Sinz, Fabian H.

[["dc.bibliographiccitation.firstpage","2715"],["dc.bibliographiccitation.issue","11"],["dc.bibliographiccitation.journal","The Plant Cell"],["dc.bibliographiccitation.lastpage","2734"],["dc.bibliographiccitation.volume","28"],["dc.contributor.author","Hartmann, Lisa"],["dc.contributor.author","Drewe-Boß, Philipp"],["dc.contributor.author","Wießner, Theresa"],["dc.contributor.author","Wagner, Gabriele"],["dc.contributor.author","Geue, Sascha"],["dc.contributor.author","Lee, Hsin-Chieh"],["dc.contributor.author","Obermüller, Dominik M."],["dc.contributor.author","Kahles, André"],["dc.contributor.author","Behr, Jonas"],["dc.contributor.author","Sinz, Fabian H."],["dc.contributor.author","Rätsch, Gunnar"],["dc.contributor.author","Wachter, Andreas"],["dc.date.accessioned","2021-04-28T06:40:31Z"],["dc.date.available","2021-04-28T06:40:31Z"],["dc.date.issued","2016"],["dc.description.abstract","Plants use light as source of energy and information to detect diurnal rhythms and seasonal changes. Sensing changing light conditions is critical to adjust plant metabolism and to initiate developmental transitions. Here, we analyzed transcriptome-wide alterations in gene expression and alternative splicing (AS) of etiolated seedlings undergoing photomorphogenesis upon exposure to blue, red, or white light. Our analysis revealed massive transcriptome reprogramming as reflected by differential expression of ∼20% of all genes and changes in several hundred AS events. For more than 60% of all regulated AS events, light promoted the production of a presumably protein-coding variant at the expense of an mRNA with nonsense-mediated decay-triggering features. Accordingly, AS of the putative splicing factor REDUCED RED-LIGHT RESPONSES IN CRY1CRY2 BACKGROUND1, previously identified as a red light signaling component, was shifted to the functional variant under light. Downstream analyses of candidate AS events pointed at a role of photoreceptor signaling only in monochromatic but not in white light. Furthermore, we demonstrated similar AS changes upon light exposure and exogenous sugar supply, with a critical involvement of kinase signaling. We propose that AS is an integration point of signaling pathways that sense and transmit information regarding the energy availability in plants."],["dc.identifier.doi","10.1105/tpc.16.00508"],["dc.identifier.pmid","27803310"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/84516"],["dc.language.iso","en"],["dc.relation.eissn","1532-298X"],["dc.relation.issn","1040-4651"],["dc.title","Alternative Splicing Substantially Diversifies the Transcriptome during Early Photomorphogenesis and Correlates with the Energy Availability in Arabidopsis"],["dc.type","journal_article"],["dc.type.internalPublication","no"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.journal","eLife"],["dc.bibliographiccitation.volume","9"],["dc.contributor.author","Cadwell, Cathryn R."],["dc.contributor.author","Scala, Federico"],["dc.contributor.author","Fahey, Paul G."],["dc.contributor.author","Kobak, Dmitry"],["dc.contributor.author","Mulherkar, Shalaka"],["dc.contributor.author","Sinz, Fabian H."],["dc.contributor.author","Papadopoulos, Stelios"],["dc.contributor.author","Tan, Zheng H."],["dc.contributor.author","Johnsson, Per"],["dc.contributor.author","Hartmanis, Leonard"],["dc.contributor.author","Li, Shuang"],["dc.contributor.author","Cotton, Ronald J."],["dc.contributor.author","Tolias, Kimberley F."],["dc.contributor.author","Sandberg, Rickard"],["dc.contributor.author","Berens, Philipp"],["dc.contributor.author","Jiang, Xiaolong"],["dc.contributor.author","Tolias, Andreas Savas"],["dc.date.accessioned","2021-04-28T06:11:24Z"],["dc.date.available","2021-04-28T06:11:24Z"],["dc.date.issued","2020"],["dc.description.abstract","Clones of excitatory neurons derived from a common progenitor have been proposed to serve as elementary information processing modules in the neocortex. To characterize the cell types and circuit diagram of clonally related excitatory neurons, we performed multi-cell patch clamp recordings and Patch-seq on neurons derived from Nestin-positive progenitors labeled by tamoxifen induction at embryonic day 10.5. The resulting clones are derived from two radial glia on average, span cortical layers 2-6, and are composed of a random sampling