Katja Nowick

Katja Nowick
Freie Universität Berlin | FUB · Institute of Biology

30.94
 · 
PhD

About

96
Publications
7,426
Reads
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1,426
Citations
Introduction
I am broadly interested in how genomic changes lead to phenotypic changes. My main focus is on the evolution of transcriptional regulators (transcription factors and lncRNAs) and gene regulatory networks in primates. I am most interested in molecular changes that enabled differences in cognition in humans.
Research Experience
January 2011 - present
Paul-Flechsig-Institut für Hirnforschung
Position
  • Independent Research Group Leader
January 2011 - present
University of Leipzig
Position
  • Independent Research Group Leader
January 2010 - December 2010
Max Planck Institute for Molecular Genetics
Position
  • PostDoc Position

Publications

Publications (96)
Article
Full-text available
Biological and medical sciences are increasingly acknowledging the significance of gene co-expression-networks for investigating complex-systems, phenotypes or diseases. Typically , complex phenotypes are investigated under varying conditions. While approaches for comparing nodes and links in two networks exist, almost no methods for the comparison...
Article
Full-text available
Network approaches have become pervasive in many research fields. They allow for a more comprehensive understanding of complex relationships between entities as well as their group-level properties and dynamics. Many networks change over time, be it within seconds or millions of years, depending on the nature of the network. Our focus will be on co...
Article
Full-text available
The flat periwinkles, Littorina fabalis and L. obtusata, comprise two sister gastropod species that have an enormous potential to elucidate the mechanisms involved in ecological speciation in the marine realm. However, the molecular resources currently available for these species are still scarce. In order to circumvent this limitation, we used RNA...
Article
Full-text available
Background: Long non-coding RNAs (lncRNAs) play an important role in regulating gene expression and are thus important for determining phenotypes. Most attempts to measure selection in lncRNAs have focused on the primary sequence. The majority of small RNAs and at least some parts of lncRNAs must fold into specific structures to perform their biolo...
Article
Full-text available
With the discovery of increasingly more functional noncoding RNAs (ncRNAs), it becomes eminent to more strongly consider them as important players during species evolution. Although tests for negative selection of ncRNAs already exist since the beginning of this century, the SSS-test is the first one for also investigating positive selection. When...
Article
Full-text available
Differences in gene regulation have been suggested to play essential roles in the evolution of phenotypic changes. While DNA changes in cis- regulatory elements affect only the regulation of its corresponding gene, variations in gene regulatory factors (GRFs) (trans) can have a broader effect, because the expression of many target genes might be af...
Article
Full-text available
Background Lacerta viridis and L. bilineata are sister species of European green lizards (eastern and western clades respectively), which until recently were grouped together as the L. viridis complex. Genetic incompatibilities were observed between lacertid populations through crossing experiments, which led to the delineation of two separate spec...
Article
Full-text available
Research in evolutionary biology has been progressively influenced by big data such as massive genome and transcriptome sequencing data, scalar measurements of several phenotypes on tens to thousands of individuals, as well as from collecting worldwide environmental data at an increasingly detailed scale. The handling and analysis of such data requ...
Article
Full-text available
Background: Network analyses, such as of gene co-expression networks, metabolic networks and ecological networks have become a central approach for the systems-level study of biological data. Several software packages exist for generating and analyzing such networks, either from correlation scores or the absolute value of a transformed score calle...
Data
Table S6. Luciferase Assay Raw Data and Final Calculated Luciferase Activity, Related to Figure 4
Data
Table S9. List of High-Probability Targets with Peak Score from AGO2-IP, Differential Expression Analysis (DESeq2), Normalized mRNA Counts from Pre-AGO2-RIP (IN), Mean, and Gene Information, Related to Figure 4
Data
Table S10. Raw miRNA Counts from sRNA-Seq Pre (IN) and Post (IP) AGO2-RIP for WT and ΔmiR-124 (KO) for 0 dpi and 4 dpi, Related to Figure 5
Data
Table S11. Raw miRNA Counts from nCounter for WT and ΔmiR-124 (KO), 0 dpi, and 4 dpi, Related to Figure 5
Data
Table S14. Raw Counts from RNA-Seq Data for WT, ΔmiR-124 (miR124KO), and ZNF787 Overexpression (ZNF787OE) at 4 dpi, n = 3, Related to Figure 6
Data
Table S8. Differential Peak Signal from AGO2-RIP, WT to ΔmiR-124, at 4 dpi, for Transcripts in WT Cells, Related to Figure 4
Data
Table S7. Raw mRNA Counts from RNA-Seq Pre (IN) and Post (IP) AGO2-RIP for WT and ΔmiR-124, n = 3, Related to Figure 4
Data
