Anne Niknejad

Scientist (Biology), Proteomics area. Expertise in Proteome annotation. MS/MS data analysis and results comparison (data mining). Technical support for users of MS/MS identification software. In charge of functioning tests for users. Management of the Product documentation. Team player, eager to learn.

2005-2009
Senior product specialist, GeneBio S.A., Genève
Technical support for clients:

• In charge of technical support for the MS/MS identification software Phenyx
• Management of issues via dedicated software (Mantis, OTRS)
• Use of WebEx service for targeted help on client server
• Involved in client management via SalesForce software

Product documentation:

• Improvement and management of the Product documentation for users (user manual, FAQ, Troubleshooting)
• Documents production and publication (Adobe FrameMaker, WebWorks Publisher, Wiki)

User tests:

• Improvement and management of user tests regarding new Phenyx releases, setting up of automatic tests in collaboration with the development team

Involvement into the Phenyx software development team:

• Responsible for user feedback by developers in order to match client expectations

2000-2005
Annotator (biocurator), GeneProt, Inc., Meyrin-Genève
Annotation of proteomes and plateform validation

Protein annotation:

• Protein characterisation (SignalP, TMHMM, NetPhos, PairCoil)
• Domain and family search (ProDom, Prosearch)
• Assessment and user of various in-house-developed tools and graphical software. Active and strong collaboration with the tool development team
• Respect of deadlines even under great time pressure

Differential study on paired proteomes (Disease and Control):

• Chromatographic elution profil analysis
• Specific literature search
• Validation of a «differential score»

Data mining:

• Use of public tools (Blast, Fasta, ClustalW) to retrieve protein information from public (SwissProt, TrEmbl) or private (Derwent) databanks
• Use of specific genomic tools (Genscan, Genewise) to retrieve information on protein genomic structure, and visualization by graphical software (Artemis, Sanger Centre)

Integration and annotation plateform:

• Assessment of the laboratory results (MS/MS spectra leading to identification of peptides)
• Setting up of parameters and testing of the identification tools

Patent update (IP):

• Responsible inside the annotation group for updating the patents issued from data mining
• Use of the Patent-In (USPTO) software for data capture

1999-2000
Scientist, GeneBio S.A, Genève
Participation in the development of a proprietary database collecting information about a family of enzymes:

• Strong collaboration with the Oracle development team to define the structure of data capture (Java entry forms, improvement and debugging)
• On-line literature search (PubMed, NCBI)
• Extraction of experimental data from the scientific literature

Training on data mining of peptidic and genomic sequences:

• Use of public databases (SwissProt, Prosite, TrEmbl, Embl) and related public software (Blast, ClustalW…)

1999
Scientist assistant, HUG, Genève
Consultation Interdisciplinaire de Médecine et Prévention de la Violence (CIMPV, Dr. Daniel Halpérin), management of the scientific literature

1997-1998
Councillor Professional digression spent in a civic activity by the Municipality of Chêne-Bourg, Geneva

1997
Scientist, Natural History Museum of Geneva
3 months to set up a small library (RefMan) at Department of Archeozoology, Pr. Louis Chaix

1991-1996
Scientist FNRS, C.M.U. Genève
Laboratory, literature searches (MedLine) at «Département d’Anesthésiologie, Pharmacologie et Soins Intensifs de Chirurgie (APSIC)», Geneva University, Dr. Béatrice Anner

1989-1994
Teacher of Biology, Collège Calvin, Geneva
Lectures and pratical work for second year students
Lectures for Adults at the “Collège du Soir pour Adultes”

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.