Barbieri C, Blasi DE, Arango-Isaza E, [...] Bickel B, Shimizu KK (2022).

A global analysis of matches and mismatches between human genetic and linguistic histories (

PNAS, November 2022

Karve S, Wagner A (2022).

Environmental complexity is more important than mutation in driving the evolution of latent novel traits in E. coli  (

Nature Communications, October 2022

Jayakumar P, Figueiredo ART, Kümmerli R (2022).

Evolution of Quorum Sensing in Pseudomonas aeruginosa Can Occur via Loss of Function and Regulon Modulation (

mSystems, October 2022

Rayo E, Neukamm J, Tomoum N, Eppenberger P, Breidenstein A, Bouwman AS, Schuenemann VJ, Rühli FJ (2022).

Metagenomic analysis of Ancient Egyptian canopic jars (

American Journal of Biological Anthroplogy, August 2022

Akagi T, Jung K, Masuda K, Shimizu KK (2022).

Polyploidy before and after domestication of crop species (

Current Opinion in Plant Biology, July 2022

Karve S, Dasmeh P, Zheng J, Wagner A (2022).

Low protein expression enhances phenotypic evolvability by intensifying selection on folding stability (

Nature Ecology & Evolution, July 2022

Müller MC, Kunz L, Schudel S, Lawson AW, Kammerecker S, Isaksson J, Wyler M, Graf J, Sotiropoulos AG, Praz CR, Manser B, Wicker T, Bourras S, Keller B (2022).

Ancient variation of the AvrPm17 gene in powdery mildew limits the effectiveness of the introgressed rye Pm17 resistance gene in wheat (

PNAS, July 2022

Sotiropoulos AG, Arango-Isaza E, Ban T, Barbieri C, Bourras S,  [...] Müller MC, Shamanin V, Shimizu KK, Yoshihira T, Zbinden H, Keller B, Wicker T (2022).

Global genomic analyses of wheat powdery mildew reveal association of pathogen spread with historical human migration and trade (

Nature Communications, July 2022

Toll-Riera M, Olombrada M, Castro-Giner F, Wagner A (2022).

A limit on the evolutionary rescue of an Antarctic bacterium from rising temperatures (

Science Advances, July 2022

Thieme M, Brêchet A, Bourgeois Y, Keller B, Bucher E, Roulin AC (2022).

Experimentally heat-induced transposition increases drought tolerance in Arabidopsis thaliana (

New Phytologist, June 2022

Robin M, Ferrari G, Akgül G, Münger X, von Seth J, Schuenemann VJ, Dalén L, Grossen C (2022).

Ancient mitochondrial and modern whole genomes unravel massive genetic diversity loss during near extinction of Alpine ibex (

Molecular Ecology, May 2022

Russo A, Mayjonade B, Frei D, Potente G, Kellenberger RT, Frachon L, Copetti D, Studer B, Frey JE, Grossniklaus U, Schlüter PM (2022).

Low-Input High-Molecular-Weight DNA Extraction for Long-Read Sequencing From Plants of Diverse Families (

Frontiers in Plant Sciences, May 2022

Neubauer A, Ruaud S, Waller M, Frangedakis E, Li FW, Nötzold SI, Wicke S, Bailly A, Szövényi P (2022).

Step-by-step protocol for the isolation and transient transformation of hornwort protoplasts (

Applications in Plant Sciences, February 2022

Potente G, Léveillé-Bourret É, Yousefi N, Choudhury RR, Keller B, Diop SI, [...] Szövényi P, Conti E (2022).

Comparative Genomics Elucidates the Origin of a Supergene Controlling Floral Heteromorphism (

Molecular Biology and Evolution, February 2022

Rayo E, Ferrari G, Neukamm J, Akgül G, [...] Bouwman AS, Rühli FJ, Schuenemann VJ (2022).

Non-destructive extraction of DNA from preserved tissues in medical collections (

Future Science, February 2022

Figueiredo ART, Özkaya Ö, Kümmerli R, Kramer J (2022).