Table S13. Raw Counts from WT and ΔmiR-124 (KO) for 7 dpi and 14 dpi, n = 3, Related to Figures S3 and S4 and STAR Methods
Data
Table S15. Network Analysis Using Time Course Data from WT and ΔmiR-124 (KO), 0 dpi to 4 dpi, n = 7, Related to Figure 6
Data
Table S12. Raw Counts from Time Course Data for WT and ΔmiR-124 (KO) for 0 dpi to 4 dpi, n = 7, Related to Figures 3 and 6
Article
Full-text available
Non-coding RNAs regulate many biological processes including neurogenesis. The brain-enriched miR-124 has been assigned as a key player of neuronal differentiation via its complex but little understood regulation of thousands of annotated targets. To systematically chart its regulatory functions, we used CRISPR/Cas9 gene editing to disrupt all six...
Article
Full-text available
The human prefrontal cortex (PFC) differs from that of other primates with respect to size, histology, and functional abilities. Here we analyzed genome wide expression data of humans, chimpanzees, and rhesus macaques to discover evolutionary changes in transcription factor (TF) networks that may underlie these phenotypic differences. We determined...
Article
Full-text available
Biomedical sciences are increasingly recognising the relevance of gene co-expression-networks for analysing complex-systems, phenotypes or diseases. When the goal is investigating complex-phenotypes under varying conditions, it comes naturally to employ comparative network methods. While approaches for comparing two networks exist, this is not the...
Preprint
Full-text available
Background: Gene co-expression network analyses have become a central approach for the systems-level analysis of biological data. Several software packages exist for generating and analyzing such networks, either from correlation scores or the absolute value of a transformed score called weighted topological overlap (wTO). However, since some genes...
Article
Full-text available
The Human Accelerated Region 1, HAR1, is the most rapidly evolving region in the human genome. It is part of two overlapping long non-coding RNAs, has a length of only 118 nucleotides and features 18 human specific changes compared to an ancestral sequence that is extremely well conserved across non-human primates. The human HAR1 forms a stable sec...
Article
Full-text available
Differential co-expression network analyses have recently become an important step in the investigation of cellular differentiation and dysfunctional gene-regulation in cell and tissue disease-states. The resulting networks have been analyzed to identify and understand pathways associated with disorders, or to infer molecular interactions. However,...
Data
Comparison between the CSD network and a metabolic gene network built from the Human Recon 2 genome-scale reconstruction. (PDF)
Data
Tree diagram of enriched GO biological processes in the C-only network generated using a threshold sample size of 105. (TIFF)
Data
Maximum k-cores for various importance value thresholds. (TIFF)
Data
List of software used in our reconstruction and analysis. (PDF)
Data
Candidate genes for further glioma association studies. (XLSX)
Data
Tree diagram of enriched GO biological processes in the combined CSD network generated using a threshold sample size of 105. (TIFF)
Data
An overview of hub nodes for CSD networks generated at different thresholds. (PDF)
Data
Distributions of C, S and D scores for our data sets. (TIFF)
Data
Tree diagram of enriched GO biological processes in the S-only network generated using a threshold sample size of 105. (TIFF)
Data
Example run of the subsampling algorithm. (PDF)
Data
Effect of sample size on accuracy of estimates. (PDF)
Data
Top 10 DCe links in the Zhang et al [43] regulatory network: C-type, S-type and S-equivalent type. (XLS)
Data
An overview of KEGG pathways enriched in the CSD network. (XLS)
Data
Tree diagram of enriched GO biological processes in the D-only network generated using a threshold sample size of 105. (TIFF)
Article
Full-text available
After the publication of this work [1] it was noticed that there was a typesetting error in figure 5 where two additional red lines were added in the sections "gene expression profiles" and "transformed gene expression profiles". The original article was corrected to remove these lines.
Article
Full-text available
Background: Organisms typically face infection by diverse pathogens, and hosts are thought to have developed specific responses to each type of pathogen they encounter. The advent of transcriptomics now makes it possible to test this hypothesis and compare host gene expression responses to multiple pathogens at a genome-wide scale. Here, we perform...
Article
Full-text available
Cognitive abilities, such as memory, learning, language, problem solving, and planning, involve the frontal lobe and other brain areas. Not much is known yet about the molecular basis of cognitive abilities, but it seems clear that cognitive abilities are determined by the interplay of many genes. One approach for analyzing the genetic networks inv...
Article
Full-text available
A substantial fraction of phenotypic differences between closely related species are likely caused by differences in gene regulation. While this has already been postulated over 30 years ago, only few examples of evolutionary changes in gene regulation have been verified. Here we identified and investigated binding sites of the transcription factor...
