The FMI publishes over 100 articles per year in peer-reviewed publications. In 2022, our researchers authored 107 scientific publications, including 49 in journals with Impact Factor >10.

Most Cited 20 FMI Publications

PUBLICATION SEARCH

Our publication database contains all the scientific publications (articles and reviews only) in which an FMI group leader is listed PLUS the first or the last author is from the FMI. You can browse the database by the name of the group leader and by the year. The table underneath features our latest publications, in chronological order starting with the most recent one.

Group:

and/or year:

Groups & Date	Authors	Title & Journal
Rijli, F. Apr 21, 2025	Pumo G, Rijli FM	Chromatin regulation of neuronal activity-dependent gene programs in circuit formation and plasticity. Curr Opin Neurobiol. 2025 Apr 21;92:103024
Turco, M. Apr 14, 2025	Turco M, Kraft O	A holistic approach to advancing women's health. Nat Rev Bioeng. April 2025
Proteomics and protein analysis; Functional Genomics; Computational Biology; Buehler, M. Apr 3, 2025	Skribbe M, Soneson C, Stadler MB, Schwaiger M, Suma Sreechakram VN, Iesmantavicius V, Hess D, Moreno EPF, Braun S, Seebacher J, Smallwood SA, Bühler M	A comprehensive Schizosaccharomyces pombe atlas of physical transcription factor interactions with proteins and chromatin. Mol Cell. 2025 Apr 3;85(7):1426-1444.e8
Zenke, F. Mar 20, 2025	Gygax J, Zenke F	Elucidating the Theoretical Underpinnings of Surrogate Gradient Learning in Spiking Neural Networks. Neural Comput. 2025 Mar 20;:1-40
Friedrich, R.; Zenke, F. Feb 20, 2025	Meissner-Bernard C, Jenkins B, Rupprecht P, Bouldoires EA, Zenke F, Friedrich RW, Frank T	Computational functions of precisely balanced neuronal microcircuits in an olfactory memory network. Cell Rep. 2025 Feb 20;44(3):115330
Keller, G. Feb 10, 2025	Solyga M, Keller GB	Multimodal mismatch responses in mouse auditory cortex. Elife. 2025 Feb 10;13
Friedrich, R.; Zenke, F. Jan 13, 2025	Meissner-Bernard C, Zenke F, Friedrich RW	Geometry and dynamics of representations in a precisely balanced memory network related to olfactory cortex. Elife. 2025 Jan 13;13
Peters, A.; Functional Genomics; Computational Biology Jan 7, 2025	Fanourgakis G, Gaspa-Toneu L, Komarov PA, Papasaikas P, Ozonov EA, Smallwood SA, Peters AHFM	DNA methylation modulates nucleosome retention in sperm and H3K4 methylation deposition in early mouse embryos. Nat Commun. 2025 Jan 7;16(1):465
Chao, J. Jan 2, 2025	Williams TD, Michalak EM, Carey KT, Lam EYN, Anderson A, Griesbach E, Chan YC, Papasaikas P, Tan VWT, Ngo L, MacPherson L, Gilan O, Rucinski A, Rutkowska-Klute A, Zinn N, Grandi P, Bantscheff M, Prinjha RK, Dawson SJ, Chao JA, Wickramasinghe VO, Dawson MA	mRNA export factors store nascent transcripts within nuclear speckles as an adaptive response to transient global inhibition of transcription. Mol Cell. 2025 Jan 2;85(1):117-131.e7
Proteomics and protein analysis; Grosshans, H.; Computational Biology; Structural Biology Dec 01, 2024	Gudipati RK, Gaidatzis D, Seebacher J, Muehlhaeusser S, Kempf G, Cavadini S, Hess D, Soneson C, Großhans H	Deep quantification of substrate turnover defines protease subsite cooperativity. Mol Syst Biol. 2024 Dec;20(12):1303-1328
Luethi, A. Dec 01, 2024	Hagihara KM, Lüthi A	Bidirectional valence coding in amygdala intercalated clusters: A neural substrate for the opponent-process theory of motivation. Neurosci Res. 2024 Dec;209:28-33
Gasser, S.; Emeritus; Diss, G. Nov 15, 2024	Hurst V, Gerhold CB, Tarashev CVD, Challa K, Seeber A, Yamazaki S, Knapp B, Helliwell SB, Bodenmiller B, Harata M, Shimada K, Gasser SM	Loss of cytoplasmic actin filaments raises nuclear actin levels to drive INO80C-dependent chromosome fragmentation. Nat Commun. 2024 Nov 15;15(1):9910
Gasser, S.; Emeritus Nov 15, 2024	Shimada K, Tarashev CVD, Bregenhorn S, Gerhold CB, van Loon B, Roth G, Hurst V, Jiricny J, Helliwell SB, Gasser SM	TORC2 inhibition triggers yeast chromosome fragmentation through mis regulated Base Excision Repair of clustered oxidation events. Nat Commun. 2024 Nov 15;15(1):9908
Turco, M. Nov 14, 2024	Burton GJ, Jauniaux E, Cindrova-Davies T, Turco MY	The human gestational sac as a choriovitelline placenta during early pregnancy; the secondary yolk sac and organoid models. Dev Biol. 2024 Nov 14;518:28-36
Diss, G.; Structural Biology Oct 14, 2024	Bendel AM, Faure AJ, Klein D, Shimada K, Lyautey R, Schiffelholz N, Kempf G, Cavadini S, Lehner B, Diss G	The genetic architecture of protein interaction affinity and specificity. Nat Commun. 2024 Oct 14;15(1):8868
Liberali, P.; Applied Tissue Model Center Oct 7, 2024	Kahnwald M, Mählen M, Oost KC, Liberali P	Advances in optical pooled screening to map spatial complexity. Nat Biotechnol. 2024 Oct 7
Proteomics and protein analysis; Buehler, M. Oct 01, 2024	Ohsawa S, Schwaiger M, Iesmantavicius V, Hashimoto R, Moriyama H, Matoba H, Hirai G, Sodeoka M, Hashimoto A, Matsuyama A, Yoshida M, Yashiroda Y, Bühler M	Nitrogen signaling factor triggers a respiration-like gene expression program in fission yeast. EMBO J. 2024 Oct;43(20):4604-4624
Caroni, P. Sep 20, 2024	Parrini M, Caroni P, Spolidoro M	Protocol to investigate the gradual selection and deployment of goal-oriented search strategies during unsupervised navigation in mice. STAR Protoc. 2024 Sep 20;5(3):103290
Schuebeler, D. Sep 19, 2024	Grand RS, Pregnolato M, Baumgartner L, Hoerner L, Burger L, Schübeler D	Genome access is transcription factor-specific and defined by nucleosome position. Mol Cell. 2024 Sep 19;84(18):3455-3468.e6
Roska, B. Aug 21, 2024	Müllner FE, Roska B	Individual thalamic inhibitory interneurons are functionally specialized toward distinct visual features. Neuron. 2024 Aug 21;112(16):2765-2782.e9
Keller, G. Aug 01, 2024	Keller GB, Sterzer P	Predictive Processing: A Circuit Approach to Psychosis. Annu Rev Neurosci. 2024 Aug;47(1):85-101
Buehler, M. Jul 29, 2024	Schwaiger M, Mohn F, Bühler M, Kaaij LJT	guidedNOMe-seq quantifies chromatin states at single allele resolution for hundreds of custom regions in parallel. BMC Genomics. 2024 Jul 29;25(1):732
Keller, G. Jul 26, 2024	Yogesh B, Keller GB	Cholinergic input to mouse visual cortex signals a movement state and acutely enhances layer 5 responsiveness. Elife. 2024 Jul 26;12
