List of works - Martin Eisenacher

A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics

scientific article published in 2022

A combination of two electrophoretical approaches for detailed proteome-based characterization of SCLC subtypes

scientific article

A community proposal to integrate proteomics activities in ELIXIR

scientific article

A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects.

scientific article

A practical data processing workflow for multi-OMICS projects

scientific article

A proteomics sample metadata representation for multiomics integration and big data analysis

scientific article published in 2021

A standardized framing for reporting protein identifications in mzIdentML 1.2

scientific article

A structured proteomic approach identifies 14-3-3Sigma as a novel and reliable protein biomarker in panel based differential diagnostics of liver tumors

scientific article published on 5 November 2014

Amyloid beta a4 precursor protein-binding family B member 1 (FE65) interactomics revealed synaptic vesicle glycoprotein 2A (SV2A) and sarcoplasmic/endoplasmic reticulum calcium ATPase 2 (SERCA2) as new binding proteins in the human brain

scientific article

An easy-to-use Decoy Database Builder software tool, implementing different decoy strategies for false discovery rate calculation in automated MS/MS protein identifications

scientific article published in March 2008

Analysis of disease-associated protein expression using quantitative proteomics—fibulin-5 is expressed in association with hepatic fibrosis.

scientific article published on 6 April 2015

Annexin A10 optimally differentiates between intrahepatic cholangiocarcinoma and hepatic metastases of pancreatic ductal adenocarcinoma: a comparative study of immunohistochemical markers and panels.

scientific article published on 29 March 2017

Applications in brain proteomics: 8(th) HUPO Brain Proteome Project Workshop 7 October 2007, Seoul, Korea

scientific article published in May 2008

Autoimmune profiling with protein microarrays in clinical applications

scientific article published on 07 March 2014

BIONDA: a free database for a fast information on published biomarkers

scientific article

BioInfra.Prot: A comprehensive proteomics workflow including data standardization, protein inference, expression analysis and data publication.

scientific article

Boolean modeling techniques for protein co-expression networks in systems medicine.

scientific article

CalibraCurve: A Tool for Calibration of Targeted MS-Based Measurements

scientific article published on 22 February 2020

Characterization of Cerebrospinal Fluid via Data-Independent Acquisition Mass Spectrometry

scientific article published on 12 September 2018

Circulating U2 small nuclear RNA fragments as a diagnostic and prognostic biomarker in lung cancer patients.

scientific article

Combined enrichment of neuromelanin granules and synaptosomes from human substantia nigra pars compacta tissue for proteomic analysis ⬇️

scientific article published on August 3, 2013

Comparison of alternative MS/MS and bioinformatics approaches for confident phosphorylation site localization

scientific article published on 3 January 2014

Comparison of label-free and label-based strategies for proteome analysis of hepatoma cell lines.

scientific article published on 14 August 2013

Comprehensive proteomic analysis of Penicillium verrucosum

scientific article published on 7 March 2017

Computational proteomics in the post-identification era

scientific article published on 01 January 2014

Controlled vocabularies and ontologies in proteomics: overview, principles and practice

scientific article

Correction: The Proteome of Human Liver Peroxisomes: Identification of Five New Peroxisomal Constituents by a Label-Free Quantitative Proteomics Survey.

scientific article published on 16 October 2013

Data handling and processing in proteomics

scientific article published on 01 June 2009

Detection of patient subgroups with differential expression in omics data: a comprehensive comparison of univariate measures

scientific article (publication date: 2013)

