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List of works by Daniel Hoffmann

A Pro-Inflammatory Gut Microbiome Characterizes SARS-CoV-2 Infected Patients and a Reduction in the Connectivity of an Anti-Inflammatory Bacterial Network Associates With Severe COVID-19

scientific article published on 17 November 2021

A multiobjective evolutionary method for the design of peptidic mimotopes

scientific article published in January 2006

A network of trans-cortical capillaries as mainstay for blood circulation in long bones

scientific article published on 21 January 2019

A new approach to inhibit human β-tryptase by protein surface binding of four-armed peptide ligands with two different sets of arms

scientific article published in February 2013

A new class of supramolecular ligands stabilizes 14-3-3 protein–protein interactions by up to two orders of magnitude

scientific article published on 01 December 2018

A simple structure-based model for the prediction of HIV-1 co-receptor tropism

scientific article published on August 2014

A small set of succinct signature patterns distinguishes Chinese and non-Chinese HIV-1 genomes

scientific article

A structural role for glycosylation: lessons from the hp model.

scientific article published on January 1998

Adaptation of the hepatitis B virus core protein to CD8(+) T-cell selection pressure.

scientific article published on 25 March 2015

Amino acid substitutions within HLA-B*27-restricted T cell epitopes prevent recognition by hepatitis delta virus-specific CD8+ T cells.

scientific article

AmpliconDuo: A Split-Sample Filtering Protocol for High-Throughput Amplicon Sequencing of Microbial Communities

scientific article published on 2 November 2015

An additional glucose dehydrogenase from Sulfolobus solfataricus: fine-tuning of sugar degradation?

scientific article published on 01 January 2011

An altered heparan sulfate structure in the articular cartilage protects against osteoarthritis

scientific article published on 18 April 2020

An emerging role of Sonic hedgehog shedding as a modulator of heparan sulfate interactions

scientific article

Atoh8 acts as a regulator of chondrocyte proliferation and differentiation in endochondral bones

scientific article published on 26 August 2019

Backbone rigidity and static presentation of guanidinium groups increases cellular uptake of arginine-rich cell-penetrating peptides

scientific article

Band-flip and kink as novel structural motifs in α-(1→4)-d-glucose oligosaccharides. Crystal structures of cyclodeca- and cyclotetradecaamylose

article published in 1999

Bayesian Data Integration Questions Classic Study on Protease Self-Digest Kinetics

scientific article published on 19 June 2020

Biallelic loss of function of the promyelocytic leukaemia zinc finger (PLZF) gene causes severe skeletal defects and genital hypoplasia

scientific article published on 8 July 2008

Biased IGH VDJ gene repertoire and clonal expansions in B cells of chronically hepatitis C virus-infected individuals

scientific article published on 14 December 2017

CD8+ T-cell response promotes evolution of hepatitis C virus nonstructural proteins

scientific article published on 2 March 2011

Ca2+ coordination controls sonic hedgehog structure and its Scube2-regulated release

scientific article published on 4 August 2017

Chondrocytes respond to an altered heparan sulfate composition with distinct changes of heparan sulfate structure and increased levels of chondroitin sulfate

scientific article published on 19 March 2020

Compensatory mutations at the HIV cleavage sites p7/p1 and p1/p6-gag in therapy-naive and therapy-experienced patients.

scientific article published in January 2006

Complexity of the human memory B-cell compartment is determined by the versatility of clonal diversification in germinal centers

scientific article

Computational methods for the design of effective therapies against drug resistant HIV strains

scientific article

Computational model predicts protein binding sites of a luminescent ligand equipped with guanidiniocarbonyl-pyrrole groups

Correction: A Small Set of Succinct Signature Patterns Distinguishes Chinese and Non-Chinese HIV-1 Genomes

DNA-methylation patterns imply a common cellular origin of virus- and UV-associated Merkel cell carcinoma

scientific article published on 19 October 2021

Design of a modular protein-based MRI contrast agent for targeted application.

scientific article

Differential escape of HCV from CD8 T cell selection pressure between China and Germany depends on the presenting HLA class I molecule

article

Differential selection in HIV-1 gp120 between subtype B and East Asian variant B'.

scientific article

Dual activity inhibition of threonine aspartase 1 by a single bisphosphate ligand

Escape from a dominant HLA-B*15-restricted CD8+ T cell response against hepatitis C virus requires compensatory mutations outside the epitope.

scientific article published on 9 November 2011

Estimating HIV evolutionary pathways and the genetic barrier to drug resistance

scientific article published on 28 April 2005

Estimating affinities of calcium ions to proteins

scientific article

Evolution of HIV resistance during treatment interruption in experienced patients and after restarting a new therapy

scientific article

Evolutionary Pareto-optimization of stably folding peptides

scientific article

Granulocytic myeloid-derived suppressor cells suppress virus-specific CD8+ T cell responses during acute Friend retrovirus infection

scientific article

Gut microbiota in HIV-infected individuals linked to coronary heart disease

article

Hepatitis B virus particles activate B cells through the TLR2-MyD88-mTOR axis

scientific article published on 04 January 2021

Identification of significant features by the Global Mean Rank test

scientific article

IgGeneUsage: differential gene usage in immune repertoires

scientific article published on 12 March 2020

Improved Bevirimat resistance prediction by combination of structural and sequence-based classifiers

scientific article

Interpol: An R package for preprocessing of protein sequences ⬇️

scientific article published on June 17, 2011

Learning multiple evolutionary pathways from cross-sectional data

scientific article

Locating Large Flexible Ligands on Proteins

scientific article published on 21 December 2017

Machine learning on normalized protein sequences.

