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Azim Dehghani Amirabad

Azim Dehghani Amirabad

Max-Planck-Institut für Informatik
High-throughput Genomics & Systems Biology

Campus E1 7
66123 Saarbrücken, Germany
email:   azim.dehghani@mpi-inf.mpg.de
phone:   +49 681 302 71924
fax:   +49 681 9325 3099
room:   309 (Building E1.7)

About

I have joined MIT CSAIL as a postdoctoral researcher in the Computational Biology team. I'm interested in the interplay between theory and experiment in the computational biology. I'm broadly interested in anything related to computational regulatory genomics and machine learning. My research revolves around development and application of principled machine learning methods for interpreting complex biological data sets.

Prior to joining MPI as a Ph.D. student, I worked as an assistant in MPI's High-throughput Genomics & Systems Biology by Marcel H. Schulz, contributing to projects in the area of epi-genomics and transcriptomics data analysis.

I spent Summer 2017 in the computational biology lab at Massachusetts Institute of Technology (MIT), USA, developing a multi-omics data integration approach for personalized de novo pathway mining in biological systems.

Publications

  • Multi-task learning of transcript isoform regulatory network
    Azim Dehghani Amirabad , Marcel H. Schulz
    In submission
  • Large-scale inference of competing endogeneous RNA networks with sparse partial correlation
    Markus List, Azim Dehghani Amirabad , Dennis Kostka, Marcel H. Schulz
    Bioinformatics (Proceedings of ISMB), 2019. (full text)

  • Multitask regression for context-specific prioritization of miRNA targets in transcripts
    Azim Dehghani Amirabad , Marcel H. Schulz
    Proceedings of German Conference for Bioinformatics 2016 (full text)

  • Transgenic expression of the RNA binding protein IMP2 stabilizes miRNA targets in murine microsteatosis
    Azim Dehghani Amirabad , Pathmanaban Ramasamy, Marina Wierz, Karl Nordström, Sonja M. Kessler, Marcel H. Schulz, Martin Simon
    Molecular Basis of Disease 2018 (full text)

  • More than the Killer Trait: Infection with the Bacterial Endosymbiont Caedibacter taeniospiralis Causes Transcriptomic Modulation in Paramecium Host
    Katrin Grosser, Pathmanaban Ramasamy, Azim Dehghani Amirabad, Marcel H. Schulz, Gilles Gasparoni, Martin Simon, and Martina Schrallhammer
    Genome Biol Evol. 2018 (full text)

  • Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction
    F Schmidt , N Gasparoni, G Gasparoni, K Gianmoena, C Cadenas, JK Polansky, P Ebert, KJV Nordström, M Barann, A Sinha, S Fröhler, J Xiong, A Dehghani Amirabad, F Behjati Ardakani, B Hutter, G Zipprich, B Felder, E Jürgen Eils, B Brors, W Chen, JG Hengstler, A Hamann, T Lengauer, P Rosenstiel, J Walter, MH Schulz
    Nucleic Acids Research, 29 November 2016
    (full text)

  • Epigenetic reprogramming in memory formation of human CD4+ T cells
    Durek P, Nordström KJV, Gasparoni G, Kressler C, Almeida M, Salhab A, Bassler K, Ulas T, Schmidt F, Xiong J, Glažar P, Klironomos F, Sinha A, Kinkley S, Yang X, Amirabad AD, Ardakani FB, Feuerbach L, Gorka O, Ebert P, Müller F, Li N, Frischbutter S, Schlickeiser S, Cendon C, Fröhler S, Felder B, Gasparoni N, Imbusch CD, Hutter B, Zipprich G, Tauchmann Y, Reinke S, Wassilew G, Hoffmann U, Arrigoni L, Richter AS, Sieverling L, Chang HD, Syrbe U, Manke T, Kalus U, Eils J, Brors B, Ruland J, Lengauer T, Rajewsky N, Chen W, Schulz MH, Dong J, Sawitzki B, Chung HR, Rosenstiel P, Schultze JP, Radbruch A, Walter J, Hamann A, Polansky JK
    Cell Immunity, Volume 45, Issue 5, 15 November 2016, (full text)

  • Epigenetic regulation of serotype expression antagonizes transcriptome dynamics in Paramecium tetraurelia
    M Cheaib, A Dehghani Amirabad, KJV Nordstroem, MH Schulz, M Simon
    DNA Research, Oxford Journals. 2015 Jun (full text)

  • Attenuation of NF-kB and activation of Nrf2 signaling by 1,2,4-triazine derivatives, protects neuron-like PC12 cells against apoptosis
    Tusi SK1, Ansari N, Amini M, Amirabad AD, Shafiee A, Khodagholi F
    Apoptosis. 2010 Jun;15(6):738-51 (full text)

  • Inhibition of LPS-induced apoptosis in differentiated-PC12 cells by new triazine derivatives through NF-kB-mediated suppression of COX-2.
    Ansari N1, Khodagholi F, Ramin M, Amini M, Irannejad H, Dargahi L, Amirabad AD
    Neurochem Int. 2010 Dec (full text)

  • Talks

  • POSTIT: Multi-task learning to infer transcript isoform regulation from epi-genomics and transcriptomics data
    Azim Dehghani Amirabad, Marcel H. Schulz
    Recomb-CCB 2018
  • Why asking for miRNA-gene interactions is wrong: A new paradigm for miRNA target prediction with expression data
    Azim Dehghani Amirabad , Marcel H. Schulz
    Presented at ISMB-SIG 2016 @ UAI 2016 Workshop on Machine Learning for Health

  • Multitask regression for context-specific prioritization of miRNA targets in transcripts
    Azim Dehghani Amirabad , Marcel H. Schulz
    Presented at German Conference for Biofinformatics 2016 and Recomb-CCB 2016 ( full text)

    Posters

  • POSTIT: Multi-task learning to infer transcript isoform regulation from epi-genomics and transcriptomics data
    Azim Dehghani Amirabad, Marcel H. Schulz
    Recomb 2018
  • Inferring Gene Regulatory Programs with Mixtures of Sparse Multi-Task Regression Models
    Tobias Heinen, Azim Dehghani Amirabad, Florian Schmidt, Marcel H. Schulz
    Recomb 2018
  • Gene structure aware method for miRNA target prediction reveals two prevalent genome-wide mechanisms for miRNA action
    Azim Dehghani Amirabad, Marcel H. Schulz
    The Non-Coding Genome 2015, EMBL Heidelberg, Germany.
  • On the power of RNA-seq for predicting miRNA-transcript interactions
    Azim Dehghani Amirabad, Marcel H. Schulz
    ISMB/ECCB 2015, Dublin, Ireland.
  • Exploiting RNA-Seq data to the fullest: Models for miRNA-transcript target interactions
    Azim Dehghani Amirabad, Marcel H. Schulz
    ECCB, Strasbourg, France, 2014

    Services

  • Sub-Reviewer: Recomb 2016
  • Sub-Reviewer: ISMB 2017
  • Software Tools

  • SPONGE: In this project, I designed, developed and implemented an algorithm for null distribution simulation for genralized sparse partial correlation with application to ceRNA network reconstruction from RNA-seq data.
  • FSMTR: An R package for solving sparse multi-task regressions for large scale problems (Comming soon! )
  • Teaching and Advising

  • Teaching assistant for seminar Probabilistic Methods for the Analysis of Next Generation Sequencing Data by Marcel H. Schulz WS 2016/17.
  • Teaching assistant for seminar Probabilistic Methods for the Analysis of Next Generation Sequencing Data by Marcel H. Schulz WS 2015/16.
  • Co-advised the Master's Thesis of Tobias Heinen
  • Co-advised the Bachelore's Thesis of Eva Paul

    Honors and Awards

  • DAADA fellowship for doctorial reseach visit at MIT
  • Travel fellowship for German Conference on Bioinformatics 2016
  • Travel fellowship for ISMB-SIG 2016
  • International Max Planck Research School for Computer Science ( IMPRS-CS ) PhD Fellowship
  • Ranked as top 0.01% out of more than 400,000 participants in competitive national University entrance examination for the B.Sc. degree, 2006

    Private

    "There are far, far better things ahead than any we leave behind." C.S. Lewis