of transcriptomic cell types. We find an interaction between shared lineage and connection type: related neurons are more likely to be connected vertically across cortical layers, but not laterally within the same layer. These findings challenge the view that related neurons show uniformly increased connectivity and suggest that integration of vertical intra-clonal input with lateral inter-clonal input may represent a developmentally programmed connectivity motif supporting the emergence of functional circuits."],["dc.identifier.doi","10.7554/eLife.52951"],["dc.identifier.pmid","32134385"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/84513"],["dc.language.iso","en"],["dc.relation.issn","2050-084X"],["dc.title","Cell type composition and circuit organization of clonally related excitatory neurons in the juvenile mouse neocortex"],["dc.type","journal_article"],["dc.type.internalPublication","no"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","2060"],["dc.bibliographiccitation.issue","12"],["dc.bibliographiccitation.journal","Nature Neuroscience"],["dc.bibliographiccitation.lastpage","2065"],["dc.bibliographiccitation.volume","22"],["dc.contributor.author","Walker, Edgar Y."],["dc.contributor.author","Sinz, Fabian H."],["dc.contributor.author","Cobos, Erick"],["dc.contributor.author","Muhammad, Taliah"],["dc.contributor.author","Froudarakis, Emmanouil"],["dc.contributor.author","Fahey, Paul G."],["dc.contributor.author","Ecker, Alexander S."],["dc.contributor.author","Reimer, Jacob"],["dc.contributor.author","Pitkow, Xaq"],["dc.contributor.author","Tolias, Andreas S."],["dc.date.accessioned","2020-03-18T10:48:38Z"],["dc.date.available","2020-03-18T10:48:38Z"],["dc.date.issued","2019"],["dc.description.abstract","Finding sensory stimuli that drive neurons optimally is central to understanding information processing in the brain. However, optimizing sensory input is difficult due to the predominantly nonlinear nature of sensory processing and high dimensionality of the input. We developed 'inception loops', a closed-loop experimental paradigm combining in vivo recordings from thousands of neurons with in silico nonlinear response modeling. Our end-to-end trained, deep-learning-based model predicted thousands of neuronal responses to arbitrary, new natural input with high accuracy and was used to synthesize optimal stimuli-most exciting inputs (MEIs). For mouse primary visual cortex (V1), MEIs exhibited complex spatial features that occurred frequently in natural scenes but deviated strikingly from the common notion that Gabor-like stimuli are optimal for V1. When presented back to the same neurons in vivo, MEIs drove responses significantly better than control stimuli. Inception loops represent a widely applicable technique for dissecting the neural mechanisms of sensation."],["dc.identifier.doi","10.1038/s41593-019-0517-x"],["dc.identifier.pmid","31686023"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/63343"],["dc.language.iso","en"],["dc.relation.eissn","1546-1726"],["dc.relation.issn","1097-6256"],["dc.relation.issn","1546-1726"],["dc.title","Inception loops discover what excites neurons most using deep predictive models"],["dc.type","journal_article"],["dc.type.internalPublication","no"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","413"],["dc.bibliographiccitation.journal","Advances in Neural Information Processing Systems"],["dc.bibliographiccitation.lastpage","421"],["dc.bibliographiccitation.volume","26"],["dc.contributor.author","Sinz, Fabian H."],["dc.contributor.author","Stöckl, A."],["dc.contributor.author","Grewe, J."],["dc.contributor.author","Benda, J."],["dc.date.accessioned","2021-04-28T11:33:11Z"],["dc.date.available","2021-04-28T11:33:11Z"],["dc.date.issued","2013"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/84538"],["dc.title","Least Informative Dimensions"],["dc.type","journal_article"],["dc.type.internalPublication","no"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","3409"],["dc.bibliographiccitation.journal","Journal of Machine Learning Research"],["dc.bibliographiccitation.lastpage","3451"],["dc.bibliographiccitation.volume","11"],["dc.contributor.author","Sinz, Fabian"],["dc.contributor.author","Bethge, M."],["dc.date.accessioned","2021-04-28T07:02:44Z"],["dc.date.available","2021-04-28T07:02:44Z"],["dc.date.issued","2010"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/84535"],["dc.relatedmaterial.material","https://sinzlab.org/errata/2019-12-20-lpnestederrata.html"],["dc.title","Lp-nested