Article
We sequenced the mitochondrial genome of the Western green lizard (Lacerta bilineata) using Illumina technology and additional Sanger sequencing. The assembled 17 086 bp mitogenome had a GC content of 40.32% and consisted of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region (CR), with a gene order identical to the chord...
Article
Full-text available
Function is a central concept in biological theories and explanations. Yet discussions about function are often based on a narrow understanding of biological systems and processes, such as idealized molecular systems or simple evolutionary, i.e., selective, dynamics. Conflicting conceptions of function continue to be used in the scientific literatu...
Article
Full-text available
Over the last decade, methods have been developed for the reconstruction of gene trees that take into account the species tree. Many of these methods have been based on the probabilistic duplication-loss model, which describes how a gene-tree evolves over a species-tree with respect to duplication and losses, as well as extension of this model, e.g...
Article
Full-text available
Deciphering the molecular basis of how modern human phenotypes have evolved is one of the most fascinating challenges in biology. Here, we will focus on the roles of gene regulatory factors (GRFs), in particular transcription factors (TFs) and long non-coding RNAs (lncRNAs) during human evolution. We will present examples of TFs and lncRNAs that ha...
Article
Full-text available
To fully understand human biology and link genotype to phenotype, the phase of DNA variants must be known. Here we present a comprehensive analysis of haplotype-resolved genomes to assess the nature and variation of haplotypes and their pairs, diplotypes, in European population samples. We use a set of 14 haplotype-resolved genomes generated by fos...
Article
Deciphering the molecular basis of how modern human phenotypes have evolved is one of the most fascinating challenges in biology. Here, we will focus on the roles of gene regulatory factors (GRFs), in particular transcription factors (TFs) and long non-coding RNAs (lncRNAs) during human evolution. We will present examples of TFs and lncRNAs that ha...
Conference Paper
Full-text available
Background / Purpose: We present a genomic comparison of the Anoles carolinensis to the next generation sequencing (NGS) data of the Lacerta viridis . Both were expected to diverge around 60-80 Mya, and differ in terms of the number of chromosomes and nature of sex-chromosomes. They are both from the order Squamata but from different suborders i....
Poster
Full-text available
Specifi cation of the problem under study? Does a given long Krüuppel-type ZF-protein bind to DNA?
Conference Paper
Full-text available
Cognition is determined by function and interplay of several hundred if not thousand genes with a considerable overlap in the phenotypes and genes causing different cognitive diseases. We argue that these diseases should not be studied in isolation, but that data allowing to study them should be integrated. Ultimately, this will allow researchers t...
Article
The mechanisms of speciation have been one of the most debated topics in evolutionary biology. Among all reproductive barriers, postzygotic reproductive isolation is perhaps the one that has attracted the most attention from geneticists. Despite remarkable advances in the identification of loci involved in Drosophila speciation, little is known abo...
Article
Full-text available
Independent determination of both haplotype sequences of an individual genome is essential to relate genetic variation to genome function, phenotype, and disease. To address the importance of phase, we have generated the most complete haplotype-resolved genome to date, "Max Planck One" (MP1), by fosmid pool-based next generation sequencing. Virtual...
Data
Pair wise number of high-confidence and all-inclusive orthologous loci and number of orthologous loci in hominids and all four primates. (XLSX)
Data
ZNF domains with human or chimpanzee specific DNA-contacting amino acids. (XLSX)
Data
For the different types of functional domains in KZNFs the number of loci that gained or lost such domains in a lineage-specific way are given. (XLSX)
Data
Gene and Pseudogene Nomenclature (DOCX)
Data
Expression of KZNF genes with human or chimpanzee specific ZNF domain changes and Ka/Ks>1. Out of eleven such genes we could obtain expression information from five human and chimpanzee tissues for five genes. The darker the field, the higher the percentage of individuals (ranging from 0 to 100%) expressing the gene in a given tissue. (TIF)
Data
Ten genes that were not assigned official gene symbols by the Human Genome Organization (HUGO) before publication of this manuscript. (XLSX)
Data
Number of KZNF loci in orthologous clusters of human, chimpanzee, orangutan, and rhesus macaque. (XLSX)
Data
A snapshot of human chromosome 8:11870862-12350861 compared to the related chimapanzee region in the synteny browser. This example highlights a region with whole gene duplication in addition to smaller duplications affecting domain architecture. Human was chosen as the reference for this display. Loci are depicted by rectangles. Orthologous loci ar...