Developing new methods to answer old and new questions in neurodegenerative diseases: 21(st) Workshop of the HUPO Brain Proteome Project (HBPP) 23-24 January 2014, Honolulu, Hawaii

scientific article published on 22 April 2014

Development of data representation standards by the human proteome organization proteomics standards initiative

scientific article

Diagnostic value of the impairment of olfaction in Parkinson's disease

scientific article

Differential proteomic and tissue expression analyses identify valuable diagnostic biomarkers of hepatocellular differentiation and hepatoid adenocarcinomas

scientific article published on 22 August 2015

Digital droplet PCR-based chimerism analysis for monitoring of hematopoietic engraftment after allogeneic stem cell transplantation

scientific article published on 21 June 2019

Direct-acting antivirals-based therapy decreases hepatic fibrosis serum biomarker microfibrillar-associated protein 4 in hepatitis C patients

scientific article published on 19 November 2018

Distinction between human cytochrome P450 (CYP) isoforms and identification of new phosphorylation sites by mass spectrometry

scientific article published on 2 October 2008

Dynamic changes of the Caenorhabditis elegans proteome during ontogenesis assessed by quantitative analysis with 15N metabolic labeling

scientific article

Enabling BioSharing - a report on the Annual Spring Workshop of the HUPO-PSI April 11-13, 2011, EMBL-Heidelberg, Germany

scientific article

Evaluation of the biomarker candidate MFAP4 for non-invasive assessment of hepatic fibrosis in hepatitis C patients

scientific article published on 04 July 2016

FE65 regulates and interacts with the Bloom syndrome protein in dynamic nuclear spheres - potential relevance to Alzheimer's disease

scientific article published on 9 April 2013

Factor inhibiting HIF-1 (FIH-1) modulates protein interactions of apoptosis-stimulating p53 binding protein 2 (ASPP2).

scientific article published on 19 April 2013

Find pairs: the module for protein quantification of the PeakQuant software suite

scientific article published on 21 August 2012

From proteomics data representation to public data flow: a report on the HUPO-PSI workshop September 2011, Geneva, Switzerland

scientific article published on February 2012

Functional metagenomics of the Thioredoxin superfamily

scientific article published on 24 December 2020

Getting a grip on proteomics data - Proteomics Data Collection (ProDaC).

scientific article

Glyoxalase 1-knockdown in human aortic endothelial cells - effect on the proteome and endothelial function estimates

scientific article published on 29 November 2016

Guidelines for reporting quantitative mass spectrometry based experiments in proteomics.

scientific article published on 14 March 2013

High Performance Proteomics: 7th HUPO Brain Proteome Project Workshop March 7-9, 2007 Wellcome Trust Conference Centre, Hinxton, UK.

scientific article published in August 2007

Highly immunoreactive IgG antibodies directed against a set of twenty human proteins in the sera of patients with amyotrophic lateral sclerosis identified by protein array

scientific article

Human Brain Proteome Project - 12th HUPO BPP Workshop. 26 September 2009, Toronto, Canada

scientific article

IGFBP1 in epithelial circulating tumor cells as a potential response marker to selective internal radiation therapy in hepatocellular carcinoma

scientific article published on 01 January 2014

Identification of novel biomarker candidates for the immunohistochemical diagnosis of cholangiocellular carcinoma.

scientific article

Identification of proteins that mediate the pro-viral functions of the interferon stimulated gene 15 in hepatitis C virus replication

scientific article published on December 2013

Immunohistochemical Markers Distinguishing Cholangiocellular Carcinoma (CCC) from Pancreatic Ductal Adenocarcinoma (PDAC) Discovered by Proteomic Analysis of Microdissected Cells

scientific article published on 7 December 2015

Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases

scientific article published on 13 January 2021

Implementing data standards: a report on the HUPOPSI workshop September 2009, Toronto, Canada

scientific article published in May 2010

Important issues in planning a proteomics experiment: statistical considerations of quantitative proteomic data

scientific article

Improving the default data analysis workflow for large autoimmune biomarker discovery studies with ProtoArrays.

scientific article

In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics.

