Data Integration: With Bioinformatics to Biological Knowledge

Program

• • Poster presentation
  • P-III-0763

  Overcoming notorious challenges in prokaryotic genome annotation: identifying missed small proteins with proteogenomics and Ribo-seq and consolidating genome annotations

  • Christian Ahrens (Zurich / CH)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0764

  Evaluating Phospho-peptides quantification across various acquisition methods and bioinformatic tools: novel standards and their utility in algorithm development

  • Pinar Altiner (Toulouse / FR)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0765

  Complex portal: a resource for functionally annotated macromolecular complexes

  • Sucharitha Balu (Cambridge / GB)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0766

  Autoprot: a modular package for processing, analysis and visualization of mass spectrometry proteomics data in Python

  • Julian Bender (Wuerzburg / DE)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0767

  Cross talk between Parkinson's disease and Alzheimer's disease in identification of concordant and discordant marker

  • Deeptarup Biswas (Mumbai / IN)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0768

  Integrating proteomics and PTM data for comprehensive multi-omics analysis

  • Tim Blokker (Hamburg / DE)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0769

  ProteoBench: a community-curated platform for comparison of proteomics data analysis workflows

  • Robbin Bouwmeester (Ghent / BE)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0770

  The annotation of post-translation modifications in UniProtKB

  • Emily Bowler-Barnett (Hinxton / GB)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0771

  PROTzilla – an open-source analysis platform for proteomics and peptidomics data for paper-ready visualizations

  • Selena Braune (Potsdam / DE)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0772

  Linking the human metabolome and proteome in UniProtKB through Rhea

  • Lionel Breuza (Geneva / CH)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0773

  Confident protein datasets for liquid-liquid phase separation studies

  • Michał Burdukiewicz (Białystok / PL)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0774

  Enhancing biomolecule detection with a multi-Omic co-clustering model in mass spectrometry: incorporating additional spatial constraints for detecting latent patterns in imaging

  • Giulia Capitoli (Vedano al Lambro / IT)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0776

  Peptide ranking strategy towards targeted workflow verification in brain disorders

  • Deeptarup Biswas (Mumbai / IN)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0777

  QSample: a quality control system to monitor user's samples in proteomics core facilities

  • Cristina Chiva (Barcelona / ES)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0778

  Serving your proteomics analysis needs – the Core Unit for Bioinformatics (CUBiMed.RUB) in Bochum and de.NBI 2.0 / ELIXIR-DE

  • Martin Eisenacher (Bochum / DE)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0779

  A shiny application to create a library from DDA data for DIA-NN analysis and its visualization

  • Amr Elguoshy (Niigata / JP)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0780

  Investigating the phenotypic proteome of Triple Negative Breast Cancer (TNBC) for precision medicine

  • Akram Emdadi (Stockholm / SE)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0782

  A comprehensive and accurate representation of human gene functions from large-scale evolutionary modeling and experimental gene ontology annotation

  • Marc Feuermann (Geneva / CH)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0783

  To be or not to be – a non-canonical ORF MS-detectable?

  • Ivo Fierro-Monti (Hinxton / GB)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0784

  CopyProtR: An R package for evaluating proteomics data in its genomic context

  • Dennis Friedel (Heidelberg / DE)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0785

  Paradigm shift in biomarker translation: an innovative and automated pipeline to generate and select clinical-grade signature peptides during DIA discovery

  • Qin Fu (Beverly Hills, CA / US)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0786

  Deciphering cross-cohort metabolic signatures of immune responses and their implications for disease pathogenesis

  • Jianbo Fu (Zurich / CH)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0787

  The uncharted territories of EGF signaling: a deep-dive via short-time phosphoproteomics and network models

  • Martin Garrido-Rodriguez (Heidelberg / DE)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0788

  Integrating statistical tests for differential analysis in quantitative proteomics: enhancing power while controlling false discoveries

  • Quentin Giai Gianetto (Paris / FR)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0789

  Estimating the taxonomic composition of complex samples using metaproteomics and machine learning

  • Hamid Hachemi (Codolet / FR)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0790

  Integrated Omics-Based Knowledgebase BrainProt™ and BDDF: Advancing the Identification of Druggable Proteins

  • Ankit Halder (Mumbai / IN)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0791

  From post-translational modifications to proteoforms

  • Yannick Hartmaring (Potsdam / DE)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0792

  Exploring dynamic behavior with SmartPhos: an integrated pipeline for low-input, high-throughput Phosphoproteomics in clinical samples

  • Barbara Helm (Heidelberg / DE)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0793