Proteomics and protein analysis; Buehler, M.; Structural Biology Jul 19, 2024	Ahel J, Pandey A, Schwaiger M, Mohn F, Basters A, Kempf G, Andriollo A, Kaaij L, Hess D, Bühler M	ChAHP2 and ChAHP control diverse retrotransposons by complementary activities. Genes Dev. 2024 Jul 19;38(11-12):554-568
Liberali, P. Jul 11, 2024	Liberali P, Schier AF	The evolution of developmental biology through conceptual and technological revolutions. Cell. 2024 Jul 11;187(14):3461-3495
Thoma, N. Jul 10, 2024	Carminati M, Vecchia L, Stoos L, Thomä NH	Pioneer factors: Emerging rules of engagement for transcription factors on chromatinized DNA. Curr Opin Struct Biol. 2024 Jul 10;88:102875
Zenke, F. Jul 5, 2024	Nilsson M, Miccini R, Laroche C, Piechowiak T, Zenke F	Resource-Efficient Speech Quality Prediction through Quantization Aware Training and Binary Activation Maps. Interspeech 2024
Diss, G. Jun 24, 2024	Bendel AM, Skendo K, Klein D, Shimada K, Kauneckaite-Griguole K, Diss G	Optimization of a deep mutational scanning workflow to improve quantification of mutation effects on protein-protein interactions. BMC Genomics. 2024 Jun 24;25(1):630
Keller, G. Jun 13, 2024	O'Toole SM, Keller GB	Sample collection protocol for single-cell RNA sequencing of functionally identified neuronal populations in vivo STAR Protoc. 2024 Jun 13;5(2):103135
Schuebeler, D.; Giorgetti, L. Jun 01, 2024	Iurlaro M, Masoni F, Flyamer IM, Wirbelauer C, Iskar M, Burger L, Giorgetti L, Schübeler D	Systematic assessment of ISWI subunits shows that NURF creates local accessibility for CTCF. Nat Genet. 2024 Jun;56(6):1203-1212
Grosshans, H.; Computational Biology May 22, 2024	Nahar S, Morales Moya LJ, Brunner J, Hendriks GJ, Towbin B, Hauser YP, Brancati G, Gaidatzis D, Großhans H	Dynamics of miRNA accumulation during C. elegans larval development. Nucleic Acids Res. 2024 May 22;52(9):5336-5355
Liberali, P.; Tsiairis, C. May 01, 2024	Moos F, Suppinger S, de Medeiros G, Oost KC, Boni A, Rémy C, Weevers SL, Tsiairis C, Strnad P, Liberali P	Open-top multi sample dual-view light-sheet microscope for live imaging of large multicellular systems. Nat Methods. 2024 May;21(5):798-803
Caroni, P. Apr 16, 2024	Bhandari K, Kanodia H, Donato F, Caroni P	Selective vulnerability of the ventral hippocampus-prelimbic cortex axis parvalbumin interneuron network underlies learning deficits of fragile X mice. Cell Rep. 2024 Apr 16;43(5):114124
Zenke, F. Apr 8, 2024	Axel Laborieux, Friedemann Zenke	Improving equilibrium propagation without weight symmetry through Jacobian homeostasis ICLR 2024
Keller, G. Apr 5, 2024	Heindorf M, Keller GB	Antipsychotic drugs selectively decorrelate long-range interactions in deep cortical layers. Elife. 2024 Apr 5;12
Computational Biology; Chao, J.; Giorgetti, L. Feb 16, 2024	Hochstoeger T, Papasaikas P, Piskadlo E, Chao JA	Distinct roles of LARP1 and 4EBP1/2 in regulating translation and stability of 5'TOP mRNAs. Sci Adv. 2024 Feb 16;10(7):eadi7830
Chao, J. Feb 15, 2024	Hochstoeger T, Chao JA	Towards a molecular understanding of the 5'TOP motif in regulating translation of ribosomal mRNAs. Semin Cell Dev Biol. 2024 Feb 15;154(Pt B):99-104
Peters, A.; Cell sorting (FACS) Feb 14, 2024	Gill ME, Kohler H, Peters AHFM	Isolation of Mouse Germ Cells by FACS Using Hoechst 33342 and SYTO16 Double Staining. Methods Mol Biol. 2024;2770:53-62
Matthias, P. Feb 01, 2024	Wang L, Shi S, Unterreiner A, Kapetanovic R, Ghosh S, Sanchez J, Aslani S, Xiong Y, Hsu CL, Donovan KA, Farady CJ, Fischer ES, Bornancin F, Matthias P	HDAC6/aggresome processing pathway importance for inflammasome formation is context-dependent J Biol Chem. 2024 Feb;300(2):105638
Thoma, N. Jan 23, 2024	Oleinikovas V, Gainza P, Ryckmans T, Fasching B, Thomä NH	From Thalidomide to Rational Molecular Glue Design for Targeted Protein Degradation. Annu Rev Pharmacol Toxicol. 2024 Jan 23;64:291-312
Computational Biology; Friedrich, R. Jan 22, 2024	Anneser L, Satou C, Hotz HR, Friedrich RW	Molecular organization of neuronal cell types and neuromodulatory systems in the zebrafish telencephalon. Curr Biol. 2024 Jan 22;34(2):298-312.e4
Caroni, P. Jan 8, 2024	Parrini M, Tricot G, Caroni P, Spolidoro M	Circuit mechanisms of navigation strategy learning in mice. Curr Biol. 2024 Jan 8;34(1):79-91.e4
Thoma, N.; Structural Biology Jan 01, 2024	Kozicka Z, Suchyta DJ, Focht V, Kempf G, Petzold G, Jentzsch M, Zou C, Di Genua C, Donovan KA, Coomar S, Cigler M, Mayor-Ruiz C, Schmid-Burgk JL, Häussinger D, Winter GE, Fischer ES, Slabicki M, Gillingham D, Ebert BL, Thomä NH	Design principles for cyclin K molecular glue degraders. Nat Chem Biol. 2024 Jan;20(1):93-102
Matthias, P. Dec 26, 2023	Artcibasova A, Wang L, Anchisi S, Yamauchi Y, Schmolke M, Matthias P, Stelling J	A quantitative model for virus uncoating predicts influenza A infectivity. Cell Rep. 2023 Dec 26;42(12):113558
Peters, A. Dec 21, 2023	Gill ME, Rohmer A, Erkek-Ozhan S, Liang CY, Chun S, Ozonov EA, Peters AHFM	De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression. Genome Res. 2023 Dec 21;33(12):2060-78
Cell sorting (FACS); Computational Biology; Bentires-Alj, M. Dec 8, 2023	Hamelin B, Obradovic MMS, Sethi A, Kloc M, Münst S, Beisel C, Eschbach K, Kohler H, Soysal S, Vetter M, Weber WP, Stadler MB, Bentires-Alj M	Single-cell Analysis Reveals Inter- and Intratumour Heterogeneity in Metastatic Breast Cancer. J Mammary Gland Biol Neoplasia. 2023 Dec 8;28(1):26
Zenke, F. Nov 01, 2023	Julian Rossbroich, Friedemann Zenke	Dis-inhibitory neuronal circuits can control the sign of synaptic plasticity NeurIPS Proceedings, 37th Conference on Neural Information Processing Systems (NeurIPS 2023)
Zenke, F. Nov 01, 2023	Halvagal MS, Zenke F	The combination of Hebbian and predictive plasticity learns invariant object representations in deep sensory networks. Nat Neurosci. 2023 Nov;26(11):1906-1915
Zenke, F. Oct 27, 2023	Manu Srinath Halvagal, Axel Laborieux, Friedemann Zenke	An eigenspace view reveals how predictor networks and stop-grads provide implicit variance regularization NeurIPS Proceedings
Zenke, F. Oct 27, 2023	Manu Srinath Halvagal, Axel Laborieux, Friedemann Zenke	Implicit variance regularization in non-contrastive SSL NeurIPS 2023, Advances in Neural Information Processing Systems 36