scientific article published on 4 August 2016

Individual profiling of circulating tumor cell composition and therapeutic outcome in patients with hepatocellular carcinoma

scientific article published in August 2013

Integrated Fourier Transform Infrared Imaging and Proteomics for Identification of a Candidate Histochemical Biomarker in Bladder Cancer

scientific article published on 12 February 2019

Inter-Lab Proteomics: Data Mining in Collaborative Projects on the Basis of the HUPO Brain Proteome Project’s Pilot Studies ⬇️

scientific article published on January 1, 2011

Intestinal amino acid availability via PEPT-1 affects TORC1/2 signaling and the unfolded protein response

scientific article

Let me infuse this for you - A way to solve the first YPIC challenge

scientific article published on 01 March 2019

Lipidomic and proteomic characterization of platelet extracellular vesicle subfractions from senescent platelets

scientific article published on 21 October 2014

Low-bias phosphopeptide enrichment from scarce samples using plastic antibodies

scientific article

Maintaining standardization: an update of the HUPO Brain Proteome Project

scientific article published on April 2008

Managing the data explosion. A report on the HUPO-PSI Workshop. August 2008, Amsterdam, The Netherlands

scientific article published in February 2009

Mass analysis peptide sequence prediction (MAPSP).

scientific article published on 24 February 2006

MicroRNA-30c as a novel diagnostic biomarker for primary and secondary B-cell lymphoma of the CNS.

scientific article

MicroRNAs from urinary exosomes as alternative biomarkers in the differentiation of benign and malignant prostate diseases

scientific article published on 01 January 2022

Modeling and managing experimental data using FuGE.

scientific article

Monocytes-neutrophils-ratio as predictive marker for failure of first induction therapy in AML

scientific article published on 18 April 2019

Noninvasive diagnosis of urothelial cancer in urine using DNA hypermethylation signatures-Gender matters

scientific article published on 16 May 2019

Novel immunohistochemical markers differentiate intrahepatic cholangiocarcinoma from benign bile duct lesions

scientific article published on 04 January 2016

Observations from the Proteomics Bench

scholarly article

One Sample, One Shot - Evaluation of sample preparation protocols for the mass spectrometric proteome analysis of human bile fluid without extensive fractionation.

scientific article published on 05 December 2016

PAA: an R/bioconductor package for biomarker discovery with protein microarrays

scientific article

PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface

scientific article published on 10 June 2015

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets

scientific article

Peek a peak: a glance at statistics for quantitative label-free proteomics.

scientific article published on April 2010

ProCon - PROteomics CONversion tool

scientific article published on 13 July 2015

Protein Biomarker Discovery Using Human Blood Plasma Microparticles

scientific article published on 01 January 2019

Protein Inference Using PIA Workflows and PSI Standard File Formats

scientific article published on 05 December 2018

Protein inference using PIA workflows and PSI standard file formats

scholarly article published 23 September 2018

Protein variability in cerebrospinal fluid and its possible implications for neurological protein biomarker research

scientific article published in PLoS ONE

Proteome Analysis of a Hepatocyte-Specific BIRC5 (Survivin)-Knockout Mouse Model during Liver Regeneration

article

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

scientific article (publication date: March 2014)

Proteomic differences between hepatocellular carcinoma and nontumorous liver tissue investigated by a combined gel-based and label-free quantitative proteomics study.

scientific article

Proteomics Data Collection - 2nd ProDaC Workshop 5 October 2007, Seoul, Korea

scientific article published in April 2008

Proteomics Data Collection - 3rd ProDaC workshop April 22nd 2008, Toledo, Spain

scientific article published in October 2008

Proteomics Data Collection - 5th ProDaC Workshop: 4 March 2009, Kolympari, Crete, Greece.

scientific article published in July 2009

Proteomics Data Collection – The 1st ProDaC workshop 26 April 2007 Ecole Normale Supérieur, Lyon, France

article

Proteomics Standards Initiative Extended FASTA Format

scientific article published on 23 May 2019

Proteomics characterization of mouse kidney peroxisomes by tandem mass spectrometry and protein correlation profiling

scientific journal article

Proteomics data collection (ProDaC): publishing and collecting proteomics data sets in public repositories using standard formats

scientific article

Proteomics data collection--4th ProDaC workshop 15 August 2008, Amsterdam, The Netherlands

scientific article

Proteomics for everyday use: activities of the HUPO Brain Proteome Project during the 5th HUPO World Congress

scientific article published in April 2007

Proteomics of rimmed vacuoles define new risk allele in inclusion body myositis.

