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Vollenweider V, Roncoroni F, Kümmerli R (2024).
Pyoverdine-antibiotic combination treatment: its efficacy and effects on resistance evolution in Escherichia coli (https://doi.org/10.1093/femsml/uqae021)
microLife, October 2024
Leinweber A, Laffont C, Lardi M, Eberl L, Pessi G, Kümmerli R (2024).
RNA-Seq reveals that Pseudomonas aeruginosa mounts growth medium-dependent competitive responses when sensing diffusible cues from Burkholderia cenocepacia (https://doi.org/10.1038/s42003-024-06618-3)
Communications Biology, August 2024
Russo A, Alessandrini M, El Baidouri M, [...]Wicker T, Xu S, Grossniklaus U,
Schlüter PM (2024).
Genome of the early spider-orchid Ophrys sphegodes provides insights into sexual deception and pollinator adaptation (https://doi.org/10.1038/s41467-024-50622-4)
Nature Communications, July 202
Kofler XV, Grossniklaus U, Schiestl FP, Frachon L (2024).
Uncovering genes involved in pollinator-driven mating system shifts and selfing syndrome evolution in Brassica rapa (https://doi.org/10.1111/nph.19880)
New Phytologist, June 2024
Passmore S, Wood ALC, Barbieri C, Shilton D, Daikoku H, Atkinson QD, Savage PE (2024).
Global musical diversity is largely independent of linguistic and genetic histories (https://doi.org/10.1038/s41467-024-48113-7)
Nature Communications, May 2024
Urban, C, Blom AA, Avanzi C, [...] Schuenemann VJ (2024).
Ancient Mycobacterium leprae genome reveals medieval English red squirrels as animal leprosy host (https://doi.org/10.1016/j.cub.2024.04.006)
Current Biology, May 2024
Wilkin S, Lanigan LT, Montes N, Sharma M, Avanzi C, Sejdiu D, [...] Schuenemann VJ (2024).
Sequential trypsin and ProAlanase digestions unearth immunological protein biomarkers shrouded by skeletal collagen (https://doi.org/10.1016/j.isci.2024.109663)
iScience, May 2024
Horvath R, Minadakis N, Bourgeois Y, Roulin AC (2024).
The evolution of transposable elements in Brachypodium distachyon is governed by purifying selection, while neutral and adaptive processes play a minor role (https://doi.org/10.7554/eLife.93284.3)
eLife, April 2024
Minadakis N, Kaderli L, Horvath R, Xu W, Thieme M, Woods DP, Roulin AC (2024).
Polygenic architecture of flowering time and its relationship with local environments in the grass Brachypodium distachyon (https://doi.org/10.1093/genetics/iyae042)
Genetics, March 2024
Thieme M, Minadakis N, Himber C, [...] Roulin AC (2024).
Transposition of HOPPLA in siRNA-deficient plants suggests a limited effect of the environment on retrotransposon mobility in Brachypodium distachyon (https://doi.org/10.1371/journal.pgen.1011200)
PLoS Genetics, March 2024
Majander K, Pla-Díaz M, du Plessis L, Arora N, [...] Schuenemann VJ (2024).
Redefining the treponemal history through pre-Columbian genomes from Brazil (https://doi.org/10.1038/s41586-023-06965-x)
Nature, January 2024
Neubauer A, Aros-Mualin D, Mariscal V, Szövényi P (2024).
Challenging the term symbiosis in plant-microbe associations to create an understanding across sciences. (https://doi.org/10.1111/jipb.13588)
Journal of Integrative Plant Biology, January 2024
Stockenhuber R, Akiyama R, Tissot N, Milosavljevic S, [...] Shimizu KK (2024).
The UV RESISTANCE LOCUS 8-Mediated UV-B Response Is Required Alongside CRYPTOCHROME 1 For Plant Survival Under Sunlight In Field Conditions. (https://doi.org/10.1093/pcp/pcad113)
Plant & Cell Physiology, January 2024
Loosli T, Hossmann S, Ingle SM, Okhai H, Kusejko K, Mouton J, Bellecave P, van Sighem A, Stecher A, d’Arminio Monforte A, Gill MJ, Sabin CA, Maartens G, Günthard HF, Sterne JAC, Lessells R, Egger M, Kouyos R (2023).
