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List of works by Frank Eisenhaber

10 years for the Journal of Bioinformatics and Computational Biology (2003-2013) -- a retrospective

scientific article published on 21 May 2014

A CH domain-containing N terminus in NuMA?

scientific article

A Reversible Association between Smc Coiled Coils Is Regulated by Lysine Acetylation and Is Required for Cohesin Association with the DNA.

scientific article published on 3 September 2016

A decade after the first full human genome sequencing: when will we understand our own genome?

scientific article published on 22 June 2012

A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus

scientific article

A new piece in the puzzle of the novel avian-origin influenza A (H7N9) virus.

scientific article

A sensitive predictor for potential GPI lipid modification sites in fungal protein sequences and its application to genome-wide studies for Aspergillus nidulans, Candida albicans, Neurospora crassa, Saccharomyces cerevisiae and Schizosaccharomyces p

scientific article published in March 2004

A simple shortcut to unsupervised alignment-free phylogenetic genome groupings, even from unassembled sequencing reads

scientific article published on 2 December 2013

ANNIE: integrated de novo protein sequence annotation

scientific article published on 23 April 2009

Active site CP-loop dynamics modulate substrate binding, catalysis, oligomerization, stability, over-oxidation and recycling of 2-Cys Peroxiredoxins

scientific article published on 20 February 2018

All that glitters is not gold--founder effects complicate associations of flu mutations to disease severity

scientific article

AllerCatPro-prediction of protein allergenicity potential from the protein sequence

scientific article published on 01 September 2019

Application of a sensitive collection heuristic for very large protein families: evolutionary relationship between adipose triglyceride lipase (ATGL) and classic mammalian lipases

scientific article published on 21 March 2006

Are knowledge-based potentials derived from protein structure sets discriminative with respect to amino acid types?

scientific article

Are knowledge-based potentials derived from protein structure sets discriminative with respect to amino acid types?

scholarly article by Shamil R. Sunyaev published in May 1998

Arxes: retrotransposed genes required for adipogenesis

scientific journal article

Automated annotation of GPI anchor sites: case study C. elegans

scientific article published in July 2000

Automatic phylogenetic classification of bacterial beta-lactamase sequences including structural and antibiotic substrate preference information

scientific article

Benchmarking selected computational gene network growing tools in context of virus-host interactions

scientific article

Beware of moving targets: reference proteome content fluctuates substantially over the years

scientific article published on 7 August 2012

Biomolecular pathway databases

scientific article published on January 2010

Blom7alpha is a novel heterogeneous nuclear ribonucleoprotein K homology domain protein involved in pre-mRNA splicing that interacts with SNEVPrp19-Pso4.

scientific article published on 29 July 2009

Brief overview of bioinformatics activities in Singapore

scientific article published on 25 September 2009

Can molecular mechanisms of biological processes be extracted from expression profiles? Case study: endothelial contribution to tumor-induced angiogenesis

scientific article

Characterization of targeting domains by sequence analysis: glycogen-binding domains in protein phosphatases

scientific article

Charged residues next to transmembrane regions revisited: "Positive-inside rule" is complemented by the "negative inside depletion/outside enrichment rule"

scientific article

Cleaning of raw peptide MS/MS spectra: improved protein identification following deconvolution of multiply charged peaks, isotope clusters, and removal of background noise

scientific article published in October 2006

Comparison of atomic solvation parameter sets: Applicability and limitations in protein folding and binding

scholarly article by Andre H. Juffer published in August 1996

Comparison of atomic solvation parametric sets: applicability and limitations in protein folding and binding

scientific article

Correction: Brief Overview of Bioinformatics Activities in Singapore.

scientific article published on 4 November 2009

Crystal structure of the p14/MP1 scaffolding complex: how a twin couple attaches mitogen-activated protein kinase signaling to late endosomes

scientific article

Crystallographic and solution studies of NAD(+)- and NADH-bound alkylhydroperoxide reductase subunit F (AhpF) from Escherichia coli provide insight into sequential enzymatic steps

scientific article

DOUTfinder--identification of distant domain outliers using subsignificant sequence similarity

scientific article

Darkness in the Human Gene and Protein Function Space: Widely Modest or Absent Illumination by the Life Science Literature and the Trend for Fewer Protein Function Discoveries Since 2000

scientific article published on 30 October 2018

Databases of protein-protein interactions and complexes

scientific article published on January 2010

Detecting atypical examples of known domain types by sequence similarity searching: the SBASE domain library approach

scientific article

Discovering novel SNPs that are correlated with patient outcome in a Singaporean cancer patient cohort treated with gemcitabine-based chemotherapy.

