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.

Groups & Date Authors Title & Journal
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

Proteomics and protein analysis; Buehler, M.; Structural Biology
Jul 3, 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 3

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

Liberali, P.
Jun 13, 2024
Liberali P, Schier AF

The evolution of developmental biology through conceptual and technological revolutions.
Cell. 2024 Jun 13

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

Keller, G.
May 20, 2024
Sterzer P, Keller GB

Predictive processing: Layer-specific prediction error signals in human cortex.
Curr Biol. 2024 May 20;34(10):R496-R498

Friedrich, R.; Zenke, F.
May 10, 2024
Claire Meissner-Bernard, Friedemann Zenke, Rainer W. Friedrich

Geometry and dynamics of representations in a precisely balanced memory network related to olfactory cortex
Elife. 2024 May 10;13

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 multisample dual-view light-sheet microscope for live imaging of large multicellular systems.
Nat Methods. 2024 May;21(5):798-803

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

Keller, G.
Feb 29, 2024
Keller GB, Sterzer P

Predictive Processing: A Circuit Approach to Psychosis.
Annu Rev Neurosci. 2024 Feb 29

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

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

Matthias, P.
Jan 8, 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 Jan 8;:105638

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

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

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

Schuebeler, D.; Buehler, M.
May 30, 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 May 30;42(6):112569

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 &delta; 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&nbsp;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

Gasser, S.
Apr 01, 2020
Harr JC, Schmid CD, Muñoz-Jiménez C, Romero-Bueno R, Kalck V, Gonzalez-Sandoval A, Hauer MH, Padeken J, Askjaer P, Mattout A, Gasser SM

Loss of an H3K9me anchor rescues laminopathy-linked changes in nuclear organization and muscle function in an Emery-Dreifuss muscular dystrophy model
Genes Dev. 2020 Apr 1;34(7-8):560-579

Grosshans, H.
Mar 30, 2020
Azzi C, Aeschimann F, Neagu A, Großhans H

A branched heterochronic pathway directs juvenile-to-adult transition through two LIN-29 isoforms
Elife. 2020 Mar 30;9

Proteomics and protein analysis; Buehler, M.
Mar 19, 2020
Tuck AC, Rankova A, Arpat AB, Liechti LA, Hess D, Iesmantavicius V, Castelo-Szekely V, Gatfield D, Bühler M

Mammalian RNA Decay Pathways Are Highly Specialized and Widely Linked to Translation
Mol Cell. 2020 Mar 19;77(6):1222-1236.e13

Friedrich, R.
Mar 2, 2020
Huang KH, Rupprecht P, Frank T, Kawakami K, Bouwmeester T, Friedrich RW

A virtual reality system to analyze neural activity and behavior in adult zebrafish.
Nat Methods. 2020 Mar;17(3):343-351

Friedrich, R.
Mar 01, 2020
Wanner AA, Friedrich RW

Whitening of odor representations by the wiring diagram of the olfactory bulb
Nat Neurosci. 2020 Mar;23(3):433-442

Buehler, M.
Mar 01, 2020
Duempelmann L, Skribbe M, Bühler M

Small RNAs in the Transgenerational Inheritance of Epigenetic Information
Trends Genet. 2020 Mar;36(3):203-214

Giorgetti, L.
Feb 20, 2020
McCord RP, Kaplan N, Giorgetti L

Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function
Mol Cell. 2020 Feb 20;77(4):688-708

Proteomics and protein analysis; Facility for Advanced Imaging and Microscopy; Computational Biology; Betschinger, J.
Jan 15, 2020
Mayer D, Stadler MB, Rittirsch M, Hess D, Lukonin I, Winzi M, Smith A, Buchholz F, Betschinger J

Zfp281 orchestrates interconversion of pluripotent states by engaging Ehmt1 and Zic2
EMBO J. 2020 Jan 15;39(2):e102591

Computational Biology
Jan 01, 2020
Hadziselimovic F, Verkauskas G, Vincel B, Stadler MB

Testicular expression of long non-coding RNAs is affected by curative GnRHa treatment of cryptorchidism
Basic Clin Androl. 2019;29:18

Bleichert, F.
Dec 01, 2019
Bleichert F

Mechanisms of replication origin licensing: a structural perspective
Curr Opin Struct Biol. 2019 Dec;59:195-204

