Publications

2019

Soneson C, Love MI, Patro R, Hussain S, Malhotra D, Robinson MD (2019).

A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs (http://doi.org/10.26508/lsa.201800175)

Life Science Alliance, February 2019

2018

Müller MC, Praz CR, Sotiropoulos AG, Menardo F, Kunz L, Schudel S, Oberhänsli S, Poretti M, Wehrli A, Bourras S, Keller B, Wicker T (2018).

A chromosome‐scale genome assembly reveals a highly dynamic effector repertoire of wheat powdery mildew (https://doi.org/10.1111/nph.15529)

New Phytologist, November 2018


Bourgeois Y, Stritt C, Walser JC, Gordon SP, Vogel JP, Roulin AC (2018).

Genome-wide scans of selection highlight the impact of biotic and abiotic constraints in natural populations of the model grass Brachypodium distachyon (https://doi.org/10.1111/tpj.14042)

The Plant Journal, October 2018


Butaité E, Kramer J, Wyder S, Kümmerli R (2018).

Environmental determinants of pyoverdine production, exploitation and competition in natural Pseudomonas communities ( https://doi.org/10.1111/1462-2920.14355 )

Environmental Microbiology, October 2018


Rezzoagli C, Wilson D, Weigert M, Wyder S, Kümmerli R (2018).

Probing the evolutionary robustness of two repurposed drugs targeting iron uptake in Pseudomonas aeruginosa https://doi.org/10.1093/emph/eoy026 )

Evolution, Medicine, and Public Health, September 2018


Ferrari G, Lischer HEL, Neukamm J, Rayo E, Borel N, Pospischil A, Rühli F, Bouwman AS, Campana MG (2018).

Assessing Metagenomic Signals Recovered from Lyuba, a 42,000-Year-Old Permafrost-Preserved Woolly Mammoth Calf (https://doi.org/10.3390/genes9090436)

Genes, August 2018


Townsend SW, Engesser S, Stoll S, Zuberbühler K, Bickel B (2018).

Compositionality in animals and humans (https://doi.org/10.1371/journal.pbio.2006425)

PLoS Biology, August 2018


Danneels B, Pinto-Carbó M, Carlier A (2018).

Patterns of Nucleotide Deletion and Insertion Inferred from Bacterial Pseudogenes (https://doi.org/10.1093/gbe/evy140)

Genome Biology and Evolution, July 2018


Giesen A, Schäfer MA, Blanckenhorn W (2018).

Geographic patterns of postzygotic isolation between two closely related widespread dung fly species (Sepsis cynipsea and Sepsis neocynipsea; Diptera: Sepsidae) (https://doi.org/10.1111/jzs.12239)

Journal of Zoological Systematics and Evolutionary Research, July 2018


Leigh DM, Lischer HEL, Grossen C, Keller LF (2018).

Batch effects in a multiyear sequencing study: False biological trends due to changes in read lengths (https://doi.org/10.1111/1755-0998.12779)

Molecular Ecology Resources, Special Issue: Association Mapping in Natural Populations, July 2018


Kellenberger RT, Desurmont GA, Schlüter PM & Schiestl FP (2018).

Trans-generational inheritance of herbivory-induced phenotypic changes in Brassica rapa (https://doi.org/10.1038/s41598-018-21880-2)

Scientific Reports, February 2018


Stritt C, Gordon SP, Wicker T, Vogel JP, Roulin AC (2018).

Recent activity in expanding populations and purifying selection have shaped transposable element landscapes across natural accessions of the mediterranean grass Brac)hypodium distachyon (https://doi.org/10.1093/gbe/evx276)

Genome Biology and Evolution, January 2018


Praz CR, Menardo F, Robinson MD, Müller MC, Wicker T, Bourras S, Keller B (2018).

Non-parent of Origin Expression of Numerous Effector Genes Indicates a Role of Gene Regulation in Host Adaption of the Hybrid Triticale Powdery Mildew Pathogen (https://doi.org/10.3389/fpls.2018.00049)

Frontiers in Plant Sciences, January 2018

2017

Collier K, Townsend SW, Manser MB (2017).

Call concatenation in wild meerkats (https://doi.org/10.1016/j.anbehav.2016.12.014)

Animal Behaviour, December 2017


Tschanz-Lischer H, Shimizu K (2017).

Reference-guided de novo assembly approach improves genome reconstruction for related species. (https://doi.org/10.1186/s12859-017-1911-6)

BMC Bioinformatics, November 2017


Giesen A, Blanckenhorn WU, Schäfer MA (2017).