scientific article

Discovery of a novel splice variant of Fcar (CD89) unravels sequence segments necessary for efficient secretion: A story of bad signal peptides and good ones that nevertheless do not make it.

scientific article

Eco1 is a novel acetyltransferase that can acetylate proteins involved in cohesion

scientific article

Effect of the additional cysteine 503 of vancomycin-resistant Enterococcus faecalis (V583) alkylhydroperoxide reductase subunit F (AhpF) and the mechanism of AhpF and subunit C assembling

scientific article published on 30 April 2019

Enzymes and auxiliary factors for GPI lipid anchor biosynthesis and post-translational transfer to proteins

scientific article (publication date: April 2003)

Erratum to Wolfgang Benetka et al., Cell Cycle Volume 7, Issue 23; pp. 3709-3719

scholarly article published in Cell Cycle

Erratum to: Charged residues next to transmembrane regions revisited: "Positive-inside rule" is complemented by the "negative inside depletion/outside enrichment rule".

scientific article published on 18 August 2017

Essential role of the flexible linker on the conformational equilibrium of bacterial peroxiredoxin reductase for effective regeneration of peroxiredoxin

scientific article

Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries

scientific article

Exo70, a subunit of the exocyst complex, interacts with SNEV(hPrp19/hPso4) and is involved in pre-mRNA splicing

scientific article published on August 2011

Experimental testing of predicted myristoylation targets involved in asymmetric cell division and calcium-dependent signalling

scientific article published on 13 December 2008

Extending Asia Pacific bioinformatics into new realms in the "-omics" era

scientific article

Farnesylation or geranylgeranylation? Efficient assays for testing protein prenylation in vitro and in vivo

scientific article published on 28 February 2006

Fat mobilization in adipose tissue is promoted by adipose triglyceride lipase

scientific article

Finite-size effects in transcript sequencing count distribution: its power-law correction necessarily precedes downstream normalization and comparative analysis

scientific article published on 12 February 2018

Function of a membrane-embedded domain evolutionarily multiplied in the GPI lipid anchor pathway proteins PIG-B, PIG-M, PIG-U, PIG-W, PIG-V, and PIG-Z

scientific article published on 15 May 2018

Functional Classification of Super-Large Families of Enzymes Based on Substrate Binding Pocket Residues for Biocatalysis and Enzyme Engineering Applications

scientific article published on 02 August 2021

Genome-wide loss-of-function analysis of deubiquitylating enzymes for zebrafish development

scientific article

Genomics-driven discovery of a biosynthetic gene cluster required for the synthesis of BII-Rafflesfungin from the fungus Phoma sp. F3723

article

Glycosylphosphatidylinositol lipid anchoring of plant proteins. Sensitive prediction from sequence- and genome-wide studies for Arabidopsis and rice

scientific article

Guest Editorial for the International Conference on Genome Informatics (GIW 2013).

scientific article

HPMV: human protein mutation viewer - relating sequence mutations to protein sequence architecture and function changes

scientific article published on 27 October 2015

Hidden localization motifs: naturally occurring peroxisomal targeting signals in non-peroxisomal proteins

scientific article

Homology-based fold predictions for Mycoplasma genitalium proteins

scientific article

How bioinformatics influences health informatics: usage of biomolecular sequences, expression profiles and automated microscopic image analyses for clinical needs and public health

scientific article

Human Rif1, ortholog of a yeast telomeric protein, is regulated by ATM and 53BP1 and functions in the S-phase checkpoint

scientific article

Human Scc4 is required for cohesin binding to chromatin, sister-chromatid cohesion, and mitotic progression

scientific article

Hydration of B-DNA: Comparison between the water network around poly(dG) · poly(dC) and poly(dG-dC) · poly(dG-dC) on the basis of Monte Carlo computations

scientific article published on 01 March 1989

Hydrophobic regions on protein surfaces. Derivation of the solvation energy from their area distribution in crystallographic protein structures

scientific article published on August 1996

Hydrophobic regions on protein surfaces: definition based on hydration shell structure and a quick method for their computation

scientific article published in December 1996

Identification and engineering of 32 membered antifungal macrolactone notonesomycins

scientific article published on 19 March 2020

Identification of New Targets Using Expression Profiles

Induction of short interspersed nuclear repeat-containing transcripts in epithelial cells upon infection with a chicken adenovirus.

