Publications

Ansermet, C., Centeno, G., Pradervand, S., Harmacek, D., Garcia, A., Daraspe, J., Kocherlakota, S., Baes, M., Bignon, Y., and Firsov, D. (2022a). Renal tubular peroxisomes are dispensable for normal kidney function. JCI Insight 7, e155836.

Ansermet, C., Centeno, G., Bignon, Y., Ortiz, D., Pradervand, S., Garcia, A., Menin, L., Gachon, F., Yoshihara, H.AI., and Firsov, D. (2022b). Dysfunction of the circadian clock in the kidney tubule leads to enhanced kidney gluconeogenesis and exacerbated hyperglycemia in diabetes. Kidney International 101, 563–573.

Blattner, L., Lucek, K., Beck, N., Berner, D., and Fumetti, S. (2022). Intra‐Alpine Islands: Population genomic inference reveals high degree of isolation between freshwater spring habitats. Diversity and Distributions 28, 291–305.

Fuertes Marraco, S.A., Alpern, D., Lofek, S., Lourenco, J., Bovay, A., Maby-El Hajjami, H., Delorenzi, M., Deplancke, B., and Speiser, D.E. (2022). Shared acute phase traits in effector and memory human CD8 T cells. Current Research in Immunology 3, 1–12.

Sepporta, M.-V., Praz, V., Balmas Bourloud, K., Joseph, J.-M., Jauquier, N., Riggi, N., Nardou-Auderset, K., Petit, A., Scoazec, J.-Y., Sartelet, H., Renella, R., and Mühlethaler-Mottet, A. (2022). TWIST1 expression is associated with high-risk neuroblastoma and promotes primary and metastatic tumor growth. Commun Biol 5, 42.

Somerville, V., Berthoud, H., Schmidt, R.S., Bachmann, H.-P., Meng, Y.H., Fuchsmann, P., von Ah, U., and Engel, P. (2022). Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures. ISME J 16, 388–399.

Waskow, A., Guihur, A., Howling, A., and Furno, I. (2022). RNA Sequencing of Arabidopsis thaliana Seedlings after Non-Thermal Plasma-Seed Treatment Reveals Upregulation in Plant Stress and Defense Pathways. IJMS 23, 3070.

Anchimiuk, A., Lioy, V.S., Bock, F.P., Minnen, A., Boccard, F., and Gruber, S. (2021). A low Smc flux avoids collisions and facilitates chromosome organization in Bacillus subtilis. ELife 10, e65467.

Antar, H., Soh, Y.-M., Zamuner, S., Bock, F.P., Anchimiuk, A., Rios, P.D.L., and Gruber, S. (2021). Relief of ParB autoinhibition by parS DNA catalysis and recycling of ParB by CTP hydrolysis promote bacterial centromere assembly. Sci. Adv. 7, eabj2854.

Arguello, J.R., Abuin, L., Armida, J., Mika, K., Chai, P.C., and Benton, R. (2021). Targeted molecular profiling of rare olfactory sensory neurons identifies fate, wiring, and functional determinants. ELife 10, e63036.

Aruanno, M., Gozel, S., Mouyna, I., Parker, J.E., Bachmann, D., Flamant, P., Coste, A.T., Sanglard, D., and Lamoth, F. (2021). Insights in the molecular mechanisms of an azole stress adapted laboratory-generated Aspergillus fumigatus strain. Medical Mycology 59, 763–772.

Baumgaertner, P., Sankar, M., Herrera, F., Benedetti, F., Barras, D., Thierry, A.-C., Dangaj, D., Kandalaft, L.E., Coukos, G., Xenarios, I., Guex, N., and Harari, A. (2021). Unsupervised Analysis of Flow Cytometry Data in a Clinical Setting Captures Cell Diversity and Allows Population Discovery. Front. Immunol. 12, 633910.

Bire, S., Dusserre, Y., Bigot, Y., and Mermod, N. (2021). PiggyBac transposase and transposon derivatives for gene transfer targeting the ribosomal DNA loci of CHO cells. Journal of Biotechnology 341, 103–112.

Bruand, M., Barras, D., Mina, M., Ghisoni, E., Morotti, M., Lanitis, E., Fahr, N., Desbuisson, M., Grimm, A., Zhang, H., Chong, C., Dagher, J., Chee, S., Tsianou, T., Dorier, J., Stevenson, B.J., Iseli, C., Ronet, C., Bobisse, S., Genolet, R., et al. (2021). Cell-autonomous inflammation of BRCA1-deficient ovarian cancers drives both tumor-intrinsic immunoreactivity and immune resistance via STING. Cell Reports 36, 109412.

Busi, S.B., Bourquin, M., Fodelianakis, S., Michoud, G., Kohler, T.J., Peter, H., Pramateftaki, P., Styllas, M., Tolosano, M., De Staercke, V., Schön, M., de Nies, L., Marasco, R., Daffonchio, D., Ezzat, L., Wilmes, P., and Battin, T.J. (2021). Genomic and metabolic adaptations of biofilms to ecological windows of opportunities in glacier-fed streams (Microbiology).

Charmoy, M., Wyss, T., Delorenzi, M., and Held, W. (2021). PD-1+ Tcf1+ CD8+ T cells from established chronic infection can form memory while retaining a stableimprint of persistent antigen exposure. Cell Rep 36, 109672.

Clemente, F., Unterländer, M., Dolgova, O., Amorim, C.E.G., Coroado-Santos, F., Neuenschwander, S., Ganiatsou, E., Cruz Dávalos, D.I., Anchieri, L., Michaud, F., Winkelbach, L., Blöcher, J., Arizmendi Cárdenas, Y.O., Sousa da Mota, B., Kalliga, E., Souleles, A., Kontopoulos, I., Karamitrou-Mentessidi, G., Philaniotou, O., Sampson, A., et al. (2021). The genomic history of the Aegean palatial civilizations. Cell 184, 2565-2586.e21.

Cristinelli, S., Angelino, P., Janowczyk, A., Delorenzi, M., and Ciuffi, A. (2021). HIV Modifies the m6A and m5C Epitranscriptomic Landscape of the Host Cell. Front.Virol. 1, 714475.

Das, S., Bernasconi, E., Koutsokera, A., Wurlod, D.-A., Tripathi, V., Bonilla-Rosso, G., Aubert, J.-D., Derkenne, M.-F., Mercier, L., Pattaroni, C., Rapin, A., von Garnier, C., Marsland, B.J., Engel, P., and Nicod, L.P. (2021). A prevalent and culturable microbiota links ecological balance to clinical stability of the human lung after transplantation. Nat Commun 12, 2126.

Dubey, M., Hadadi, N., Pelet, S., Carraro, N., Johnson, D.R., and van der Meer, J.R. (2021). Environmental connectivity controls diversity in soil microbial communities. Commun Biol 4, 492.

Duraiswamy, J., Turrini, R., Minasyan, A., Barras, D., Crespo, I., Grimm, A.J., Casado, J., Genolet, R., Benedetti, F., Wicky, A., Ioannidou, K., Castro, W., Neal, C., Moriot, A., Renaud-Tissot, S., Anstett, V., Fahr, N., Tanyi, J.L., Eiva, M.A., Jacobson, C.A., et al. (2021). Myeloid antigen-presenting cell niches sustain antitumor T cells and license PD-1 blockade via CD28 costimulation. Cancer Cell 39, 1623-1642.e20.

Feller, A.F., Ogi, V., Seehausen, O., and Meier, J.I. (2021). Identification of a novel sex determining chromosome in cichlid fishes that acts as XY or ZW in different lineages. Hydrobiologia 848, 3727–3745.