Chao, J. Oct 16, 2023	Eichenberger BT, Griesbach E, Mitchell J, Chao JA	Following the Birth, Life, and Death of mRNAs in Single Cells. Annu Rev Cell Dev Biol. 2023 Oct 16;39:253-275
Computational Biology Sep 21, 2023	Hadziselimovic F, Verkauskas G, Stadler MB	Epigenetics, cryptorchidism, and infertility. Basic Clin Androl. 2023 Sep 21;33(1):24
Keller, G. Sep 20, 2023	O'Toole SM, Oyibo HK, Keller GB	Molecularly targetable cell types in mouse visual cortex have distinguishable prediction error responses. Neuron. 2023 Sep 20;111(18):2918-2928.e8
Proteomics and protein analysis; Computational Biology Sep 11, 2023	Charlotte Soneson , Vytautas Iesmantavicius, Daniel Hess, Michael B Stadler, Jan Seebacher	einprot: flexible, easy-to-use, reproducible workflows for statistical analysis of quantitative proteomics data Journal of Open Source Software, sept 2023 8(89), 5750
Rijli, F. Sep 01, 2023	Selleri L, Rijli FM	Shaping faces: genetic and epigenetic control of craniofacial morphogenesis. Nat Rev Genet. 2023 Sep;24(9):610-626
Proteomics and protein analysis; Buehler, M. Aug 01, 2023	Flemr M, Schwaiger M, Hess D, Iesmantavicius V, Ahel J, Tuck AC, Mohn F, Bühler M	Mouse nuclear RNAi-defective 2 promotes splicing of weak 5' splice sites. RNA. 2023 Aug;29(8):1140-1165
Proteomics and protein analysis; Grosshans, H.; Computational Biology Jul 20, 2023	Welte T, Goulois A, Stadler MB, Hess D, Soneson C, Neagu A, Azzi C, Wisser MJ, Seebacher J, Schmidt I, Estoppey D, Nigsch F, Reece-Hoyes J, Hoepfner D, Großhans H	Convergence of multiple RNA-silencing pathways on GW182/TNRC6. Mol Cell. 2023 Jul 20;83(14):2478-2492.e8
Schuebeler, D.; Proteomics and protein analysis; Thoma, N.; Structural Biology Jul 5, 2023	Michael AK, Stoos L, Crosby P, Eggers N, Nie XY, Makasheva K, Minnich M, Healy KL, Weiss J, Kempf G, Cavadini S, Kater L, Seebacher J, Vecchia L, Chakraborty D, Isbel L, Grand RS, Andersch F, Fribourgh JL, Schübeler D, Zuber J, Liu AC, Becker PB, Fierz B, Partch CL, Menet JS, Thomä NH	Cooperation between bHLH transcription factors and histones for DNA access. Nature. 2023 Jul;619(7969):385-393
Computational Biology; Bentires-Alj, M. Jul 3, 2023	Couto JP, Vulin M, Jehanno C, Coissieux MM, Hamelin B, Schmidt A, Ivanek R, Sethi A, Bräutigam K, Frei AL, Hager C, Manivannan M, Gómez-Miragaya J, Obradovic MM, Varga Z, Koelzer VH, Mertz KD, Bentires-Alj M	Nicotinamide N-methyltransferase sustains a core epigenetic program that promotes metastatic colonization in breast cancer. EMBO J. 2023 Jul 3;42(13):e112559
Schuebeler, D.; Thoma, N. Jul 01, 2023	Isbel L, Iskar M, Durdu S, Weiss J, Grand RS, Hietter-Pfeiffer E, Kozicka Z, Michael AK, Burger L, Thomä NH, Schübeler D	Readout of histone methylation by Trim24 locally restricts chromatin opening by p53. Nat Struct Mol Biol. 2023 Jul;30(7):948-957
Schuebeler, D.; Buehler, M. Jun 27, 2023	Gil N, Perry RB, Mukamel Z, Tuck A, Bühler M, Ulitsky I	Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus. Cell Rep. 2023 Jun 27;42(6):112569
Computational Biology; Bentires-Alj, M. Jun 9, 2023	Amante RJ, Jehanno C, De Silva D, Coissieux MM, Ackerknecht M, Romanet V, Sethi A, Hamelin B, Preca BT, Piscuoglio S, Ng CKY, Mohseni M, Bentires-Alj M	PI3K inhibition circumvents resistance to SHP2 blockade in metastatic triple-negative breast cancer. J Mammary Gland Biol Neoplasia. 2023 Jun 9;28(1):13
Keller, G. Jun 7, 2023	Jordan R, Keller GB	The locus coeruleus broadcasts prediction errors across the cortex to promote sensorimotor plasticity. Elife. 2023 Jun 7;12
Cell sorting (FACS); Computational Biology; Rijli, F. Jun 5, 2023	Kessler S, Minoux M, Joshi O, Ben Zouari Y, Ducret S, Ross F, Vilain N, Salvi A, Wolff J, Kohler H, Stadler MB, Rijli FM	A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest. Nat Commun. 2023 Jun 5;14(1):3242
Giorgetti, L.; Tsiairis, C. Jun 5, 2023	Roth G, Misailidis G, Pappa M, Ferralli J, Tsiairis CD	Unidirectional and phase-gated signaling synchronizes murine presomitic mesoderm cells. Dev Cell. 2023 Jun 5;58(11):967-980.e4
Giorgetti, L. Jun 01, 2023	Mach P, Giorgetti L	Integrative approaches to study enhancer-promoter communication. Curr Opin Genet Dev. 2023 Jun;80:102052
Computational Biology; Diss, G. Jun 01, 2023	Soneson C, Bendel AM, Diss G, Stadler MB	mutscan-a flexible R package for efficient end-to-end analysis of multiplexed assays of variant effect data. Genome Biol. 2023 Jun 1;24(1):132
Cell sorting (FACS); Facility for Advanced Imaging and Microscopy; Computational Biology; Liberali, P. Jun 01, 2023	Suppinger S, Zinner M, Aizarani N, Lukonin I, Ortiz R, Azzi C, Stadler MB, Vianello S, Palla G, Kohler H, Mayran A, Lutolf MP, Liberali P	Multimodal characterization of murine gastruloid development. Cell Stem Cell. 2023 Jun 1;30(6):867-884.e11
Animal facility; Facility for Advanced Imaging and Microscopy; Roska, B. Apr 27, 2023	Munz M, Bharioke A, Kosche G, Moreno-Juan V, Brignall A, Rodrigues TM, Graff-Meyer A, Ulmer T, Haeuselmann S, Pavlinic D, Ledergerber N, Gross-Scherf B, Rózsa B, Krol J, Picelli S, Cowan CS, Roska B	Pyramidal neurons form active, transient, multilayered circuits perturbed by autism-associated mutations at the inception of neocortex. Cell. 2023 Apr 27;186(9):1930-1949.e31
Computational Biology; Bentires-Alj, M. Apr 18, 2023	Auf der Maur P, Trefny MP, Baumann Z, Vulin M, Correia AL, Diepenbruck M, Kramer N, Volkmann K, Preca BT, Ramos P, Leroy C, Eichlisberger T, Buczak K, Zilli F, Okamoto R, Rad R, Jensen MR, Fritsch C, Zippelius A, Stadler MB, Bentires-Alj M	N-acetylcysteine overcomes NF1 loss-driven resistance to PI3Kα inhibition in breast cancer. Cell Rep Med. 2023 Apr 18;4(4):101002
Peters, A. Apr 01, 2023	Gaspa-Toneu L, Peters AH	Nucleosomes in mammalian sperm: conveying paternal epigenetic inheritance or subject to reprogramming between generations? Curr Opin Genet Dev. 2023 Apr;79:102034
Keller, G. Feb 22, 2023	Vasilevskaya A, Widmer FC, Keller GB, Jordan R	Locomotion-induced gain of visual responses cannot explain visuomotor mismatch responses in layer 2/3 of primary visual cortex. Cell Rep. 2023 Feb 22;42(3):112096
Chao, J.; Giorgetti, L. Feb 16, 2023	Dave P, Roth G, Griesbach E, Mateju D, Hochstoeger T, Chao JA	Single-molecule imaging reveals translation-dependent destabilization of mRNAs. Mol Cell. 2023 Feb 16;83(4):589-606.e6