scientific article

Proteomics today: bioinformatics at its best. Proteomics and Bioinformatics -- an inseparable couple

scientific article published on 01 November 2008

Quality meets quantity - quality control, data standards and repositories

scientific article

Quantitative Secretome Analysis of Activated Jurkat Cells Using Click Chemistry-Based Enrichment of Secreted Glycoproteins

scientific article published on 03 October 2016

Quantitative Tissue Proteomics Analysis Reveals Versican as Potential Biomarker for Early-Stage Hepatocellular Carcinoma

scientific article published on 2 December 2015

Quantitative proteome analysis of plasma microparticles for the characterization of HCV-induced hepatic cirrhosis and hepatocellular carcinoma.

scientific article published on 19 June 2017

Quantitative proteome analysis reveals the correlation between endocytosis-associated proteins and hepatocellular carcinoma dedifferentiation.

scientific article published on 9 August 2016

Redox proteomics uncovers peroxynitrite-sensitive proteins that help Escherichia coli to overcome nitrosative stress

scientific article published on 21 May 2013

Reproducibility, Specificity and Accuracy of Relative Quantification Using Spectral Library-based Data-independent Acquisition

scientific article published on 07 November 2019

Search and decoy: the automatic identification of mass spectra.

scientific article published in January 2012

Sense and nonsense of pathway analysis software in proteomics.

scientific article published on 14 November 2011

Spatial and molecular resolution of diffuse malignant mesothelioma heterogeneity by integrating label-free FTIR imaging, laser capture microdissection and proteomics

scientific article

Spatial proteomics revealed a CX3CL1-dependent crosstalk between the urothelium and relocated macrophages through IL-6 during an acute bacterial infection in the urinary bladder

scientific article published on 28 February 2020

Study of Early Leaf Senescence inArabidopsis thalianaby Quantitative Proteomics Using Reciprocal14N/15N Labeling and Difference Gel Electrophoresis

Systematic Comparison of Label-Free, SILAC, and TMT Techniques to Study Early Adaption toward Inhibition of EGFR Signaling in the Colorectal Cancer Cell Line DiFi

scientific article published on 14 January 2020

The HUPO Brain Proteome project wish list--summary of the 9(th) HUPO BPP Workshop 9-10 January 2008, Barbados

scientific article published in June 2008

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary

scientific article (publication date: 2013)

The Human Proteome Organization-Proteomics Standards Initiative Quality Control Working Group: Making Quality Control More Accessible for Biological Mass Spectrometry.

scientific article

The PRIDE database and related tools and resources in 2019: improving support for quantification data

scientific article

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

scientific article published on 01 January 2022

The Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.

scientific article

The amino acid's backup bone - storage solutions for proteomics facilities

scientific article

The bacterial proteogenomic pipeline

scientific article published on 8 December 2014

The challenge of on-tissue digestion for MALDI MSI- a comparison of different protocols to improve imaging experiments

scientific article published on 17 February 2015

The membrane proteome of sensory cilia to the depth of olfactory receptors

scientific article

The mzIdentML data standard for mass spectrometry-based proteomics results

scientific article (publication date: July 2012)

The mzIdentML data standard version 1.2, supporting advances in proteome informatics.

scientific article

The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics

scientific article (publication date: August 2013)

The proteome of human liver peroxisomes: identification of five new peroxisomal constituents by a label-free quantitative proteomics survey

scientific article

Tissue-based quantitative proteome analysis of human hepatocellular carcinoma using tandem mass tags

scientific article published on 28 July 2016

Toward a Successful Clinical Neuroproteomics The 11th HUPO Brain Proteome Project Workshop 3 March, 2009, Kolymbari, Greece

scientific article

Transcriptome and Proteome Analysis in LUHMES Cells Overexpressing Alpha-Synuclein

scientific article published on 11 April 2022

Using Laboratory Information Management Systems as central part of a proteomics data workflow

scientific article

Varying survival of motoneurons and activation of distinct molecular mechanism in response to altered peripheral myelin protein 22 gene dosage.

scientific article

mzIdentML: An Open Community-Built Standard Format for the Results of Proteomics Spectrum Identification Algorithms ⬇️

scientific article published on January 1, 2011

mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics

scientific article published on 13 February 2019

List of works by Martin Eisenacher

A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics

A combination of two electrophoretical approaches for detailed proteome-based characterization of SCLC subtypes

A community proposal to integrate proteomics activities in ELIXIR

A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects.