scientific article published in May 2003

Integrated tools for biomolecular sequence-based function prediction as exemplified by the ANNOTATOR software environment

scientific article published in January 2010

International Conference on Genome Informatics (GIW 2013) in Singapore: Introduction to the systems biology contributions

scientific article

Investigation of causes of oseltamivir chemoprophylaxis failures during influenza A (H1N1-2009) outbreaks

scientific article

Is LGI2 the candidate gene for partial epilepsy with pericentral spikes?

scientific article

Isolation and Identification of an Anthracimycin Analogue from Nocardiopsis kunsanensis, a Halophile from a Saltern, by Genomic Mining Strategy.

scientific article published on 21 May 2018

Key roles of the Escherichia coli AhpC C-terminus in assembly and catalysis of alkylhydroperoxide reductase, an enzyme essential for the alleviation of oxidative stress

scientific article

Kleisins: a superfamily of bacterial and eukaryotic SMC protein partners

scientific article

Knockout of the non-essential gene SUGCT creates diet-linked, age-related microbiome disbalance with a diabetes-like metabolic syndrome phenotype

scientific article published on 13 November 2019

Linking transcriptional mediators via the GACKIX domain super family.

scientific article

Low resolution solution structure of an enzymatic active AhpC10:AhpF2 ensemble of the Escherichia coli Alkyl hydroperoxide Reductase

scientific article published on 13 November 2015

Low-resolution structure of the soluble domain GPAA1 (yGPAA170–247) of the glycosylphosphatidylinositol transamidase subunit GPAA1 from Saccharomyces cerevisiae ⬇️

scientific article published on March 28, 2013

MYRbase: analysis of genome-wide glycine myristoylation enlarges the functional spectrum of eukaryotic myristoylated proteins

scientific article

Mapping the sequence mutations of the 2009 H1N1 influenza A virus neuraminidase relative to drug and antibody binding sites

scientific article published on 20 May 2009

Molecular cloning and characterization of EndoGlyx-1, an EMILIN-like multisubunit glycoprotein of vascular endothelium

scientific article

Molecular cloning and characterization of endosialin, a C-type lectin-like cell surface receptor of tumor endothelium

scientific article (publication date: 9 March 2001)

Molecular mechanism of the Escherichia coli AhpC in the function of a chaperone under heat-shock conditions

scientific article published in Scientific Reports

Molecular processes during fat cell development revealed by gene expression profiling and functional annotation

scientific article

More than 1,001 problems with protein domain databases: transmembrane regions, signal peptides and the issue of sequence homology

scientific article

Motif discovery with data mining in 3D protein structure databases: discovery, validation and prediction of the U-shape zinc binding ("Huf-Zinc") motif

scientific article

Motif refinement of the peroxisomal targeting signal 1 and evaluation of taxon-specific differences

scientific article published in May 2003

Myristoylation of viral and bacterial proteins

scientific article published on April 2004

N-terminal N-myristoylation of proteins: prediction of substrate proteins from amino acid sequence

scientific article

N-terminal N-myristoylation of proteins: refinement of the sequence motif and its taxon-specific differences

scientific article published in April 2002

NMR studies reveal a novel grab and release mechanism for efficient catalysis of the bacterial 2-Cys peroxiredoxin machinery

scientific article published on 24 September 2015

Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins

scientific article published on 25 October 2011

Novel SNP improves differential survivability and mortality in non-small cell lung cancer patients

scientific article

Novel insights into the vancomycin-resistant Enterococcus faecalis (V583) alkylhydroperoxide reductase subunit F.

scientific article published on 18 September 2017

Nuclear import of a lipid-modified transcription factor: mobilization of NFAT5 isoform a by osmotic stress

scientific article published on 15 November 2011

On filtering false positive transmembrane protein predictions

scientific article

On the necessity of different statistical treatment for Illumina BeadChip and Affymetrix GeneChip data and its significance for biological interpretation

scientific article

On the necessity of dissecting sequence similarity scores into segment-specific contributions for inferring protein homology, function prediction and annotation

scientific article

PSIC: profile extraction from sequence alignments with position-specific counts of independent observations

scientific article published in May 1999

Parameterization of disorder predictors for large-scale applications requiring high specificity by using an extended benchmark dataset

scientific article

PaxGenes: Evolution and Function

article

Pds5 cooperates with cohesin in maintaining sister chromatid cohesion.

scientific article

Phosphorylation-induced autoinhibition regulates the cytoskeletal protein Lethal (2) giant larvae.

