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Th17 cell plasticity towards a T-bet-dependent Th1 phenotype is required for bacterial control in Staphylococcus aureus infection
Bartsch P, Kilian C, Hellmig M, Paust H, Borchers A, Sivayoganathan A, Enk L, Zhao Y, Shaikh N, Büttner H, Wong M, Puelles V, Wiech T, Flavell R, Huber T, Turner J, Bonn S, Huber S, Gagliani N, Mittrücker H, Rohde H, Panzer U, Krebs C
PLOS PATHOG. 2022;18(4):e1010430.

Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice
Schepanski S, Chini M, Sternemann V, Urbschat C, Thiele K, Sun T, Zhao Y, Poburski M, Woestemeier A, Thieme M, Zazara D, Alawi M, Fischer N, Heeren J, Vladimirov N, Woehler A, Puelles V, Bonn S, Gagliani N, Hanganu-Opatz I, Arck P
NAT COMMUN. 2022;13(1):.

Neuronal cholesterol synthesis is essential for repair of chronically demyelinated lesions in mice
Berghoff S, Spieth L, Sun T, Hosang L, Depp C, Sasmita A, Vasileva M, Scholz P, Zhao Y, Krueger-Burg D, Wichert S, Brown E, Michail K, Nave K, Bonn S, Odoardi F, Rossner M, Ischebeck T, Edgar J, Saher G
CELL REP. 2021;37(4):.

Hippocampal neurons respond to brain activity with functional hypoxia
Butt U, Steixner-Kumar A, Depp C, Sun T, Hassouna I, Wüstefeld L, Arinrad S, Zillmann M, Schopf N, Fernandez Garcia-Agudo L, Mohrmann L, Bode U, Ronnenberg A, Hindermann M, Goebbels S, Bonn S, Katschinski D, Miskowiak K, Nave K, Ehrenreich H
MOL PSYCHIATR. 2021;26(6):1790-1807.

Towards Explainable End-to-End Prostate Cancer Relapse Prediction from H&E Images Combining Self-Attention Multiple Instance Learning with a Recurrent Neural Network
Dietrich E, Fuhlert P, Ernst A, Sauter G, Lennartz E, Stiehl S, Zimmermann M, Bonn S
2021. Machine Learning for Health (ML4H) 2021. Cornell University, 38-53.

DeepGRP: engineering a software tool for predicting genomic repetitive elements using Recurrent Neural Networks with attention
Hausmann F, Kurtz S
ALGORITHM MOL BIOL. 2021;16(1):20.

Altered gut microbial metabolism of essential nutrients in primary sclerosing cholangitis
Kummen M, Thingholm L, Rühlemann M, Holm K, Hansen S, Moitinho-Silva L, Liwinski T, Zenouzi R, Storm-Larsen C, Midttun Ø, McCann A, Ueland P, Høivik M, Vesterhus M, Trøseid M, Laudes M, Lieb W, Karlsen T, Bang C, Schramm C, Franke A, Hov J
GASTROENTEROLOGY. 2021;160(5):1784-1798.e0.

Histological activity despite normal ALT and IgG serum levels in patients with autoimmune hepatitis and cirrhosis
Laschtowitz A, Zachou K, Lygoura V, Pape S, Derben F, Jaeckel E, Oller-Moreno S, Weidemann S, Krech T, Piecha F, Schön G, Liebhoff A, Al Tarrah M, Heneghan M, Drenth J, Dalekos G, Taubert R, Lohse A, Schramm C
JHEP REP. 2021;3(4):100321.

Interactive gene networks with KNIT
Magruder D, Liebhoff A, Bethune J, Bonn S
BIOINFORMATICS. 2021;37(2):276-278.

Algorithmic advances in machine learning for single-cell expression analysis
Oller S, Kloiber K, Machart P, Bonn S
Current Opinion in Systems Biology. 2021;2021(25):27-33.