Facility for Advanced Imaging and Microscopy; Grosshans, H. Feb 15, 2023	Meeuse MWM, Hauser YP, Nahar S, Smith AAT, Braun K, Azzi C, Rempfler M, Großhans H	C. elegans molting requires rhythmic accumulation of the Grainyhead/LSF transcription factor GRH-1. EMBO J. 2023 Feb 15;42(4):e111895
Thoma, N.; Structural Biology Feb 15, 2023	Pla-Prats C, Cavadini S, Kempf G, Thomä NH	Recognition of the CCT5 di-Glu degron by CRL4(DCAF12) is dependent on TRiC assembly. EMBO J. 2023 Feb 15;42(4):e112253
Luethi, A. Jan 18, 2023	Massi L, Hagihara KM, Courtin J, Hinz J, Müller C, Fustiñana MS, Xu C, Karalis N, Lüthi A	Disynaptic specificity of serial information flow for conditioned fear. Sci Adv. 2023 Jan 18;9(3):eabq1637
Peters, A.; Facility for Advanced Imaging and Microscopy; Electron microscopy Jan 11, 2023	Ballmer D, Tardat M, Ortiz R, Graff-Meyer A, Ozonov EA, Genoud C, Peters AH, Fanourgakis G	HP1 proteins regulate nucleolar structure and function by secluding pericentromeric constitutive heterochromatin. Nucleic Acids Res. 2023 Jan 11;51(1):117-143
Proteomics and protein analysis; Buehler, M. Jan 9, 2023	Kuzdere T, Flury V, Schalch T, Iesmantavicius V, Hess D, Bühler M	Differential phosphorylation of Clr4(SUV39H) by Cdk1 accompanies a histone H3 methylation switch that is essential for gametogenesis. EMBO Rep. 2023 Jan 9;24(1):e55928
Arber, S. Jan 5, 2023	Yang W, Kanodia H, Arber S	Structural and functional map for forelimb movement phases between cortex and medulla. Cell. 2023 Jan 5;186(1):162-177.e18
Gasser, S.; Emeritus Jan 01, 2023	Gasser SM	Making a journal great: an ode to Terri Grodzicker. Genes Dev. 2023 Jan 1;37(1-2):25-26
Computational Biology; Tsiairis, C. Dec 23, 2022	Vogg MC, Ferenc J, Buzgariu WC, Perruchoud C, Sanchez PGL, Beccari L, Nuninger C, Le Cras Y, Delucinge-Vivier C, Papasaikas P, Vincent S, Galliot B, Tsiairis CD	The transcription factor Zic4 promotes tentacle formation and prevents epithelial transdifferentiation in Hydra. Sci Adv. 2022 Dec 23;8(51):eabo0694
Zenke, F. Dec 8, 2022	Julian Rossbroich, Julia Gygax, Friedemann Zenke	Fluctuation-driven initialization for spiking neural network training. Neuromorph Comput Eng 2 (2022) 044016
Functional Genomics; Facility for Advanced Imaging and Microscopy; Giorgetti, L. Dec 5, 2022	Mach P, Kos PI, Zhan Y, Cramard J, Gaudin S, Tünnermann J, Marchi E, Eglinger J, Zuin J, Kryzhanovska M, Smallwood S, Gelman L, Roth G, Nora EP, Tiana G, Giorgetti L	Cohesin and CTCF control the dynamics of chromosome folding. Nat Genet. 2022 Dec;54(12):1907-1918
Schuebeler, D.; Computational Biology Dec 5, 2022	Kaluscha S, Domcke S, Wirbelauer C, Stadler MB, Durdu S, Burger L, Schübeler D	Evidence that direct inhibition of transcription factor binding is the prevailing mode of gene and repeat repression by DNA methylation. Nat Genet. 2022 Dec;54(12):1895-1906
Schuebeler, D. Dec 01, 2022	Isbel L, Grand RS, Schübeler D	Generating specificity in genome regulation through transcription factor sensitivity to chromatin. Nat Rev Genet. 2022 Dec;23(12):728-740
Matthias, P.; Structural Biology Oct 19, 2022	Langousis G, Sanchez J, Kempf G, Matthias P	Expression and Crystallization of HDAC6 Tandem Catalytic Domains. Methods Mol Biol. 2023;2589:467-480
Matthias, P. Oct 19, 2022	Wang L, Sanchez J, Hess D, Matthias P	Immunoprecipitation of HDAC6 and Interacting Proteins. Methods Mol Biol. 2023;2589:493-508
Zenke, F. Sep 01, 2022	Axel Laborieux, Friedemann Zenke	Holomorphic Equilibrium Propagation Computes Exact Gradients Through Finite Size Oscillations NeurIPS 2022, Advances in Neural Information Processing Systems 35
Bentires-Alj, M. Sep 01, 2022	Vulin M, Jehanno C, Sethi A, Correia AL, Obradovic MMS, Couto JP, Coissieux MM, Diepenbruck M, Preca BT, Volkmann K, der Maur PA, Schmidt A, Münst S, Sauteur L, Kloc M, Palafox M, Britschgi A, Unterreiner V, Galuba O, Claerr I, Lopez-Romero S, Galli GG, Baeschlin D, Okamoto R, Soysal SD, Mechera R, Weber WP, Radimerski T, Bentires-Alj M	A high-throughput drug screen reveals means to differentiate triple-negative breast cancer. Oncogene. 2022 Sep;41(39):4459-4473
Gasser, S.; Emeritus; Grosshans, H. Sep 01, 2022	Padeken J, Methot SP, Gasser SM	Establishment of H3K9-methylated heterochromatin and its functions in tissue differentiation and maintenance. Nat Rev Mol Cell Biol. 2022 Sep;23(9):623-640
Caroni, P. Aug 22, 2022	Serrano M, Tripodi M, Caroni P	Strategy updating mediated by specific retrosplenial-parafascicular-basal ganglia networks. Curr Biol. 2022 Aug 22;32(16):3477-3492.e5
Ciosk, R. Aug 19, 2022	Pekec T, Lewandowski J, Komur AA, Sobanska D, Guo Y, Switonska-Kurkowska K, Malecki JM, Dubey AA, Pokrzywa W, Frankowski M, Figiel M, Ciosk R	Ferritin-mediated iron detoxification promotes hypothermia survival in Caenorhabditis elegans and murine neurons. Nat Commun. 2022 Aug 19;13(1):4883
Liberali, P. Aug 18, 2022	de Medeiros G, Ortiz R, Strnad P, Boni A, Moos F, Repina N, Challet Meylan L, Maurer F, Liberali P	Multiscale light-sheet organoid imaging framework. Nat Commun. 2022 Aug 18;13(1):4864
Thoma, N. Aug 01, 2022	Pla-Prats C, Thomä NH	Quality control of protein complex assembly by the ubiquitin-proteasome system. Trends Cell Biol. 2022 Aug;32(8):696-706
Keller, G. Jul 29, 2022	Mahringer D, Zmarz P, Okuno H, Bito H, Keller GB	Functional correlates of immediate early gene expression in mouse visual cortex. Peer Community J. 2022 Jul 29;2:e45
Chao, J.; Giorgetti, L. Jul 28, 2022	Piskadlo E, Eichenberger BT, Giorgetti L, Chao JA	Design, Labeling, and Application of Probes for RNA smFISH. Methods Mol Biol. 2022;2537:173-183
Friedrich, R.; Keller, G. Jul 22, 2022	Satou C, Neve RL, Oyibo HK, Zmarz P, Huang KH, Arn Bouldoires E, Mori T, Higashijima SI, Keller GB, Friedrich RW	A viral toolbox for conditional and transneuronal gene expression in zebrafish. Elife. 2022 Jul 22;11
Zenke, F. Jul 6, 2022	Cramer B, Stradmann Y, Schemmel J, Zenke F	The Heidelberg Spiking Data Sets for the Systematic Evaluation of Spiking Neural Networks. IEEE Trans Neural Netw Learn Syst. 2022 Jul;33(7):2744-2757
Turco, M. Jul 01, 2022	Burton GJ, Turco MY	Joan Hunt Senior award lecture: New tools to shed light on the 'black box' of pregnancy. Placenta. 2022 Jul;125:54-60