A practical data processing workflow for multi-OMICS projects

A proteomics sample metadata representation for multiomics integration and big data analysis

A standardized framing for reporting protein identifications in mzIdentML 1.2

A structured proteomic approach identifies 14-3-3Sigma as a novel and reliable protein biomarker in panel based differential diagnostics of liver tumors

Amyloid beta a4 precursor protein-binding family B member 1 (FE65) interactomics revealed synaptic vesicle glycoprotein 2A (SV2A) and sarcoplasmic/endoplasmic reticulum calcium ATPase 2 (SERCA2) as new binding proteins in the human brain

An easy-to-use Decoy Database Builder software tool, implementing different decoy strategies for false discovery rate calculation in automated MS/MS protein identifications

Analysis of disease-associated protein expression using quantitative proteomics—fibulin-5 is expressed in association with hepatic fibrosis.

Annexin A10 optimally differentiates between intrahepatic cholangiocarcinoma and hepatic metastases of pancreatic ductal adenocarcinoma: a comparative study of immunohistochemical markers and panels.

Applications in brain proteomics: 8(th) HUPO Brain Proteome Project Workshop 7 October 2007, Seoul, Korea

Autoimmune profiling with protein microarrays in clinical applications

BIONDA: a free database for a fast information on published biomarkers

BioInfra.Prot: A comprehensive proteomics workflow including data standardization, protein inference, expression analysis and data publication.

Boolean modeling techniques for protein co-expression networks in systems medicine.

CalibraCurve: A Tool for Calibration of Targeted MS-Based Measurements

Characterization of Cerebrospinal Fluid via Data-Independent Acquisition Mass Spectrometry

Circulating U2 small nuclear RNA fragments as a diagnostic and prognostic biomarker in lung cancer patients.

Combined enrichment of neuromelanin granules and synaptosomes from human substantia nigra pars compacta tissue for proteomic analysis ⬇️

Comparison of alternative MS/MS and bioinformatics approaches for confident phosphorylation site localization

Comparison of label-free and label-based strategies for proteome analysis of hepatoma cell lines.

Comprehensive proteomic analysis of Penicillium verrucosum

Computational proteomics in the post-identification era

Controlled vocabularies and ontologies in proteomics: overview, principles and practice

Correction: The Proteome of Human Liver Peroxisomes: Identification of Five New Peroxisomal Constituents by a Label-Free Quantitative Proteomics Survey.

Data handling and processing in proteomics

Detection of patient subgroups with differential expression in omics data: a comprehensive comparison of univariate measures

Developing new methods to answer old and new questions in neurodegenerative diseases: 21(st) Workshop of the HUPO Brain Proteome Project (HBPP) 23-24 January 2014, Honolulu, Hawaii

Development of data representation standards by the human proteome organization proteomics standards initiative

Diagnostic value of the impairment of olfaction in Parkinson's disease

Differential proteomic and tissue expression analyses identify valuable diagnostic biomarkers of hepatocellular differentiation and hepatoid adenocarcinomas

Digital droplet PCR-based chimerism analysis for monitoring of hematopoietic engraftment after allogeneic stem cell transplantation

Direct-acting antivirals-based therapy decreases hepatic fibrosis serum biomarker microfibrillar-associated protein 4 in hepatitis C patients

Distinction between human cytochrome P450 (CYP) isoforms and identification of new phosphorylation sites by mass spectrometry

Dynamic changes of the Caenorhabditis elegans proteome during ontogenesis assessed by quantitative analysis with 15N metabolic labeling

Enabling BioSharing - a report on the Annual Spring Workshop of the HUPO-PSI April 11-13, 2011, EMBL-Heidelberg, Germany

Evaluation of the biomarker candidate MFAP4 for non-invasive assessment of hepatic fibrosis in hepatitis C patients

FE65 regulates and interacts with the Bloom syndrome protein in dynamic nuclear spheres - potential relevance to Alzheimer's disease

Factor inhibiting HIF-1 (FIH-1) modulates protein interactions of apoptosis-stimulating p53 binding protein 2 (ASPP2).