scientific article published on February 2005

PhyloDome--visualization of taxonomic distributions of domains occurring in eukaryote protein sequence sets

scientific article

Post-translational GPI lipid anchor modification of proteins in kingdoms of life: analysis of protein sequence data from complete genomes

scientific article

Post-translational Regulation of Radioactive Iodine Therapy Response in Papillary Thyroid Carcinoma

scientific article published on 01 December 2017

Posttranslational modifications and subcellular localization signals: indicators of sequence regions without inherent 3D structure?

scientific article published on April 2007

Potential human adaptation mutation of influenza A(H5N1) virus, Canada

scientific article published on September 2014

Predicting function: from genes to genomes and back

scientific article

Prediction of lipid posttranslational modifications and localization signals from protein sequences: big-Pi, NMT and PTS1

scientific article

Prediction of peroxisomal targeting signal 1 containing proteins from amino acid sequence

scientific article

Prediction of posttranslational modification of proteins from their amino acid sequence

scientific article published on January 2010

Prediction of potential GPI-modification sites in proprotein sequences

scientific article

Prediction of secondary structural content of proteins from their amino acid composition alone. I. New analytic vector decomposition methods

scientific article published on June 1996

Prediction of secondary structural content of proteins from their amino acid composition alone. II. The paradox with secondary structural class

scientific article published on June 1996

Prediction of sequence signals for lipid post-translational modifications: insights from case studies

scientific article

Prenylation of viral proteins by enzymes of the host: Virus-driven rationale for therapy with statins and FT/GGT1 inhibitors

scientific article published on 8 September 2017

Prenylation: From bacteria to eukaryotes

article by E. S. Marakasova et al published September 2013 in Molecular Biology

Prenylation: from bacteria to eukaryotes

scientific article published on September 2013

Principles of helix-helix packing in proteins: the helical lattice superposition model

scientific article published in January 1996

Protein Prenylation: An (Almost) Comprehensive Overview on Discovery History, Enzymology, and Significance in Physiology and Disease

article by Wolfgang Benetka et al published 25 September 2006 in Monatshefte für Chemie

Protein function machinery: from basic structural units to modulation of activity.

scientific article

Protein prenyltransferases

scientific article

Protein prenyltransferases: anchor size, pseudogenes and parasites

scientific article

Protein structure prediction: recognition of primary, secondary, and tertiary structural features from amino acid sequence.

scientific article

Proteins with two SUMO-like domains in chromatin-associated complexes: the RENi (Rad60-Esc2-NIP45) family

scientific article

Purification and crystallization of yeast glycosylphosphatidylinositol transamidase subunit PIG-S (PIG-S(71-467)).

scientific article

RNAase-III enzyme Dicer maintains signaling pathways for differentiation and survival in mouse cortical neural stem cells

scientific article

Reannotation of the CELO genome characterizes a set of previously unassigned open reading frames and points to novel modes of host interaction in avian adenoviruses

scientific article

Reconstruction of gene association network reveals a transmembrane protein required for adipogenesis and targeted by PPARγ.

scientific article published on 15 June 2010

Reducing the haystack to find the needle: improved protein identification after fast elimination of non-interpretable peptide MS/MS spectra and noise reduction

scientific article

Refinement and prediction of protein prenylation motifs

scientific article

Regulation of chromatin structure by site-specific histone H3 methyltransferases

scientific article

Rotamers: to be or not to be? An analysis of amino acid side-chain conformations in globular proteins

scientific article published in March 1993

S. pombe meiotic linear elements contain proteins related to synaptonemal complex components.

scientific article published in July 2004

SNEV is an evolutionarily conserved splicing factor whose oligomerization is necessary for spliceosome assembly

scientific article

SPACER: Server for predicting allosteric communication and effects of regulation.

scientific article published on 03 June 2013

SUMO conjugation in plants

scientific article published on 23 September 2004

Sequence properties of GPI-anchored proteins near the omega-site: constraints for the polypeptide binding site of the putative transamidase

scientific article published on 01 December 1998

Similarity of molecular phenotype between known epilepsy gene LGI1 and disease candidate gene LGI2.

scientific article

Single-residue posttranslational modification sites at the N-terminus, C-terminus or in-between: To be or not to be exposed for enzyme access

scientific article published on July 2015

Sporadic human cases of swine-origin influenza before 2009 share the Sa epitope

scientific article

Structural insight into the glycosylphosphatidylinositol transamidase subunits PIG-K and PIG-S from yeast

scientific article published on 4 December 2010

Structural modelling of the lumenal domain of human GPAA1, the metallo-peptide synthetase subunit of the transamidase complex, reveals zinc-binding mode and two flaps surrounding the active site

scientific article published on 29 September 2020

Structural principles of B-DNA grooves hydration in fibers as revealed by Monte Carlo simulations and x-ray diffraction

scientific article published on 01 August 1990

Structural requirements for interaction of peroxisomal targeting signal 2 and its receptor PEX7.