Proteomics and protein analysis; Bentires-Alj, M. Jun 23, 2022	Amante RJ, Auf der Maur P, Richina V, Sethi A, Iesmantavicius V, Bonenfant D, Aceto N, Bentires-Alj M	Protein Tyrosine Phosphatase SHP2 Controls Interleukin-8 Expression in Breast Cancer Cells. J Mammary Gland Biol Neoplasia. 2022 Jun;27(2):145-153
Chao, J. Jun 22, 2022	Gómez-Puerta S, Ferrero R, Hochstoeger T, Zubiri I, Chao J, Aragón T, Voigt F	Live imaging of the co-translational recruitment of XBP1 mRNA to the ER and its processing by diffuse, non-polarized IRE1α. Elife. 2022 Jun 22;11
Computational Biology Jun 21, 2022	Hadziselimovic F, Verkauskas G, Stadler M	A novel role for CFTR interaction with LH and FGF in azoospermia and epididymal maldevelopment caused by cryptorchidism. Basic Clin Androl. 2022 Jun 21;32(1):10
Roska, B. Jun 15, 2022	Bharioke A, Munz M, Brignall A, Kosche G, Eizinger MF, Ledergerber N, Hillier D, Gross-Scherf B, Conzelmann KK, Macé E, Roska B	General anesthesia globally synchronizes activity selectively in layer 5 cortical pyramidal neurons. Neuron. 2022 Jun 15;110(12):2024-2040.e10
Rijli, F. Jun 7, 2022	Pumo GM, Kitazawa T, Rijli FM	Epigenetic and Transcriptional Regulation of Spontaneous and Sensory Activity Dependent Programs During Neuronal Circuit Development. Front Neural Circuits. 2022;16:911023
Grosshans, H. Jun 6, 2022	Stojanovski K, Großhans H, Towbin BD	Coupling of growth rate and developmental tempo reduces body size heterogeneity in C. elegans. Nat Commun. 2022 Jun 6;13(1):3132
Arber, S. Jun 01, 2022	Arber S, Costa RM	Networking brainstem and basal ganglia circuits for movement. Nat Rev Neurosci. 2022 Jun;23(6):342-360
Peters, A.; Cell sorting (FACS) Jun 01, 2022	Gill ME, Kohler H, Peters AHFM	Dual DNA staining enables isolation of multiple sub-types of post-replicative mouse male germ cells. Cytometry A. 2022 Jun;101(6):529-536
Peters, A. May 18, 2022	Kawamura YK, Peters AHFM	Maternal enzyme reprograms paternal DNA for healthy offspring. Nature. 2022 May;605(7911):621-622
Arber, S.; Caroni, P. May 4, 2022	Krüttner S, Falasconi A, Valbuena S, Galimberti I, Bouwmeester T, Arber S, Caroni P	Absence of familiarity triggers hallmarks of autism in mouse model through aberrant tail-of-striatum and prelimbic cortex signaling. Neuron. 2022 May 4;110(9):1468-1482.e5
Schuebeler, D.; Computational Biology; Rijli, F. Apr 28, 2022	Machlab D, Burger L, Soneson C, Rijli FM, Schübeler D, Stadler MB	monaLisa: an R/Bioconductor package for identifying regulatory motifs. Bioinformatics. 2022 Apr 28;38(9):2624-2625
Matthias, P.; Structural Biology Apr 26, 2022	Wang L, Moreira EA, Kempf G, Miyake Y, Oliveira Esteves BI, Fahmi A, Schaefer JV, Dreier B, Yamauchi Y, Alves MP, Plückthun A, Matthias P	Disrupting the HDAC6-ubiquitin interaction impairs infection by influenza and Zika virus and cellular stress pathways. Cell Rep. 2022 Apr 26;39(4):110736
Luethi, A. Apr 15, 2022	d'Aquin S, Szonyi A, Mahn M, Krabbe S, Gründemann J, Lüthi A	Compartmentalized dendritic plasticity during associative learning. Science. 2022 Apr 15;376(6590):eabf7052
Matthias, P.; Structural Biology Apr 15, 2022	Langousis G, Cavadini S, Boegholm N, Lorentzen E, Kempf G, Matthias P	Structure of the ciliogenesis-associated CPLANE complex. Sci Adv. 2022 Apr 15;8(15):eabn0832
Cell sorting (FACS); Functional Genomics; Giorgetti, L. Apr 13, 2022	Zuin J, Roth G, Zhan Y, Cramard J, Redolfi J, Piskadlo E, Mach P, Kryzhanovska M, Tihanyi G, Kohler H, Eder M, Leemans C, van Steensel B, Meister P, Smallwood S, Giorgetti L	Nonlinear control of transcription through enhancer-promoter interactions. Nature. 2022 Apr;604(7906):571-577
Tsiairis, C. Apr 2, 2022	Ferenc J, Tsiairis CD	Studying Mechanical Oscillations During Whole-Body Regeneration in Hydra. Methods Mol Biol. 2022;2450:619-633
Proteomics and protein analysis; Bleichert, F. Feb 25, 2022	Schmidt JM, Yang R, Kumar A, Hunker O, Seebacher J, Bleichert F	A mechanism of origin licensing control through autoinhibition of S. cerevisiae ORC·DNA·Cdc6. Nat Commun. 2022 Feb 25;13(1):1059
Keller, G. Feb 16, 2022	Widmer FC, O'Toole SM, Keller GB	NMDA receptors in visual cortex are necessary for normal visuomotor integration and skill learning. Elife. 2022 Feb 16;11
Gasser, S.; Proteomics and protein analysis; Emeritus Feb 01, 2022	Delaney CE, Methot SP, Kalck V, Seebacher J, Hess D, Gasser SM, Padeken J	SETDB1-like MET-2 promotes transcriptional silencing and development independently of its H3K9me-associated catalytic activity. Nat Struct Mol Biol. 2022 Feb;29(2):85-96
Rijli, F. Jan 31, 2022	Kitazawa T, Minoux M, Ducret S, Rijli FM	Different Ectopic Hoxa2 Expression Levels in Mouse Cranial Neural Crest Cells Result in Distinct Craniofacial Anomalies and Homeotic Phenotypes. J Dev Biol. 2022 Jan 31;10(1)
Rijli, F. Jan 31, 2022	Kitazawa Taro, Maryline Minoux, Sebastien Ducret, Filippo M. Rijli	Different Ectopic Hoxa2 Expression Levels in Mouse Cranial Neural Crest Cells Result in Distinct Craniofacial Anomalies and Homeotic Phenotypes J Dev Biol, Jan 2022
Zenke, F. Jan 25, 2022	Cramer B, Billaudelle S, Kanya S, Leibfried A, Grübl A, Karasenko V, Pehle C, Schreiber K, Stradmann Y, Weis J, Schemmel J, Zenke F	Surrogate gradients for analog neuromorphic computing. Proc Natl Acad Sci U S A. 2022 Jan 25;119(4)
Luethi, A. Jan 7, 2022	Courtin J, Bitterman Y, Müller S, Hinz J, Hagihara KM, Müller C, Lüthi A	A neuronal mechanism for motivational control of behavior. Science. 2022 Jan 7;375(6576):eabg7277
Keller, G. Jan 01, 2022	Garner AR, Keller GB	A cortical circuit for audio-visual predictions. Nat Neurosci. 2022 Jan;25(1):98-105
Chao, J. Jan 01, 2022	Mateju D, Chao JA	Stress granules: regulators or by-products? FEBS J. 2022 Jan;289(2):363-373
Gasser, S.; Proteomics and protein analysis Dec 17, 2021	Challa K, Seebacher J, Gasser SM	Sucrose gradient chromatin enrichment for quantitative proteomics analysis in budding yeast. STAR Protoc. 2021 Dec 17;2(4):100825
Zenke, F. Dec 13, 2021	Wu YK, Zenke F	Nonlinear transient amplification in recurrent neural networks with short-term plasticity. Elife. 2021 Dec 13;10
Functional Genomics; Computational Biology; Tsiairis, C. Dec 10, 2021	Ferenc J, Papasaikas P, Ferralli J, Nakamura Y, Smallwood S, Tsiairis CD	Mechanical oscillations orchestrate axial patterning through Wnt activation in Hydra. Sci Adv. 2021 Dec 10;7(50):eabj6897