Find pairs: the module for protein quantification of the PeakQuant software suite

From proteomics data representation to public data flow: a report on the HUPO-PSI workshop September 2011, Geneva, Switzerland

Functional metagenomics of the Thioredoxin superfamily

Getting a grip on proteomics data - Proteomics Data Collection (ProDaC).

Glyoxalase 1-knockdown in human aortic endothelial cells - effect on the proteome and endothelial function estimates

Guidelines for reporting quantitative mass spectrometry based experiments in proteomics.

High Performance Proteomics: 7th HUPO Brain Proteome Project Workshop March 7-9, 2007 Wellcome Trust Conference Centre, Hinxton, UK.

Highly immunoreactive IgG antibodies directed against a set of twenty human proteins in the sera of patients with amyotrophic lateral sclerosis identified by protein array

Human Brain Proteome Project - 12th HUPO BPP Workshop. 26 September 2009, Toronto, Canada

IGFBP1 in epithelial circulating tumor cells as a potential response marker to selective internal radiation therapy in hepatocellular carcinoma

Identification of novel biomarker candidates for the immunohistochemical diagnosis of cholangiocellular carcinoma.

Identification of proteins that mediate the pro-viral functions of the interferon stimulated gene 15 in hepatitis C virus replication

Immunohistochemical Markers Distinguishing Cholangiocellular Carcinoma (CCC) from Pancreatic Ductal Adenocarcinoma (PDAC) Discovered by Proteomic Analysis of Microdissected Cells

Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases

Implementing data standards: a report on the HUPOPSI workshop September 2009, Toronto, Canada

Important issues in planning a proteomics experiment: statistical considerations of quantitative proteomic data

Improving the default data analysis workflow for large autoimmune biomarker discovery studies with ProtoArrays.

In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics.

Individual profiling of circulating tumor cell composition and therapeutic outcome in patients with hepatocellular carcinoma

Integrated Fourier Transform Infrared Imaging and Proteomics for Identification of a Candidate Histochemical Biomarker in Bladder Cancer

Inter-Lab Proteomics: Data Mining in Collaborative Projects on the Basis of the HUPO Brain Proteome Project’s Pilot Studies ⬇️

Intestinal amino acid availability via PEPT-1 affects TORC1/2 signaling and the unfolded protein response

Let me infuse this for you - A way to solve the first YPIC challenge

Lipidomic and proteomic characterization of platelet extracellular vesicle subfractions from senescent platelets

Low-bias phosphopeptide enrichment from scarce samples using plastic antibodies

Maintaining standardization: an update of the HUPO Brain Proteome Project

Managing the data explosion. A report on the HUPO-PSI Workshop. August 2008, Amsterdam, The Netherlands

Mass analysis peptide sequence prediction (MAPSP).

MicroRNA-30c as a novel diagnostic biomarker for primary and secondary B-cell lymphoma of the CNS.

MicroRNAs from urinary exosomes as alternative biomarkers in the differentiation of benign and malignant prostate diseases

Modeling and managing experimental data using FuGE.

Monocytes-neutrophils-ratio as predictive marker for failure of first induction therapy in AML

Noninvasive diagnosis of urothelial cancer in urine using DNA hypermethylation signatures-Gender matters

Novel immunohistochemical markers differentiate intrahepatic cholangiocarcinoma from benign bile duct lesions

Observations from the Proteomics Bench

One Sample, One Shot - Evaluation of sample preparation protocols for the mass spectrometric proteome analysis of human bile fluid without extensive fractionation.

PAA: an R/bioconductor package for biomarker discovery with protein microarrays

PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface