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Prof. Dr. Katja Nowick

Katja_Nowick

Professorin

Adresse
Königin-Luise-Str. 1/3
Raum 101a
12161 Berlin

Dr. Nowick performed her doctoral work at the Max-Planck Institute for Evolutionary Anthropology in Dr. Svante Pääbo’s lab on transcriptome evolution in primates and the functional characterization of FOXP2. She joined Dr. Lisa Stubbs’s lab at the Lawrence Livermore National Laboratory for her postdoctoral work in 2006 to study the evolution of zinc finger transcription factors in primates. The lab relocated in 2008 to the University of Illinois at Urbana-Champaign. In 2010 Dr. Nowick returned to Germany, to join the department of Dr. Hans Lehrach at the Max-Planck Institute for Molecular Genetics in Berlin. In 2011, she received an Advanced Postdoc award from the Volkswagen Foundation to start her own independent research group at the University of Leipzig within the group of Dr. Peter Stadler. The focus of her work since then is on how changes in gene regulatory factors, such as transcription factors and non-coding RNAs, and their networks contributed to species evolution. In 2016, she was appointed as professor for Bioinformatics at the University of Hohenheim. In summer 2017, she accepted the offer from Freie Universität to become a professor for Human Biology. Being affiliated with the Institutes for Biology and Bioinformatics, the group continues to employ wet-lab, genomics, transcriptomics, and computational methods to functionally study the molecular basis of primate and brain evolution. She is a founder of the “Programming for Evolutionary Biology” school and an editor for the journal Molecular Biology and Evolution (MBE).

Triant, D.A., Nowick, K. and Shelest, E. (2021) Editorial: Gene Regulation as a Driver of Adaptation and Speciation. Front. Genet. 12:793933. doi: 10.3389/fgene.2021.793933

Jovanovic, V.M., Sarfert, M., Reyna-Blanco, C.S., Indrischek, H., Valdivia, D.I., Shelest, E., Nowick, K. (2021) Positive Selection in Gene Regulatory Factors Suggests Adaptive Pleiotropic Changes During Human Evolution. Front Genet. 2021 May 17;12:662239. doi: 10.3389/fgene.2021.662239

Kolora S.R.R., Gysi, D.M., Schaffer, S., Grimm-Seyfarth A, Szabolcs, M.,  Faria R., Henle K., Stadler P.F., Schlegel M., Nowick, K. (2021) Accelerated evolution of tissue-specific genes mediates divergence amidst gene flow in European green lizards. Genome Biol Evol. 2021 May 14;evab109. doi: 10.1093/gbe/evab109

Gysi, D.M., Fragoso, T. de M., Zebardast, F., Bertoli, W., Busskamp, V., Almaas, E., and Nowick, K. (2020) Whole transcriptomic network analysis using Co-expression Differential Network Analysis (CoDiNA). PLoS One, 2020

Gysi, D.M. and Nowick K. (2020) Headline Review Interface: Construction, comparison and evolution of networks in life sciences and other disciplines. J R Soc Interface. 2020 May;17(166):20190610.  doi: 10.1098/rsif.2019.0610.  Epub 2020 May 6

Marques J.P, Sotelo G, Galindo J, Chaube P, Costa D, Afonso S, Panova M, Nowick K, Butlin R, Hollander J, Faria R. (2020) Transcriptomic resources for evolutionary studies in flat periwinkles and related species. Scientific Data 2020 Mar 3;7(1):73.  doi: 10.1038/s41597-020-0408-8

Nowick K, Walter Costa MB, Höner Zu Siederdissen C, Stadler PF. (2019). Selection Pressures on RNA Sequences and Structures. Evolutionary Bioinformatics Online. 2019 Aug 29;15:1176934319871919. doi: 10.1177/1176934319871919. eCollection 2019

Perdomo-Sabogal Á, Nowick K. (2019). Genetic Variation in Human Gene Regulatory Factors Uncovers Regulatory Roles in Local Adaptation and Disease. Genome Biology and Evolution. 2019 Aug 1;11(8):2178-2193. doi: 10.1093/gbe/evz131

Walter Costa, MB., Hӧner zu Siederdissen, C., Dunjic, M., Stadler, PF., and Nowick, K. (2019). SSS-test: A Novel Test for Detecting Positive Selection on RNA Secondary Structure. BMC Bioinformatics. 2019 Mar 21;20(1):151.  doi: 10.1186/s12859-019-2711-y