Flaugnatti, N., Isaac, S., Lemos Rocha, L.F., Stutzmann, S., Rendueles, O., Stoudmann, C., Vesel, N., Garcia-Garcera, M., Buffet, A., Sana, T.G., Rocha, E.P.C., and Blokesch, M. (2021). Human commensal gut Proteobacteria withstand type VI secretion attacks through immunity protein-independent mechanisms. Nat Commun 12, 5751.

Fortuna, A., Bähre, H., Visca, P., Rampioni, G., and Leoni, L. (2021). The two Pseudomonas aeruginosa DksA stringent response proteins are largely interchangeable at the whole transcriptome level and in the control of virulence‐related traits. Environ Microbiol 23, 5487–5504.

González-Loyola, A., Bovay, E., Kim, J., Lozano, T.W., Sabine, A., Renevey, F., Arroz-Madeira, S., Rapin, A., Wypych, T.P., Rota, G., Durot, S., Velin, D., Marsland, B., Guarda, G., Delorenzi, M., Zamboni, N., Luther, S.A., and Petrova, T.V. (2021a). FOXC2 controls adult lymphatic endothelial specialization, function, and gut lymphatic barrier preventing multiorgan failure. Sci. Adv. 7, eabf4335.

González-Loyola, A., Bovay, E., Kim, J., Lozano, T.W., Sabine, A., Renevey, F., Arroz-Madeira, S., Rapin, A., Wypych, T.P., Rota, G., Durot, S., Velin, D., Marsland, B., Guarda, G., Delorenzi, M., Zamboni, N., Luther, S.A., and Petrova, T.V. (2021b). FOXC2 controls adult lymphatic endothelial specialization, function, and gut lymphatic barrier preventing multiorgan failure. Sci. Adv. 7, eabf4335.

Hill, V., Akarsu, H., Barbarroja, R.S., Cippà, V.L., Kuhnert, P., Heller, M., Falquet, L., Heller, M., Stoffel, M.H., Labroussaa, F., and Jores, J. (2021). Minimalistic mycoplasmas harbor different functional toxin-antitoxin systems. PLoS Genet 17, e1009365.

de Jonge, K., Tillé, L., Lourenco, J., Maby-El Hajjami, H., Nassiri, S., Racle, J., Gfeller, D., Delorenzi, M., Verdeil, G., Baumgaertner, P., and Speiser, D.E. (2021). Inflammatory B cells correlate with failure to checkpoint blockade in melanoma patients. OncoImmunology 10, 1873585.

Kaushal, A., Mohana, G., Dorier, J., Özdemir, I., Omer, A., Cousin, P., Semenova, A., Taschner, M., Dergai, O., Marzetta, F., Iseli, C., Eliaz, Y., Weisz, D., Shamim, M.S., Guex, N., Lieberman Aiden, E., and Gambetta, M.C. (2021). CTCF loss has limited effects on global genome architecture in Drosophila despite critical regulatory functions. Nat Commun 12, 1011.

Kawecki, T.J., Erkosar, B., Dupuis, C., Hollis, B., Stillwell, R.C., and Kapun, M. (2021). The Genomic Architecture of Adaptation to Larval Malnutrition Points to a Trade-off with Adult Starvation Resistance in Drosophila. Molecular Biology and Evolution 38, 2732–2749.

Labiano, S., Roh, V., Godfroid, C., Hiou-Feige, A., Romero, J., Sum, E., Rapp, M., Boivin, G., Wyss, T., Simon, C., Bourhis, J., Umaña, P., Trumpfheller, C., Tolstonog, G.V., Vozenin, M.-C., and Romero, P. (2021). CD40 Agonist Targeted to Fibroblast Activation Protein α Synergizes with Radiotherapy in Murine HPV-Positive Head and Neck Tumors. Clin Cancer Res 27, 4054–4065.

Meylan, P., Pich, C., Winkler, C., Ginster, S., Mury, L., Sgandurra, M., Dreos, R., Frederick, D.T., Hammond, M., Boland, G.M., and Michalik, L. (2021a). Low expression of the PPARγ-regulated gene thioredoxin-interacting protein accompanies human melanoma progression and promotes experimental lung metastases. Sci Rep 11, 7847.

Meylan, P., Pich, C., Winkler, C., Ginster, S., Mury, L., Sgandurra, M., Dreos, R., Frederick, D.T., Hammond, M., Boland, G.M., and Michalik, L. (2021b). Low expression of the PPARγ-regulated gene thioredoxin-interacting protein accompanies human melanoma progression and promotes experimental lung metastases. Sci Rep 11, 7847.

Mika, K., Cruchet, S., Chai, P.C., Prieto-Godino, L.L., Auer, T.O., Pradervand, S., and Benton, R. (2021). Olfactory receptor–dependent receptor repression in Drosophila. Sci. Adv. 7, eabe3745.

Morales, M., Sentchilo, V., Hadadi, N., and van der Meer, J.R. (2021). Genome-wide gene expression changes of Pseudomonas veronii 1YdBTEX2 during bioaugmentation in polluted soils. Environmental Microbiome 16, 8.

Ortiz, D., Pekár, S., Bilat, J., and Alvarez, N. (2021). Poor performance of DNA barcoding and the impact of RAD loci filtering on the species delimitation of an Iberian ant-eating spider. Molecular Phylogenetics and Evolution 154, 106997.

Özel Duygan, B.D., Gaille, C., Fenner, K., and van der Meer, J.R. (2021a). Assessing Antibiotics Biodegradation and Effects at Sub-inhibitory Concentrations by Quantitative Microbial Community Deconvolution. Front. Environ. Sci. 9, 737247.

Özel Duygan, B.D., Rey, S., Leocata, S., Baroux, L., Seyfried, M., and van der Meer, J.R. (2021b). Assessing Biodegradability of Chemical Compounds from Microbial Community Growth Using Flow Cytometry. MSystems 6, e01143-20.

Park, H.-S., Papanastasi, E., Blanchard, G., Chiticariu, E., Bachmann, D., Plomann, M., Morice-Picard, F., Vabres, P., Smahi, A., Huber, M., Pich, C., and Hohl, D. (2021). ARP-T1-associated Bazex–Dupré–Christol syndrome is an inherited basal cell cancer with ciliary defects characteristic of ciliopathies. Commun Biol 4, 544.

Reis, R.S., Deforges, J., Schmidt, R.R., Schippers, J.H.M., and Poirier, Y. (2021). An antisense noncoding RNA enhances translation via localized structural rearrangements of its cognate mRNA. The Plant Cell 33, 1381–1397.

Ren, G., Zhang, X., Li, Y., Ridout, K., Serrano-Serrano, M.L., Yang, Y., Liu, A., Ravikanth, G., Nawaz, M.A., Mumtaz, A.S., Salamin, N., and Fumagalli, L. (2021). Large-scale whole-genome resequencing unravels the domestication history of Cannabis sativa. Sci. Adv. 7, eabg2286.

Schmid-Siegert, E., Richard, S., Luraschi, A., Mühlethaler, K., Pagni, M., and Hauser, P.M. (2021). Expression Pattern of the Pneumocystis jirovecii Major Surface Glycoprotein Superfamily in Patients with Pneumonia. The Journal of Infectious Diseases 223, 310–318.

Schönecker, L., Schnydrig, P., Brodard, I., Thomann, A., Hemphill, A., Rodriguez-Campos, S., Perreten, V., Jores, J., and Kittl, S. (2021). Trueperella pecoris sp. nov. isolated from bovine and porcine specimens. International Journal of Systematic and Evolutionary Microbiology 71.

Sflomos, G., Battista, L., Aouad, P., De Martino, F., Scabia, V., Stravodimou, A., Ayyanan, A., Ifticene‐Treboux, A., RLS, Bucher, P., Fiche, M., Ambrosini, G., and Brisken, C. (2021). Intraductal xenografts show lobular carcinoma cells rely on their own extracellular matrix and LOXL1. EMBO Mol Med 13.

Shamseddin, M., De Martino, F., Constantin, C., Scabia, V., Lancelot, A., Laszlo, C., Ayyannan, A., Battista, L., Raffoul, W., Gailloud‐Matthieu, M., Bucher, P., Fiche, M., Ambrosini, G., Sflomos, G., and Brisken, C. (2021). Contraceptive progestins with androgenic properties stimulate breast epithelial cell proliferation. EMBO Mol Med 13.

Sobel, J., Guay, C., Elhanani, O., Rodriguez-Trejo, A., Stoll, L., Menoud, V., Jacovetti, C., Walker, M.D., and Regazzi, R. (2021). Scrt1, a transcriptional regulator of β-cell proliferation identified by differential chromatin accessibility during islet maturation. Sci Rep 11, 8800.

Toussaint, E.F.A., Gauthier, J., Bilat, J., Gillett, C.P.D.T., Gough, H.M., Lundkvist, H., Blanc, M., Muñoz-Ramírez, C.P., and Alvarez, N. (2021). HyRAD-X Exome Capture Museomics Unravels Giant Ground Beetle Evolution. Genome Biology and Evolution 13, evab112.

Ubags, N.D., Trompette, A., Pernot, J., Nibbering, B., Wong, N.C., Pattaroni, C., Rapin, A., Nicod, L.P., Harris, N.L., and Marsland, B.J. (2021). Microbiome-induced antigen-presenting cell recruitment coordinates skin and lung allergic inflammation. Journal of Allergy and Clinical Immunology 147, 1049-1062.e7.

Vesel, N., and Blokesch, M. (2021). Pilus Production in Acinetobacter baumannii Is Growth Phase Dependent and Essential for Natural Transformation. J Bacteriol 203, e00034-21.

Amândio, A.R., Lopez-Delisle, L., Bolt, C.C., Mascrez, B., and Duboule, D. (2020). A complex regulatory landscape involved in the development of mammalian external genitals. ELife 9, e52962.

Ansermet, C., Centeno, G., Lagarrigue, S., Nikolaeva, S., Yoshihara, H.A., Pradervand, S., Barras, J., Dattner, N., Rotman, S., Amati, F., and Firsov, D. (2020). Renal tubular arginase‐2 participates in the formation of the corticomedullary urea gradient and attenuates kidney damage in ischemia‐reperfusion injury in mice. Acta Physiol 229.

Arjona, Y., Fernández‐López, J., Navascués, M., Alvarez, N., Nogales, M., and Vargas, P. (2020). Linking seascape with landscape genetics: Oceanic currents favour colonization across the Galápagos Islands by a coastal plant. J. Biogeogr. 47, 2622–2633.

Bagnoud, A., Pramateftaki, P., Bogard, M.J., Battin, T.J., and Peter, H. (2020). Microbial Ecology of Methanotrophy in Streams Along a Gradient of CH4 Availability. Front. Microbiol. 11, 771.

Berger, A., Le Fourn, V., Masternak, J., Regamey, A., Bodenmann, I., Girod, P., and Mermod, N. (2020). Overexpression of transcription factor Foxa1 and target genes remediate therapeutic protein production bottlenecks in Chinese hamster ovary cells. Biotechnology and Bioengineering 117, 1101–1116.

Bou Sleiman, M., Frochaux, M.V., Andreani, T., Osman, D., Guigo, R., and Deplancke, B. (2020). Enteric infection induces Lark-mediated intron retention at the 5′ end of Drosophila genes. Genome Biol 21, 4.

Carmona, S.J., Siddiqui, I., Bilous, M., Held, W., and Gfeller, D. (2020). Deciphering the transcriptomic landscape of tumor-infiltrating CD8 lymphocytes in B16 melanoma tumors with single-cell RNA-Seq. Oncoimmunology 9, 1737369.

Dehaene, H., Praz, V., Lhôte, P., Lopes, M., and Herr, W. (2020). THAP11F80L cobalamin disorder-associated mutation reveals normal and pathogenic THAP11 functions in gene expression and cell proliferation. PLoS ONE 15, e0224646.

Drebes Dörr, N.C., and Blokesch, M. (2020). Interbacterial competition and anti‐predatory behaviour of environmental Vibrio cholerae strains. Environ Microbiol 22, 4485–4504.

Duroy, P., Bosshard, S., Schmid‐Siegert, E., Neuenschwander, S., Arib, G., Lemercier, P., Masternak, J., Roesch, L., Buron, F., Girod, P., Xenarios, I., and Mermod, N. (2020). Characterization and mutagenesis of Chinese hamster ovary cells endogenous retroviruses to inactivate viral particle release. Biotechnology and Bioengineering 117, 466–485.

Ercolano, G., Wyss, T., Salomé, B., Romero, P., Trabanelli, S., and Jandus, C. (2020). Distinct and shared gene expression for human innate versus adaptive helper lymphoid cells. J Leukoc Biol 108, 723–737.

Feller, A.F., Selz, O.M., McGee, M.D., Meier, J.I., Mwaiko, S., and Seehausen, O. (2020a). Rapid generation of ecologically relevant behavioral novelty in experimental cichlid hybrids. Ecol Evol 10, 7445–7462.

Feller, A.F., Haesler, M.P., Peichel, C.L., and Seehausen, O. (2020b). Genetic architecture of a key reproductive isolation trait differs between sympatric and non-sympatric sister species of Lake Victoria cichlids. Proc. R. Soc. B. 287, 20200270.

Frochaux, M.V., Bou Sleiman, M., Gardeux, V., Dainese, R., Hollis, B., Litovchenko, M., Braman, V.S., Andreani, T., Osman, D., and Deplancke, B. (2020). cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel. Genome Biol 21, 6.

Fujita, S., De Bellis, D., Edel, K.H., Köster, P., Andersen, T.G., Schmid‐Siegert, E., Dénervaud Tendon, V., Pfister, A., Marhavý, P., Ursache, R., Doblas, V.G., Barberon, M., Daraspe, J., Creff, A., Ingram, G., Kudla, J., and Geldner, N. (2020). SCHENGEN receptor module drives localized ROS production and lignification in plant roots. EMBO J 39.

Gauthier, J., Pajkovic, M., Neuenschwander, S., Kaila, L., Schmid, S., Orlando, L., and Alvarez, N. (2020). Museomics identifies genetic erosion in two butterfly species across the 20th century in Finland. Mol Ecol Resour 20, 1191–1205.

Gervais, M., Labouèbe, G., Picard, A., Thorens, B., and Croizier, S. (2020). EphrinB1 modulates glutamatergic inputs into POMC-expressing progenitors and controls glucose homeostasis. PLoS Biol 18, e3000680.

Giger, S., Kovtonyuk, L.V., Utz, S.G., Ramosaj, M., Kovacs, W.J., Schmid, E., Ioannidis, V., Greter, M., Manz, M.G., Lutolf, M.P., Jessberger, S., and Knobloch, M. (2020). A Single Metabolite which Modulates Lipid Metabolism Alters Hematopoietic Stem/Progenitor Cell Behavior and Promotes Lymphoid Reconstitution. Stem Cell Reports 15, 566–576.

Guay, C., Abdulkarim, B., Tan, J.Y., Dubuis, G., Rütti, S., Laybutt, D.R., Widmann, C., Regazzi, R., and Marques, A.C. (2020). Publisher Correction: Loss-of-function of the long non-coding RNA A830019P07Rik in mice does not affect insulin expression and secretion. Sci Rep 10, 8354.

Khan, G.A., Deforges, J., Reis, R.S., Hsieh, Y.-F., Montpetit, J., Antosz, W., Santuari, L., Hardtke, C.S., Grasser, K.D., and Poirier, Y. (2020). The transcription and export complex THO/TREX contributes to transcription termination in plants. PLoS Genet 16, e1008732.

Kuhn, A., Le Fourn, V., Fisch, I., and Mermod, N. (2020). Genome‐wide analysis of single nucleotide variants allows for robust and accurate assessment of clonal derivation in cell lines used to produce biologics. Biotechnology and Bioengineering 117, 3628–3638.

Kuhnert, P., Brodard, I., Alsaaod, M., Steiner, A., Stoffel, M.H., and Jores, J. (2020). Treponema phagedenis (ex Noguchi 1912) Brumpt 1922 sp. nov., nom. rev., isolated from bovine digital dermatitis. International Journal of Systematic and Evolutionary Microbiology 70, 2115–2123.

Leblond, M.M., Tillé, L., Nassiri, S., Gilfillan, C.B., Imbratta, C., Schmittnaegel, M., Ries, C.H., Speiser, D.E., and Verdeil, G. (2020). CD40 Agonist Restores the Antitumor Efficacy of Anti-PD1 Therapy in Muscle-Invasive Bladder Cancer in an IFN I/II-Mediated Manner. Cancer Immunol Res 8, 1180–1192.

Özel Duygan, B.D., Hadadi, N., Babu, A.F., Seyfried, M., and van der Meer, J.R. (2020). Rapid detection of microbiota cell type diversity using machine-learned classification of flow cytometry data. Commun Biol 3, 379.

Pais Ferreira, D., Silva, J.G., Wyss, T., Fuertes Marraco, S.A., Scarpellino, L., Charmoy, M., Maas, R., Siddiqui, I., Tang, L., Joyce, J.A., Delorenzi, M., Luther, S.A., Speiser, D.E., and Held, W. (2020a). Central memory CD8+ T cells derive from stem-like Tcf7hi effector cells in the absence of cytotoxic differentiation. Immunity 53, 985-1000.e11.

Pais Ferreira, D., Silva, J.G., Wyss, T., Fuertes Marraco, S.A., Scarpellino, L., Charmoy, M., Maas, R., Siddiqui, I., Tang, L., Joyce, J.A., Delorenzi, M., Luther, S.A., Speiser, D.E., and Held, W. (2020b). Central memory CD8+ T cells derive from stem-like Tcf7hi effector cells in the absence of cytotoxic differentiation. Immunity 53, 985-1000.e11.

Pourcel, L., Buron, F., Garcia, F., Delaloix, M.-S., Le Fourn, V., Girod, P.-A., and Mermod, N. (2020a). Transient vitamin B5 starving improves mammalian cell homeostasis and protein production. Metabolic Engineering 60, 77–86.

Pourcel, L., Buron, F., Arib, G., Le Fourn, V., Regamey, A., Bodenmann, I., Girod, P., and Mermod, N. (2020b). Influence of cytoskeleton organization on recombinant protein expression by CHO cells. Biotechnology and Bioengineering 117, 1117–1126.

Prieto-Godino, L.L., Silbering, A.F., Khallaf, M.A., Cruchet, S., Bojkowska, K., Pradervand, S., Hansson, B.S., Knaden, M., and Benton, R. (2020). Functional integration of “undead” neurons in the olfactory system. Sci. Adv. 6, eaaz7238.

Ragusa, S., Prat-Luri, B., González-Loyola, A., Nassiri, S., Squadrito, M.L., Guichard, A., Cavin, S., Gjorevski, N., Barras, D., Marra, G., Lutolf, M.P., Perentes, J., Corse, E., Bianchi, R., Wetterwald, L., Kim, J., Oliver, G., Delorenzi, M., De Palma, M., and Petrova, T.V. (2020). Antiangiogenic immunotherapy suppresses desmoplastic and chemoresistant intestinal tumors in mice. Journal of Clinical Investigation 130, 1199–1216.

Salces‐Castellano, A., Patiño, J., Alvarez, N., Andújar, C., Arribas, P., Braojos‐Ruiz, J.J., Arco‐Aguilar, M., García‐Olivares, V., Karger, D.N., López, H., Manolopoulou, I., Oromí, P., Pérez‐Delgado, A.J., Peterman, W.E., Rijsdijk, K.F., and Emerson, B.C. (2020). Climate drives community‐wide divergence within species over a limited spatial scale: evidence from an oceanic island. Ecol Lett 23, 305–315.

Stoll, L., Rodríguez-Trejo, A., Guay, C., Brozzi, F., Bayazit, M.B., Gattesco, S., Menoud, V., Sobel, J., Marques, A.C., Venø, M.T., Esguerra, J.L.S., Barghouth, M., Suleiman, M., Marselli, L., Kjems, J., Eliasson, L., Renström, E., Bouzakri, K., Pinget, M., Marchetti, P., et al. (2020). A circular RNA generated from an intron of the insulin gene controls insulin secretion. Nat Commun 11, 5611.

Stutzmann, S., and Blokesch, M. (2020). Comparison of chitin‐induced natural transformation in pandemic Vibrio cholerae O1 El Tor strains. Environ Microbiol 22, 4149–4166.

Aruanno, M., Bachmann, D., Sanglard, D., and Lamoth, F. (2019). Link between heat shock protein 90 (Hsp90) and the mitochondrial respiratory chain in the caspofungin stress response of Aspergillus fumigatus. Antimicrob Agents Chemother AAC.00208-19, aac;AAC.00208-19v1.

Avril, A., Purcell, J., Brelsford, A., and Chapuisat, M. (2019a). Asymmetric assortative mating and queen polyandry are linked to a supergene controlling ant social organization. Mol Ecol 28, 1428–1438.

Avril, A., Zahnd, S., Djordjevic, J., and Chapuisat, M. (2019b). No mate preference associated with the supergene controlling social organization in Alpine silver ants. J Evol Biol jeb.13479.

Bast, J., Parker, D.J., Dumas, Z., Jalvingh, K.M., Tran Van, P., Jaron, K.S., Figuet, E., Brandt, A., Galtier, N., and Schwander, T. (2018). Consequences of Asexuality in Natural Populations: Insights from Stick Insects. Mol. Biol. Evol. 35, 1668–1677.

Bekliz, M., Brandani, J., Bourquin, M., Battin, T.J., and Peter, H. (2019). Benchmarking protocols for the metagenomic analysis of stream biofilm viromes. PeerJ 7, e8187.

Bosshard, S., Duroy, P.-O., and Mermod, N. (2019). A role for alternative end-joining factors in homologous recombination and genome editing in Chinese hamster ovary cells. DNA Repair 82, 102691.

Callegari, A., Sieben, C., Benke, A., Suter, D.M., Fierz, B., Mazza, D., and Manley, S. (2019). Single-molecule dynamics and genome-wide transcriptomics reveal that NF-kB (p65)-DNA binding times can be decoupled from transcriptional activation. PLoS Genet. 15, e1007891.

Can, E., Mishkovsky, M., Yoshihara, H.A.I., Kunz, N., Couturier, D.-L., Petrausch, U., Doucey, M.-A., and Comment, A. (2020). Noninvasive rapid detection of metabolic adaptation in activated human T lymphocytes by hyperpolarized 13C magnetic resonance. Sci Rep 10, 200.

Cardoso-Moreira, M., Halbert, J., Valloton, D., Velten, B., Chen, C., Shao, Y., Liechti, A., Ascenção, K., Rummel, C., Ovchinnikova, S., Mazin, P.V., Xenarios, I., Harshman, K., Mort, M., Cooper, D.N., Sandi, C., Soares, M.J., Ferreira, P.G., Afonso, S., Carneiro, M., et al. (2019). Gene expression across mammalian organ development. Nature 571, 505–509.

Castelo-Szekely, V., De Matos, M., Tusup, M., Pascolo, S., Ule, J., and Gatfield, D. (2019). Charting DENR-dependent translation reinitiation uncovers predictive uORF features and links to circadian timekeeping via Clock. Nucleic Acids Res. 47, 5193–5209.

Cattaneo, P., Graeff, M., Marhava, P., and Hardtke, C.S. (2019). Conditional effects of the epigenetic regulator JUMONJI 14 in Arabidopsis root growth. Development 146.

Chai, P.C., Cruchet, S., Wigger, L., and Benton, R. (2019). Sensory neuron lineage mapping and manipulation in the Drosophila olfactory system. Nat Commun 10, 643.

Cossard, G.G., Toups, M.A., and Pannell, J.R. (2019). Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. Annals of Botany 123, 1119–1131.

Dangaj, D., Bruand, M., Grimm, A.J., Ronet, C., Barras, D., Duttagupta, P.A., Lanitis, E., Duraiswamy, J., Tanyi, J.L., Benencia, F., Conejo-Garcia, J., Ramay, H.R., Montone, K.T., Powell, D.J., Gimotty, P.A., Facciabene, A., Jackson, D.G., Weber, J.S., Rodig, S.J., Hodi, S.F., et al. (2019). Cooperation between Constitutive and Inducible Chemokines Enables T Cell Engraftment and Immune Attack in Solid Tumors. Cancer Cell 35, 885-900.e10.

Deforges, J., Reis, R.S., Jacquet, P., Sheppard, S., Gadekar, V.P., Hart-Smith, G., Tanzer, A., Hofacker, I.L., Iseli, C., Xenarios, I., and Poirier, Y. (2019a). Control of Cognate Sense mRNA Translation by cis-Natural Antisense RNAs. Plant Physiol. 180, 305–322.

Deforges, J., Reis, R.S., Jacquet, P., Vuarambon, D.J., and Poirier, Y. (2019b). Prediction of regulatory long intergenic non-coding RNAs acting in trans through base-pairing interactions. BMC Genomics 20, 601.

Delaneau, O., Zazhytska, M., Borel, C., Giannuzzi, G., Rey, G., Howald, C., Kumar, S., Ongen, H., Popadin, K., Marbach, D., Ambrosini, G., Bielser, D., Hacker, D., Romano, L., Ribaux, P., Wiederkehr, M., Falconnet, E., Bucher, P., Bergmann, S., Antonarakis, S.E., et al. (2019). Chromatin three-dimensional interactions mediate genetic effects on gene expression. Science 364.

Dobrowolski, C., Valadkhan, S., Graham, A.C., Shukla, M., Ciuffi, A., Telenti, A., and Karn, J. (2019). Entry of Polarized Effector Cells into Quiescence Forces HIV Latency. MBio 10.

Ellegaard, K.M., and Engel, P. (2019). Genomic diversity landscape of the honey bee gut microbiota. Nat Commun 10, 446.

Ellegaard, K.M., Brochet, S., Bonilla‐Rosso, G., Emery, O., Glover, N., Hadadi, N., Jaron, K.S., Meer, J.R., Robinson‐Rechavi, M., Sentchilo, V., Tagini, F., SAGE class 2016-17, and Engel, P. (2019). Genomic changes underlying host specialization in the bee gut symbiont Lactobacillus Firm5. Mol Ecol 28, 2224–2237.

Ercolano, G., Wyss, T., Salomé, B., Romero, P., Trabanelli, S., and Jandus, C. (2020). Distinct and shared gene expression for human innate versus adaptive helper lymphoid cells. J. Leukoc. Biol. 108, 723–737.

Feulner, P.G.D., and Seehausen, O. (2019). Genomic insights into the vulnerability of sympatric whitefish species flocks. Mol Ecol 28, 615–629.

Frankish, A., Diekhans, M., Ferreira, A.-M., Johnson, R., Jungreis, I., Loveland, J., Mudge, J.M., Sisu, C., Wright, J., Armstrong, J., Barnes, I., Berry, A., Bignell, A., Carbonell Sala, S., Chrast, J., Cunningham, F., Di Domenico, T., Donaldson, S., Fiddes, I.T., García Girón, C., et al. (2019). GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Res. 47, D766–D773.

Galvāo, V.C., Fiorucci, A.-S., Trevisan, M., Franco-Zorilla, J.M., Goyal, A., Schmid-Siegert, E., Solano, R., and Fankhauser, C. (2019). PIF transcription factors link a neighbor threat cue to accelerated reproduction in Arabidopsis. Nat Commun 10, 4005.

Golumbeanu, M., Desfarges, S., Hernandez, C., Quadroni, M., Rato, S., Mohammadi, P., Telenti, A., Beerenwinkel, N., and Ciuffi, A. (2019a). Proteo-Transcriptomic Dynamics of Cellular Response to HIV-1 Infection. Sci Rep 9, 213.

Golumbeanu, M., Desfarges, S., Hernandez, C., Quadroni, M., Rato, S., Mohammadi, P., Telenti, A., Beerenwinkel, N., and Ciuffi, A. (2019b). Proteo-Transcriptomic Dynamics of Cellular Response to HIV-1 Infection. Sci Rep 9, 213.

Gudkova, D., Dergai, O., Praz, V., and Herr, W. (2019). HCF-2 inhibits cell proliferation and activates differentiation-gene expression programs. Nucleic Acids Res. 47, 5792–5808.

Hendrikx, S., Coso, S., Prat-Luri, B., Wetterwald, L., Sabine, A., Franco, C.A., Nassiri, S., Zangger, N., Gerhardt, H., Delorenzi, M., and Petrova, T.V. (2019). Endothelial Calcineurin Signaling Restrains Metastatic Outgrowth by Regulating Bmp2. Cell Rep 26, 1227-1241.e6.

Hoedjes, K.M., van den Heuvel, J., Kapun, M., Keller, L., Flatt, T., and Zwaan, B.J. (2019). Distinct genomic signals of lifespan and life history evolution in response to postponed reproduction and larval diet in Drosophila. Evol Lett 3, 598–609.

Hoekstra, M.M., Emmenegger, Y., Hubbard, J., and Franken, P. (2019). Cold-inducible RNA-binding protein (CIRBP) adjusts clock-gene expression and REM-sleep recovery following sleep deprivation. ELife 8, e43400.

Hollis, B., Koppik, M., Wensing, K.U., Ruhmann, H., Genzoni, E., Erkosar, B., Kawecki, T.J., Fricke, C., and Keller, L. (2019). Sexual conflict drives male manipulation of female postmating responses in Drosophila melanogaster. Proc. Natl. Acad. Sci. U.S.A. 116, 8437–8444.

Hor, C.N., Yeung, J., Jan, M., Emmenegger, Y., Hubbard, J., Xenarios, I., Naef, F., and Franken, P. (2019). Sleep-wake-driven and circadian contributions to daily rhythms in gene expression and chromatin accessibility in the murine cortex. Proc. Natl. Acad. Sci. U.S.A. 116, 25773–25783.

Jan, M., Gobet, N., Diessler, S., Franken, P., and Xenarios, I. (2019). A multi-omics digital research object for the genetics of sleep regulation. Sci Data 6, 258.

Ji, H., Chen, Y., Castillo-Armengol, J., Dreos, R., Moret, C., Niederhäuser, G., Delacuisine, B., Lopez-Mejia, I.C., Denechaud, P.-D., and Fajas, L. (2020). CDK7 Mediates the Beta-Adrenergic Signaling in Thermogenic Brown and White Adipose Tissues. IScience 23, 101163.

Koto, A., Motoyama, N., Tahara, H., McGregor, S., Moriyama, M., Okabe, T., Miura, M., and Keller, L. (2019). Oxytocin/vasopressin-like peptide inotocin regulates cuticular hydrocarbon synthesis and water balancing in ants. Proc. Natl. Acad. Sci. U.S.A. 116, 5597–5606.

Layer, M., Adler, A., Reynaert, E., Hernandez, A., Pagni, M., Morgenroth, E., Holliger, C., and Derlon, N. (2019). Organic substrate diffusibility governs microbial community composition, nutrient removal performance and kinetics of granulation of aerobic granular sludge. Water Res X 4, 100033.

Luong-Gardiol, N., Siddiqui, I., Pizzitola, I., Jeevan-Raj, B., Charmoy, M., Huang, Y., Irmisch, A., Curtet, S., Angelov, G.S., Danilo, M., Juilland, M., Bornhauser, B., Thome, M., Hantschel, O., Chalandon, Y., Cazzaniga, G., Bourquin, J.-P., Huelsken, J., and Held, W. (2019). γ-Catenin-Dependent Signals Maintain BCR-ABL1+ B Cell Acute Lymphoblastic Leukemia. Cancer Cell 35, 649-663.e10.

Magalhães, B., Senn, L., and Blanc, D.S. (2019). High-Quality Complete Genome Sequences of Three Pseudomonas aeruginosa Isolates Retrieved from Patients Hospitalized in Intensive Care Units. Microbiol Resour Announc 8, MRA.01624-18, e01624-18.

Magalhães, B., Valot, B., Abdelbary, M.M.H., Prod’hom, G., Greub, G., Senn, L., and Blanc, D.S. (2020). Combining Standard Molecular Typing and Whole Genome Sequencing to Investigate Pseudomonas aeruginosa Epidemiology in Intensive Care Units. Front. Public Health 8, 3.

Matthey-Doret, C., van der Kooi, C.J., Jeffries, D.L., Bast, J., Dennis, A.B., Vorburger, C., and Schwander, T. (2019). Mapping of Multiple Complementary Sex Determination Loci in a Parasitoid Wasp. Genome Biol Evol 11, 2954–2962.

Mavoungou, L.O., Neuenschwander, S., Pham, U., Iyer, P.S., and Mermod, N. (2019). Characterization of mesoangioblast cell fate and improved promyogenic potential of a satellite cell-like subpopulation upon transplantation in dystrophic murine muscles. Stem Cell Research 41, 101619.

Meier, J.I., Stelkens, R.B., Joyce, D.A., Mwaiko, S., Phiri, N., Schliewen, U.K., Selz, O.M., Wagner, C.E., Katongo, C., and Seehausen, O. (2019). The coincidence of ecological opportunity with hybridization explains rapid adaptive radiation in Lake Mweru cichlid fishes. Nat Commun 10, 5391.

Merienne, N., Meunier, C., Schneider, A., Seguin, J., Nair, S.S., Rocher, A.B., Le Gras, S., Keime, C., Faull, R., Pellerin, L., Chatton, J.-Y., Neri, C., Merienne, K., and Déglon, N. (2019). Cell-Type-Specific Gene Expression Profiling in Adult Mouse Brain Reveals Normal and Disease-State Signatures. Cell Reports 26, 2477-2493.e9.

Minocha, S., Villeneuve, D., Praz, V., Moret, C., Lopes, M., Pinatel, D., Rib, L., Guex, N., and Herr, W. (2019). Rapid Recapitulation of Nonalcoholic Steatohepatitis upon Loss of Host Cell Factor 1 Function in Mouse Hepatocytes. Mol. Cell. Biol. 39.

Moysés-Oliveira, M., Di-Battista, A., Zamariolli, M., Meloni, V.A., Bragagnolo, S., Christofolini, D.M., Steiner, C.E., Kosyakova, N., Liehr, T., Reymond, A., and Melaragno, M.I. (2019). Breakpoint mapping at nucleotide resolution in X-autosome balanced translocations associated with clinical phenotypes. Eur. J. Hum. Genet. 27, 760–771.

Parker, D.J., Djordjevic, J., and Schwander, T. (2019a). Olfactory Proteins in Timema Stick Insects. Front. Ecol. Evol. 7, 101.

Parker, D.J., Bast, J., Jalvingh, K., Dumas, Z., Robinson-Rechavi, M., and Schwander, T. (2019b). Repeated Evolution of Asexuality Involves Convergent Gene Expression Changes. Mol. Biol. Evol. 36, 350–364.

Parker, D.J., Bast, J., Jalvingh, K., Dumas, Z., Robinson-Rechavi, M., and Schwander, T. (2019c). Sex-biased gene expression is repeatedly masculinized in asexual females. Nat Commun 10, 4638.

Roh, V., Hiou‐Feige, A., Misetic, V., Rivals, J., Sponarova, J., Teh, M., Ferreira Lopes, S., Truan, Z., Mermod, M., Monnier, Y., Hess, J., Tolstonog, G.V., and Simon, C. (2020). The transcription factor FOXM1 regulates the balance between proliferation and aberrant differentiation in head and neck squamous cell carcinoma. J. Pathol. 250, 107–119.

Salomé, B., Gomez-Cadena, A., Loyon, R., Suffiotti, M., Salvestrini, V., Wyss, T., Vanoni, G., Ruan, D.F., Rossi, M., Tozzo, A., Tentorio, P., Bruni, E., Riether, C., Jacobsen, E.-M., Jandus, P., Conrad, C., Hoenig, M., Schulz, A., Michaud, K., Della Porta, M.G., et al. (2019). CD56 as a marker of an ILC1-like population with NK cell properties that is functionally impaired in AML. Blood Adv 3, 3674–3687.

Sarropoulos, I., Marin, R., Cardoso-Moreira, M., and Kaessmann, H. (2019). Developmental dynamics of lncRNAs across mammalian organs and species. Nature 571, 510–514.

Scheidweiler, D., Peter, H., Pramateftaki, P., de Anna, P., and Battin, T.J. (2019). Unraveling the biophysical underpinnings to the success of multispecies biofilms in porous environments. ISME J 13, 1700–1710.

Siddiqui, I., Schaeuble, K., Chennupati, V., Fuertes Marraco, S.A., Calderon-Copete, S., Pais Ferreira, D., Carmona, S.J., Scarpellino, L., Gfeller, D., Pradervand, S., Luther, S.A., Speiser, D.E., and Held, W. (2019). Intratumoral Tcf1+PD-1+CD8+ T Cells with Stem-like Properties Promote Tumor Control in Response to Vaccination and Checkpoint Blockade Immunotherapy. Immunity 50, 195-211.e10.

Unzu, C., Planet, E., Brandenberg, N., Fusil, F., Cassano, M., Perez‐Vargas, J., Friedli, M., Cosset, F., Lutolf, M.P., Wildhaber, B.E., and Trono, D. (2019). Pharmacological Induction of a Progenitor State for the Efficient Expansion of Primary Human Hepatocytes. Hepatology 69, 2214–2231.

Veltsos, P., Ridout, K.E., Toups, M.A., González-Martínez, S.C., Muyle, A., Emery, O., Rastas, P., Hudzieczek, V., Hobza, R., Vyskot, B., Marais, G.A.B., Filatov, D.A., and Pannell, J.R. (2019). Early Sex-Chromosome Evolution in the Diploid Dioecious Plant Mercurialis annua. Genetics 212, 815–835.

Yeganeh, M., Praz, V., Carmeli, C., Villeneuve, D., Rib, L., Guex, N., Herr, W., Delorenzi, M., Hernandez, N., and CycliX consortium (2019). Differential regulation of RNA polymerase III genes during liver regeneration. Nucleic Acids Res. 47, 1786–1796.

Aguilar-Bultet, L., Nicholson, P., Rychener, L., Dreyer, M., Gözel, B., Origgi, F.C., Oevermann, A., Frey, J., and Falquet, L. (2018). Genetic Separation of Listeria monocytogenes Causing Central Nervous System Infections in Animals. Front Cell Infect Microbiol 8, 20.

Al Shareef, S.M., Basit, S., Li, S., Pfister, C., Pradervand, S., Lecendreux, M., Mayer, G., Dauvilliers, Y., Salpietro, V., Houlden, H., BaHammam, A.S., and Tafti, M. (2018). Kleine-Levin syndrome is associated with LMOD3 variants. J Sleep Res e12718.

Bell, E., Lamminmäki, T., Alneberg, J., Andersson, A.F., Qian, C., Xiong, W., Hettich, R.L., Balmer, L., Frutschi, M., Sommer, G., and Bernier-Latmani, R. (2018). Biogeochemical Cycling by a Low-Diversity Microbial Community in Deep Groundwater. Front Microbiol 9, 2129.

Bovay, E., Sabine, A., Prat-Luri, B., Kim, S., Son, K., Willrodt, A.-H., Olsson, C., Halin, C., Kiefer, F., Betsholtz, C., Jeon, N.L., Luther, S.A., and Petrova, T.V. (2018). Multiple roles of lymphatic vessels in peripheral lymph node development. J. Exp. Med. 215, 2760–2777.

Castro, W., Chelbi, S.T., Niogret, C., Ramon-Barros, C., Welten, S.P.M., Osterheld, K., Wang, H., Rota, G., Morgado, L., Vivier, E., Raeber, M.E., Boyman, O., Delorenzi, M., Barras, D., Ho, P.-C., Oxenius, A., and Guarda, G. (2018). The transcription factor Rfx7 limits metabolism of NK cells and promotes their maintenance and immunity. Nat. Immunol. 19, 809–820.

Dammone, G., Karaz, S., Lukjanenko, L., Winkler, C., Sizzano, F., Jacot, G., Migliavacca, E., Palini, A., Desvergne, B., Gilardi, F., and Feige, J.N. (2018). PPARγ Controls Ectopic Adipogenesis and Cross-Talks with Myogenesis During Skeletal Muscle Regeneration. Int J Mol Sci 19.

De Luca, S., Nicholson, P., Magistrali, C.F., García-Martín, A.B., Rychener, L., Zeeh, F., Frey, J., and Perreten, V. (2018). Transposon-associated lincosamide resistance lnu(C) gene identified in Brachyspira hyodysenteriae ST83. Vet. Microbiol. 214, 51–55.

De-Kayne, R., and Feulner, P.G.D. (2018). A European Whitefish Linkage Map and Its Implications for Understanding Genome-Wide Synteny Between Salmonids Following Whole Genome Duplication. G3 g3.200552.2018.

Diessler, S., Jan, M., Emmenegger, Y., Guex, N., Middleton, B., Skene, D.J., Ibberson, M., Burdet, F., Götz, L., Pagni, M., Sankar, M., Liechti, R., Hor, C.N., Xenarios, I., and Franken, P. (2018). A systems genetics resource and analysis of sleep regulation in the mouse. PLoS Biol. 16, e2005750.

Dogar, A.M., Pauchard-Batschulat, R., Grisoni-Neupert, B., Richman, L., Paillusson, A., Pradervand, S., Hagenbüchle, O., Ambrosini, G., Schmid, C.D., Bucher, P., and Kühn, L.C. (2018). Short-lived AUF1 p42-binding mRNAs of RANKL and BCL6 have two distinct instability elements each. PLoS ONE 13, e0206823.

Erkosar, B., Yashiro, E., Zajitschek, F., Friberg, U., Maklakov, A.A., van der Meer, J.R., and Kawecki, T.J. (2018). Host diet mediates a negative relationship between abundance and diversity of Drosophila gut microbiota. Ecol Evol 8, 9491–9502.

Feulner, P.G.D., Schwarzer, J., Haesler, M.P., Meier, J.I., and Seehausen, O. (2018). A Dense Linkage Map of Lake Victoria Cichlids Improved the Pundamilia Genome Assembly and Revealed a Major QTL for Sex-Determination. G3 8, 2411–2420.

Golumbeanu, M., Cristinelli, S., Rato, S., Munoz, M., Cavassini, M., Beerenwinkel, N., and Ciuffi, A. (2018). Single-Cell RNA-Seq Reveals Transcriptional Heterogeneity in Latent and Reactivated HIV-Infected Cells. Cell Rep 23, 942–950.

Groeneveld, S., Faget, J., Zangger, N., and Meylan, E. (2018). Snail mediates repression of the Dlk1-Dio3 locus in lung tumor-infiltrating immune cells. Oncotarget 9, 32331–32345.

Gueneau, L., Fish, R.J., Shamseldin, H.E., Voisin, N., Tran Mau-Them, F., Preiksaitiene, E., Monroe, G.R., Lai, A., Putoux, A., Allias, F., Ambusaidi, Q., Ambrozaityte, L., Cimbalistienė, L., Delafontaine, J., Guex, N., Hashem, M., Kurdi, W., Jamuar, S.S., Ying, L.J., Bonnard, C., et al. (2018). KIAA1109 Variants Are Associated with a Severe Disorder of Brain Development and Arthrogryposis. Am. J. Hum. Genet. 102, 116–132.

Harumoto, T., and Lemaitre, B. (2018). Male-killing toxin in a bacterial symbiont of Drosophila. Nature 557, 252–255.

Iyer, P.S., Mavoungou, L.O., Ronzoni, F., Zemla, J., Schmid-Siegert, E., Antonini, S., Neff, L.A., Dorchies, O.M., Jaconi, M., Lekka, M., Messina, G., and Mermod, N. (2018). Autologous Cell Therapy Approach for Duchenne Muscular Dystrophy using PiggyBac Transposons and Mesoangioblasts. Mol. Ther. 26, 1093–1108.

Jang, S.M., Kauzlaric, A., Quivy, J.-P., Pontis, J., Rauwel, B., Coluccio, A., Offner, S., Duc, J., Turelli, P., Almouzni, G., and Trono, D. (2018). KAP1 facilitates reinstatement of heterochromatin after DNA replication. Nucleic Acids Research 46, 8788–8802.

Lucas, E.R., and Keller, L. (2018). Elevated expression of ageing and immunity genes in queens of the black garden ant. Exp. Gerontol. 108, 92–98.

Masclaux, F.G., Wyss, T., Mateus-Gonzalez, I.D., Aletti, C., and Sanders, I.R. (2018). Variation in allele frequencies at the bg112 locus reveals unequal inheritance of nuclei in a dikaryotic isolate of the fungus Rhizophagus irregularis. Mycorrhiza 28, 369–377.

Masson, F., Calderon Copete, S., Schüpfer, F., Garcia-Arraez, G., and Lemaitre, B. (2018). In Vitro Culture of the Insect Endosymbiont Spiroplasma poulsonii Highlights Bacterial Genes Involved in Host-Symbiont Interaction. MBio 9, e00024-18, /mbio/9/2/mBio.00024-18.atom.

Matthey, N., Drebes Dörr, N.C., and Blokesch, M. (2018). Long-Read-Based Genome Sequences of Pandemic and Environmental Vibrio cholerae Strains. Microbiol Resour Announc 7, e01574-18, /mra/7/23/e01574-18.atom.

Meibom, K.L., Cabello, E.M., and Bernier-Latmani, R. (2018). The Small RNA RyhB Is a Regulator of Cytochrome Expression in Shewanella oneidensis. Front Microbiol 9, 268.

Merienne, N., Vachey, G., de Longprez, L., Meunier, C., Zimmer, V., Perriard, G., Canales, M., Mathias, A., Herrgott, L., Beltraminelli, T., Maulet, A., Dequesne, T., Pythoud, C., Rey, M., Pellerin, L., Brouillet, E., Perrier, A.L., du Pasquier, R., and Déglon, N. (2017). The Self-Inactivating KamiCas9 System for the Editing of CNS Disease Genes. Cell Rep 20, 2980–2991.