scientific article

Metabolism of cancer cells commonly responds to irradiation by a transient early mitochondrial shutdown

scientific article published on 28 October 2021

Methods for optimizing antiviral combination therapies

scientific article

Mtreemix: a software package for learning and using mixture models of mutagenetic trees

scientific article published on 18 January 2005

Mutations in Hepatitis D Virus Allow It to Escape Detection by CD8 T Cells and Evolve at the Population Level

scientific article published on 12 February 2019

Parameters Influencing Baseline HIV-1 Genotypic Tropism Testing Related to Clinical Outcome in Patients on Maraviroc

scientific article

Parental origin and functional relevance of a de novo UBE3A variant

scientific article published on 8 October 2010

Pareto Optimization Identifies Diverse Set of Phosphorylation Signatures Predicting Response to Treatment with Dasatinib

scientific article

Partial reduction and two-step modification of proteins for identification of disulfide bonds.

scientific article

Photoaffinity labelling of the human GM2-activator protein. Mechanistic insight into ganglioside GM2 degradation.

scientific article

Predicting Bevirimat resistance of HIV-1 from genotype

scientific article

Prediction of co-receptor usage of HIV-1 from genotype

scientific article published in April 2010

Predominance of Central Memory T Cells with High T-Cell Receptor Repertoire Diversity is Associated with Response to PD-1/PD-L1 Inhibition in Merkel Cell Carcinoma

scientific article published on 13 January 2020

Prevalence of C-terminal gag cleavage site mutations in HIV from therapy-naïve patients.

scientific article published on 24 December 2008

Prevalence of minor variants of HIV strains at reverse transcriptase position 103 in therapy-naïve patients and their impact on the virological failure

scientific article published on 17 April 2009

Protein dynamics with off-lattice Monte Carlo moves

scientific article published on 01 April 1996

Proteolytic processing of palmitoylated Hedgehog peptides specifies the 3-4 intervein region of the Drosophila wing. ⬇️

scientific article published on 9 March 2018

Protistan community analysis: key findings of a large-scale molecular sampling

scientific article

Quantitative Assessment of Molecular Dynamics Sampling for Flexible Systems

scientific article published on 13 January 2017

Quantitative Comparison of Abundance Structures of Generalized Communities: From B-Cell Receptor Repertoires to Microbiomes

scientific article

Rapid Uptake of Pre-Exposure Prophylaxis (PrEP) after Significant Price Reduction in Germany Highlights Importance of PrEP Accessibility

scientific article published on 13 March 2020

Rational Design, Binding Studies and Crystal Structure Evaluation of the First Ligand Targeting the Dimerization Interface of the 14-3-3ζ Adapter Protein.

scientific article

Role of Gag mutations in PI resistance in the Swiss HIV cohort study: bystanders or contributors?

scientific article published on 20 December 2016

Rpd3-dependent boundary formation at telomeres by removal of Sir2 substrate

scientific article

SearchXLinks. A program for the identification of disulfide bonds in proteins from mass spectra

scientific article published on 01 February 2006

SeqFeatR for the Discovery of Feature-Sequence Associations

scientific article published on 5 January 2016

Signaling domain of Sonic Hedgehog as cannibalistic calcium-regulated zinc-peptidase

scientific article

Signaling systems affecting the severity of multiple osteochondromas.

scientific article published on 12 March 2018

Single-domain parvulins constitute a specific marker for recently proposed deep-branching archaeal subgroups

scientific article

Sonic hedgehog shedding results in functional activation of the solubilized protein.

scientific article published on June 2011

Specific inhibition of the Survivin-CRM1 interaction by peptide-modified molecular tweezers

Strain-Induced "Band Flips" in Cyclodecaamylose and Higher Homologues

scientific article published in March 1998

Structure of HIV-1 quasi-species as early indicator for switches of co-receptor tropism.

scientific article

Structures of the Common Cyclodextrins and Their Larger Analogues-Beyond the Doughnut

scientific article published in July 1998

Tenofovir resistance and resensitization

scientific article published on November 2003

The B-cell epitope of the monoclonal anti-factor VIII antibody ESH8 characterized by peptide array analysis

scientific article published on 01 March 2008

The amino acid substitutions rtP177G and rtF249A in the reverse transcriptase domain of hepatitis B virus polymerase reduce the susceptibility to tenofovir.

scientific article

The antiretroviral potency of emtricitabine is approximately 3-fold higher compared to lamivudine in dual human immunodeficiency virus type 1 infection/competition experiments in vitro

scientific article published on 17 March 2010

The enzyme-binding region of human GM2-activator protein

scientific article published on March 2006

The imprinted NPAP1/C15orf2 gene in the Prader-Willi syndrome region encodes a nuclear pore complex associated protein

scientific article

The normal-mode entropy in the MM/GBSA method: effect of system truncation, buffer region, and dielectric constant

scientific article published on 02 August 2012

Trade-off shapes diversity in eco-evolutionary dynamics

scientific article published on 17 August 2018

Transient domain interactions enhance the affinity of the mitotic regulator Pin1 toward phosphorylated peptide ligands.

scientific article

Treatment of Chronic Hepatitis B Virus Infection Using Small Molecule Modulators of Nucleocapsid Assembly: Recent Advances and Perspectives

scientific article published on 29 March 2019

Two-stage method for protein-ligand docking

scientific article published in October 1999

Virus-Induced Type I Interferon Deteriorates Control of Systemic Pseudomonas Aeruginosa Infection

scientific article published on 27 July 2015

Widespread regulation of gene expression in the Drosophila genome by the histone acetyltransferase dTip60.

scientific article published in December 2009

Wnt5a is a transcriptional target of Gli3 and Trps1 at the onset of chondrocyte hypertrophy

scientific article published on 21 September 2019

intePareto: an R package for integrative analyses of RNA-Seq and ChIP-Seq data

scientific article published on 29 December 2020

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