Kolora S.R.R., Weigert A., Saffari A., Kehr S., Costa M.B.W., Spröer C., Indrischek H., Chintalapati M., Lohse K., Doose G., Overmann J., Bunk B., Bleidorn C., Grimm-Seyfarth A., Henle K., Nowick K, Faria R., Stadler P.F., Schlegel M. (2018). Divergent evolution in the genomes of closely-related lacertids, Lacerta viridis and L. bilineata and implications for speciation. Gigascience. 2018 Dec 10. doi: 10.1093/gigascience/giy160

Gysi, D.M., Voigt, A., Fragoso, T. de M., Almaas, E., and Nowick, K. (2018). wTO: an R package for computing weighted topological overlap and consensus networks with an integrated visualization tool. BMC Bioinformatics 2018 Oct 24;19(1):392. doi: 10.1186/s12859-018-2351-7

Kutsche, L.K., Gysi, D.M.*, Fallmann, J., Lenk, K., Petri, R., Swiersy, A., Klapper, S.D., Pircs, K., Khattak, S., Stadler, P.F., Jakobsson, J., Nowick, K. and Busskamp, V. (2018) Combined experimental and system-level analyses reveal the complex regulatory network of miR-124 during human neurogenesis, Cell Systems 2018 Oct 24;7(4):438-452.e8. doi: 10.1016/j.cels.2018.08.011 (*my PhD student is shared first author)

Berto, S. and Nowick, K. (2018) Species-specific changes in a primate transcription factor network provide insights into the molecular evolution of the primate prefrontal cortex, Genome Biology and Evolution 2018 Jul 30. doi: 10.1093/gbe/evy149

Faria, R., Triant, D., Perdomo‑Sabogal, A., Overduin, B., Bleidorn, C., Bermudez Santana, C.I., Langenberger, D., Dall’Olio, G.M., Indrischek, H., Aerts, J., Engelhardt, J., Engelken, J., Liebal, K., Fasold, M., Robb, S., Grath, S., Raj Kolora, S.R., Carvalho, T., Salzburger, W., Jovanovic, V. and Nowick, K. (2018) Introducing evolutionary biologists to the analysis of big data: guidelines to organize extended bioinformatics training courses, Evolution: Education and Outreach doi.org/10.1186/s12052-018-0080-z

Walter Costa, MB., Hӧner zu Siederdissen, C., Tulpan, D., Stadler, PF., Nowick, K. (2018) Temporal ordering of substitutions in RNA evolution: Uncovering the structural evolution of the Human Accelerated Region 1, Journal of Theoretical Biology 2018; 438:143-150. doi.org/10.1016/j.jtbi.2017.11.015

Voigt, A., Nowick, K.*, Almaas, E. (2017) A composite network of conserved and tissue specific gene interactions reveals possible genetic interactions in glioma, PLoS Computational Biology doi: 10.1371/journal.pcbi.1005739 (*shared corresponding author)

Doublet, V., Poeschl, Y., Gogol-Döring, A., Alaux, C., Annoscia, D., Aurori, C., Barribeau, SM., Bedoya-Reina, OC., Brown, MJF., Bull, JC., Flenniken, ML., Galbraith, DA., Genersch, E., Gisder, S. Grosse, I., Holt, HL., Hultmark, D., Lattorff, HMG., Le Conte, Y., Manfredini, F., McMahon, DP., Moritz, RFA., Nazzi, F. Niño, EL., Nowick, K., van Rij, RP., Paxton, RJ. and Grozinger, CM. (2017) Unity in defence: honeybee workers exhibit conserved molecular responses to diverse pathogens, BMC Genomics (2017) 18:207. DOI 10.1186/s12864-017-3597-6

Berto, S., Perdomo-Sabogal, A., Gerighausen, D., Qin, J., Nowick, K. (2016) A transcription factor consensus network of the human frontal lobe: insights into the molecular mechanisms of human cognitive abilities, Frontiers in Genetics: Special on Systems biology of transcriptional regulation

Perdomo-Sabogal, A., Nowick, K.*, Piccini, I., Sudbrak, R.,  Lehrach, H., Yaspo, ML., Warnatz, HJ.†, Querfurth, R.*† (2016) Human lineage-specific transcriptional regulation through GA binding protein transcription factor alpha (GABPa), Molecular Biology and Evolution 2016 May; 33(5):1231-44. doi: 10.1093/molbev/msw007 (*shared corresponding author)

Laubichler, M., Stadler, P., Prohaska, S., Nowick, K. (2015) The Relativity of Biological Function, Theory in Biosciences, 10/2015