Protein phosphorylation in depolarized synaptosomes: Dissecting primary effects of calcium from synaptic vesicle cycling
Silbern I, Pan K, Fiosins M, Bonn S, Rizzoli S, Fornasiero E, Urlaub H, Jahn R
MOL CELL PROTEOMICS. 2021;20:.

Landscape of T-cell repertoires with public COVID-19-associated T-cell receptors in pre-pandemic risk cohorts
Simnica D, Schultheiß C, Mohme M, Paschold L, Willscher E, Fitzek A, Püschel K, Matschke J, Ciesek S, Sedding D, Zhao Y, Gagliani N, Maringer Y, Walz J, Heide J, Schulze-Zur-Wiesch J, Binder M
CLIN TRANSL IMMUNOL. 2021;10(9):e1340.

Pro-cachectic factors link experimental and human chronic kidney disease to skeletal muscle wasting programs
Solagna F, Tezze C, Lindenmeyer M, Lu S, Wu G, Liu S, Zhao Y, Mitchell R, Meyer C, Omairi S, Kilic T, Paolini A, Ritvos O, Pasternack A, Matsakas A, Kylies D, Wiesch J, Turner J, Wanner N, Nair V, Eichinger F, Menon R, Martin I, Klinkhammer B, Hoxha E, Cohen C, Tharaux P, Boor P, Ostendorf T, Kretzler M, Sandri M, Kretz O, Puelles V, Patel K, Huber T
J CLIN INVEST. 2021;131(11):.

Deep Learning-Based Bias Transfer for Overcoming Laboratory Differences of Microscopic Images
Thebille A, Dietrich E, Klaus M, Gernhold L, Lennartz E, Kuppe C, Kramann R, Huber T, Sauter G, Puelles V, Zimmermann M, Bonn S
2021. Annual Conference on Medical Image Understanding and Analysis. Papież B, Yaqub M, Jiao J, Namburete A, Noble J (eds.). 1. ed. Oxford: Springer Nature Switzerland AG, 322-336.

Bias-invariant RNA-sequencing metadata annotation
Wartmann H, Heins S, Kloiber K, Bonn S
GIGASCIENCE. 2021;10(9):giab064.

Clonal expansion and activation of tissue-resident memory-like Th17 cells expressing GM-CSF in the lungs of severe COVID-19 patients
Zhao Y, Kilian C, Turner J, Bosurgi L, Roedl K, Bartsch P, Gnirck A, Cortesi F, Schultheiß C, Hellmig M, Enk L, Hausmann F, Borchers A, Wong M, Paust H, Siracusa F, Scheibel N, Herrmann M, Rosati E, Bacher P, Kylies D, Jarczak D, Lütgehetmann M, Pfefferle S, Steurer S, Zur Wiesch J, Puelles V, Sperhake J, Addo M, Lohse A, Binder M, Huber S, Huber T, Kluge S, Bonn S, Panzer U, Gagliani N, Krebs C
SCI IMMUNOL. 2021;6(56):.

Single-cell biology to decode the immune cellular composition of kidney inflammation.
Zhao Y, Panzer U, Bonn S, Krebs C
CELL TISSUE RES. 2021;385(2):435-443.

Deep learning-based molecular morphometrics for kidney biopsies
Zimmermann M, Klaus M, Wong M, Thebille A, Gernhold L, Kuppe C, Halder M, Kranz J, Wanner N, Braun F, Wulf S, Wiech T, Panzer U, Krebs C, Hoxha E, Kramann R, Huber T, Bonn S, Puelles V
JCI INSIGHT. 2021;6(7):e144779.

Explainable Deep Learning for Augmentation of Small RNA Expression Profiles
Fiosina J, Fiosins M, Bonn S
J COMPUT BIOL. 2020.

CRISPLD1: a novel conserved target in the transition to human heart failure
Khadjeh S, Hindmarsh V, Weber F, Cyganek L, Vidal R, Torkieh S, Streckfuss-Bömeke K, Lbik D, Tiburcy M, Mohamed B, Bonn S, Toischer K, Hasenfuss G
BASIC RES CARDIOL. 2020;115(3):27.

