Publications

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

 

Kolora SRR, Weigert A, Saffari A, Kehr S, Costa MBW, 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 PF, 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

 

Gysi, D.M., Voigt, A., Fragoso, T. de M., Almaas, E., and Nowick, K. (2018)  CoDiNA: an R Package for Co-expression Differential Network Analysis in n Dimensions, arXiv:1802.00828 [stat.CO]

 

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.

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