Siderophores drive invasion dynamics in bacterial communities through their dual role as public good versus public bad (

Ecology Letters, January 2022

Izuno A, Onoda Y, Amada G, Kobayashi K, Mukai M, Isagi Y, Shimizu KK (2022).

Demography and selection analysis of the incipient adaptive radiation of a Hawaiian woody species (

PLoS Genetics, January 2022

Kakui H, Tsuchimatsu T, Yamazaki M, Hatakeyama M, Shimizu KK (2022).

Pollen Number and Ribosome Gene Expression Altered in a Genome-Editing Mutant of REDUCED POLLEN NUMBER1 Gene (

Frontiers in Plant Science, January 2022

Murer L, Petkidis A, Vallet T, Vignuzzi M, Greber UF (2022).

Chemical evolution of Rhinovirus identifies capsid-destabilizing mutations driving low pH-independent genome uncoating (

Journal of Virology, January 2022

Pla-Díaz M, Sánchez-Busó L, Giacani L, [...] Schuenemann VJ, Nieselt K, Arora N, González-Candelas F (2022).

Evolutionary Processes in the Emergence and Recent Spread of the Syphilis Agent, Treponema pallidum (

Molecular Biology and Evolution, January 2022

Stritt C, Gimmi EL, Wyler M, Bakali AH, Skalska A, Hasterok R, Mur LAJ, Pecchioni N, Roulin AC (2022).

Migration without interbreeding: evolutionary history of a highly selfing Mediterranean grass inferred from whole genomes (

Molecular Ecology, January 2022


Müller MC, Kunz L, Graf J, Schudel S, Keller B (2021).

Host Adaptation Through Hybridization: Genome Analysis of Triticale Powdery Mildew Reveals Unique Combination of Lineage-Specific Effectors (

Molecular Plant-Microbe Interactions, December 2021

Wicker T, Stritt C, Sotiropoulos AG, Poretti M, Pozniak C, Walkowiak S, Gundlach H, Stein N (2021).

Transposable Element Populations Shed Light on the Evolutionary History of Wheat and the Complex Co-Evolution of Autonomous and Non-Autonomous Retrotransposons (

Advanced Genetics, December 2021

Frangedakis E, Waller M, Nishiyama T, Tsukaya H, Xu X, Yue Y, Tjahjadi M, Gunadi A, Van Eck J, Li F-W, Szövényi P, Sakakibara K (2021).

An Agrobacterium-mediated stable transformation technique for the hornwort model Anthoceros agrestis (

New Phytologist, November 2021

Aivelo T, Lemoine M, Tschirren B (2021).

Elevational Changes in Bacterial Microbiota Structure and Diversity in an Arthropod-Disease Vector (

Microbial Ecology, October 2021

Bai Y, Caussinus E, Leo S, Bosshardt F, Myachina F, Rot G, Robinson MD, Lehner CF (2021).

A cis-regulatory element promoting increased transcription at low temperature in cultured ectothermic Drosophila cells (

BMC Genomics, October 2021

Lankheet I, Vicente M, Barbieri C, Schlebusch C (2021).

The performance of common SNP arrays in assigning African mitochondrial haplogroups (

BMC Genomic Data, October 2021

Leigh DM, Lischer HEL, Guillaume F, Grossen C, Günther T (2021).

Disentangling adaptation from drift in bottlenecked and reintroduced populations of Alpine ibex (

Molecular Ecology Resources, October 2021

Ng KKS, Kobayashi MJ, Fawcett JA [...] Shimizu KK (2021).

The genome of Shorea leprosula (Dipterocarpaceae) highlights the ecological relevance of drought in aseasonal tropical rainforests (

Communications Biology, October 2021

Pfrengle S, Neukamm J, [...] Schuenemann VJ (2021).

Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes (

BMC Biology, October 2021

Roquis D, Robertson M, Yu L, Thieme M, Julkowska M, Bucher E (2021).

Genomic impact of stress-induced transposable element mobility in Arabidopsis (

Nucleic Acids Research, October 2021

Urban C, Blom AA, Pfrengle S, Walker-Meikle K, Stone AC, Inskip SA, Schuenemann VJ (2021).