Pathogen-induced tissue-resident memory TH17 (TRM17) cells amplify autoimmune kidney disease
Krebs C, Reimers D, Zhao Y, Paust H, Bartsch P, Nuñez S, Rosemblatt M, Hellmig M, Kilian C, Borchers A, Enk L, Zinke M, Becker M, Schmid J, Klinge S, Wong M, Puelles V, Schmidt C, Bertram T, Stumpf N, Hoxha E, Meyer-Schwesinger C, Lindenmeyer M, Cohen C, Rink M, Kurts C, Franzenburg S, Koch-Nolte F, Turner J, Riedel J, Huber S, Gagliani N, Huber T, Wiech T, Rohde H, Bono M, Bonn S, Panzer U, Mittrücker H
SCI IMMUNOL. 2020;5(50):.

Realistic in silico generation and augmentation of single-cell RNA-seq data using generative adversarial networks
Marouf M, Machart P, Bansal V, Kilian C, Magruder D, Krebs C, Bonn S
NAT COMMUN. 2020;11(1):166.

Neuropathology of patients with COVID-19 in Germany: a post-mortem case series
Matschke J, Lütgehetmann M, Hagel C, Sperhake J, Schröder A, Edler C, Mushumba H, Fitzek A, Allweiss L, Dandri M, Dottermusch M, Heinemann A, Pfefferle S, Schwabenland M, Sumner Magruder D, Bonn S, Prinz M, Gerloff C, Püschel K, Krasemann S, Aepfelbacher M, Glatzel M
LANCET NEUROL. 2020;19(11):919-929.

Deep learning-based cell composition analysis from tissue expression profiles
Menden K, Marouf M, Oller S, Dalmia A, Magruder D, Kloiber K, Heutink P, Bonn S
SCI ADV. 2020;6(30):eaba2619.

SEAweb: the small RNA Expression Atlas web application
Rahman R, Liebhoff A, Bansal V, Fiosins M, Rajput A, Sattar A, Magruder D, Madan S, Sun T, Gautam A, Heins S, Liwinski T, Bethune J, Trenkwalder C, Fluck J, Mollenhauer B, Bonn S
NUCLEIC ACIDS RES. 2020;48(D1):D204-D219.

SUMOylation controls the neurodevelopmental function of the transcription factor Zbtb20
Ripamonti S, Shomroni O, Rhee J, Chowdhury K, Jahn O, Hellmann K, Bonn S, Brose N, Tirard M
J NEUROCHEM. 2020;154(6):647-661.

Organ-specific small non-coding RNA responses in domestic (Sudani) ducks experimentally infected with highly pathogenic avian influenza virus (H5N1)
Samir M, Vidal R, Abdallah F, Capece V, Seehusen F, Geffers R, Hussein A, Ali A, Bonn S, Pessler F
RNA BIOL. 2020;17(1):112-124.

Functional hypoxia drives neuroplasticity and neurogenesis via brain erythropoietin
Wakhloo D, Scharkowski F, Curto Y, Javed Butt U, Bansal V, Steixner-Kumar A, Wüstefeld L, Rajput A, Arinrad S, Zillmann M, Seelbach A, Hassouna I, Schneider K, Qadir Ibrahim A, Werner H, Martens H, Miskowiak K, Wojcik S, Bonn S, Nacher J, Nave K, Ehrenreich H
NAT COMMUN. 2020;11(1):1313.

Tagger-A Swiss army knife for multiomics to dissect cell type-specific mechanisms of gene expression in mice
Kaczmarczyk L, Bansal V, Rajput A, Rahman R, Krzyżak W, Degen J, Poll S, Fuhrmann M, Bonn S, Jackson W
PLOS BIOL. 2019;17(8):e3000374.

