role for translational control in Toxoplasma gondii by Hassan, Musa A, Vasquez, Juan J, Guo-Liang, Chew, Meissner, Markus, Nicolai Siegel, T

“…The lytic cycle of the protozoan parasite Toxoplasma gondii, which involves a brief sojourn in the extracellular space, is characterized by defined…”
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Comparative ribosome profiling reveals extensive translational complexity in different Trypanosoma brucei life cycle stages by Vasquez, Juan-José, Hon, Chung-Chau, Vanselow, Jens T, Schlosser, Andreas, Siegel, T Nicolai

“…While gene expression is a fundamental and tightly controlled cellular process that is regulated at multiple steps, the exact contribution of each step remains…”
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Noncoding RNAs as emerging regulators of Plasmodium falciparum virulence gene expression by Vembar, Shruthi S, Scherf, Artur, Siegel, T Nicolai

“…Highlights • Small and long noncoding RNAs are abundant in Plasmodium falciparum blood stages. • Subtelomeric and intronic ncRNAs may determine singular var…”
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H2B.V demarcates divergent strand-switch regions, some tDNA loci, and genome compartments in Trypanosoma cruzi and affects parasite differentiation and host cell invasion by Rosón, Juliana Nunes, Vitarelli, Marcela de Oliveira, Costa-Silva, Héllida Marina, Pereira, Kamille Schmitt, Pires, David da Silva, Lopes, Leticia de Sousa, Cordeiro, Barbara, Kraus, Amelie J, Cruz, Karin Navarro Tozzi, Calderano, Simone Guedes, Fragoso, Stenio Perdigão, Siegel, T Nicolai, Elias, Maria Carolina, da Cunha, Julia Pinheiro Chagas

“…Histone variants play a crucial role in chromatin structure organization and gene expression. Trypanosomatids have an unusual H2B variant (H2B.V) that is known…”
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Four histone variants mark the boundaries of polycistronic transcription units in Trypanosoma brucei by Siegel, T Nicolai, Hekstra, Doeke R, Kemp, Louise E, Figueiredo, Luisa M, Lowell, Joanna E, Fenyo, David, Wang, Xuning, Dewell, Scott, Cross, George A M

“…Unusually for a eukaryote, genes transcribed by RNA polymerase II (pol II) in Trypanosoma brucei are arranged in polycistronic transcription units. With one…”
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Exploiting CRISPR-Cas9 technology to investigate individual histone modifications by Vasquez, Juan-José, Wedel, Carolin, Cosentino, Raul O, Siegel, T Nicolai

“…Abstract Despite their importance for most DNA-templated processes, the function of individual histone modifications has remained largely unknown because in…”
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Evidence for a Shared Nuclear Pore Complex Architecture That Is Conserved from the Last Common Eukaryotic Ancestor by DeGrasse, Jeffrey A., DuBois, Kelly N., Devos, Damien, Siegel, T. Nicolai, Sali, Andrej, Field, Mark C., Rout, Michael P., Chait, Brian T.

“…The nuclear pore complex (NPC) is a macromolecular assembly embedded within the nuclear envelope that mediates bidirectional exchange of material between the…”
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Genome-wide analysis of chromatin structures in Trypanosoma brucei using high-resolution MNase-ChIP-seq by Wedel, Carolin, Siegel, T. Nicolai

“…Specific DNA-protein interactions are the basis for many important cellular mechanisms like the regulation of gene expression or replication. Knowledge about…”
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Cell-to-Cell Heterogeneity in Trypanosomes by Luzak, Vanessa, López-Escobar, Lara, Siegel, T. Nicolai, Figueiredo, Luisa M

“…Recent developments in single-cell and single-molecule techniques have revealed surprising levels of heterogeneity among isogenic cells. These advances have…”
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Spatial integration of transcription and splicing in a dedicated compartment sustains monogenic antigen expression in African trypanosomes by Faria, Joana, Luzak, Vanessa, Müller, Laura S. M., Brink, Benedikt G., Hutchinson, Sebastian, Glover, Lucy, Horn, David, Siegel, T. Nicolai

“…Highly selective gene expression is a key requirement for antigenic variation in several pathogens, allowing evasion of host immune responses and maintenance…”
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Rapid Identification of Ischemic Injury in Renal Tissue by Mass-Spectrometry Imaging by van Smaalen, T. C, Ellis, S. R, Mascini, N. E, Siegel, T. Porta, Cillero-Pastor, B, Hillen, L. M, van Heurn, L. W. E, Peutz-Kootstra, C. J, Heeren, R. M. A

“…The increasing analytical speed of mass-spectrometry imaging (MSI) has led to growing interest in the medical field. Acute kidney injury is a severe disease…”
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