Raj Kolora, SR., Faria, R., Weigert, A., Schaffer, S., Grimm, A., Henle, K., Sahyon, A., Stadler, PF., Nowick, K., Bleidorn, C., Schlegel, M. (2015) The complete mitochondrial genome of Lacerta bilineata and comparison with its closely related congener L. viridis, Mitochondrial DNA 2015 Dec 28:1-3

Mahmudi, O., Sennblad, B., Arvestad, L., Nowick, K., Lagergren, J. (2015) Gene-Pseudogene Evolution: a Probabilistic Approach,  BMC Genomics , 16 (Suppl 10):S12

Hoehe, M., Church, G.M., Lehrach, H., Kroslak, T., Palczewski, S., Nowick, K., Schulz, S., Suk, E.K., Huebsch, T. (2014) Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes, Nature Communications 01/2014; 5:5569

Andrés, AM. and Nowick, K. (2014) Editorial overview: Genetics of human evolution: The genetics of human origins, Current Opinion in Genetics and Development 11/2014

Kolora, R., Weigert, A., Gerth, M., Sahyoun, A., Stadler, PF., Henle, K., Bleidorn, C., Nowick, K., Schlegel, M. (2014) An NGS-based approach for the comparison of lizard species to detect genome divergence and rearrangements, Next Generation Sequencing Conference (NGS) 2014 09/2014

Perdomo-Sabogal, A., Kanton, S., Walter, M.B.C., Nowick, K. (2014) The roles of gene regulatory factors in the history of human evolution, Current Opinion in Genetics and Development 9;29C: 60-67

Zaveri, A., Nowick, K., Lehmann, J. (2013) Towards Biomedical Data Integration for Analyzing the Evolution of Cognition, Proceedings of Ontology and Data in Life Sciences Workshop (ODLS)

Nowick, K., Carneiro M., Faria R. (2013) A prominent role of KRAB-ZNF transcription factors in mammalian speciation? Trends in Genetics 29: 130-139

Nowick, K., Fields, C., Gernat, T., Caetano-Anolles, D., Kholina, N., Stubbs, L. (2011) Gain, loss and divergence in primate zinc-finger genes: a rich resource for evolution of gene regulatory differences between species, PLoS One 6: e21553

Suk, E.K., McEwen, G.K., Duitama, J., Nowick, K., Schulz, S., Palczewski, S., Schreiber, S., Holloway, D., McLaughlin S., Peckham, H., Lee, C., Huebsch, T., and Hoehe, M.R. (2011) A comprehensively molecular haplotype-resolved genome of a European individual. Genome Research 10: 1672-85

Nowick, K., Hamilton, A.T., Zhang, H., Tran-Gyamfi, M., and Stubbs, L. (2010) Rapid sequence and expression divergence suggests selection for novel function in primate-specific KRAB-ZNF transcription factors, Molecular Biology and Evolution 27, 2606-17

Nowick, K. and Stubbs, L. (2010) Lineage-specific Transcription Factors and the Evolution of Gene Regulatory Networks, Briefings in Functional Genomics 9, 65-78

Nowick, K., Gernat, T., Almaas, E. and Stubbs, L. (2009) Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain, PNAS 106, 22358-63

Nowick, K., Huntley, S., and Stubbs, L. (2009) Rapid expansion and divergence suggest a central and distinct role for KRAB-ZNF genes in vertebrate evolution. In Yoshida, K. (ed), Focus on Zinc Finger Protein Research. Research Signpost, 13-29

Farkas, L.M., Haffner, C., Giger, T., Khaitovich, P., Nowick, K., Birchmeier, C., Paabo, S. and Huttner, W.B. (2008) Insulinoma-associated 1 has a panneurogenic role and promotes the generation and expansion of basal progenitors in the developing mouse neocortex, Neuron 60, 40-55

Stroud, J.C., Wu, Y., Bates, D.L., Han, A., Nowick, K., Paabo, S., Tong, H. Chen, L. (2006) Structure of the forkhead domain of FOXP2 bound to DNA, Structure 14, 159-166

Khaitovich, P., Hellmann, I., Enard, W., Nowick, K., Leinweber, M., Franz, H., Weiss, G., Lachmann, M. and Paabo, S. (2005) Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees, Science 309, 1850-1854

Enard, W., Ebersberger, I., Fischer, A., Heissig, F., Hellmann, I., Höffner, B., Khaitovich, P., Kitano, T., Köhler, K., Metzler, D., Nickel, B., Przeworski, M., Schwarz, C., Nowick, K., Wiebe, V., Winkler, M., Zöllner, S., and Pääbo, S.: Functional genomics in the chimpanzee. In: Progress-Report 1999-2002.