HIV-1 drug resistance in people on dolutegravir-based antiretroviral therapy: a collaborative cohort analysis (https://doi.org/10.1016/S2352-3018(23)00228-X)
The Lancet HIV, October 2023
Menéndez LP, Barbieri C, López Cruz IG, Schmelzle T, Breidenstein A, Barquera R, Borzi G, Schuenemann VJ, Sánchez-Villagra MR (2023).
On Roth’s “human fossil” from Baradero, Buenos Aires Province, Argentina: morphological and genetic analysis (https://doi.org/10.1186/s13358-023-00293-3)
Swiss Journal of Palaeontology, October 2023
Akiyama R, Goto T, Tameshige T, [...] Shimizu-Inatsugi R, Shimizu KK (2023).
Seasonal pigment fluctuation in diploid and polyploid Arabidopsis revealed by machine learning-based phenotyping method PlantServation. (https://doi.org/10.1038/s41467-023-41260-3)
Nature Communications, September 2023
Minadakis N, Williams H, Horvath R, Cakovic D, Stritt C, Thieme M, Bourgeois YXC, Roulin AC (2023).
The demographic history of the wild crop relative Brachypodium distachyon is shaped by distinct past and present ecological niches (https://doi.org/10.24072/pcjournal.319
Peer Community Journal, September 2023
Wang K, Prüfer K, Krause-Kyora B, Childebayeva A, Schuenemann VJ, Coia V, Maixner F, Zink A, Schiffels S, Krause J (2023).
High-coverage genome of the Tyrolean Iceman reveals unusually high Anatolian farmer ancestry. (https://doi.org/10.1016/j.xgen.2023.100377)
Cell Genomics, September 2023
Wilkin S, Hommel P, Ventresca Miller A, Boivin N, Pedergnana A, Shishlina N, Trifonov V (2023).
Curated cauldrons: Preserved proteins from early copper-alloy vessels illuminate feasting practices in the Caucasian steppe. (https://doi.org/10.1016/j.isci.2023.107482 )
iScience, September 2023
Giesen A, Blanckenhorn WU, Schäfer MA, Shimizu KK, Shimizu-Inatsugi R, Misof B, Podsiadlowski L, Niehuis O, Lischer HEL, Aeschbacher S, Kapun M (2023).
Geographic Variation in Genomic Signals of Admixture Between Two Closely Related European Sepsid Fly Species (https://doi.org/10.1007/s11692-023-09612-5)
Evolutionary Biology, August 2023
Sun J, Okada M, Tameshige T, Shimizu-Inatsugi R, Akiyama R, Nagano AJ, Sese J, Shimizu KK (2023).
A low-coverage 3′ RNA-seq to detect homeolog expression in polyploid wheat (https://doi.org/10.1093/nargab/lqad067)
NAR Genomics and Bioinformatics, July 2023
Arango-Isaza E, Capodiferro MR, Aninao MJ, [...] Shimizu KK, Barbieri C (2023).
The genetic history of the Southern Andes from present-day Mapuche ancestry (https://doi.org/10.1016/j.cub.2023.05.013)
Current Biology, June 2023
Schmeing S,Robinson MD (2023).
Gapless provides combined scaffolding, gap filling, and assembly correction with long reads (https://doi.org/10.26508/lsa.202201471)
Life Science Alliance, May 2023
Frangedakis E, Marron AO, Waller M, Neubauer A, Tse SW, Yue Y, Ruaud S, Waser L, Sakakibara K, Szövényi P (2023).
What can hornworts teach us? (https://doi.org/10.3389/fpls.2023.1108027)
Frontiers in Plant Sciences, March 2023
Kunz L, Sotiropoulos AG, Graf J, Razavi M, Keller B & Müller MC (2023).