symmetric distributions"],["dc.type","journal_article"],["dc.type.internalPublication","no"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","aac9462"],["dc.bibliographiccitation.issue","6264"],["dc.bibliographiccitation.journal","Science"],["dc.bibliographiccitation.volume","350"],["dc.contributor.author","Jiang, Xiaolong"],["dc.contributor.author","Shen, Shan"],["dc.contributor.author","Cadwell, Cathryn R."],["dc.contributor.author","Berens, Philipp"],["dc.contributor.author","Sinz, Fabian"],["dc.contributor.author","Ecker, Alexander S."],["dc.contributor.author","Patel, Saumil"],["dc.contributor.author","Tolias, Andreas S."],["dc.date.accessioned","2020-04-01T11:50:43Z"],["dc.date.available","2020-04-01T11:50:43Z"],["dc.date.issued","2015"],["dc.description.abstract","Since the work of Ramón y Cajal in the late 19th and early 20th centuries, neuroscientists have speculated that a complete understanding of neuronal cell types and their connections is key to explaining complex brain functions. However, a complete census of the constituent cell types and their wiring diagram in mature neocortex remains elusive. By combining octuple whole-cell recordings with an optimized avidin-biotin-peroxidase staining technique, we carried out a morphological and electrophysiological census of neuronal types in layers 1, 2/3, and 5 of mature neocortex and mapped the connectivity between more than 11,000 pairs of identified neurons. We categorized 15 types of interneurons, and each exhibited a characteristic pattern of connectivity with other interneuron types and pyramidal cells. The essential connectivity structure of the neocortical microcircuit could be captured by only a few connectivity motifs."],["dc.identifier.doi","10.1126/science.aac9462"],["dc.identifier.pmid","26612957"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/63434"],["dc.language.iso","en"],["dc.relation.eissn","1095-9203"],["dc.relation.issn","0036-8075"],["dc.title","Principles of connectivity among morphologically defined cell types in adult neocortex"],["dc.type","journal_article"],["dc.type.internalPublication","no"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","e1002889"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","PLoS Computational Biology"],["dc.bibliographiccitation.volume","9"],["dc.contributor.author","Sinz, Fabian"],["dc.contributor.author","Bethge, Matthias"],["dc.date.accessioned","2021-04-28T06:40:44Z"],["dc.date.available","2021-04-28T06:40:44Z"],["dc.date.issued","2013"],["dc.description.abstract","Divisive normalization in primary visual cortex has been linked to adaptation to natural image statistics in accordance to Barlow's redundancy reduction hypothesis. Using recent advances in natural image modeling, we show that the previously studied static model of divisive normalization is rather inefficient in reducing local contrast correlations, but that a simple temporal contrast adaptation mechanism of the half-saturation constant can substantially increase its efficiency. Our findings reveal the experimentally observed temporal dynamics of divisive normalization to be critical for redundancy reduction."],["dc.identifier.doi","10.1371/journal.pcbi.1002889"],["dc.identifier.pmid","23382664"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/84519"],["dc.language.iso","en"],["dc.relation.eissn","1553-7358"],["dc.title","Temporal adaptation enhances efficient contrast gain control on natural images"],["dc.type","journal_article"],["dc.type.internalPublication","no"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.contributor.author","Cadwell, C. R."],["dc.contributor.author","Jiang, X."],["dc.contributor.author","Sinz, F. H."],["dc.contributor.author","Berens, P."],["dc.contributor.author","Fahey, P. G."],["dc.contributor.author","Yatsenko, D."],["dc.contributor.author","Froudarakis, E."],["dc.contributor.author","Ecker, A. S."],["dc.contributor.author","Cotton, R. J."],["dc.contributor.author","Tolias, A. S."],["dc.date.accessioned","2020-04-02T13:43:07Z"],["dc.date.available","2020-04-02T13:43:07Z"],["dc.date.issued","2016"],["dc.description.abstract","The neocortex carries out