The long noncoding RNA neuroLNC regulates presynaptic activity by interacting with the neurodegeneration-associated protein TDP-43
Keihani S, Kluever V, Mandad S, Bansal V, Rahman R, Fritsch E, Gomes L, Gärtner A, Kügler S, Urlaub H, Wren J, Bonn S, Rizzoli S, Fornasiero E
SCI ADV. 2019;5(12):eaay2670.

Violent aggression predicted by multiple pre-adult environmental hits
Mitjans M, Seidel J, Begemann M, Bockhop F, Moya-Higueras J, Bansal V, Wesolowski J, Seelbach A, Ibáñez M, Kovacevic F, Duvar O, Fañanás L, Wolf H, Ortet G, Zwanzger P, Klein V, Lange I, Tänzer A, Dudeck M, Penke L, van Elst L, Bittner R, Schmidmeier R, Freese R, Müller-Isberner R, Wiltfang J, Bliesener T, Bonn S, Poustka L, Müller J, Arias B, Ehrenreich H
MOL PSYCHIATR. 2019;24(10):1549-1564.

DNA Methyltransferase 1 Controls Nephron Progenitor Cell Renewal and Differentiation
Wanner N, Vornweg J, Combes A, Wilson S, Plappert J, Rafflenbeul G, Puelles V, Rahman R, Liwinski T, Lindner S, Grahammer F, Kretz O, Wlodek M, Romano T, Moritz K, Boerries M, Busch H, Bonn S, Little M, Bechtel-Walz W, Huber T
J AM SOC NEPHROL. 2019;30(1):63-78.

Genome-wide association study results for educational attainment aid in identifying genetic heterogeneity of schizophrenia
Bansal V, Mitjans M, Burik C, Linnér R, Okbay A, Rietveld C, Begemann M, Bonn S, Ripke S, de Vlaming R, Nivard M, Ehrenreich H, Koellinger P
NAT COMMUN. 2018;9(1):3078.

Upregulation of miR-370 and miR-543 is associated with reduced expression of heat shock protein 40 in spinocerebellar ataxia type 3
Evert B, Nalavade R, Jungverdorben J, Matthes F, Weber S, Rajput A, Bonn S, Brüstle O, Peitz M, Krauß S
PLOS ONE. 2018;13(8):e0201794.

Targeting myelin lipid metabolism as a potential therapeutic strategy in a model of CMT1A neuropathy
Fledrich R, Abdelaal T, Rasch L, Bansal V, Schütza V, Brügger B, Lüchtenborg C, Prukop T, Stenzel J, Rahman R, Hermes D, Ewers D, Möbius W, Ruhwedel T, Katona I, Weis J, Klein D, Martini R, Brück W, Müller W, Bonn S, Bechmann I, Nave K, Stassart R, Sereda M
NAT COMMUN. 2018;9(1):3025.

Precisely measured protein lifetimes in the mouse brain reveal differences across tissues and subcellular fractions
Fornasiero E, Mandad S, Wildhagen H, Alevra M, Rammner B, Keihani S, Opazo F, Urban I, Ischebeck T, Sakib M, Fard M, Kirli K, Centeno T, Vidal R, Rahman R, Benito E, Fischer A, Dennerlein S, Rehling P, Feussner I, Bonn S, Simons M, Urlaub H, Rizzoli S
NAT COMMUN. 2018;9(1):4230.

Molecular Evolution and Functional Divergence of the IgLON Family
Kubick N, Brösamle D, Mickael M
EVOL BIOINFORM. 2018;14:1176934318775081.

Regional and subtype-dependent miRNA signatures in sporadic Creutzfeldt-Jakob disease are accompanied by alterations in miRNA silencing machinery and biogenesis
Llorens F, Thüne K, Martí E, Kanata E, Dafou D, Díaz-Lucena D, Vivancos A, Shomroni O, Zafar S, Schmitz M, Michel U, Fernández-Borges N, Andréoletti O, Del Río J, Díez J, Fischer A, Bonn S, Sklaviadis T, Torres J, Ferrer I, Zerr I
PLOS PATHOG. 2018;14(1):e1006802.

The codon sequences predict protein lifetimes and other parameters of the protein life cycle in the mouse brain
Mandad S, Rahman R, Centeno T, Vidal R, Wildhagen H, Rammner B, Keihani S, Opazo F, Urban I, Ischebeck T, Kirli K, Benito E, Fischer A, Yousefi R, Dennerlein S, Rehling P, Feussner I, Urlaub H, Bonn S, Rizzoli S, Fornasiero E
SCI REP-UK. 2018;8(1):16913.

Oasis 2: improved online analysis of small RNA-seq data
Rahman R, Gautam A, Bethune J, Sattar A, Fiosins M, Magruder D, Capece V, Shomroni O, Bonn S
BMC BIOINFORMATICS. 2018;19(1):54.

Epigenetic alterations in longevity regulators, reduced life span, and exacerbated aging-related pathology in old father offspring mice
Xie K, Ryan D, Pearson B, Henzel K, Neff F, Vidal R, Hennion M, Lehmann I, Schleif M, Schröder S, Adler T, Rathkolb B, Rozman J, Schütz A, Prehn C, Mickael M, Weiergräber M, Adamski J, Busch D, Ehninger G, Matynia A, Jackson W, Wolf E, Fuchs H, Gailus-Durner V, Bonn S, Hrabě de Angelis M, Ehninger D
P NATL ACAD SCI USA. 2018;115(10):E2348-E2357.

The landscape of human mutually exclusive splicing
Hatje K, Rahman R, Vidal R, Simm D, Hammesfahr B, Bansal V, Rajput A, Mickael M, Sun T, Bonn S, Kollmar M
MOL SYST BIOL. 2017;13(12):.

Severe DCM phenotype of patient harboring RBM20 mutation S635A can be modeled by patient-specific induced pluripotent stem cell-derived cardiomyocytes
Streckfuss-Bömeke K, Tiburcy M, Fomin A, Luo X, Li W, Fischer C, Özcelik C, Perrot A, Sossalla S, Haas J, Vidal R, Rebs S, Khadjeh S, Meder B, Bonn S, Linke W, Zimmermann W, Hasenfuss G, Guan K
J MOL CELL CARDIOL. 2017;113:9-21.

Letzte Aktualisierung aus dem FIS: 09.12.2022 - 03:47 Uhr

Bookchapters

  • ISBRA 2019: Bioinformatics Research and Applications
    Deep Learning and Random Forest-Based Augmentation of sRNA Expression Profiles
    Jelena Fiosina, Maksims Fiosins, Stefan Bonn
    Conference paper, 09 May 2019

Software

SEA ( https://sea.dzne.de ): SEA, the small RNA expression atlas, is a web application that allows querying, visualization, and analysis of small RNA expression information for over 30.000 small RNAs, over 2000 samples, hundreds of diseases, over 7 organisms, and plenty of tissues and cell types. SEA is fully interactive and lightning fast and a perfect showcase for the 'knowledge-bases' we build.

Oasis & Oasis 2 ( https://oasis.dzne.de ): Oasis, the online analysis of small RNAs, is a web application that allows for the detection, differential expression, and classification analysis of small RNAs. It is interactive, fast, and heavily used in the research community.

Memory Epigenome Browser ( https://memory-epigenome-browser.dzne.de ): The memory epigenome browser allows to select, visualize, and download over 200 cell type-specific epigenetic and transcriptomic datasets before and after learning. It is part of our manuscript on the epigenetic basis of learning and memory (Halder et al. Nature Neuroscience 2016).

GRAND: Graphs as nested dictionaries is a framework that allows for fast and memory efficient graph operations and interactive visualization. It is a free python package that can read many standard graph formats and supports many standard graph operations (e.g. search, shortest path).