The broad use of the Pm8 resistance gene in wheat resulted in hypermutation of the AvrPm8 gene in the powdery mildew pathogen (https://doi.org/10.1186/s12915-023-01513-5)
BMC Biology, February 2023
Waller M, Frangedakis E, Marron AO, Sauret-Gueto S, Rever J, Sabbagh CRR, Hibberd JM, Haseloff J, Renzaglia KS, Szövényi P (2023).
An optimised transformation protocol for Anthoceros agrestis and three more hornwort species. (https://doi.org/10.1111/tpj.16161)
The Plant Journal, February 2023
Sotiropoulos AG, Sánchez-Martín J, [...]Wicker T, Keller B (2022).
A fictional field case study to understand the genetic basis of host-fungal pathogen interactions using the wheat powdery mildew-wheat pathosystem (https://doi.org/10.1080/00219266.2022.2147574)
Journal of Biological Education, December 2022
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 (https://doi.org/10.1073/pnas.2122084119)
PNAS, November 2022
Hasterok R, Catalan P, Hazen SP,Roulin AC, Vogel JP, Wang K, Mur LAJ (2022).
Brachypodium: 20 years as a grass biology model system; the way forward? (https://doi.org/10.1016/j.tplants.2022.04.008)
Trends in Plant Science, October 2022
Shimizu KK (2022).
Robustness and the generalist niche of polyploid species: Genome shock or gradual evolution? (https://doi.org/10.1016/j.pbi.2022.102292)
Current Opinion in Plant Biology, October 2022
Karve S, Wagner A (2022).
Environmental complexity is more important than mutation in driving the evolution of latent novel traits in E. coli (https://doi.org/10.1038/s41467-022-33634-w)
Nature Communications, October 2022
Figueiredo ART, Kümmerli R (2022).
Evolution of Quorum Sensing in Pseudomonas aeruginosa Can Occur via Loss of Function and Regulon Modulation (https://doi.org/10.1128/msystems.00354-22)
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 (https://doi.org/10.1002/ajpa.24600)
American Journal of Biological Anthroplogy, August 2022
Akagi T, Jung K, Masuda K, Shimizu KK (2022).
Polyploidy before and after domestication of crop species (https://doi.org/10.1016/j.pbi.2022.102255)
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 (https://doi.org/10.1038/s41559-022-01797-w)
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 (https://doi.org/10.1073/pnas.2108808119)
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 (https://doi.org/10.1038/s41467-022-31975-0)
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 (https://doi.org/10.1126/sciadv.abk3511)
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 (https://doi.org/10.1111/nph.18322)
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 (https://doi.org/10.1111/mec.16503)
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 (https://doi.org/10.3389/fpls.2022.883897)
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 (https://doi.org/10.1002/aps3.11456)
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 (https://doi.org/10.1093/molbev/msac035)
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 (https://doi.org/10.2144/btn-2021-0014)
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 (https://doi.org/10.1111/ele.13912)
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 (https://doi.org/10.1371/journal.pgen.1009987)
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 (https://doi.org/10.3389/fpls.2021.768584)
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 (https://doi.org/10.1128/JVI.01060-21)
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 (https://doi.org/10.1093/molbev/msab318)
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 (https://doi.org/10.1111/mec.16207)
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 (https://doi.org/10.1094/MPMI-05-21-0111-SC)
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 (https://doi.org/10.1002/ggn2.202100022)
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 (https://doi.org/10.1111/nph.17524)
New Phytologist, November 2021
Aivelo T, Lemoine M, Tschirren B (2021).
Elevational Changes in Bacterial Microbiota Structure and Diversity in an Arthropod-Disease Vector (https://doi.org/10.1007/s00248-021-01879-5)
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 (https://doi.org/10.1186/s12864-021-08057-4)
BMC Genomics, October 2021
Lankheet I, Vicente M, Barbieri C, Schlebusch C (2021).
The performance of common SNP arrays in assigning African mitochondrial haplogroups (https://doi.org/10.1186/s12863-021-01000-2)
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 (https://doi.org/10.1111/1755-0998.13442)
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 (https://doi.org/10.1038/s42003-021-02682-1)
Communications Biology, October 2021
Pfrengle S, Neukamm J, [...] Schuenemann VJ (2021).
Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes (https://doi.org/10.1186/s12915-021-01120-2)
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 (https://doi.org/10.1093/nar/gkab828)
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 (https://doi.org/10.3389/fmicb.2021.762263)
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 (https://doi.org/10.1057/s41599-021-00881-z)
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 (https://doi.org/10.3389/fpls.2021.715985)
Frontiers in Plant Sciences, September 2021
Mittelstrass J, Sperone FG, Horton MW (2021).
Using transects to disentangle the environmental drivers of plant-microbiome assembly (https://doi.org/10.1111/pce.14190)
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 (https://doi.org/10.1111/1365-2656.13598)
Journal of Animal Ecology, September 2021
Figueiredo ART, Wagner A, Kümmerli R (2021).
Ecology drives the evolution of diverse social strategies in Pseudomonas aeruginosa (https://doi.org/10.1111/mec.16119)
Molecular Ecology, August 2021
Endosperm and Seed Transcriptomes Reveal Possible Roles for Small RNA Pathways in Wild Tomato Hybrid Seed Failure (https://doi.org/10.1093/gbe/evab107)
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 (https://doi.org/10.1126/sciadv.abd9223)
Science Advances, August 2021
Stritt C, Thieme M, Roulin AC (2021).
Rare transposable elements challenge the prevailing view of transposition dynamics in plants (https://doi.org/10.1002/ajb2.1709)
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 (https://doi.org/10.1093/cid/ciab628)
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 (https://doi.org/10.1186/s12864-021-07845-2)
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 (https://doi.org/10.7554/eLife.67388)
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 (https://doi.org/10.1093/ofid/ofab046)
Open Forum Infectious Diseases, May 2021
Gerber R, Robinson MD (2021).
Censcyt: censored covariates in differential abundance analysis in cytometry (https://doi.org/10.1186/s12859-021-04125-4)
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 (https://doi.org/10.1186/s13059-021-02368-1)
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 (https://doi.org/10.1111/tpj.15214)
The Plant Journal, May 2021
Szövényi P, Gunadi A, Li FW (2021).
Charting the genomic landscape of seed-free plants (https://doi.org/10.1038/s41477-021-00888-z)
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 (https://doi.org/10.1038/s42003-021-01908-6)
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 (https://doi.org/10.1111/nph.17101)
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 (https://doi.org/10.1038/s41598-021-83719-7)
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 (https://doi.org/10.1111/nph.17075)
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 (https://doi.org/10.26508/lsa.202001004)
Life Science Alliance, March 2021
Schmeing S, Robinson MD (2021).
ReSeq simulates realistic Illumina high-throughput sequencing data (https://doi.org/10.1186/s13059-021-02265-7)
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 (https://doi.org/10.1111/nph.16874)
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 (https://doi.org/10.1093/pcp/pcaa152)
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 (https://doi.org/10.2144/btn-2020-0100)
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 (https://doi.org/10.1111/1442-1984.12304)
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 (https://doi.org/10.1371/journal.pbio.3000916)
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 (https://doi.org/10.1038/s41586-020-2961-x)
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 (https://doi.org/10.1093/gbe/evaa180)
Genome Biology and Evolution, November 2020
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Variola virus genome sequenced from an eighteenth-century museum specimen supports the recent origin of smallpox (https://doi.org/10.1098/rstb.2019.0572)
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 (https://doi.org/10.1098/rstb.2019.0569)
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 (https://doi.org/10.3389/fgene.2020.567262)
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 (https://doi.org/10.1016/j.jaa.2020.101233)
Journal of Anthropological Archaeology, October 2020
Collier K, Radford AN, Stoll S, Watson SK, Manser MB, Bickel B, Townsend SW (2020).
Dwarf mongoose alarm calls: investigating a complex non-human animal call (https://doi.org/10.1098/rspb.2019.2514)
Proceedings of the Royal Society B, September 2020
Figueiredo ART, Kümmerli R (2020).
Microbial Mutualism: Will You Still Need Me, Will You Still Feed Me? (https://doi.org/10.1016/j.cub.2020.07.002)
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 (https://doi.org/10.3389/fgene.2020.565854)
Frontiers in Genetics, September 2020
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Genetic and Methylome Variation in Turkish Brachypodium Distachyon Accessions Differentiate Two Geographically Distinct Subpopulations (https://doi.org/10.3390/ijms21186700)
International Journal of Molecular Sciences, September 2020
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Ancient Bacterial Genomes Reveal a High Diversity of Treponema pallidum Strains in Early Modern Europe (https://doi.org/10.1016/j.cub.2020.07.058)
Current Biology, August 2020
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2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals (https://doi.org/10.1186/s12915-020-00839-8)
BMC Biology, August 2020
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Single residues in the LRR domain of the wheat PM3A immune receptor can control the strength and the spectrum of the immune response (https://doi.org/10.1111/tpj.14917)
The Plant Journal, July 2020
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Phenotypic responses to temperature in the ciliate Tetrahymena thermophila (https://doi.org/10.1002/ece3.6486)
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 (https://doi.org/10.1098/rspb.2020.0652)
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 (https://doi.org/10.3389/fpls.2020.00747)
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 (https://doi.org/10.1098/rsbl.2020.0244)
Biology Letters, June 2020
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Adaptive reduction of male gamete number in the selfing plant Arabidopsis thaliana (https://doi.org/10.1038/s41467-020-16679-7)
Nature Communications, June 2020
Figueiredo ART, Kramer J (2020).
Cooperation and Conflict Within the Microbiota and Their Effects On Animal Hosts (https://doi.org/10.3389/fevo.2020.00132)
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A Paleogenomic Reconstruction of the Deep Population History of the Andes (https://doi.org/10.1016/j.cell.2020.04.015)
Cell, May 2020
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Origin and Health Status of First-Generation Africans from Early Colonial Mexico (https://doi.org/10.1016/j.cub.2020.04.002)
Current Biology, April 2020
From zygote to a multicellular soma: Body size affects optimal growth strategies under cancer risk (https://doi.org/10.1111/eva.12969)
Evolutionary Applications, April 2020
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Fermentation Ability of Gut Microbiota of Wild Japanese Macaques in the Highland and Lowland Yakushima: In Vitro Fermentation Assay and Genetic Analyses (https://doi.org/10.1007/s00248-020-01515-8)
Microbial Ecology, April 2020
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Artificial selection reveals the role of transcriptional constraints in the maintenance of life history variation (https://doi.org/10.1002/evl3.166)
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A pseudomolecule‐scale genome assembly of the liverwort Marchantia polymorpha (https://doi.org/10.1111/tpj.14602)
The Plant Journal, March 2020
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New Phytologist, March 2020
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Bacterial siderophores in community and host interactions (https://doi.org/10.1038/s41579-019-0284-4)
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Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts (https://doi.org/10.1038/s41477-020-0618-2)
Nature Plants, March 2020
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Domestication of High-Copy Transposons Underlays the Wheat Small RNA Response to an Obligate Pathogen (https://doi.org/10.1093/molbev/msz272 )
Molecular Biology and Evolution, March 2020
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BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty (https://doi.org/10.1186/s13059-020-01967-8)
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 (https://doi.org/10.1016/j.plaphy.2020.01.021)
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 (https://doi.org/10.1111/jzs.12327)
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Grossen C, Guillaume F, Keller LF, Croll D (2020).
Purging of highly deleterious mutations through severe bottlenecks in Alpine ibex (https://doi.org/10.1038/s41467-020-14803-1)
Nature Communications, February 2020
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The influence of host genetics on the microbiome (https://doi.org/10.12688/f1000research.20835.1)
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Evolution under pH stress and high population densities leads to increased density‐dependent fitness in the protist Tetrahymena thermophila (https://doi.org/10.1111/evo.13921)
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Trait-dependent resemblance of the flowering phenology and floral morphology of the allopolyploid Cardamine flexuosa to those of the parental diploids in natural habitats (https://doi.org/10.1007/s10265-019-01164-0)
Journal of Plant Research, January 2020
Diverse ways to think about cancer: What can we learn about cancer by studying it across the tree of life? (http://dx.doi.org/10.7203/metode.10.14593)
Mètode Science Studies Journal, December 2019
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Human mitochondrial DNA lineages in the Iron-Age Fennoscandia suggest incipient admixture and eastern introduction of farming-related maternal ancestry (https://doi.org/10.1038/s41598-019-51045-8 )
Scientific Reports, November 2019
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A Phylogenomic Analysis of the Floral Transcriptomes of Sexually Deceptive and Rewarding European Orchids, Ophrys and Gymnadenia (https://doi.org/10.3389/fpls.2019.01553)
Frontiers in Plant Science, November 2019
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Diversity, dynamics and effects of LTR retrotransposons in the model grass Brachypodium distachyon (https://doi.org/10.1111/nph.16308)
New Phytologist, November 2019
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Open Forum Infectious Diseases, October 2019
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Maleness-on-the-Y (MoY) orchestrates male sex determination in major agricultural fruit fly pests. (https://doi.org/10.1126/science.aax1318)
Science, September 2019
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Large-scale mitogenomic analysis of the phylogeography of the Late Pleistocene cave bear (https://doi.org/10.1038/s41598-019-47073-z)
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 (https://doi.org/10.1097/QAI.0000000000002077)
Journal of Acquired Immune Deficiency Syndromes, August 2019
The current genomic landscape of western South America: Andes, Amazonia and Pacific Coast (https://doi.org/10.1093/molbev/msz174)
Molecular Biology and Evolution, July 2019
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A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes (https://doi.org/10.1038/s41467-019-11272-z)
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Microbial life cycles link global modularity in regulation to mosaic evolution (https://doi.org/10.1038/s41559-019-0939-6)
Nature Ecology & Evolution, July 2019
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The AvrPm3-Pm3 effector-NLR interactions control both race-specific resistance and host-specificity of cereal mildews on wheat (https://doi.org/10.1038/s41467-019-10274-1)
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 (https://doi.org/10.1111/nph.15529)
New Phytologist, March 2019
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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
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Consistent Reanalysis of Genome-wide Imprinting Studies in Plants Using Generalized Linear Models Increases Concordance across Datasets (https://doi.org/10.1038/s41598-018-36768-4)
Scientific Reports, February 2019
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Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome (https://doi.org/10.1038/s41598-018-37208-z)
Scientific Reports, January 2019
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Measurements of hybrid fertility and a test of mate preference for two house mouse races with massive chromosomal divergence. (https://doi.org/10.1186/s12862-018-1322-y )
BMC Evolutionary Biology, January 2019
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A Single Point Mutation in the Rhinovirus 2B Protein Reduces the Requirement for Phosphatidylinositol 4-Kinase Class III Beta in Viral Replication (https://doi.org/10.1128/JVI.01462-18)
Journal of Virology, December 2018
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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
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Probing the evolutionary robustness of two repurposed drugs targeting iron uptake in Pseudomonas aeruginosa ( https://doi.org/10.1093/emph/eoy026 )
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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
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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 (https://doi.org/10.1016/j.cub.2018.05.068)
Current Biology, August 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).
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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
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Frontiers in Plant Sciences, January 2018
Collier K, Townsend SW, Manser MB (2017).
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BMC Evolutionary Biology, October 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)
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2,000 Year old β‐thalassemia case in Sardinia suggests malaria was endemic by the Roman period (https://doi.org/10.1002/ajpa.23278)
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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)
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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)
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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)
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PLoS ONE, November 2016
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The genetic architecture of freezing tolerance varies across the range of Arabidopsis thaliana (http://dx.doi.org/10.1111/pce.12812)
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Conserved but Attenuated Parental Gene Expression in Allopolyploids: Constitutive Zinc Hyperaccumulation in the Allotetraploid Arabidopsis kamchatica (https://doi.org/10.1093/molbev/msw141)
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The Cardamine hirsuta genome offers insight into the evolution of morphological diversity (http://dx.doi.org/10.1038/nplants.2016.167)
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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)
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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
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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)
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