Thoma, N.; Structural Biology Nov 15, 2021	Mohamed WI, Schenk AD, Kempf G, Cavadini S, Basters A, Potenza A, Abdul Rahman W, Rabl J, Reichermeier K, Thomä NH	The CRL4<sup>DCAF1</sup> cullin-RING ubiquitin ligase is activated following a switch in oligomerization state. EMBO J. 2021 Nov 15;40(22):e108008
Gasser, S.; Cell sorting (FACS); Emeritus; Grosshans, H.; Computational Biology Nov 4, 2021	Methot SP, Padeken J, Brancati G, Zeller P, Delaney CE, Gaidatzis D, Kohler H, van Oudenaarden A, Großhans H, Gasser SM	H3K9me selectively blocks transcription factor activity and ensures differentiated tissue integrity. Nat Cell Biol. 2021 Nov;23(11):1163-1175
Turco, M. Nov 01, 2021	Sheridan MA, Zhao X, Fernando RC, Gardner L, Perez-Garcia V, Li Q, Marsh SGE, Hamilton R, Moffett A, Turco MY	Characterization of primary models of human trophoblast. Development. 2021 Nov 1;148(21)
Chao, J. Nov 01, 2021	Mitchell J, Chao JA	Single-molecule mRNA and translation imaging in neurons. Biochem Soc Trans. 2021 Nov 1;49(5):2221-2227
Liberali, P. Oct 18, 2021	Lukonin I, Zinner M, Liberali P	Organoids in image-based phenotypic chemical screens. Exp Mol Med. 2021 Oct;53(10):1495-1502
Liberali, P. Oct 01, 2021	Yang Q, Liberali P	Collective behaviours in organoids. Curr Opin Cell Biol. 2021 Oct;72:81-90
Gasser, S.; Emeritus Oct 01, 2021	Hurst V, Challa K, Shimada K, Gasser SM	Cytoskeleton integrity influences XRCC1 and PCNA dynamics at DNA damage. Mol Biol Cell. 2021 Oct 1;32(20):br6
Gasser, S.; Proteomics and protein analysis; Emeritus Sep 27, 2021	Hurst V, Challa K, Jonas F, Forey R, Sack R, Seebacher J, Schmid CD, Barkai N, Shimada K, Gasser SM, Poli J	A regulatory phosphorylation site on Mec1 controls chromatin occupancy of RNA polymerases during replication stress. EMBO J. 2021 Sep 27;:e108439
Betschinger, J. Sep 14, 2021	Waehle V, Ungricht R, Hoppe PS, Betschinger J	The tumor suppressor WT1 drives progenitor cell progression and epithelialization to prevent Wilms tumorigenesis in human kidney organoids. Stem Cell Reports. 2021 Sep 14;16(9):2107-2117
Friedrich, R. Sep 01, 2021	Rupprecht P, Carta S, Hoffmann A, Echizen M, Blot A, Kwan AC, Dan Y, Hofer SB, Kitamura K, Helmchen F, Friedrich RW	A database and deep learning toolbox for noise-optimized, generalized spike inference from calcium imaging. Nat Neurosci. 2021 Sep;24(9):1324-1337
Gasser, S.; Emeritus; Protein structure Sep 01, 2021	Shimada K, Tsai-Pflugfelder M, Vijeh Motlagh ND, Delgoshaie N, Fuchs J, Gut H, Gasser SM	The stabilized Pol31-Pol3 interface counteracts Pol32 ablation with differential effects on repair. Life Sci Alliance. 2021 Sep;4(9)
Giorgetti, L. Aug 21, 2021	Zhan Y, Giorgetti L, Tiana G	Polymer Folding Simulations from Hi-C Data. Methods Mol Biol. 2022;2301:259-265
Arber, S. Aug 19, 2021	Ferreira-Pinto MJ, Kanodia H, Falasconi A, Sigrist M, Esposito MS, Arber S	Functional diversity for body actions in the mesencephalic locomotor region. Cell. 2021 Aug 19;184(17):4564-4578.e18
Schuebeler, D.; Proteomics and protein analysis; Functional Genomics; Thoma, N. Aug 01, 2021	Grand RS, Burger L, Gräwe C, Michael AK, Isbel L, Hess D, Hoerner L, Iesmantavicius V, Durdu S, Pregnolato M, Krebs AR, Smallwood SA, Thomä N, Vermeulen M, Schübeler D	BANP opens chromatin and activates CpG-island-regulated genes. Nature. 2021 Aug;596(7870):133-137
Schuebeler, D.; Proteomics and protein analysis; Functional Genomics; Betschinger, J. Aug 01, 2021	Olivieri D, Paramanathan S, Bardet AF, Hess D, Smallwood SA, Elling U, Betschinger J	The BTB-domain transcription factor ZBTB2 recruits chromatin remodelers and a histone chaperone during the exit from pluripotency. J Biol Chem. 2021 Aug;297(2):100947
Proteomics and protein analysis; Facility for Advanced Imaging and Microscopy; Chao, J.; Structural Biology Jul 23, 2021	Nörpel J, Cavadini S, Schenk AD, Graff-Meyer A, Hess D, Seebacher J, Chao JA, Bhaskar V.	Structure of the human C9orf72-SMCR8 complex reveals a multivalent protein interaction architecture. PLoS Biol. 2021 Jul 23;19(7):e3001344
Facility for Advanced Imaging and Microscopy; Chao, J.; Giorgetti, L. Jul 21, 2021	Eichenberger BT, Zhan Y, Rempfler M, Giorgetti L, Chao JA	deepBlink: threshold-independent detection and localization of diffraction-limited spots. Nucleic Acids Res. 2021 Jul 21;49(13):7292-7297
Thoma, N. Jul 15, 2021	Kozicka Z, Thomä NH	Haven't got a glue: Protein surface variation for the design of molecular glue degraders. Cell Chem Biol. 2021 Jul 15;28(7):1032-1047
Friedrich, R. Jul 8, 2021	Friedrich RW, Wanner AA	Dense Circuit Reconstruction to Understand Neuronal Computation: Focus on Zebrafish. Annu Rev Neurosci. 2021 Jul 8;44:275-293
Matthias, P. Jul 8, 2021	Moreira EA, Yamauchi Y, Matthias P	How Influenza Virus Uses Host Cell Pathways during Uncoating. Cells. 2021 Jul 8;10(7)
Thoma, N. Jul 8, 2021	Michael AK, Thomä NH	Reading the chromatinized genome. Cell. 2021 Jul 8;184(14):3599-3611
Luethi, A. Jul 6, 2021	Whittle N, Fadok J, MacPherson KP, Nguyen R, Botta P, Wolff SBE, Müller C, Herry C, Tovote P, Holmes A, Singewald N, Lüthi A, Ciocchi S	Central amygdala micro-circuits mediate fear extinction. Nat Commun. 2021 Jul 6;12(1):4156
Facility for Advanced Imaging and Microscopy; Liberali, P. Jul 01, 2021	Yang Q, Xue SL, Chan CJ, Rempfler M, Vischi D, Maurer-Gutierrez F, Hiiragi T, Hannezo E, Liberali P	Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. Nat Cell Biol. 2021 Jul;23(7):733-744
Computational Biology; Buehler, M.; Structural Biology Jun 22, 2021	Shimada Y, Carl SH, Skribbe M, Flury V, Kuzdere T, Kempf G, Bühler M	An enhancer screen identifies new suppressors of small-RNA-mediated epigenetic gene silencing. PLoS Genet. 2021 Jun 22;17(6):e1009645
Proteomics and protein analysis; Grosshans, H.; Computational Biology Jun 3, 2021	Gudipati RK, Braun K, Gypas F, Hess D, Schreier J, Carl SH, Ketting RF, Großhans H	Protease-mediated processing of Argonaute proteins controls small RNA association. Mol Cell. 2021 Jun 3;81(11):2388-2402.e8
