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Recent news
2025
2025, I am officially on the academic job market! Feel free to reach out to me if you are aware of a position in genomics and computational biology.
2025-04-22, I submitted the revised manuscript "EvANI benchmarking workflow for evolutionary distance estimation", Preprint.
2025-04-20, We are submitting three manuscripts to the orthology special issue of the Journal of Molecular Evolution; one as the first author "Quest for orthologs in the era of data deluge and AI", another that I'm the second to last author "Reconstructing evolutionary histories with hierarchical orthologous groups", and as the last author with our former intern, Ali "OrthoXML-tools: a toolkit for manipulating OrthoXML files for orthology data" , Code.
2025-04-12, It's my pleasure to contribute to the GIAB small variant benchmark set for human genome sample HG002 using the Q100 T2T assembly using the personlzied pangenome approach.
2025-03-00, I'm glad that the work led by Fahimeh, the PhD student who I supervised in Lausanne, has been published in the Abstract Collection of - European Journal of Human Genetics , titled "cfCNV: an optimized pipeline for detecting copy number variations for cell free DNA data", previously presented at the European Society of Human Genetics Conference (ESHG).
2025-00-00, The study section for reviewing my grant seems to be paused.
2025-01-07, Our collabrative work (accross three continents) on copy number variation of C. elegans is now published Genome Biology and Evolution .
2024-01-03, FastOMA is online in Nature methods!
2024
2024-11-14, I'm presenting a poster at Biological Data Science, Cold Spring Harbor Laboratory, New York, on "ANI, are you OK? Challenges for k-mer-based estimation of evolutionary distances"
2024-10-19, Our Quest for Orthologs Benchmark Service paper is accepted for publication in NAR Genomics and Bioinformatics!
2024-10-19, The GIAB genomic stratifications is published in Nature Communication!
2024-10-15, The Quest for Orthologs consortium is published a piece in Genome Biology and Evolution discussing the challanges in the era of biodiversity genomics.
2024-10-15, I have submitted a grant application. Wish me luck!
2024-10-02, The Minimizer review paper, with great viz for teaching, has been accepted for publication in Genome Biology!
2024-09-06, I've submitted the ANI evaluation abstract to the Biological Data Science! Meet you at CSHL in November 2024.
2024-07-25, FastOMA has been accepted for publication in Nature methods.
2024-06-00, we submitted the revised version of the FastOMA manuscript.
2024-06-03, we received the comments from 3 reviewes for the Minimizer manuscript from Genome Biology.
2024-05-13, we submited the revised manuscriot of the GIAB stratification project.
2024-05-01, starting a new PostDoc position at JHU.
2024-04-25, Sara's paper got published in BMC Genomics.
2024-04-01, sad moments of saying goodbye to friends in Lausanne.
2024-02-20, the status of FastOMA paper submission changed to "All Reviewers Assigned".
2024-01-19, we received a major revision for Sara's paper from BMC Genomics.
2024-01-19, congrats to Arun, our master student, who defended his thesis!
2024-01-16, we submitted the FastOMA manuscript!
2024-01-02, I gave a talk on k-mer approaches at Sharif university.
2023
2023-12-07, we are organsing the QfO8 meeting which will be held in Montreal, Submit your abstract now!
2023-11-07, we submitted the GIAB genomic stratifications manuscript.
2023-11-06, I gave a talk on computional comparative genomics at the Botanical Garden, University of Zurich.
2023-10-23, the OMA 2024 paper got accepted in the NAR journal.
2023-07-27, Sina presented FastOMA in ISMB/ECCB, France!
2023-07-04, Sara defended her master project!
2023-06-01, Fahimeh, who will be our visiting researcher, started her project on copy number variations.
2023-02-07, congragts to Alina, our former intern, who will start her DPhil at Oxford soon!
2022
2022-11-18, Sina gave a lecture as part of the Reviews in Quantitative Biology course.
2022-09-12, Sina presented in ECCB/QfO about BioQA summer project.
2022-08-23, Ali, our research intern, presented his poster at EPFL.
2022-03-17, OMAmo paper is accpeted for publication in Bioinformatics.
2021
2022-10-20, we submitted the OMAmo paper.
2021-09-12, I presented the PhaseRE project on "Identifying recombination location per sample using long reads." in the Basel Computational Biology Conference.
2021-05-01, I arrived in Lausanne (Switzerlands) to start a PostDoc at Department of Computational Biology, the University of Lausanne.
2021-03-01, I've got promoted to the manager of Bioinformatics Department in Life and Me company.
2020
2020-11-22, Alireza's paper on graph total variation got accepted!
2020-00-00, I've started to work for the Life and Me company as a bioinformatic analyst.
2020-09-09, I've submitted a proposal for the Marie Curie Postdoc fellowship (but I didn't get it in the end).
2020-07-28, I defended my PhD thesis with an excellence rank. Hurray!
2020-07-21, The panel of NDORMS-Oxford informed me that they will not be offering me the PostDoc position
2020-07-17, I've got accepted to work as a postdoc in UCL. Unfortunately, I couldn't proceed!
2020-05-05, I've got rejected after an interview with CafeBazaar for a data scientist position.
2019
2019-08-06, Proud to receive an offer letter from Human Genome Sequencing Center as an Exchange visitor.
2019-03-26, My first first-author paper, HapMC, is published in PLOS one, after several rejection in other lower IF journals.
2019-03-21, I had an Skype interview with [The Jackson Laboratory](www.jax.org) as a computational sciences summer intern (but in the end I didn't get it.)
2018-10-14, I've arrived in the Netherlands to join the WUR bioinformatics group as a guest researcher.
2015-09-23, I've started my PhD at Iran university of science and technology.
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