scientific article published on 5 November 2011

Structure of the hydration envelope of the B-form of polydeoxyribonucleotides poly(dA-dC).poly(dG-dT) and poly(dA-dG).poly(dTs-dT) from the data of Monte-Carlo simulation

scientific article

Structure of the hydration shells of oligo(dA-dT)·oligo(dA-dT) and oligo(dA)·oligo(dT) tracts in B-type conformation on the basis of Monte Carlo calculations

scientific article published in 1990

Structure, mechanism and ensemble formation of the alkylhydroperoxide reductase subunits AhpC and AhpF from Escherichia coli

scientific article

Synthesizing non-natural parts from natural genomic template

scientific article

TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter.

scientific article published in January 2004

TPR subunits of the anaphase-promoting complex mediate binding to the activator protein CDH1

scientific article (publication date: 2 September 2003)

Tachyon search speeds up retrieval of similar sequences by several orders of magnitude

scientific article

Taxonomy workbench

scientific article

The 160K Natural Organism Library, a unique resource for natural products research

scientific article published on 01 July 2018

The Brix domain protein family -- a key to the ribosomal biogenesis pathway?

scientific article published in June 2001

The Geographic Variation of Surveillance and Zoonotic Spillover Potential of Influenza Viruses in Domestic Poultry and Swine

scientific article published on 27 November 2018

The Janus-faced E-values of HMMER2: extreme value distribution or logistic function?

scientific article

The Recipe for Protein Sequence-Based Function Prediction and Its Implementation in the ANNOTATOR Software Environment

scientific article

The STIR-domain superfamily in signal transduction, development and immunity

scientific article

The Tudor domain 'Royal Family': Tudor, plant Agenet, Chromo, PWWP and MBT domains

scientific article (publication date: February 2003)

The WD40 propeller domain of Cdh1 functions as a destruction box receptor for APC/C substrates

scientific article

The highly pathogenic H7N3 avian influenza strain from July 2012 in Mexico acquired an extended cleavage site through recombination with host 28S rRNA

scientific article published on May 2013

The ring between ring fingers (RBR) protein family

scientific article published on January 2007

The substrate specificity profile of human granzyme A.

scientific article

To kill or to be killed: pangenome analysis of Escherichia coli strains reveals a tailocin specific for pandemic ST131

scientific article published on 01 January 2022

To kill or to be killed: pangenome analysis of Escherichia coli strains reveals a tailocin specific for pandemic ST131

scientific article published in 2022

Toward Allosterically Increased Catalytic Activity of Insulin-Degrading Enzyme against Amyloid Peptides

scientific article published on 16 December 2016

Towards Complete Sets of Farnesylated and Geranylgeranylated Proteins

scientific article published on 15 August 2007

Towards complete sets of farnesylated and geranylgeranylated proteins

scientific article

Transamidase subunit GAA1/GPAA1 is a M28 family metallo-peptide-synthetase that catalyzes the peptide bond formation between the substrate protein's omega-site and the GPI lipid anchor's phosphoethanolamine

scientific article

Transition steps in peroxide reduction and a molecular switch for peroxide robustness of prokaryotic peroxiredoxins

scientific article

Translational Informatics Management System (TIMS): Towards OMICS based clinical data management for long term curation of clinical studies

scientific article published on 03 August 2019

Transmembrane helix: simple or complex

scientific article

Two fission yeast homologs of Drosophila Mei-S332 are required for chromosome segregation during meiosis I and II.

scientific article published in February 2004

Ubiquitylation in plants: a post-genomic look at a post-translational modification

scientific article

Unix interfaces, Kleisli, bucandin structure, etc. -- the heroic beginning of bioinformatics in Singapore

scientific article published on 5 June 2014

Wanted: subcellular localization of proteins based on sequence ⬇️

scientific article published on April 1, 1998

brakeless is required for lamina targeting of R1-R6 axons in the Drosophila visual system

scientific article published in June 2000

dissectHMMER: a HMMER-based score dissection framework that statistically evaluates fold-critical sequence segments for domain fold similarity

scientific article published in August 2015

pkaPS: prediction of protein kinase A phosphorylation sites with the simplified kinase-substrate binding model

scientific article published on 12 January 2007

xHMMER3x2: Utilizing HMMER3's speed and HMMER2's sensitivity and specificity in the glocal alignment mode for improved large-scale protein domain annotation

scientific article

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