Anne Niknejad

Expertise in biocuration and scientific literature management. Biocuration of transcriptomic data. Biocuration of chemical data for genome-scale metabolic networks. Experienced in clinical data harmonization (CDISC, OMOP). Expertise in proteome annotation, MS/MS data analysis and data mining.

2021: Biocuration Career Award

2010-present
Biocurator at bgee.org:

• Responsible for expression data curation
• Curation of anatomical homology relationships between animal species
• Creation of species-specific developmental ontologies

Biocurator at Vital-IT, Swiss Institute of Bioinformatics:

• Literature mining for various projects
• Curation of chemical data for MetaNetX platform
• Clinical data harmonization for European IMI projects

French: Native language
English: Good written & spoken practices
German: Basic written knowledge
Persian: Good spoken pratices

• Auditor to the Training courses of the Swiss Institute of Bioinformatics (SIB, 1999)
• Master of Biology (1990), Geneva University, Faculty of Sciences, Animal physiology department: «étude d’un facteur vasoactif, l’endothéline»
• High School diploma (Latin and classic Greek), Collège Rousseau, Geneva

• Pierre-Alain Binz, Anne Niknejad, Nicolas Budin, Olivier Evalet, Alexandre Masselot. Validation approaches in Protein Identification with Phenyx: not only FDR. SFEAP 2008, Tours (F), October 6-8, 2008
• Pierre-Alain Binz, Alexandre Masselot, Nicolas Budin, Anne Niknejad, Daniel Walther, Gerard Bouchet, Stéphane Pelhâtre, Sébastien Catherinet, Andreas Quandt, David Bouyssié, Ron D. Appel. Mass Spectrometry data interpretation in proteomics: What data is in my data? SMAP 2007, Pau (F), September 17-20, 2007
• Pierre-Alain Binz, Alexandre Masselot, Roman Mylonas, David Bouyssié, Anne Niknejad, Nicolas Budin, Ron Appel. Validation of protein and peptide identification from mass spectrometry data: peaklist issues. ProteomLux 2006, Luxembourg (Lux), Oct 11-14, 2006
• Pierre-Alain Binz, Alexandre Masselot, Roman Mylonas, David Bouyssié, Anne Niknejad, Ron Appel. Garbage in – Garbage out : The peak list issue in proteomics. 7th Siena meeting from Genome to Proteome: Back to the Future, Siena (I), Sept 3-7 2006
• Pierre-Alain Binz, Nicolas Budin, Anne Niknejad, Olivier Evalet, Daniel Walther, Ron D. Appel, Alexandre Masselot. Around Phenyx: where delivering peptides and protein identification and characterization is only a starting point. ABRF 2006, Long Beach (USA), Feb.2006
• I. Cusin, A. Bairoch, N. Barrillat, T. Baussant, C. Boiteau, L. Bougueleret, N. Budin, S. Carraud, D. Chiappe, N. Christmann, J. Colinge, I. Fasso, A. Gleizes, E. Gonzalez-Couto, F. Grange, D. Hochstrasser, A. Karmine, T. Kowall, S. Lagache, E. Mahe, H. Mattou, M. Moniatte, A. Niknejad, F. Perret, N. Pinaud, S. Reffas, P-O. Regamey, P-A. Rey, P. Rodriguez-Tome, K. Rose, G. Rossellat, C. Saudrais, C. Zwahlen Proteomic study of serum from 2500 pregnant women at first and third trimester of pregnancy.  From genome to proteome: biomarker discovery and imaging proteomes, 6th Sienna meeting, Sienna 2004.

• Pierre-Alain Binz, Nicolas Budin, Anne Niknejad, Olivier Evalet, Alexandre Masselot. How to choose and define a protein identification strategy adapted to an experimental workflow. ABRF 2006, Long Beach (USA), Feb.2006
• Pierre-Alain Binz, Nicolas Budin, Anne Niknejad, Alexandre Masselot. On the manipulation and comparison of protein and peptide identification results from MS data: walking on eggs in the peaks jungle. ABRF 2007, Tampa (USA) Mars 31-April 3, 2007

• Co-inventor, International patent application for "SECRETED POLYPEPTIDE SPECIES ASSOCIATED WITH CARDIOVASCULAR DISORDERS", published as: WO 04/089987.
• Co-inventor, International patent application for "SECRETED POLYPEPTIDE SPECIES ASSOCIATED WITH CARDIOVASCULAR DISORDERS", published as: WO 04/090551.
• Co-inventor, International patent application for "HUMAN ARGININE-RICH PROTEIN-RELATED COMPOSITIONS", published as: WO02/079246. Abandoned
• Co-inventor, International patent application for "Q9UL33/Q9NZZ4 AND Q9H5P3 SPLICE VARIANTS", published as: WO03/004532. Abandoned
• Co-inventor, International patent application for "CARCINOMA-RELATED PEPTIDES", published as: WO03/005033.
• Co-inventor, International patent application for "GENE ENCODING SERINE PROTEASES",published as: WO03/064641. Abandoned
• Co-inventor, International patent application for "ENGINEERED HUMAN KUNITZ-TYPE PROTEASE INHIBITOR", published as: WO03/070770.
• Co-inventor, International patent application for "SECRETED PEPTIDES", published as: WO04/005332.
• Co-inventor, International patent application for "SECRETED PEPTIDES", published as: WO04/005338.