  Reactome biomolecular pathways database – update

  • Henning Hermjakob (Hinxton / GB)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0794

  Spectra-sum method for protein qunatification from LC-MS/MS data with TMT-labeling

  • Heeyoun Hwang (Cheongju-si / KR)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0795

  Machine learning unlocks new insights in ovarian cancer proteomics

  • Ekaterina Ilgisonis (Moscow / RU)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0796

  Spatial proteomic analysis of breast cancer heterogeneity unravels mechanisms of cancer cell phenotypic plasticity

  • Shiri Karagach (Rehovot / IL)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0797

  Evaluating knowledge graphs for disease prediction and therapeutic drug recommendation using proteomics data

  • Daniel Kautzner (Bielefeld / DE)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0798

  TIMS DIA-NN 3.0: improved algorithms to enhance peptide detection with confidence and accuracy

  • Jonathan Krieger (Mississauga / CA)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0799

  The PRIDE Affinity-proteomics Archive (PRIDE-AP): making affinity proteomics datasets FAIR

  • Deepti Kundu (Cambridge / GB)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0800

  Input normalization and PTM stoichiometry calculations in Spectronaut^®

  • Veronique Laforte (Schlieren / CH)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0801

  A protein sequence-based deep transfer learning framework for identifying human proteome-wide deubiquitinase-substrate interactions

  • Dong Li (Beijing / CN)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0802

  Reproducibility-optimized multi-group statistic and survival analysis

  • Markus Lindén (Turku / FI)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0803

  Semares – a semantic and FAIR technology framework for proteomics and multi-omics data integration, analysis and visualization

  • Thomas Lingner (Goettingen / DE)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0804

  Functional analysis of (phospho)-proteomic data with rROMA enables per-sample pathway and kinase activity quantification

  • Stephane Liva (Paris / FR)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0805

  Functional analysis of MS-based proteomics data: from protein groups to networks

  • Marie Locard-Paulet (Toulouse / FR)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0806

  PhosX: data-driven kinase activity inference from phosphoproteomics experiments

  • Alessandro Lussana (Hinxton / GB)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0807

  Modeling multipartite networks integrating high-throughput phospho-proteomics (ModPhosphoNet)

  • Loredana Martignetti (Paris / FR)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0808

  A Common Data Analysis Pipeline (CDAP) for data independent acquisition mass spectrometry data

  • Aaron Maurais (Seattle, WA / US)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0809

  Molecular complex navigator: a new way to visualise related complexes in complex portal

  • Juan Jose Medina Reyes (Cambridge / GB)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0810

  A pipeline for designing proteogeno-typic peptide standards to quantify variants: the potential of neutrophil elastase in proteogenomics

  • Yassene Mohammed (Leiden / NL)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0811

  PTMNavigator: interactive visualization of differentially regulated post-translational modifications in cellular signaling pathways

  • Julian Müller (Freising / DE)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0812

  KPOP: Korea ProteOme rePository for open access proteomics data

  • Eunok Paek (Seoul / KR)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0813

  Liver proteome analysis in 111 knock-out mouse models provides crucial references for the function of genes influencing metabolic processes

  • Areum Nam (Seoul / KR)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0814

  Are we there yet? Assessing the readiness of single-cell proteomics to answer biological hypotheses

  • Alyssa A Nitz (Provo, UT / US)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0815

  Single nucleus RNA sequencing analysis combined with in vitro validation in human dopaminergic neurons reveals aspects of idiopathic Parkinson's disease pathology

  • Sofia Notopoulou (Thessaloniki / GR)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0816

  The UniProt KnowledgeBase – supporting proteomics research

  • Sandra Orchard (Hinxton / GB)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0817

  SimpliFi in a box: multiomics data analysis on private servers

  • Jim Palmeri (Fairport, NY / US)
  • John Wilson (Fairport, NY / US)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0818

  Complete quantitative data-independent acquisition mass spectrometry workflow using Nextflow

  • Mats Daniel Perk (Turku / FI)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0819

  Uniquome: construction and decoding of a novel proteomic atlas that contains new peptide entities

  • Vasileios Pierros (Athens / GR)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0820

  OutCyte UPS 2.0: a representation learning based new tool for leaderless protein secretion prediction

  • Gereon Poschmann (Duesseldorf / DE)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0821

  Integrating quantitative proteomics and pharmacoproteomics for reliable biomarker discovery in Alzheimer's disease

  • Murih Pusparum (Mol / BE)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0822

  Leveraging MD 2.0 to support proteomics-based biomarker discovery

  • Anna Quaglieri (Melbourne / AU)
  • Mark Condina (Melbourne / AU)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0823