Bentires-Alj, M. Jun 2, 2021	Correia AL, Guimaraes JC, Auf der Maur P, De Silva D, Trefny MP, Okamoto R, Bruno S, Schmidt A, Mertz K, Volkmann K, Terracciano L, Zippelius A, Vetter M, Kurzeder C, Weber WP, Bentires-Alj M	Hepatic stellate cells suppress NK cell-sustained breast cancer dormancy. Nature. 2021 Jun;594(7864):566-571
Luethi, A. Jun 01, 2021	Hagihara KM, Bukalo O, Zeller M, Aksoy-Aksel A, Karalis N, Limoges A, Rigg T, Campbell T, Mendez A, Weinholtz C, Mahn M, Zweifel LS, Palmiter RD, Ehrlich I, Lüthi A, Holmes A	Intercalated amygdala clusters orchestrate a switch in fear state. Nature. 2021 Jun;594(7863):403-407
Matthias, P.; Cell sorting (FACS); Computational Biology May 27, 2021	Song S, Cao C, Choukrallah MA, Tang F, Christofori G, Kohler H, Wu F, Fodor BD, Frederiksen M, Willis SN, Jackson JT, Nutt SL, Dirnhofer S, Stadler MB, Matthias P	OBF1 and Oct factors control the germinal center transcriptional program. Blood. 2021 May 27;137(21):2920-2934
Luethi, A. May 19, 2021	Mahn M, Saraf-Sinik I, Patil P, Pulin M, Bitton E, Karalis N, Bruentgens F, Palgi S, Gat A, Dine J, Wietek J, Davidi I, Levy R, Litvin A, Zhou F, Sauter K, Soba P, Schmitz D, Lüthi A, Rost BR, Wiegert JS, Yizhar O	Efficient optogenetic silencing of neurotransmitter release with a mosquito rhodopsin. Neuron. 2021 May 19;109(10):1621-1635.e8
Grosshans, H.; Tsiairis, C. May 17, 2021	Tsiairis C, Großhans H	Gene expression oscillations in C. elegans underlie a new developmental clock. Curr Top Dev Biol. 2021;144:19-43
Gasser, S. May 01, 2021	Fuchs J, Cheblal A, Gasser SM	Underappreciated Roles of DNA Polymerase δ in Replication Stress Survival. Trends Genet. 2021 May;37(5):476-487
Peters, A.; Proteomics and protein analysis; Functional Genomics; Computational Biology; Betschinger, J. Apr 28, 2021	Olivieri D, Castelli E, Kawamura YK, Papasaikas P, Lukonin I, Rittirsch M, Hess D, Smallwood SA, Stadler MB, Peters AHFM, Betschinger J	Cooperation between HDAC3 and DAX1 mediates lineage restriction of embryonic stem cells. EMBO J. 2021 Apr 28;:e106818
Luethi, A. Apr 01, 2021	Fustiñana MS, Eichlisberger T, Bouwmeester T, Bitterman Y, Lüthi A	State-dependent encoding of exploratory behaviour in the amygdala. Nature. 2021 Apr;592(7853):267-271
Peters, A. Apr 01, 2021	Stäubli A, Peters AH	Mechanisms of maternal intergenerational epigenetic inheritance. Curr Opin Genet Dev. 2021 Apr;67:151-162
Facility for Advanced Imaging and Microscopy; Chao, J.; Structural Biology Apr 01, 2021	Bhaskar V, Desogus J, Graff-Meyer A, Schenk AD, Cavadini S, Chao JA	Dynamic association of human Ebp1 with the ribosome. RNA. 2021 Apr;27(4):411-419
Felsenberg, J. Apr 01, 2021	Felsenberg J	Changing memories on the fly: the neural circuits of memory re-evaluation in Drosophila melanogaster. Curr Opin Neurobiol. 2021 Apr;67:190-198
Zenke, F. Mar 26, 2021	Zenke F, Vogels TP	The Remarkable Robustness of Surrogate Gradient Learning for Instilling Complex Function in Spiking Neural Networks. Neural Comput. 2021 Mar 26;33(4):899-925
Computational Biology Mar 18, 2021	Hadziselimovic F, Verkauskas G, Stadler MB	Molecular clues in the regulation of mini-puberty involve neuronal DNA binding transcription factor NHLH2. Basic Clin Androl. 2021 Mar 18;31(1):6
Chao, J. Mar 16, 2021	Daniel Mateju Jeffrey A. Chao	Stress granules: Regulators or by-products? FASEB J, 16 March 2021
Chiquet-Ehrismann, R.; Histology/ Antibody/ FACS; Proteomics and protein analysis Mar 12, 2021	Hendaoui I, Lahmar A, Campo L, Mebarki S, Bichet S, Hess D, Degen M, Kchir N, Charrada-Ben Farhat L, Hefaiedh R, Ruiz C, Terracciano LM, Tucker RP, Hendaoui L, Chiquet-Ehrismann R	Tenascin-W Is a Novel Stromal Marker in Biliary Tract Cancers. Front Immunol. 2020;11:630139
Cell sorting (FACS); Computational Biology; Rijli, F. Mar 01, 2021	Kitazawa T, Machlab D, Joshi O, Maiorano N, Kohler H, Ducret S, Kessler S, Gezelius H, Soneson C, Papasaikas P, López-Bendito G, Stadler MB, Rijli FM	A unique bipartite Polycomb signature regulates stimulus-response transcription during development. Nat Genet. 2021 Mar;53(3):379-391
Schuebeler, D.; Computational Biology Mar 01, 2021	Iurlaro M, Stadler MB, Masoni F, Jagani Z, Galli GG, Schübeler D	Mammalian SWI/SNF continuously restores local accessibility to chromatin. Nat Genet. 2021 Mar;53(3):279-287
Gasser, S.; Proteomics and protein analysis Feb 18, 2021	Challa K, Schmid CD, Kitagawa S, Cheblal A, Iesmantavicius V, Seeber A, Amitai A, Seebacher J, Hauer MH, Shimada K, Gasser SM	Damage-induced chromatome dynamics link Ubiquitin ligase and proteasome recruitment to histone loss and efficient DNA repair. Mol Cell. 2021 Feb 18;81(4):811-829.e6
Zenke, F. Feb 17, 2021	Zenke F, Bohté SM, Clopath C, Comsa IM, Göltz J, Maass W, Masquelier T, Naud R, Neftci EO, Petrovici MA, Scherr F, Goodman DFM	Visualizing a joint future of neuroscience and neuromorphic engineering. Neuron. 2021 Feb 17;109(4):571-575
Arber, S. Feb 01, 2021	Ruder L, Schina R, Kanodia H, Valencia-Garcia S, Pivetta C, Arber S	A functional map for diverse forelimb actions within brainstem circuitry. Nature. 2021 Feb;590(7846):445-450
Computational Biology Jan 11, 2021	Soneson C, Srivastava A, Patro R, Stadler MB	Preprocessing choices affect RNA velocity results for droplet scRNA-seq data. PLoS Comput Biol. 2021 Jan 11;17(1):e1008585
Zenke, F. Jan 8, 2021	Friedemann Zenke, Emre O. Neftci	Brain-Inspired Learning on Neuromorphic Substrates. Proceedings of the IEEE, 8 Jan 2021
Gasser, S. Jan 7, 2021	Forey R, Barthe A, Tittel-Elmer M, Wery M, Barrault MB, Ducrot C, Seeber A, Krietenstein N, Szachnowski U, Skrzypczak M, Ginalski K, Rowicka M, Cobb JA, Rando OJ, Soutourina J, Werner M, Dubrana K, Gasser SM, Morillon A, Pasero P, Lengronne A, Poli J	A Role for the Mre11-Rad50-Xrs2 Complex in Gene Expression and Chromosome Organization. Mol Cell. 2021 Jan 7;81(1):183-197.e6
Gasser, S. Jan 01, 2021	Padeken J, Methot S, Zeller P, Delaney CE, Kalck V, Gasser SM	Argonaute NRDE-3 and MBT domain protein LIN-61 redundantly recruit an H3K9me3 HMT to prevent embryonic lethality and transposon expression. Genes Dev. 2021 Jan 1;35(1-2):82-101
Facility for Advanced Imaging and Microscopy; Chao, J.; Giorgetti, L. Dec 23, 2020	Mateju D, Eichenberger B, Voigt F, Eglinger J, Roth G, Chao JA	Single-Molecule Imaging Reveals Translation of mRNAs Localized to Stress Granules Cell. 2020 Dec 23;183(7):1801-1812.e13