complex mental processes such as perception and cognition through the interactions of billions of neurons connected by trillions of synapses. Recent studies suggest that excitatory cortical neurons with a shared developmental lineage are more likely to be synaptically connected to each other than to nearby, unrelated neurons [1, 2]. However, the precise wiring diagram between clonally related neurons is unknown, and the impact of cell lineage on neural computation remains controversial. Here we show that vertical connections linking neurons across cortical layers are specifically enhanced between clonally related neurons (Fig. 1). In contrast, lateral connections within a cortical layer preferentially occur between unrelated neurons (Fig. 1). Importantly, we observed these connection biases for distantly related cousin cells, suggesting that cell lineage influences a larger fraction of connections than previously thought. A simple quantitative model of cortical connectivity based on our empirically measured connection probabilities reveals that both increased vertical connectivity and decreased lateral connectivity between cousins promote the convergence of shared input onto clonally related neurons, providing a novel circuit-level mechanism by which clonal units form functional cell assemblies with similar tuning properties [3, 4]. Taken together, our data suggest that the integration of feedforward, intra-columnar input with lateral, inter-columnar information may represent a fundamental principle of cortical computation that is established, at least initially, by developmental programs."],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/63538"],["dc.language.iso","en"],["dc.notes.preprint","yes"],["dc.relation.conference","AREADNE 2016: Research in Encoding And Decoding of Neural Ensembles"],["dc.relation.eventend","2016-06-26"],["dc.relation.eventlocation","Santorini, Greece"],["dc.relation.eventstart","2016-06-22"],["dc.relation.iserratumof","yes"],["dc.title","Cell Lineage Directs teh Precise Assembly of Excitatory Neocortical Circuits"],["dc.type","conference_paper"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","2809"],["dc.bibliographiccitation.issue","11"],["dc.bibliographiccitation.journal","Neural Computation"],["dc.bibliographiccitation.lastpage","2814"],["dc.bibliographiccitation.volume","25"],["dc.contributor.author","Sinz, Fabian H."],["dc.contributor.author","Bethge, Matthias"],["dc.date.accessioned","2021-04-28T06:40:39Z"],["dc.date.available","2021-04-28T06:40:39Z"],["dc.date.issued","2013-11"],["dc.description.abstract","Divisive normalization has been proposed as a nonlinear redundancy reduction mechanism capturing contrast correlations. Its basic function is a radial rescaling of the population response. Because of the saturation of divisive normalization, however, it is impossible to achieve a fully independent representation. In this letter, we derive an analytical upper bound on the inevitable residual redundancy of any saturating radial rescaling mechanism."],["dc.identifier.doi","10.1162/NECO_a_00505"],["dc.identifier.pmid","23895047"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/84518"],["dc.language.iso","en"],["dc.relation.eissn","1530-888X"],["dc.relation.issn","0899-7667"],["dc.title","What is the limit of redundancy reduction with divisive normalization?"],["dc.type","journal_article"],["dc.type.internalPublication","no"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.contributor.author","Fahey, Paul G."],["dc.contributor.author","Muhammad, Taliah"],["dc.contributor.author","Smith, Cameron"],["dc.contributor.author","Froudarakis, Emmanouil"],["dc.contributor.author","Cobos, Erick"],["dc.contributor.author","Fu, Jiakun"],["dc.contributor.author","Walker, Edgar Y."],["dc.contributor.author","Yatsenko, Dimitri"],["dc.contributor.author","Sinz, Fabian H."],["dc.contributor.author","Reimer, Jacob"],["dc.contributor.author","Tolias, Andreas S."],["dc.date.accessioned","2021-04-28T06:41:08Z"],["dc.date.available","2021-04-28T06:41:08Z"],["dc.date.issued","2019"],["dc.identifier.doi","10.1101/745323"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/84523"],["dc.title","A global map of orientation tuning in mouse visual cortex"],["dc.type","preprint"],["dc.type.internalPublication","no"],["dspace.entity.type","Publication"]]