Behavioural mechanisms of reproductive isolation between two hybridizing dung fly species (https://doi.org/10.1016/j.anbehav.2017.08.008)

Animal Behaviour, October 2017, Pages 155–166


Menardo F, Praz CR, Wicker T & Keller B (2017).

Rapid turnover of effectors in grass powdery mildew (Blumeria graminis) (https://doi.org/10.1186/s12862-017-1064-2)

BMC Evolutionary Biology, October 2017


Wyder S, Raissig MT, Grossniklaus U (2017).

Consistent Reanalysis of Genome-wide Imprinting Studies in Plants Using Generalized Linear Models Increases Concordance across Datasets (https://doi.org/10.1101/180745)

bioRxiv, October 2017


Briskine R, Paape T, Shimizu-Inatsugi R, Nishiyama T, Akama S, Sese J, Shimizu KK (2017).

Genome assembly and annotation of Arabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology (http://dx.doi.org/10.1111/1755-0998.12604)

Molecular Ecology Resources, September 2017, Pages 1025–1036


Butaité E, Baumgartner M, Wyder S, Kümmerli R (2017).

Siderophore cheating and cheating resistance shape competition for iron in soil and freshwater Pseudomonas communities ( https://doi.org/10.1038/s41467-017-00509-4 )

Nature Communications, September 2017


Collier K, Radford AN, Townsend SW, Manser MB (2017).

Wild dwarf mongooses produce general alert and predator-specific alarm calls ( https://doi.org/10.1093/beheco/arx091)

Behavioral Ecology, September 2017, Pages 1293–1301


Viganó C, Haas C, Rühli FJ, Bouwman A (2017).

2,000 Year old β‐thalassemia case in Sardinia suggests malaria was endemic by the Roman period (https://doi.org/10.1002/ajpa.23278)

American Journal of Physical Anthropology, July 2017


Baumgartner M, Roffler S, Wicker T, Pernthaler J (2017).

Letting go: bacterial genome reduction solves the dilemma of adapting to predation mortality in a substrate-restricted environment (http://dx.doi.org/10.1038/ismej.2017.87)

The ISME Journal, June 2017


Izuno A, Kitayama K, Onoda Y, Tsujii Y, Hatakeyama M, Nagano AJ, Honjo MN, Shimizu-Inatsugi R, Kudoh H, Shimizu KK, Isagi Y (2017).

The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha (Myrtaceae) (http://dx.doi.org/10.1111/mec.14016)

Molecular Ecology, March 2017, Pages 1515–1532


Menardo F, Wicker T, Keller B (2017).

Reconstructing the Evolutionary History of Powdery Mildew Lineages (Blumeria graminis) at Different Evolutionary Time Scales with NGS Data (https://doi.org/10.1093/gbe/evx008)

Genome Biology and Evolution, February 2017, Pages 446–456


Shimizu-Inatsugi R, Terada A, Hirose K, Kudoh H, Sese J, Shimizu KK (2017).

Plant adaptive radiation mediated by polyploid plasticity in transcriptomes (http://dx.doi.org/10.1111/mec.13738)

Molecular Ecology, January 2017, Pages 193–207

 

2016

Baumgartner M, Neu TR, Blom JF, Pernthaler J (2016).

Protistan predation interferes with bacterial long-term adaptation to substrate restriction by selecting for defence morphotypes (https://doi.org/10.1111/jeb.12957)

Journal of Evolutionary Biology, November 2016, Pages 2297–2310


Kellenberger RT, Schlüter PM, Schiestl FP (2016).

Herbivore-Induced DNA Demethylation Changes Floral Signalling and Attractiveness to Pollinators in Brassica rapa (https://doi.org/10.1371/journal.pone.0166646)

PLoS ONE, November 2016


Horton MW, Willems G, Sasaki E, Koornneef M, Nordborg M (2016).

The genetic architecture of freezing tolerance varies across the range of Arabidopsis thaliana (http://dx.doi.org/10.1111/pce.12812)

Plant, Cell & Environment, November 2016, Pages 2570–2579


Paape T, Hatakeyama M, Shimizu-Inatsugi R, Cereghetti T, Onda Y, Kenta T, Sese J, Shimizu KK (2016).

Conserved but Attenuated Parental Gene Expression in Allopolyploids: Constitutive Zinc Hyperaccumulation in the Allotetraploid Arabidopsis kamchatica (https://doi.org/10.1093/molbev/msw141)

Molecular Biology and Evolution, November 2016, Pages 2781–2800


Gan X, Hay A, Kwantes M, Haberer G, Hallab A, Ioio RD, Hofhuis H, Pieper B, Cartolano M, Neumann U, Nikolov LA, Song B, Hajheidari M, Briskine R, Kougioumoutzi E, Vlad D, Broholm S, Hein J, Meksem K, Lightfoot D, Shimizu KK, Shimizu-Inatsugi R, Imprialou M, Kudrna D, Wing R, Sato S, Huijser P, Filatov D, Mayer KFX, Mott R, Tsiantis M (2016).