Keller, G. Dec 23, 2020	Jordan R, Keller GB	Opposing Influence of Top-down and Bottom-up Input on Excitatory Layer 2/3 Neurons in Mouse Primary Visual Cortex. Neuron. 2020 Dec 23;108(6):1194-1206.e5
Facility for Advanced Imaging and Microscopy; Liberali, P. Dec 01, 2020	Zinner M, Lukonin I, Liberali P	Design principles of tissue organisation: How single cells coordinate across scales. Curr Opin Cell Biol. 2020 Dec;67:37-45
Chao, J. Dec 01, 2020	Dave P, Chao JA	Insights into mRNA degradation from single-molecule imaging in living cells. Curr Opin Struct Biol. 2020 Dec;65:89-95
Matthias, P.; Proteomics and protein analysis Nov 18, 2020	Saito M, Iestamantavicius V, Hess D, Matthias P	Monitoring Acetylation of the RNA Helicase DDX3X, a Protein Critical for Formation of Stress Granules. Methods Mol Biol. 2021;2209:217-234
Thoma, N.; Structural Biology Nov 01, 2020	Pathare GR, Decout A, Glück S, Cavadini S, Makasheva K, Hovius R, Kempf G, Weiss J, Kozicka Z, Guey B, Melenec P, Fierz B, Thomä NH, Ablasser A	Structural mechanism of cGAS inhibition by the nucleosome Nature. 2020 Nov;587(7835):668-672
Gasser, S. Oct 15, 2020	Cheblal A, Challa K, Seeber A, Shimada K, Yoshida H, Ferreira HC, Amitai A, Gasser SM	DNA Damage-Induced Nucleosome Depletion Enhances Homology Search Independently of Local Break Movement Mol Cell. 2020 Oct 15;80(2):311-326.e4
Facility for Advanced Imaging and Microscopy; Computational Biology; Liberali, P. Oct 7, 2020	Lukonin I, Serra D, Challet Meylan L, Volkmann K, Baaten J, Zhao R, Meeusen S, Colman K, Maurer F, Stadler MB, Jenkins J, Liberali P	Phenotypic landscape of intestinal organoid regeneration Nature. 2020 Oct;586(7828):275-280
Computational Biology Sep 26, 2020	Soneson C, Marini F, Geier F, Love MI, Stadler MB	ExploreModelMatrix: Interactive exploration for improved understanding of design matrices and linear models in R. F1000Res. 2020;9:512
Roska, B.; Computational Biology Sep 17, 2020	Cowan CS, Renner M, De Gennaro M, Gross-Scherf B, Goldblum D, Hou Y, Munz M, Rodrigues TM, Krol J, Szikra T, Cuttat R, Waldt A, Papasaikas P, Diggelmann R, Patino-Alvarez CP, Galliker P, Spirig SE, Pavlinic D, Gerber-Hollbach N, Schuierer S, Srdanovic A, Balogh M, Panero R, Kusnyerik A, Szabo A, Stadler MB, Orgül S, Picelli S, Hasler PW, Hierlemann A, Scholl HPN, Roma G, Nigsch F, Roska B	Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution Cell. 2020 Sep 17;182(6):1623-1640.e34
Thoma, N. Aug 01, 2020	Kassube SA, Thomä NH	Structural insights into Fe-S protein biogenesis by the CIA targeting complex. Nat Struct Mol Biol. 2020 Aug;27(8):735-742
Gasser, S.; Rass, U.; Diss, G. Jul 27, 2020	Falquet B, Ölmezer G, Enkner F, Klein D, Challa K, Appanah R, Gasser SM, Rass U	Disease-associated DNA2 nuclease-helicase protects cells from lethal chromosome under-replication Nucleic Acids Res. 2020 Jul 27;48(13):7265-7278
Zenke, F. Jul 20, 2020	Tianlin Liu, Friedemann Zenke	Finding trainable sparse networks through Neural Tangent Transfer International Conference on Machine Learning
Facility for Advanced Imaging and Microscopy; Grosshans, H.; Tsiairis, C. Jul 01, 2020	Meeuse MW, Hauser YP, Morales Moya LJ, Hendriks GJ, Eglinger J, Bogaarts G, Tsiairis C, Großhans H	Developmental function and state transitions of a gene expression oscillator in Caenorhabditis elegans Mol Syst Biol. 2020 Jul;16(7):e9498
Peters, A.; Facility for Advanced Imaging and Microscopy Jul 01, 2020	Liu Z, Tardat M, Gill ME, Royo H, Thierry R, Ozonov EA, Peters AH	SUMOylated PRC1 controls histone H3.3 deposition and genome integrity of embryonic heterochromatin EMBO J. 2020 Jul 1;39(13):e103697
Schuebeler, D.; Facility for Advanced Imaging and Microscopy; Thoma, N.; Structural Biology Jun 26, 2020	Michael AK, Grand RS, Isbel L, Cavadini S, Kozicka Z, Kempf G, Bunker RD, Schenk AD, Graff-Meyer A, Pathare GR, Weiss J, Matsumoto S, Burger L, Schübeler D, Thomä NH	Mechanisms of OCT4-SOX2 motif readout on nucleosomes Science. 2020 Jun 26;368(6498):1460-1465
Computational Biology; Buehler, M. Jun 23, 2020	Carl SH, Duempelmann L, Shimada Y, Bühler M	A fully automated deep learning pipeline for high-throughput colony segmentation and classification Biol Open. 2020 Jun 23;9(6)
Arber, S.; Cell sorting (FACS); Rijli, F. Jun 16, 2020	Maheshwari U, Kraus D, Vilain N, Holwerda SJB, Cankovic V, Maiorano NA, Kohler H, Satoh D, Sigrist M, Arber S, Kratochwil CF, Di Meglio T, Ducret S, Rijli FM	Postmitotic Hoxa5 Expression Specifies Pontine Neuron Positional Identity and Input Connectivity of Cortical Afferent Subsets Cell Rep. 2020 Jun 16;31(11):107767
Roska, B. Jun 5, 2020	Nelidova D, Morikawa RK, Cowan CS, Raics Z, Goldblum D, Scholl HPN, Szikra T, Szabo A, Hillier D, Roska B	Restoring light sensitivity using tunable near-infrared sensors Science. 2020 Jun 5;368(6495):1108-1113
Schuebeler, D.; Peters, A.; Functional Genomics; Computational Biology May 29, 2020	Ginno PA, Gaidatzis D, Feldmann A, Hoerner L, Imanci D, Burger L, Zilbermann F, Peters AHFM, Edenhofer F, Smallwood SA, Krebs AR, Schübeler D	A genome-scale map of DNA methylation turnover identifies site-specific dependencies of DNMT and TET activity Nat Commun. 2020 May 29;11(1):2680
Thoma, N.; Structural Biology May 26, 2020	Schenk AD, Cavadini S, Thomä NH, Genoud C	Live Analysis and Reconstruction of Single-Particle Cryo-Electron Microscopy Data with CryoFLARE J Chem Inf Model. 2020 May 26;60(5):2561-2569
Gasser, S.; Grosshans, H.; Computational Biology May 01, 2020	Mattout A, Gaidatzis D, Padeken J, Schmid CD, Aeschimann F, Kalck V, Gasser SM	LSM2-8 and XRN-2 contribute to the silencing of H3K27me3-marked genes through targeted RNA decay Nat Cell Biol. 2020 May;22(5):579-590
Gasser, S.; Computational Biology Apr 29, 2020	Mattout A, Gaidatzis D, Kalck V, Gasser SM	A Nuclear RNA Degradation Pathway Helps Silence Polycomb/H3K27me3-Marked Loci in Caenorhabditis elegans. Cold Spring Harb Symp Quant Biol. 2020 Apr 29
Facility for Advanced Imaging and Microscopy; Computational Biology; Chao, J.; Structural Biology Apr 7, 2020	Bhaskar V, Graff-Meyer A, Schenk AD, Cavadini S, von Loeffelholz O, Natchiar SK, Artus-Revel CG, Hotz HR, Bretones G, Klaholz BP, Chao JA	Dynamics of uS19 C-Terminal Tail during the Translation Elongation Cycle in Human Ribosomes Cell Rep. 2020 Apr 7;31(1):107473