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Temporal change of DNA methylation subclasses between matched newly diagnosed and recurrent glioblastoma
Drexler R, Khatri R, Schüller U, Eckhardt A, Ryba A, Sauvigny T, Dührsen L, Mohme M, Ricklefs T, Bode H, Hausmann F, Huber T, Bonn S, Voß H, Neumann J, Silverbush D, Hovestadt V, Suvà M, Lamszus K, Gempt J, Westphal M, Heiland D, Hänzelmann S, Ricklefs F
ACTA NEUROPATHOL. 2024;147(1):21.

Fetal lung growth predicts the risk for early-life respiratory infections and childhood asthma
Zazara D, Giannou O, Schepanski S, Pagenkemper M, Giannou A, Pincus M, Belios I, Bonn S, Muntau A, Hecher K, Diemert A, Arck P
WORLD J PEDIATR. 2024 [Epub ahead of print];2024(1):.

Performance comparison of TCR-pMHC prediction tools reveals a strong data dependency
Deng L, Ly C, Abdollahi S, Zhao Y, Prinz I, Bonn S
FRONT IMMUNOL. 2023;14:1128326.

Targeted anticonvulsive treatment of IDH-wildtype glioblastoma based on DNA methylation subclasses
Drexler R, Göttsche J, Sauvigny T, Schüller U, Khatri R, Hausmann F, Hänzelmann S, Huber T, Bonn S, Heiland D, Delev D, Venkataramani V, Winkler F, Weller J, Zeyen T, Herrlinger U, Gempt J, Ricklefs F, Dührsen L
NEURO-ONCOLOGY. 2023;25(5):1006-1008.

Epigenetic neural glioblastoma enhances synaptic integration and predicts therapeutic vulnerability
Drexler R, Khatri R, Sauvigny T, Mohme M, Maire C, Ryba A, Zghaibeh Y, Dührsen L, Salviano-Silva A, Lamszus K, Westphal M, Gempt J, Wefers A, Neumann J, Bode H, Hausmann F, Huber T, Bonn S, Jütten K, Delev D, Weber K, Harter P, Onken J, Vajkoczy P, Capper D, Wiestler B, Weller M, Snijder B, Buck A, Weiss T, Keough M, Ni L, Monje M, Silverbush D, Hovestadt V, Suvà M, Krishna S, Hervey-Jumper S, Schüller U, Heiland D, Hänzelmann S, Ricklefs F
bioRxiv. 2023.

Epigenetic profiling reveals a strong association between lack of 5-ALA fluorescence and EGFR amplification in IDH-wildtype glioblastoma
Drexler R, Sauvigny T, Schüller U, Eckhardt A, Maire C, Khatri R, Hausmann F, Hänzelmann S, Huber T, Bonn S, Bode H, Lamszus K, Westphal M, Dührsen L, Ricklefs F
NEURO-ONCOL PRACT. 2023;10(5):462-471.

Testosterone affects type I/type II interferon response of neutrophils during hepatic amebiasis
Er-Lukowiak M, Hänzelmann S, Rothe M, Moamenpour D, Hausmann F, Khatri R, Hansen C, Boldt J, Bärreiter V, Honecker B, Bea A, Groneberg M, Fehling H, Marggraff C, Cadar D, Bonn S, Sellau J, Lotter H
FRONT IMMUNOL. 2023;14:1279245.

Reduction of IFN-I responses by plasmacytoid dendritic cells in a longitudinal trans men cohort
Grünhagel B, Borggrewe M, Hagen S, Ziegler S, Henseling F, Glau L, Thiele R, Pujantell M, Sivayoganathan V, Padoan B, Claussen J, Düsedau A, Hennesen J, Bunders M, Bonn S, Tolosa E, Krebs C, Dorn C, Altfeld M
ISCIENCE. 2023;26(11):108209.

DISCERN: deep single-cell expression reconstruction for improved cell clustering and cell subtype and state detection
Hausmann F, Ergen C, Khatri R, Marouf M, Hänzelmann S, Gagliani N, Huber S, Machart P, Bonn S
GENOME BIOL. 2023;24(1):212.

Loss of TDP-43 causes ectopic endothelial sprouting and migration defects through increased fibronectin, vcam 1 and integrin α4/β1
Hipke K, Pitter B, Hruscha A, van Bebber F, Modic M, Bansal V, Lewandowski S, Orozco D, Edbauer D, Bonn S, Haass C, Pohl U, Montanez E, Schmid B
FRONT CELL DEV BIOL. 2023;11:1169962.