  AlphaFold3 and protein modifications: obvious strengths and significant challenges

  • Pathmanaban Ramasamy (Ghent / BE)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0824

  Beyond the reference code: unveiling multicoding genes and their alternative proteins and microproteins

  • Xavier Roucou (Sherbrooke / CA)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0825

  Human proteome size as a function of development of experimental technologies and bioinformatics methods

  • Elizaveta Sarygina (Moscow / RU)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0826

  Standardization efforts in metaproteomics

  • Kay Schallert (Dortmund / DE)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0827

  Systematic proteomic meta-analysis of osteoblasts, bone, and blood: identifying druggable targets, active factors, and biomarkers for bone biomaterial development

  • Johannes R. Schmidt (Leipzig / DE)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0828

  Improved protein quantification by using bipartite peptide-protein graphs

  • Karin Schork (Bochum / DE)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0829

  OmicsQ: a user-friendly and interactive platform for quantitative proteomics data analytics

  • Veit Schwämmle (Odense / DK)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0830

  MultiOmicsAgent: guided extreme gradient-boosted decision trees-based approaches for biomarker-candidate discovery in multi-omics data

  • Jens Settelmeier (Zurich / CH)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0831

  Systematic discovery and validation of degrader targets using deep proteomics screening combined with bioinformatics

  • Bachuki Shashikadze (Planegg / DE)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0832

  Digital proteome: a resource for target expression across 22 tissues in human and preclinical species

  • Polina Shichkova (Schlieren / CH)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0833

  Significantly faster library-free dia-PASEF analysis with a Spectronaut integrated workflow in ProteoScape

  • Grzegorz Skoraczynski (Schlieren / CH)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0834

  BrainProt™: unraveling insights into meningioma tumorigenesis and neurological signaling cascades

  • Sanjeeva Srivastava (Mumbai / IN)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0835

  Relative quantification of proteins and of post-translational modifications with shared peptides: a weight-based approach

  • Mateusz Staniak (Wrocław / PL)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0837

  AliceDB – database and bioinformatic tool for identification of natural protein variants based on mass spectrometry measurements

  • Marcel Thiel (Gdansk / PL)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0838

  Multilayer data integration and cross-validation of human protein atlas datasets: a generative artificial intelligence driven roadmap to validate DNA target gene predictions of KRAB ZNF proteins

  • Hans-Juergen Thiesen (Rostock / DE)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0839

  deTELpy: a Python package for high throughput detection of amino acid substitutions in mass spectrometry datasets

  • Agnes Toth-Petroczy (Dresden / DE)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0840

  Disease-specific antibody databases for bottom-up proteomics

  • Xuan-Tung Trinh (Odense / DK)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0841

  Identification of candidates from high-throughput proteomic profiling of PROTAC-induced degradation

  • Nikita Verheyden (Frankfurt / DE)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0842

  Metadata matters: enhancing TBI proteomics

  • Melissa S Vorster (Stellenbosch / ZA)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0843

  A meta-analysis of brain and cerebrospinal fluid proteomic profiles of Huntington's disease animal models and human patients

  • Eleni Voukali (Libechov / CZ)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0844

  Integrated proteomics analysis of baseline protein expression in pig tissues

  • Shengbo Wang (Cambridge / GB)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0845

  Prolfquapp: protein differential expression analysis with advanced R tools and dynamic visual reporting

  • Witold Wolski (Zurich / CH)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0846

  Enhancing Mass Spectrometry Imaging Accuracy via Spatially Informed Mass Recalibration

  • Witold Wolski (Zurich / CH)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0847

  Integrating MSstats with INDRA for enhanced interpretation of proteomic differential analysis results

  • Anthony Wu (Medford, OR / US)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0848

  BioLadder: a bioinformatic platform primarily focused on proteomic data analysis

  • Songfeng Wu (Beijing / CN)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0849

  Cell type deconvolution of bulk proteome samples

  • Måns Zamore (Lund / SE)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0850

  DORSSAA: Drug-target interactOmics resource based on stability/solubility alteration assay

  • Ehsan Zangene (Helsinki / FI)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0851

  A data processing pipeline to streamline and evaluate report tables from different mass spectrometry data processing software

  • Tanja Ziesmann (Mainz / DE)

   Data Integration: With Bioinformatics to Biological Knowledge
• • Poster presentation
  • P-III-0852

  The sky is the limit: a cloud-based proteomics platform for the masses

  • Daniel Zolg (Garching / DE)

   Data Integration: With Bioinformatics to Biological Knowledge