Curriculum Vitae

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name Center for Computational and Theoretical Biology
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date of birth The tag birthday is only available for users.
profession The tag profession is only available for users.
institution The tag institution is only available for users.

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my publications

Transcriptome survey of the anhydrobiotic tardigrade Milnesium tardigradum in comparison with Hypsibius dujardini and Richtersius coronifer. In BMC Genomics, (11) 1: 168, Year 2010.
The virtual ecologist approach: simulating data and observers. In Oikos, (119) 4: 622--635, Blackwell Publishing Ltd, Year 2010.
Benchmarking novel approaches for modelling species range dynamics. In Global Change Biology, (22) 8: 2651--2664, Year 2016.
WHAMY is a novel actin polymerase promoting myoblast fusion, macrophage cell motility and sensory organ development in Drosophila. In J. Cell. Sci., (129) 3: 604--620, Year 2016.
Protein interaction networks--more than mere modules. In PLoS Comput. Biol., (6) e1000659, Year 2010.
Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees. In Biol Direct, (5) 4-4, Year 2010.
proovread: large-scale high accuracy PacBio correction through iterative short read consensus. In Bioinformatics, Oxford University Press (OUP), Year 2014.
ISAAC - InterSpecies Analysing Application using Containers. In BMC Bioinformatics, (15) 1: 18, Year 2014.
The characterization of the circadian clock in the olive fly Bactrocera oleae (Diptera: Tephritidae) reveals a Drosophila-like organization. In Scientific Reports, (8) 1: 816, Year 2018.
Closely related receptor complexes differ in their ABA selectivity and sensitivity. In The Plant Journal, (61) 1: 25--35, Wiley Online Library, Year 2010.
DNA-Metabarcoding – ein neuer Blick auf organismische Diversität. In BioSpektrum, (22) 147-150, Year 2016.
Correlation and process in species distribution models: bridging a dichotomy. In Journal of Biogeography, (39) 12: 2119--2131, Blackwell Publishing Ltd, Year 2012.
Chromosomal evolution in Pleurothallidinae (Orchidaceae: Epidendroideae) with emphasis on the genus Acianthera: chromosome numbers and heterochromatin. In Botanical Journal of the Linnean Society, (178) 102-120, Year 2015.
Biodiversity dynamics on islands: explicitly
counting for causality in mechanistic models
In Diversity, (9) 3: Year 2017.
TBro: visualization and management of de novo transcriptomes.. In Database, (2016) Year 2016.
The bilaterian roots of cordon-bleu. In BMC Res Notes, (6) 1: 393, Year 2013.
Keeping the Cape Lowland archipelago afloat. (Biodiversity in southern Africa. Volume 3: Implications for landuse and management) 151-179, Klaus Hess Publishers, Göttingen & Windhoek, Year 2010.
Delineating probabilistic species pools in ecology and biogeography. In Global Ecology and Biogeography , (25) 489-501, Year 2016.
Shaping tissues by balancing active forces and geometric constraints. In Journal of Physics D: Applied Physics, (49) 5: 053001, IOP Publishing, Year 2015.
Connectivity, not frequency, determines the fate of a morpheme. In PLoS ONE, (8) 7: e69945, Year 2013.
Leishmania donovani HslV does not interact stably with HslU proteins. In Int J Parasitol, (42) 4: 329-339, Year 2012.
AraPheno: a public database for Arabidopsis thaliana phenotypes. In Nucleic acids research, (45) D1: D1054--D1059, Oxford University Press, Year 2017.
Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus adults in active and anhydrobiotic state. In PLoS ONE, (7) 9: e45682, Public Library of Science, Year 2012.
Variation in structural location and amino acid conservation of functional sites in protein domain families. In BMC Bioinformatics, (6) 210, Year 2005.
Flagship umbrella species needed for conservation of overlooked biodiversity. In Conservation Biology, (31) 481-485, Year 2017.
Natural allelic variation of the AZI1 gene controls root growth under zinc-limiting condition. In PLOS Genetics, (14) 4: 1-23, Public Library of Science, Year 2018.
Functional leaf traits of vascular epiphytes: vertical trends within the forest, intra- and interspecific trait variability, and taxonomic signals. In Functional Ecology, (30) 188-198, Year 2016.
Using compensatory base change analysis of internal transcribed spacer 2 secondary structures to identify three new species in Paramacrobiotus (Tardigrada). In Organisms Diversity & Evolution, (10) 4: 287-296, Springer-Verlag, Year 2010.
Multiple alleles at a single locus control seed dormancy in Swedish Arabidopsis. In Elife, (5) e22502, eLife Sciences Publications Limited, Year 2016.
Molecular characterization of antimicrobial peptide genes of the carpenter ant Camponotus floridanus. In PLoS One, (7) 8: Year 2012.
Impacts of past habitat loss and future climate change on the range dynamics of South African Proteaceae. In Diversity and Distributions, (19) 4: 363--376, Year 2013.
Morpheme networks reveal language dynamics. Actes des 11es Journées Internationales d'Analyse Statistique des Données Textuelles / Proceedings of the 11th International Conference on the Statistical Analysis of Textual Data. Year 2012.
Formin’ cellular structures. In Communicative & Integrative Biology, (6) 6: e27634, Year 2013.
Proteomic Analysis of Tardigrades: Towards a Better Understanding of Molecular Mechanisms by Anhydrobiotic Organisms. In PLoS ONE, (5) 3: e9502, Public Library of Science, Year 2010.
FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms. In PLOS Computational Biology, (13) 1: 1-21, Public Library of Science, Year 2017.
The ITS2 Database II: homology modelling RNA structure for molecular systematics. In Nucleic Acids Res., (36) D377--380, Year 2008.
Bacterial Diversity and Community Structure in Two Bornean Nepenthes Species with Differences in Nitrogen Acquisition Strategies. In Microbial Ecology, (71) 938–953, Year 2016.
ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments. In Nucleic Acids Res., (44) 8: e77, Year 2016.
proovread: large-scale high-accuracy PacBio correction through iterative short read consensus. In Bioinformatics, Year 2014.
A kinome of 2600 in the ciliate Paramecium tetraurelia. In FEBS Lett., (583) 3589--3592, Year 2009.
ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales). In BMC Evol Biol, (8) 218-218, Year 2008.
Dieta de coruja murucututu (Pulsatrix perspicillata perspicillata Lathan, 1790) no Campus de UFRPE, Recife, PE. VI Congresso de Ecologia do Brasil. (Volume III) 273-274, Federal University of Ceará, Fortaleza, Year 2003.
Modelling interaction sites in protein domains with interaction profile hidden Markov models. In Bioinformatics, (22) 2851--2857, Year 2006.
Monophyletic clades of Macaranga pollinating thrips with high specificity to host plant taxonomic sections. In Biological Journal of the Linnean Society, (116) 3: 558–570, Year 2015.
bcgTree: automatized phylogenetic tree building from bacterial core genomes. In Genome, (59) 783-791, Year 2016.
Tensile forces drive a reversible fibroblast-to-myofibroblast transition during tissue growth in engineered clefts. In Science Advances, (4) 1: eaao4881, Year 2018.
The geography of the Anthropocene differs between the land and the sea. Year submitted.
A kinome of 2600 in the ciliate Paramecium tetraurelia. In FEBS Lett, (583) 22: 3589-3592, Year 2009.
Scrutinizing the immune defence inventory of Camponotus floridanus applying total transcriptome sequencing. In BMC Genomics, (16) 1: Springer Science $ Business Media, Year 2015.
Stress response in tardigrades: differential gene expression of molecular chaperones. In Cell Stress Chaperones, (15) 4: 423-430, Year 2010.
Genome of a tardigrade: Horizontal gene transfer or bacterial contamination?. In Proceedings of the National Academy of Sciences, (113) 22: E3054-E3056, Year 2016.
An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations. In Nature genetics, (44) 7: 825--830, Nature Research, Year 2012.
A map of local adaptation in Arabidopsis thaliana. In Science, (334) 6052: 86--89, American Association for the Advancement of Science, Year 2011.
Transcriptome analysis in tardigrade species reveals specific molecular pathways for stress adaptations. In Bioinform Biol Insights, (6) 69-96, Year 2012.
1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. In Cell, (166) 2: 481--491, Year 2016.
Different evolutionary modifications as a guide to rewire two-component systems. In Bioinform Biol Insights, (6) 97-128, Year 2012.
Gradual conversion of cellular stress patterns into pre-stressed matrix architecture during in vitro tissue growth. In Journal of The Royal Society Interface, (13) 118: The Royal Society, Year 2016.
Evolutionary flexibility of protein complexes. In BMC Evol. Biol., (9) 155, Year 2009.
Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden. In Nature genetics, (45) 8: 884--890, Nature Research, Year 2013.
Identification of divergent WH2 motifs by HMM-HMM alignments. In BMC Res Notes, (8) 1: 18, Year 2015.
Estimating demographic models for the range dynamics of plant species. In Global Ecology and Biogeography, (19) 1: 85--97, Blackwell Publishing Ltd, Year 2010.
The AraGWAS Catalog: a curated and standardized Arabidopsis thaliana GWAS catalog. In Nucleic Acids Research, gkx954, Year 2017.
Atlantic forest fragments in Pernambuco and Alagoas and theirs bromeliads: distribution, composition, richness and conservation. (Fragments of the Atlantic Forest of Northeast Brazil: Biodiversity, Conservation and the Bromeliads) 101-131, Andrea Jakobsson Estúdio, Rio de Janeiro, Year 2006.
GER1, a GDSL motif-encoding gene from rice is a novel early light-and jasmonate-induced gene. In Plant Biology, (9) 01: 32--40, Georg Thieme Verlag Stuttgart KGtextperiodcentered New York, Year 2007.
Synthesis of novel derivatives of oxindole, their urease inhibition and molecular docking studies.. Year 2015.
Regulators of PP2C phosphatase activity function as abscisic acid sensors. In Science, (324) 5930: 1064--1068, American Association for the Advancement of Science, Year 2009.
Branchfall as a demographic filter for epiphyte communities: Lessons from a forest floor-based sampling. In PloS one, (10) e0128019, Year 2015.
Computational integration of genomic traits into 16S rDNA microbiota sequencing studies. In Gene, Year 2014.
4SALE--a tool for synchronous RNA sequence and secondary structure alignment and editing. In BMC Bioinformatics, (7) 498, Year 2006.
Generalist social bees maximize diversity intake in plant species-rich and resource-abundant environments. In Ecosphere, (8) 3: e01758--n/a, Year 2017.
Linking ecological niche, community ecology and biogeography: insights from a mechanistic niche model. In Journal of Biogeography, (39) 12: 2212--2224, Year 2012.
Venus flytrap carnivorous lifestyle builds on herbivore defense strategies. In Genome Res., (26) 6: 812--825, Year 2016.
ITS2 Database V: Twice as Much. In Molecular Biology and Evolution, (32) 11: 3030-3032, Year 2015.
The protein composition of the digestive fluid from the venus flytrap sheds light on prey digestion mechanisms. In Mol. Cell Proteomics, (11) 11: 1306--1319, Year 2012.
Leaf growth response to mild drought: natural variation in Arabidopsis sheds light on trait architecture. In The Plant Cell, (28) 10: 2417--2434, American Society of Plant Biologists, Year 2016.
Internal Transcribed Spacer 2 (nu ITS2 rRNA) Sequence-Structure Phylogenetics: Towards an Automated Reconstruction of the Green Algal Tree of Life. In PLoS ONE, (6) 2: e16931, Public Library of Science, Year 2011.
Integrating stochasticity into community ecology. Year submitted.
Gating of the two-pore cation channel AtTPC1 in the plant vacuole is based on a single voltage-sensing domain. In Plant Biol (Stuttg), (18) 5: 750--760, Year 2016.
Release from prey preservation behavior via prey switch allowed diversification of cuticular hydrocarbon profiles in digger wasps. In Evolution, (in press) Year 2017.
chloroExtractor: extraction and assembly of the chloroplast genome from whole genome shotgun data. In The Journal of Open Source Software, (3) 21: 464, The Open Journal, Year 2018.
The ITS2 Database III--sequences and structures for phylogeny. In Nucleic Acids Res, (38) Database issue: 275-279, Year 2010.
reper: Genome-wide identification, classification and quantification of repetitive elements without an assembled genome. In The Journal of Open Source Software, (3) 22: 527, The Open Journal, Year 2018.
The Small World of Osteocytes: Connectomics of the Lacuno-Canalicular
Network in Bone.
In New Journal of Physics, (19) 073019, Year 2017.
Integrating community assembly and biodiversity reveals new dimensions of ecosystem functions: the Community Assembly and the Functioning of Ecosystems (CAFE) approach. In Ecology Letters, (21) 167–180, Year 2018.
Detecting species-site dependencies in large multiple sequence alignments. In Nucleic Acids Res., (37) 5959--5968, Year 2009.
biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format. In F1000Research, (5) 2348, F1000 Research, Ltd., Year 2016.
Positive selection in tick saliva proteins of the Salp15 family. In J. Mol. Evol., (68) 186--191, Year 2009.
A comprehensive analysis of human proteins’ binding sites and its implications for drug
Advancements in Life Sciences "International Quarterly Journal of Biological Sciences", Year 2015.
Spatial scaling of extinction rates: theory and data reveal non-linearity, and a major upscaling and downscaling challenge. In Global Ecology and Biogeography, (27) 2-13, Year 2018.
Process, correlation and parameter fitting in species distribution models: a response to Kriticos et al. 2012. In Journal of Biogeography, (40) 611-613, Year 2013.
Infection of Soybean Plants with the Insect Bacterial Symbiont Burkholderia gladioli and Evaluation of Plant Fitness. In BIO-PROTOCOL, (7) 24: Bio-Protocol, LLC, Year 2017.
Evolutionary and Structural Analyses of the Mammalian Haloacid Dehalogenase-Type Phosphatases AUM and Chronophin Provide Insight into the Basis of their Different Substrate Specificities. In J. Biol. Chem., (289) 6: 3416-31, Year 2014.
Bioinformatics identifies tardigrade molecular adaptations including the DNA-j family and first steps towards dynamical modelling. In Journal of Zoological Systematics and Evolutionary Research, (49) 120--126, Blackwell Publishing Ltd, Year 2011.
Molecular phylogeny of the neotropical genus Christensonella (Orchidaceae, Maxillariinae): species delimitations and insights into chromosome evolution. In Annals of Botany, (102) 491-507: Year 2008.
Oceanic island biogeography through the lens of the general dynamic model: assessment and prospect. In Biological Reviews, (92) 830-853, Blackwell Publishing Ltd, Year 2017.
FENNEC - Functional Exploration of Natural Networks and Ecological Communities. In bioRxiv, Cold Spring Harbor Laboratory, Year 2017.
FHOD proteins in actin dynamics-a formin' class of its own. In Small GTPases, (5) 2: 1--6, Year 2014.
Partially-supervised protein subclass discovery with simultaneous annotation of functional residues. In BMC Struct. Biol., (9) 68, Year 2009.
ITS2 Database V: Twice as Much. In Mol. Biol. Evol., (32) 11: 3030--3032, Year 2015.
Linear and nonlinear rheology of living cells. In Annual Review of Materials Research, (41) 75--97, Annual Reviews, Year 2011.
Modeling the long-term dynamics of tropical forests: from leaf traits to whole-tree growth patterns. In Ecological Monographs, Year submitted.
Reptiles as reservoirs of bacterial infections: real threat or methodological bias?. In Microbial Ecology, (70) 3: 579-84, Year 2015.
Genetic Components of Root Architecture Remodeling in Response to Salt Stress. In The Plant Cell, American Society of Plant Biologists, Year 2017.
Evolution of an RNP assembly system: a minimal SMN complex facilitates formation of UsnRNPs in Drosophila melanogaster. In Proc. Natl. Acad. Sci. U.S.A., (105) 10045--10050, Year 2008.
Karyotype diversity and genome size variation in Neotropical Maxillariinae orchids. In Plant Biology, (19) 298-308, Year 2017.
Honey bee foraging ecology: Season but not landscape diversity shapes the amount and diversity of collected pollen. In PLoS one, (in press) Year 2017.
Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades. In BMC Genomics, (10) 469-469, Year 2009.
Computational integration of genomic traits into 16S rDNA microbiota sequencing studies . In Gene , (549) 1: 186 - 191, Year 2014.
Effects of time and isolation on plant diversity: testing island biogeography theory with an eco-evolutionary model. In bioRxiv, 100289: Year 2017.
Mechanistic models in macroecology and biogeography: state-of-art and prospects. In Ecography, (40) 267-280: Year 2017.
A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota. In RNA, (11) 361--364, Year 2005.
Distinguishing species. In RNA, (13) 1469--1472, Year 2007.
Impaired induction of the jasmonate pathway in the rice mutant hebiba. In Plant Physiology, (133) 4: 1820--1830, American Society of Plant Biologists, Year 2003.
biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format. In F1000Research, (5) 2348, F1000 Research, Ltd., Year 2017.
ITS2 database IV: interactive taxon sampling for internal transcribed spacer 2 based phylogenies. In Mol. Phylogenet. Evol., (63) 3: 585--588, Year 2012.
Nuclear localization of the mutant protein phosphatase abi1 is required for insensitivity towards ABA responses in Arabidopsis. In The Plant Journal, (54) 5: 806--819, Blackwell Publishing Ltd, Year 2008.
Function of phytochelatin synthase in catabolism of glutathione-conjugates. In The Plant Journal, (49) 4: 740--749, Wiley Online Library, Year 2007.
Effects of Harvesting Flowers from Shrubs on the Persistence and Abundance of Wild Shrub Populations at Multiple Spatial Extents. In Conservation Biology, (25) 1: 73--84, Blackwell Publishing Inc, Year 2011.
Human HAD phosphatases: structure, mechanism, and roles in health and disease. In FEBS J., (280) 2: 549--571, Year 2013.
5.8S-28S rRNA interaction and HMM-based ITS2 annotation. In Gene, (430) 50--57, Year 2009.
How type 1 fimbriae help Escherichia coli to evade extracellular antibiotics. In Scientific Reports, (6) 18109, The Author(s), Year 2016.
Phylogeny of Oedogoniales, Chaetophorales and Chaetopeltidales (Chlorophyceae): inferences from sequence-structure analysis of ITS2. In Ann Bot, (109) 1: 109-116, Year 2012.
The advantages and limitations of trait analysis with GWAS: a review. In Plant Methods, (9) 29-29, Year 2013.
Biogeographic, climatic and spatial drivers differentially affect α-, β- and γ-diversities on oceanic archipelagos. In Proceedings of the Royal Society of London B: Biological Sciences, (281) 1784: Year 2014.
Arabidopsis thaliana AUCSIA-1 regulates auxin biology and physically interacts with a kinesin-related protein. In PloS one, (7) 7: e41327, Public Library of Science, Year 2012.
Late Quaternary climate change shapes island biodiversity. In Nature, (532) 7597: 99--102, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved., Year 2016.
Genome of a tardigrade: Horizontal gene transfer or bacterial contamination?. In Proc. Natl. Acad. Sci. U.S.A., Year 2016.
A mixed-model approach for genome-wide association studies of correlated traits in structured populations. In Nature genetics, (44) 9: 1066--1071, Nature Research, Year 2012.
Evolutionary Distances in the Twilight Zone---A Rational Kernel Approach. In PLoS ONE, (5) 12: e15788, Public Library of Science, Year 2010.
Contact of myeloma cells induces a characteristic transcriptome signature in skeletal precursor cells--Implications for myeloma bone disease. In Bone, (93) 155--166, Elsevier, Year 2016.
Antibiotic-producing symbionts dynamically transition between plant pathogenicity and insect-defensive mutualism. In Nature Communications, (8) 15172--, The Author(s), Year 2017.
Species richness change across spatial scales. Year submitted.
Crown galls of grapevine (Vitis vinifera) host distinct microbiota. In Applied and Environmental Microbiology, (82) 5542-5552, Year 2016.
Cell sheet mechanics: How geometrical constraints induce the detachment of cell sheets from concave surfaces . In Acta Biomaterialia , (45) 85 - 97, Year 2016.
The ITS2 Database. In J Vis Exp, 61: Year 2012.
Heterochromatin diversity and its co-localization with 5S and 45S rDNA sites in chromosomes of four Maxillaria species (Orchidaceae). In Genetics and Molecular Biology, (29) 659 - 664, scielo, Year 2006.
Coalignment of osteocyte canaliculi and collagen fibers in human osteonal bone. In Journal of Stuctural Biology, (199) 177-186, Year 2017.
How to understand species’ niches and range dynamics: a demographic research agenda for biogeography. In Journal of Biogeography, (39) 12: 2146--2162, Blackwell Publishing Ltd, Year 2012.
Word formation is aware of morpheme family size. In PLoS ONE, (9) 4: e93978, Year 2014.

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