One Health Approaches to Trace Mycobacterium leprae’s Zoonotic Potential Through Time (

Frontiers in Microbiology, October 2021

Aguirre-Fernández G, Barbieri C, Graff A, Pérez de Arce J, Moreno H, Sánchez-Villagra MR (2021).

Cultural macroevolution of musical instruments in South America (

Humanities and Social Sciences Communications, September 2021

Halstead-Nussloch G, Tanaka T, Copetti D, Paape T, Kobayashi f, Hatakeyama M, [...] Shimizu KK, Handa H (2021).

Multiple Wheat Genomes Reveal Novel Gli-2 Sublocus Location and Variation of Celiac Disease Epitopes in Duplicated α-Gliadin Genes (

Frontiers in Plant Sciences, September 2021

Mittelstrass J, Sperone FG, Horton MW (2021).

Using transects to disentangle the environmental drivers of plant-microbiome assembly (

Plant, Cell & Environment, September 2021

Moerman F, Fronhofer EA, Altermatt F, Wagner A (2021).

Selection on growth rate and local adaptation drive genomic adaptation during experimental range expansions in the protist Tetrahymena thermophila (

Journal of Animal Ecology, September 2021

Figueiredo ART, Wagner A, Kümmerli R (2021).

Ecology drives the evolution of diverse social strategies in Pseudomonas aeruginosa (

Molecular Ecology, August 2021

Florez-Rueda AMFiscalini F, Roth M, Grossniklaus U, Städler T (2021).

Endosperm and Seed Transcriptomes Reveal Possible Roles for Small RNA Pathways in Wild Tomato Hybrid Seed Failure (

Genome Biology and Evolution, August 2021

Matsumae H, Ranacher P, Savage PE, Blasi  DE, Currie TE, Koganebuchi K, Nishida N, Sato T, Tanabe H, Tajima A, Brown S, Stoneking M, Shimizu KK, Oota H, Bickel B (2021).

Exploring correlations in genetic and cultural variation across language families in northeast Asia (

Science Advances, August 2021

Stritt C, Thieme M, Roulin AC (2021).

Rare transposable elements challenge the prevailing view of transposition dynamics in plants (

American Journal of Botany, August 2021

Nguyen H, Hampel B, Garcia Nuñez D, Battegay M, Hachfeld A, Bernasconi E, Calmy A, Cavassini M, Vernazza P, Fellay J, Rudolph H, Huber M, Leuzinger K, Perreau M, Scherrer A,  Ramette AN, Yerly S, Günthard HF, Kouyos RD, Kusejko K,  the Swiss HIV Cohort Study (2021).

Identifying and Characterizing Trans women in the Swiss HIV Cohort Study as an Epidemiologically Distinct Risk Group (

Clinical Infectious Diseases, July 2021

Milosavljevic S, Kuo T, Decarli S, Mohn L, Sese J, Shimizu KK, Shimizu-Inatsugi R & Robinson MD (2021).

ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw (

BMC Genomics, July 2021

Nguyen H, Thorball CW, Fellay J, Böni J, Yerly S, [...], Günthard HF, Kouyos RD, The Swiss HIV Cohort Study (2021).

Systematic screening of viral and human genetic variation identifies antiretroviral resistance and immune escape link (

eLife, June 2021

Brown JA, Mbunkah HA, Lejone TI, [...] Metzner KJ, Günthard HF, Labhardt ND, Kouyos RD, Tschumi N (2021).

Emergence of Human Immunodeficiency Virus-1 Drug Resistance During the 3-Month World Health Organization-Recommended Enhanced Adherence Counseling Period in the CART-1 Cohort Study (

Open Forum Infectious Diseases, May 2021

Gerber R, Robinson MD (2021).

Censcyt: censored covariates in differential abundance analysis in cytometry (

BMC Bioinformatics, May 2021

Huang R, Soneson C, Germain P-L, Schmidt TSB, Von Mering C, Robinson MD (2021).

treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses (

BMC Genome Biology, May 2021

Manser B, Koller T, Praz CR, Roulin AC, [...], Keller B, Sánchez-Martín J (2021).

Identification of specificity-defining amino acids of the wheat immune receptor Pm2 and powdery mildew effector AvrPm2 (

The Plant Journal, May 2021

Szövényi P, Gunadi A, Li FW (2021).

Charting the genomic landscape of seed-free plants (

Nature Plants, April 2021

Abrouk M, Athiyannan N, Müller T, Pailles Y, Stritt C, Roulin AC, [...] Keller B, Krattinger SG (2021).

Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color (

Communications Biology, March 2021

Akiyama R, Sun J, Hatakeyama M, Lischer HEL, [...] Shimizu KK, Shimizu‐Inatsugi R (2021).

Fine‐scale empirical data on niche divergence and homeolog expression patterns in an allopolyploid and its diploid progenitor species (

New Phytologist, March 2021

Baumann C, Pfrengle S, Münzel SC, Molak M, Feuerborn TR, Breidenstein A, [...] Bocherens H, Schuenemann VJ (2021).

A refined proposal for the origin of dogs: the case study of Gnirshöhle, a Magdalenian cave site (

Scientific Reports, March 2021

Hewitt T, Müller MC, Molnár I, Mascher M, Holušová K, Šimková H, Kunz L, [...] Keller B, Lagudah E, Zhang P (2021).

A highly differentiated region of wheat chromosome 7AL encodes a Pm1a immune receptor that recognizes its corresponding AvrPm1a effector from Blumeria graminis (

New Phytologist, March 2021

Lütge A, Zyprych-Walczak J, Brykczynska Kunzmann U, Crowell HL, Calini D, Malhotra D, Soneson C, Robinson MD (2021).

CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq data (

Life Science Alliance, March 2021

Schmeing S, Robinson MD (2021).

ReSeq simulates realistic Illumina high-throughput sequencing data (

Genome Biology, February 2021

Frangedakis E, Shimamura M, Villarreal JC, Li FW, Tomaselli M, Waller M, Sakakibara K, Renzaglia KS, Szövényi P (2021).

The hornworts: morphology, evolution and development (

New Phytologist, January 2021

Shimizu KK, Copetti D, Okada M, Wicker T, Tameshige T, Hatakeyama M, Shimizu-Inatsugi R, [...] Handa H (2020).

De Novo Genome Assembly of the Japanese Wheat Cultivar Norin 61 Highlights Functional Variation in Flowering Time and Fusarium Resistance Genes in East Asian Genotypes (

Plant and Cell Physiology, January 2021


Furtwängler A, Neukamm J, Böhme L, Reiter E, Vollstedt M, Arora N, [...] Krause J, Schuenemann VJ, Herbig A (2020).

Comparison of target enrichment strategies for ancient pathogen DNA (

Biotechniques, December 2020

Shimizu‐Inatsugi R, Milosavljevic S, Shimizu KK, Schaepman‐Strub G, Tanoi K, Sato Y (2020).

Metal accumulation and its effect on leaf herbivory in an allopolyploid species Arabidopsis kamchatica inherited from a diploid hyperaccumulator A. halleri (

Plant Species Biology, December 2020

Aubier TG, Galipaud M, Erten EY, Kokko H (2020).

Transmissible cancers and the evolution of sex under the Red Queen hypothesis (

PLOS Biology, November 2020

Walkowiak S, Gao L, [...] Shimizu-Inatsugi R, [...] Shimizu KK, [...] Keller B, [...] Wicker T, Pozniak CJ (2020).

Multiple wheat genomes reveal global variation in modern breeding (

Nature, November 2020

Wyler M, Stritt C, Walser JC, Baroux C, Roulin AC (2020).

Impact of transposable elements on methylation and gene expression across natural accessions of Brachypodium distachyon (

Genome Biology and Evolution, November 2020

Ferrari G, Neukamm J, [...] Rühli F, Bouwman A, Schuenemann VJ (2020).

Variola virus genome sequenced from an eighteenth-century museum specimen supports the recent origin of smallpox (

Philosophical Transactions of the Royal Society B, October 2020

Morozova I, Kasianov A, Bruskin S, Neukamm J, Molak M, Batieva E, Pudło A, Rühli FJ, Schuenemann VJ (2020).

New ancient Eastern European Yersinia pestis genomes illuminate the dispersal of plague in Europe (

Philosophical Transactions of the Royal Society B, October 2020

Sun J, Shimizu-Inatsugi R, Hofhuis H, Shimizu K, Hay A, Shimizu KK, Sese J (2020).

A Recently Formed Triploid Cardamine insueta Inherits Leaf Vivipary and Submergence Tolerance Traits of Parents (

Frontiers in Genetics, October 2020

Urban M, Barbieri C (2020).

North and South in the ancient Central Andes: Contextualizing the archaeological record with evidence from linguistics and molecular anthropology (

Journal of Anthropological Archaeology, October 2020

Figueiredo ART, Kümmerli R (2020).

Microbial Mutualism: Will You Still Need Me, Will You Still Feed Me? (

Current Biology, September 2020

Paape T, Akiyama R, Cereghetti T, Onda Y, Hirao AS, Kenta T, Shimizu KK (2020.

Experimental and Field Data Support Range Expansion in an Allopolyploid Arabidopsis Owing to Parental Legacy of Heavy Metal Hyperaccumulation (

Frontiers in Genetics, September 2020

Skalska A, Stritt C, Wyler M, [...] Roulin AC, Hasterok R, Mur LAJ (2020).

Genetic and Methylome Variation in Turkish Brachypodium Distachyon Accessions Differentiate Two Geographically Distinct Subpopulations (

International Journal of Molecular Sciences, September 2020

Majander K, Pfrengle S, [...] Arora N, Akgül G, [...] Schuenemann VJ (2020).

Ancient Bacterial Genomes Reveal a High Diversity of Treponema pallidum Strains in Early Modern Europe (

Current Biology, August 2020

Neukamm J, Pfrengle S, [...] Schuenemann VJ (2020).

2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals (

BMC Biology, August 2020

Lindner S, Keller B, Singh SP, Hasenkamp Z, Jung E, Müller MC, Bourras S, Keller B (2020).

Single residues in the LRR domain of the wheat PM3A immune receptor can control the strength and the spectrum of the immune response (

The Plant Journal, July 2020

Weber de Melo V, Lowe R, Hurd PJ, Petchey O (2020).

Phenotypic responses to temperature in the ciliate Tetrahymena thermophila (

Ecology and Evolution, July 2020

Cairns J, Moermann F, Fronhofer EA, Altermatt F, Hiltunen T (2020).

Evolution in interacting species alters predator life-history traits, behaviour and morphology in experimental microbial communities (

Proceedings of the Royal Society B, June 2020

Kirbis A, Waller M, Ricca M, Bont Z, Neubauer A, Goffinet B, Szövényi P (2020).

Transcriptional Landscapes of Divergent Sporophyte Development in Two Mosses, Physcomitrium (Physcomitrella) patens and Funaria hygrometrica (

Frontiers in Plant Science, June 2020

Moerman F, Fronhofer EA, Wagner A, Altermatt F (2020).

Gene swamping alters evolution during range expansions in the protist Tetrahymena thermophila (

Biology Letters, June 2020

Tsuchimatsu T, Kakui H, [...] Grossniklaus U, Kanaoka MM, Lenhard M, Nordborg M, Shimizu KK (2020).

Adaptive reduction of male gamete number in the selfing plant Arabidopsis thaliana (

Nature Communications, June 2020

Figueiredo ART, Kramer J (2020).

Cooperation and Conflict Within the Microbiota and Their Effects On Animal Hosts (

Frontiers in Ecology and Evolution, May 2020

Nakatsuka N, Lazaridis I, Barbieri C, [...] Fehren-Schmitz L (2020).

A Paleogenomic Reconstruction of the Deep Population History of the Andes (

Cell, May 2020

Barquera R, Lamnidis TC, [...] Barbieri C, [...] Krause J (2020).

Origin and Health Status of First-Generation Africans from Early Colonial Mexico (

Current Biology, April 2020

Erten EY, Kokko H (2020).

From zygote to a multicellular soma: Body size affects optimal growth strategies under cancer risk (

Evolutionary Applications, April 2020

Hanya G, Tackmann J, [..] von Mering C, Shimizu-Inatsugi R, Hayakawa T, Shimizu KK & Ushida K (2020).

Fermentation Ability of Gut Microbiota of Wild Japanese Macaques in the Highland and Lowland Yakushima: In Vitro Fermentation Assay and Genetic Analyses (

Microbial Ecology, April 2020

Pick JL, Hatakeyama M, Ihle KE, [...] Shimizu‐Inatsugi R, Shimizu KK, Tschirren B (2020).

Artificial selection reveals the role of transcriptional constraints in the maintenance of life history variation (

Evolution Letters, April 2020

Diop SI, Subotic O, Giraldo‐Fonseca A, Waller M, Kirbis A, Neubauer A, Potente G, [...] Grossniklaus U, McDaniel SF, Szövényi P (2020).

A pseudomolecule‐scale genome assembly of the liverwort Marchantia polymorpha (

The Plant Journal, March 2020

Gerke P, Szövényi P, Neubauer A, Lenz H, Gutmann B, McDowell R, Small I, Schallenberg‐Rüdinger M, Knoop V (2020).

Towards a plant model for enigmatic U‐to‐C RNA editing: the organelle genomes, transcriptomes, editomes and candidate RNA editing factors in the hornwort Anthoceros agrestis (

New Phytologist, March 2020

Kramer J, Özkaya Ö, Kümmerli R (2020).

Bacterial siderophores in community and host interactions (

Nature Reviews Microbiology, March 2020

Li F, Nishiyama T, Waller M, [...] Diop IS, [...] Kirbis A, [...] Neubauer A, [...] Szövényi P (2020).

Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts (

Nature Plants, March 2020

Poretti M, Praz CR, Meile L, Kälin C, Schaefer LK, Schläfli M, Widrig V, Sanchez-Vallet A, Wicker T, Bourras S (2020).

Domestication of High-Copy Transposons Underlays the Wheat Small RNA Response to an Obligate Pathogen ( )

Molecular Biology and Evolution, March 2020

Tiberi S, Robinson MD (2020).

BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty (

Genome Biology, March 2020

Wyder S, Rivera A, Valdés AE, Cañal MJ, Gagliardini V, Fernández H, Grossniklaus U (2020).

Differential gene expression profiling of one- and two-dimensional apogamous gametophytes of the fern Dryopteris affinis ssp. affinis (

Plant Physiology and Biochemistry, March 2020

Baur J, Giesen A, Rohner PT, Blanckenhorn WU, Schäfer MA (2020).

Exaggerated male forelegs are not more differentiated than wing morphology in two widespread sister species of black scavenger flies (

Journal of Zoological Systematics and Evolutionary Research, February 2020

Grossen C, Guillaume F, Keller LF, Croll D (2020).

Purging of highly deleterious mutations through severe bottlenecks in Alpine ibex (

Nature Communications, February 2020

Tabrett A, Horton MW (2020).

The influence of host genetics on the microbiome (

F1000Research, February 2020

Moerman F, Arquint A, Merkli S, Wagner A, Altermatt F, Fronhofer EA (2020).

Evolution under pH stress and high population densities leads to increased density‐dependent fitness in the protist Tetrahymena thermophila (

Evolution, January 2020

Akiyama R, Milosavljevic S, Leutenegger M, Shimizu-Inatsugi R (2020).

Trait-dependent resemblance of the flowering phenology and floral morphology of the allopolyploid Cardamine flexuosa to those of the parental diploids in natural habitats (

Journal of Plant Research, January 2020



Erten EY, Kokko H (2019).

Diverse ways to think about cancer: What can we learn about cancer by studying it across the tree of life? (

Mètode Science Studies Journal, December 2019

Izuno A, Wicker T, Hatakeyama M, Copetti D, Shimizu KK (2019).

Updated Genome Assembly and Annotation for Metrosideros polymorpha, an Emerging Model Tree Species of Ecological Divergence ()

G3: Genes, Genomes, Genetics, November 2019

Översti S, Majander K, Salmela E, Salo K, Arppe L, Belskiy S, Etu-Sihvola H, Laakso V, Mikkola E, Pfrengle S, Putkonen M, Taavitsainen JP, Vuoristo K, Wessman A, Sajantila A, Oinonen M, Haak W, Schuenemann VJ, Krause J, Palo JU, Onkamo P. (2019).

Human mitochondrial DNA lineages in the Iron-Age Fennoscandia suggest incipient admixture and eastern introduction of farming-related maternal ancestry ( )

Scientific Reports, November 2019

Piñeiro Fernández L, Byers KJRP, Cai J, Sedeek KEM, Kellenberger RT, Russo A, Qi W, Aquino Fournier C, Schlüter PM (2019).

A Phylogenomic Analysis of the Floral Transcriptomes of Sexually Deceptive and Rewarding European Orchids, Ophrys and Gymnadenia (

Frontiers in Plant Science, November 2019

Stritt C, Wyler M, Gimmi EL, Pippel M, Roulin AC (2019).

Diversity, dynamics and effects of LTR retrotransposons in the model grass Brachypodium distachyon (

New Phytologist, November 2019

Olearo F, Nguyen H, Bonnet F, Yerly S, Wandeler G, Stoeckle M, Cavassini M, Scherrer A, Costagiola D, Schmid P, Günthard HF, Bernasconi E, Boeni J, D’arminio Monforte A, Zazzi M, Rossetti B, Neau D, Bellecave P, Rijnders B, Reiss P, Wit F, Kouyos R, Calmy A (2019).

Impact of the M184V/I Mutation on the Efficacy of Abacavir/Lamivudine/Dolutegravir Therapy in Human Immunodeficiency Virus Treatment-Experienced Patients (

Open Forum Infectious Diseases, October 2019

Meccariello A, Salvemini M, Primo P, Hall B, Koskinioti P, Dalíková M, Gravina A, Gucciardino MA, Forlenza F, Gregoriou ME, Ippolito D, Monti SM, Petrella V, Perrotta MM, Schmeing S, Ruggiero A, Scolari F, Giordano E, Tsoumani KT, Marec F, Windbichler N, Arunkumar KP, Bourtzis K, Mathiopoulos KD, Ragoussis J, Vitagliano L, Tu Z, Papathanos PA, Robinson MD, Saccone G (2019).

Maleness-on-the-Y (MoY) orchestrates male sex determination in major agricultural fruit fly pests. (

Science, September 2019

Gretzinger J, Molak M, Reiter E, Pfrengle S, Urban C, Neukamm J, Blant M, Conard NJ, Cupillard C, Dimitrijević V, Drucker DG, Hofman-Kamińska E, Kowalczyk R, Krajcarz MT, Krajcarz M, Münzel SC, Peresani M, Romandini M, Rufí I, Soler J, Terlato G, Krause J, Bocherens H, Schuenemann VJ (2019).

Large-scale mitogenomic analysis of the phylogeography of the Late Pleistocene cave bear (

Scientific Reports, August 2019

Nguyen H, Thorball CW, Fellay J, Böni J, Yerly S, Perreau M, Klimkait T, Kusejko K, Bachmann N, Chaudron S, Paioni P, Thurnheer MC, Battegay M, Cavassini M,  Vernazza P, Bernasconi E, Günthard HF, Kouyos R (2019).

HIV Transmission Chains Exhibit Greater HLA-B Homogeneity Than Randomly Expected (

Journal of Acquired Immune Deficiency Syndromes, August 2019

Barbieri CBarquera RArias LSandoval JR, Acosta OZurita CAguilar-Campos A, Tito-Álvarez AM, Serrano-Osuna R, Gray R, Mafessoni F, Heggarty PShimizu KKFujita RStoneking MPugach I, Fehren-Schmitz L (2019).

The current genomic landscape of western South America: Andes, Amazonia and Pacific Coast (

Molecular Biology and Evolution, July 2019

Soneson C, Yao Y, Bratus-Neuenschwander A, Patrignani A, Robinson MD & Hussain S (2019).

A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes (

Nature Communications, July 2019

van Gestel J, Ackermann M, Wagner A (2019).

Microbial life cycles link global modularity in regulation to mosaic evolution (

Nature Ecology & Evolution, July 2019

Bourras S, Kunz L, Xue M, Praz CR, Müller MC, Kälin C, Schläfli M, Ackermann P, Flückiger S, Parlange F, Menardo F, Schaefer LK, Ben-David R, Roffler S, Oberhaensli S, Widrig V, Lindner S, Isaksson J, Wicker T, Yu D & Keller B (2019).

The AvrPm3-Pm3 effector-NLR interactions control both race-specific resistance and host-specificity of cereal mildews on wheat (

Nature Communications, May 2019

Müller MC, Praz CR, Sotiropoulos AG, Menardo F, Kunz L, Schudel S, Oberhänsli S, Poretti M, Wehrli A, Bourras S, Keller B, Wicker T (2019).

A chromosome‐scale genome assembly reveals a highly dynamic effector repertoire of wheat powdery mildew (

New Phytologist, March 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 (

Life Science Alliance, February 2019

Wyder S, Raissig MT, Grossniklaus U (2019).

Consistent Reanalysis of Genome-wide Imprinting Studies in Plants Using Generalized Linear Models Increases Concordance across Datasets (

Scientific Reports, February 2019

Bergelson J, Mittelstrass J, Horton MW (2019).

Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome (

Scientific Reports, January 2019

Grize SA, Wilwert E, Searle JB, Lindholm AK (2019).

Measurements of hybrid fertility and a test of mate preference for two house mouse races with massive chromosomal divergence. ( )

BMC Evolutionary Biology, January 2019


Roulin PS, Murer LP, Greber UF (2018).

A Single Point Mutation in the Rhinovirus 2B Protein Reduces the Requirement for Phosphatidylinositol 4-Kinase Class III Beta in Viral Replication (

Journal of Virology, December 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 (

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 ( )

Environmental Microbiology, October 2018

Beeravolu CR, Hickerson MJ, Frantz LAF, Lohse K (2018).

ABLE: blockwise site frequency spectra for inferring complex population histories and recombination (

Genome Biology, September 2018

Paape T, Briskine RV, Halstead-Nussloch G, Lischer HEL, Shimizu-Inatsugi R, Hatakeyama M, Tanaka K, Nishiyama T, Sabirov R, Sese J, Shimizu KK (2018).

Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica (

Nature Communications, September 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 )

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 (

Genes, August 2018

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

Compositionality in animals and humans (

PLoS Biology, August 2018

Whitewoods CD, Cammarata J, Nemec Venza Z, Sang S, Crook AD, Aoyama T, Wang XY, Waller M, Cuming AC, Szövényi P, Nimchuk ZL, Roeder AHK, Scanlon MJ, Harrison CJ (2018).

CLAVATA was a genetic novelty for the morphological innovation of 3D growth in land plants (

Current Biology, August 2018

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

Patterns of Nucleotide Deletion and Insertion Inferred from Bacterial Pseudogenes (

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) (

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 (

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 (

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 (

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 (

Frontiers in Plant Sciences, January 2018


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

Call concatenation in wild meerkats (

Animal Behaviour, December 2017

Tschanz-Lischer H, Shimizu K (2017).

Reference-guided de novo assembly approach improves genome reconstruction for related species. (

BMC Bioinformatics, November 2017

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

Behavioural mechanisms of reproductive isolation between two hybridizing dung fly species (

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) (

BMC Evolutionary Biology, 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 (

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 ( )

Nature Communications, September 2017

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

Wild dwarf mongooses produce general alert and predator-specific alarm calls (

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 (

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 (

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) (

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 (

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 (

Molecular Ecology, January 2017, Pages 193–207



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 (

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 (

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 (

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 (

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 (

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 (

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 (

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 (

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 (

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 (

Nature Genetics, January 2016



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 (

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 (

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) (

Annals of Botany, April 2015, Pages 763–776



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 (

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? (

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 (

Nucleic Acids Research, April 2014