Zenke, F.
Nov 01, 2019
Neftci Emre O, Mostafa Hesham, Zenke Friedemann

Surrogate Gradient Learning in Spiking Neural Networks: Bringing the Power of Gradient-based optimization to spiking neural networks
IEEE Signal Processing Magazine (Volume: 36 , Issue: 6 , Nov. 2019)

Tsiairis, C.
Nov 01, 2019
Vogg MC, Galliot B, Tsiairis CD

Model systems for regeneration: Hydra
Development. 2019 Nov 1;146(21)

Luethi, A.
Nov 01, 2019
Krabbe S, Paradiso E, d'Aquin S, Bitterman Y, Courtin J, Xu C, Yonehara K, Markovic M, Müller C, Eichlisberger T, Gründemann J, Ferraguti F, Lüthi A

Adaptive disinhibitory gating by VIP interneurons permits associative learning.
Nat Neurosci. 2019 Nov;22(11):1834-1843

Friedrich, R.
Nov 01, 2019
Frank T, Mönig NR, Satou C, Higashijima SI, Friedrich RW

Associative conditioning remaps odor representations and modifies inhibition in a higher olfactory brain area
Nat Neurosci. 2019 Nov;22(11):1844-1856

Gasser, S.; Proteomics and protein analysis; Protein structure
Oct 15, 2019
Deshpande I, Keusch JJ, Challa K, Iesmantavicius V, Gasser SM, Gut H

The Sir4 H-BRCT domain interacts with phospho-proteins to sequester and repress yeast heterochromatin
EMBO J. 2019 Oct 15;38(20):e101744

Rijli, F.
Sep 26, 2019
Kratochwil CF, Rijli FM

The Cre/Lox System to Assess the Development of the Mouse Brain.
Methods Mol Biol. 2020;2047:491-512

Bleichert, F.
Sep 12, 2019
Ekundayo B, Bleichert F

Origins of DNA replication
PLoS Genet. 2019 Sep;15(9):e1008320

Buehler, M.
Sep 5, 2019
Kaaij LJT, Mohn F, van der Weide RH, de Wit E, Bühler M

The ChAHP Complex Counteracts Chromatin Looping at CTCF Sites that Emerged from SINE Expansions in Mouse.
Cell. 2019 Sep 5;178(6):1437-1451.e14

Caroni, P.
Sep 5, 2019
Mukherjee A, Carvalho F, Eliez S, Caroni P

Long-Lasting Rescue of Network and Cognitive Dysfunction in a Genetic Schizophrenia Model
Cell. 2019 Sep 5;178(6):1387-1402.e14

Grosshans, H.; Computational Biology; Buehler, M.
Sep 01, 2019
Welte T, Tuck AC, Papasaikas P, Carl SH, Flemr M, Knuckles P, Rankova A, Bühler M, Großhans H

The RNA hairpin binder TRIM71 modulates alternative splicing by repressing MBNL1
Genes Dev. 2019 Sep 1;33(17-18):1221-1235

Chiquet-Ehrismann, R.
Aug 30, 2019
Schnellmann R, Chiquet-Ehrismann R

Preparation and Application of a Decellularized Extracellular Matrix for Identification of ADAMTS Substrates.
Methods Mol Biol. 2020;2043:275-284

Facility for Advanced Imaging and Microscopy; Chao, J.
Aug 14, 2019
Voigt F, Eglinger J, Chao JA

Quantification of mRNA Turnover in Living Cells: A Pipeline for TREAT Data Analysis.
Methods Mol Biol. 2019;2038:75-88

Giorgetti, L.
Aug 10, 2019
Tiana G, Giorgetti L

Coarse Graining of a Giant Molecular System: The Chromatin Fiber.
Methods Mol Biol. 2019;2022:399-411

Peters, A.; Facility for Advanced Imaging and Microscopy; Thoma, N.; Structural Biology
Aug 8, 2019
Rabl J, Bunker RD, Schenk AD, Cavadini S, Gill ME, Abdulrahman W, Andrés-Pons A, Luijsterburg MS, Ibrahim AFM, Branigan E, Aguirre JD, Marceau AH, Guérillon C, Bouwmeester T, Hassiepen U, Peters AHFM, Renatus M, Gelman L, Rubin SM, Mailand N, van Attikum H, Hay RT, Thomä NH

Structural Basis of BRCC36 Function in DNA Repair and Immune Regulation
Mol Cell. 2019 Aug 8;75(3):483-497.e9