The Cardamine hirsuta genome offers insight into the evolution of morphological diversity (http://dx.doi.org/10.1038/nplants.2016.167)

Nature Plants, October 2016


Pinto-Carbó M, Sieber S, Dessein S, Wicker T, Verstraete B, Gademann K, Eberl L, Carlier A (2016).

Evidence of horizontal gene transfer between obligate leaf nodule symbionts (http://dx.doi.org/10.1038/ismej.2016.27)

The ISME Journal, September 2016


Carlier A, Fehr L, Pinto-Carbó M, Schäberle T, Reher R, Dessein S, König G, Eberl L (2016).

The genome analysis of Candidatus Burkholderia crenata reveals that secondary metabolism may be a key function of the Ardisia crenata leaf nodule symbiosis (http://dx.doi.org/10.1111/1462-2920.13184)

Environmental Microbiology, August 2016, Pages 2507–2522


Novikova PY, Hohmann N, Nizhynska V, Tsuchimatsu T, Ali J, Muir G, Guggisberg A, Paape T, Schmid K, Fedorenko OM, Holm S, Säll T, Schlötterer C, Marhold K, Widmer A, Sese J, Shimizu KK, Weigel D, Krämer U, Koch MA, Nordborg M (2016).

Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism (http://dx.doi.org/10.1038/ng.3617)

Nature Genetics, July 2016


Cornetti L, Lemoine M, Hilfiker D, Morger J, Reeh K, Tschirren B (2016).

Higher genetic diversity on mountain tops: the role of historical and contemporary processes in shaping genetic variation in the bank vole (http://dx.doi.org/10.1111/bij.12723)

Biological Journal of the Linnean Society, June 2016, Pages 233–244


Menardo F, Praz CR, Wyder S, Ben-David R, Bourras S, Matsumae H, McNally KE, Parlange F, Riba A, Roffler S, Schaefer L, Shimizu KK, Valenti L, Zbinden H, Wicker T, Keller B (2016).

Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species (http://dx.doi.org/10.1038/ng.3485)

Nature Genetics, January 2016

 

2015

Morger J, Råberg L, Hille SM, Helsen S, Štefka J, Al-Sabi MM, Kapel CMO, Mappes T, Essbauer S, Ulrich RG, Bartolommei P, Mortelliti A, Balciauskas L, van den Brink NW, Rémy A, Bajer A, Cheprakov M, Korva M, García-Pérez AL, Biek R, Withenshaw S, Tschirren B (2015).

Distinct haplotype structure at the innate immune receptor Toll-like receptor 2 across bank vole populations and lineages in Europe (http://dx.doi.org/10.1111/bij.12593)

Biological Journal of the Linnean Society, September 2015, Pages 124–133


Tschirren B (2015).

Borrelia burgdorferi sensu lato infection pressure shapes innate immune gene evolution in natural rodent populations across Europe (http://dx.doi.org/10.1098/rsbl.2015.0263)

Biology Letters, May 2015


Tedder A, Helling M, Pannell JR, Shimizu-Inatsugi R, Kawagoe T, van Campen J, Sese J, Shimizu KK (2015).

Female sterility associated with increased clonal propagation suggests a unique combination of androdioecy and asexual reproduction in populations of Cardamine amara (Brassicaceae) (https://doi.org/10.1093/aob/mcv006)

Annals of Botany, April 2015, Pages 763–776

 

2014

Morger J, Banjok J, Craig PS, Rogan MT, Lun ZR, Hide G, Tschirren B (2014).

Naturally occurring Toll-like receptor 11 (TLR11) and Toll-like receptor 12 (TLR12) polymorphisms are not associated with Toxoplasma gondii infection in wild wood mice (https://doi.org/10.1016/j.meegid.2014.05.032)

Infection, Genetics and Evolution, August 2014, Pages 180-184


Collier K, Bickel B, van Schaik C, Manser MB, Townsend SW (2014).

Language evolution: Syntax before phonology? (https://doi.org/10.1098/rspb.2014.0263)

Proceedings of the Royal Society B, Biological Sciences, June 2014


Akama S, Shimizu-Inatsugi R, Shimizu KK, Sese J (2014).

Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis (https://doi.org/10.1093/nar/gkt1376)

Nucleic Acids Research, April 2014