Miyazaki, R., Yano, H., Sentchilo, V., and van der Meer, J.R. (2018). Physiological and transcriptome changes induced by Pseudomonas putida acquisition of an integrative and conjugative element. Sci Rep 8, 5550.

Moser, F.N., van Rijssel, J.C., Mwaiko, S., Meier, J.I., Ngatunga, B., and Seehausen, O. (2018). The onset of ecological diversification 50 years after colonization of a crater lake by haplochromine cichlid fishes. Proc. R. Soc. B 285, 20180171.

Mouammine, A., Eich, K., Frandi, A., and Collier, J. (2018). Control of proline utilization by the Lrp-like regulator PutR in Caulobacter crescentus. Sci Rep 8, 14677.

Moysés-Oliveira, M., Giannuzzi, G., Fish, R.J., Rosenfeld, J.A., Petit, F., Soares, M. de F., Kulikowski, L.D., Di-Battista, A., Zamariolli, M., Xia, F., Liehr, T., Kosyakova, N., Carvalheira, G., Parker, M., Seaby, E.G., Ennis, S., Gilbert, R.D., Hagelstrom, R.T., Cremona, M.L., Li, W.L., et al. (2018). Inactivation of AMMECR1 is associated with growth, bone, and heart alterations. Hum. Mutat. 39, 281–291.

Nisa, L., Barras, D., Medová, M., Aebersold, D.M., Medo, M., Poliaková, M., Koch, J., Bojaxhiu, B., Eliçin, O., Dettmer, M.S., Angelino, P., Giger, R., Borner, U., Caversaccio, M.D., Carey, T.E., Ho, L., McKee, T.A., Delorenzi, M., and Zimmer, Y. (2018). Comprehensive Genomic Profiling of Patient-matched Head and Neck Cancer Cells: A Preclinical Pipeline for Metastatic and Recurrent Disease. Mol. Cancer Res. 16, 1912–1926.

Perriot, S., Mathias, A., Perriard, G., Canales, M., Jonkmans, N., Merienne, N., Meunier, C., El Kassar, L., Perrier, A.L., Laplaud, D.-A., Schluep, M., Déglon, N., and Du Pasquier, R. (2018). Human Induced Pluripotent Stem Cell-Derived Astrocytes Are Differentially Activated by Multiple Sclerosis-Associated Cytokines. Stem Cell Reports 11, 1199–1210.

Pich, C., Meylan, P., Mastelic-Gavillet, B., Nguyen, N.T., Loyon, R., Trang, B.K., Moser, H., Moret, C., Goepfert, C., Hafner, J., Levesque, M.P., Romero, P., Jandus, C., and Michalik, L. (2018). Induction of paracrine signaling in metastatic melanoma cells by PPARγ agonist rosiglitazone activates stromal cells and enhances tumor growth. Cancer Res canres.0912.2018.

Rib, L., Villeneuve, D., Minocha, S., Praz, V., Hernandez, N., Guex, N., Herr, W., and CycliX Consortium (2018). Cycles of gene expression and genome response during mammalian tissue regeneration. Epigenetics Chromatin 11, 52.

Roh, V., Abramowski, P., Hiou-Feige, A., Cornils, K., Rivals, J.-P., Zougman, A., Aranyossy, T., Thielecke, L., Truan, Z., Mermod, M., Monnier, Y., Prassolov, V., Glauche, I., Nowrouzi, A., Abdollahi, A., Fehse, B., Simon, C., and Tolstonog, G.V. (2018). Cellular Barcoding Identifies Clonal Substitution as a Hallmark of Local Recurrence in a Surgical Model of Head and Neck Squamous Cell Carcinoma. Cell Rep 25, 2208-2222.e7.

Romiguier, J., Rolland, J., Morandin, C., and Keller, L. (2018). Phylogenomics of palearctic Formica species suggests a single origin of temporary parasitism and gives insights to the evolutionary pathway toward slave-making behaviour. BMC Evol. Biol. 18, 40.

Sardella, C., Winkler, C., Quignodon, L., Hardman, J.A., Toffoli, B., Giordano Attianese, G.M.P., Hundt, J.E., Michalik, L., Vinson, C.R., Paus, R., Desvergne, B., and Gilardi, F. (2018). Delayed Hair Follicle Morphogenesis and Hair Follicle Dystrophy in a Lipoatrophy Mouse Model of Pparg Total Deletion. J. Invest. Dermatol. 138, 500–510.

Savary, R., Masclaux, F.G., Wyss, T., Droh, G., Cruz Corella, J., Machado, A.P., Morton, J.B., and Sanders, I.R. (2018). A population genomics approach shows widespread geographical distribution of cryptic genomic forms of the symbiotic fungus Rhizophagus irregularis. ISME J 12, 17–30.

Schwalie, P.C., Dong, H., Zachara, M., Russeil, J., Alpern, D., Akchiche, N., Caprara, C., Sun, W., Schlaudraff, K.-U., Soldati, G., Wolfrum, C., and Deplancke, B. (2018). A stromal cell population that inhibits adipogenesis in mammalian fat depots. Nature 559, 103–108.

Sevestre, J., Diene, S.M., Aouiti-Trabelsi, M., Deghmane, A.-E., Tournier, I., François, P., Caron, F., and Taha, M.-K. (2018). Differential expression of hemoglobin receptor, HmbR, between carriage and invasive isolates of Neisseria meningitidis contributes to virulence: lessons from a clonal outbreak. Virulence 9, 923–929.

Tagini, F., Pillonel, T., Croxatto, A., Bertelli, C., Koutsokera, A., Lovis, A., and Greub, G. (2018). Distinct Genomic Features Characterize Two Clades of Corynebacterium diphtheriae: Proposal of Corynebacterium diphtheriae Subsp. diphtheriae Subsp. nov. and Corynebacterium diphtheriae Subsp. lausannense Subsp. nov. Front. Microbiol. 9, 1743.

Toffoli, B., Zennaro, C., Winkler, C., Giordano Attianese, G.M.P., Bernardi, S., Carraro, M., Gilardi, F., and Desvergne, B. (2018). Hemicentin 1 influences podocyte dynamic changes in glomerular diseases. Am. J. Physiol. Renal Physiol. 314, F1154–F1165.

Tripathy, R., Leca, I., van Dijk, T., Weiss, J., van Bon, B.W., Sergaki, M.C., Gstrein, T., Breuss, M., Tian, G., Bahi-Buisson, N., Paciorkowski, A.R., Pagnamenta, A.T., Wenninger-Weinzierl, A., Martinez-Reza, M.F., Landler, L., Lise, S., Taylor, J.C., Terrone, G., Vitiello, G., Del Giudice, E., et al. (2018). Mutations in MAST1 Cause Mega-Corpus-Callosum Syndrome with Cerebellar Hypoplasia and Cortical Malformations. Neuron 100, 1354-1368.e5.

Wilson, A., Fu, H., Schiffrin, M., Winkler, C., Koufany, M., Jouzeau, J.-Y., Bonnet, N., Gilardi, F., Renevey, F., Luther, S.A., Moulin, D., and Desvergne, B. (2018). Lack of Adipocytes Alters Hematopoiesis in Lipodystrophic Mice. Front Immunol 9, 2573.

Yashiro, E., Pinto-Figueroa, E., Buri, A., Spangenberg, J.E., Adatte, T., Niculita-Hirzel, H., Guisan, A., and van der Meer, J.R. (2018). Meta-scale mountain grassland observatories uncover commonalities as well as specific interactions among plant and non-rhizosphere soil bacterial communities. Sci Rep 8, 5758.