Expansion-enhanced super-resolution radial fluctuations enable nanoscale molecular profiling of pathology specimens
Kylies D, Zimmermann M, Haas F, Schwerk M, Kuehl M, Brehler M, Czogalla J, Hernandez L, Konczalla L, Okabayashi Y, Menzel J, Edenhofer I, Mezher S, Aypek H, Dumoulin B, Wu H, Hofmann S, Kretz O, Wanner N, Tomas N, Krasemann S, Glatzel M, Kuppe C, Kramann R, Banjanin B, Schneider R, Urbschat C, Arck P, Gagliani N, van Zandvoort M, Wiech T, Grahammer F, Sáez P, Wong M, Bonn S, Huber T, Puelles V
NAT NANOTECHNOL. 2023;18(4):336-342.

Pathogen detection in RNA-seq data with Pathonoia
Liebhoff A, Menden K, Laschtowitz A, Franke A, Schramm C, Bonn S
BMC BIOINFORMATICS. 2023;24(1):.

Single-cell transcriptomics reveals a mechanosensitive injury signaling pathway in early diabetic nephropathy
Liu S, Zhao Y, Lu S, Zhang T, Lindenmeyer M, Nair V, Gies S, Wu G, Nelson R, Czogalla J, Aypek H, Zielinski S, Liao Z, Schaper M, Fermin D, Cohen C, Delic D, Krebs C, Grahammer F, Wiech T, Kretzler M, Meyer-Schwesinger C, Bonn S, Huber T
GENOME MED. 2023;15(1):2.

A multi-omics dataset for the analysis of frontotemporal dementia genetic subtypes
Menden K, Francescatto M, Nyima T, Blauwendraat C, Dhingra A, Castillo-Lizardo M, Fernandes N, Kaurani L, Kronenberg-Versteeg D, Atasu B, Sadikoglou E, Borroni B, Rodriguez-Nieto S, Simon-Sanchez J, Fischer A, Craig D, Neumann M, Bonn S, Rizzu P, Heutink P
SCI DATA. 2023;10(1):849.

Transcriptional and Clonal Characterization of Cytotoxic T Cells in Crescentic Glomerulonephritis
Mueller A, Zhao Y, Cicek H, Paust H, Sivayoganathan A, Linke A, Wegscheid C, Wiech T, Huber T, Meyer-Schwesinger C, Bonn S, Prinz I, Panzer U, Tiegs G, Krebs C, Neumann K
J AM SOC NEPHROL. 2023;34(6):1003-1018.

CD4+ T cells produce GM-CSF and drive immune-mediated glomerular disease by licensing monocyte-derived cells to produce MMP12
Paust H, Song N, De Feo D, Asada N, Tuzlak S, Zhao Y, Riedel J, Hellmig M, Sivayoganathan A, Peters A, Kaffke A, Borchers A, Wenzel U, Steinmetz O, Tiegs G, Meister E, Mack M, Kurts C, von Vietinghoff S, Lindenmeyer M, Hoxha E, Stahl R, Huber T, Bonn S, Meyer-Schwesinger C, Wiech T, Turner J, Becher B, Krebs C, Panzer U
SCI TRANSL MED. 2023;15(687):.

DeePSC: A Deep Learning Model for Automated Diagnosis of Primary Sclerosing Cholangitis at Two-dimensional MR Cholangiopancreatography
Ragab H, Westhaeusser F, Ernst A, Yamamura J, Fuhlert P, Zimmermann M, Sauerbeck J, Shenas F, Özden C, Weidmann A, Adam G, Bonn S, Schramm C
RADIOL-ARTIF INTELL. 2023;5(3):e220160.

Glucocorticoids target the CXCL9/CXCL10-CXCR3 axis and confer protection against immune-mediated kidney injury
Riedel J, Robben L, Paust H, Zhao Y, Asada N, Song N, Peters A, Kaffke A, Borchers A, Tiegs G, Seifert L, Tomas N, Hoxha E, Wenzel U, Huber T, Wiech T, Turner J, Krebs C, Panzer U
JCI INSIGHT. 2023;8(1):.

Kidney outcome after mild to moderate COVID-19
Schmidt-Lauber C, Hänzelmann S, Schunk S, Petersen E, Alabdo A, Lindenmeyer M, Hausmann F, Kuta P, Renné T, Twerenbold R, Zeller T, Blankenberg S, Fliser D, Huber T
NEPHROL DIAL TRANSPL. 2023;38(9):2031-2040.

Proteomic analysis of the human hippocampus identifies neuronal pentraxin 1 (NPTX1) as synapto-axonal target in late-stage Parkinson's disease
Warth Perez Arias C, Silbern I, Caldi Gomes L, Wartmann H, Dambeck V, Fanz J, Neuenroth L, Bähr M, Outeiro T, Bonn S, Stadelmann-Nessler C, Rizzoli S, Lenz C, Urlaub H, Lingor P
J NEUROCHEM. 2023;166(5):862-874.

Multicytokine-producing CD4+ T cells characterize the livers of patients with NASH
Woestemeier A, Scognamiglio P, Zhao Y, Wagner J, Muscate F, Casar C, Siracusa F, Cortesi F, Agalioti T, Müller S, Sagebiel A, Konczalla L, Wahib R, Karstens K, Giannou A, Duprée A, Wolter S, Wong M, Mühlig A, Bielecka A, Bansal V, Zhang T, Mann O, Puelles V, Huber T, Lohse A, Izbicki J, Palm N, Bonn S, Huber S, Gagliani N
JCI INSIGHT. 2023;8(1):.

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.

Correction: 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. 2022;20(11):.

Distinct translatome changes in specific neural populations precede electroencephalographic changes in prion-infected mice
Kaczmarczyk L, Schleif M, Dittrich L, Williams R, Koderman M, Bansal V, Rajput A, Schulte T, Jonson M, Krost C, Testaquadra F, Bonn S, Jackson W
PLOS PATHOG. 2022;18(8):.

ERR2 and ERR3 promote the development of gamma motor neuron functional properties required for proprioceptive movement control
Khan M, Cherukuri P, Negro F, Rajput A, Fabrowski P, Bansal V, Lancelin C, Lee T, Bian Y, Mayer W, Akay T, Müller D, Bonn S, Farina D, Marquardt T
PLOS BIOL. 2022;20(12):.

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
CURR OPIN SYST BIOL. 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 (Hrsg.). 1. Aufl. 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: 26.02.2024 - 00:33 Uhr

Buchkapitel und Buchbesprechungen

  • 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, der "small RNA expression atlas", ist eine Webanwendung, die es ermöglicht, RNA-Expressionsdatensätze abzufragen, zu visualisieren und zu analysieren. Die SEA Datenbank enthält Informationen zu über 30.000 kleinen RNA Molekülen, 2.000 RNA-Proben, hunderten Erkrankungen, mehr als sieben Spezies und vielen verschiedenen Geweben und Zelltypen. SEA ist völlig Interaktiv und schnell. Es ist ein perfektes Beispiel für die Art von Wissensdatenbanken, die wir aufbauen.

Oasis & Oasis 2 ( https://oasis.dzne.de ): Oasis ist ein Webservice, mit dem man RNA-Datensätze analysieren kann, um Informationen darüber zu erhalten, welche kleinen RNA-Moleküle in den eigenen Datensätzen vorhanden sind. Darüber hinaus ist es möglich, für diese kleinen RNA Moleküle differentielle Expressionen zu ermitteln und auch Machine-Learning Modelle für die Klassifikation von Krankheiten zu generieren. Der Webservice ist interaktiv, schnell und wird von der Forschungsgemeinde stark benutzt.

Memory Epigenom Browser ( https://memory-epigenome-browser.dzne.de ): Der Memory Epigenom Browser ermöglicht es, über 200 Zelltyp-spezifische epigenetische und transcriptomische Datensätze vor und nach Lernvorgängen auszuwählen, zu visualisieren und herunterzuladen. Diese Daten sind Teil unserer Veröffentlichung über die epigenetischen Grundlagen von Lern- und Gedächtnisprozessen (Halder et al. Nature Neuroscience 2016).

GRAND: "Graphs as nested dictionaries" ist eine Software, die es ermöglicht, schnell und ohne großen RAM-Verbrauch Graph-Operationen und Graph-Visualisierungen durchzuführen. GRAND ist als Python-Packet frei erhältlich. Es unterstützt viele gängige Graph-Dateiformate und enthält Algorithmen für gängige Operationen wie Suche oder kürzeste Pfade.