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Sina Majidian

@sinamajidian.bsky.social
1.5K followers 1.3K following 208 posts

Hiring PhDs/Postdocs CGRLab.github.io | Assistant Professor, Data Science and AI division, Chalmers & University of Gothenburg| SciLifeLab | Formerly at JHU-Langmead, UNIL-Dessimoz, WUR

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Reposted by Sina Majidian
jakobheinz.bsky.social @jakobheinz.bsky.social · 20h
I’m excited to share our new preprint introducing HipHap, a tool for assigning long reads to haplotype-resolved diploid reference assemblies! With Max Marin, Matthew Meyerson, and @lh3lh3.bsky.social Preprint: www.biorxiv.org/content/10.6... 🧵 1/6
biorxiv.org
HipHap: Haplotype Assignment and Confidence Scoring for Diploid Reference Genomes
Diploid genome assemblies are now routinely available, but most read aligners were designed for haploid references, which have long been the gold standard. When reads are aligned to a diploid assembly...
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Ben Langmead @benlangmead.bsky.social · 30/09/2026
Have you been thinking of submitting an abstract to Genome Informatics UK this year? You still have time! The deadline is October 5. We'll see you there. coursesandconferences.wellcomeconnectingscience.org/event/genome...
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Reposted by Sina Majidian
Swiss National Science Foundation (SNSF) @snsf.ch · 30/09/2026
The SNSF will continue its successful funding from 2029 to 2032. With three key priorities, it is strengthening research that is collaborative, bold and forward-looking. It has requested 5.4 billion Swiss francs from the federal government. ➡️ sohub.io/tn9c
snf.ch
Research for the Switzerland of tomorrow
The SNSF will continue its successful funding from 2029 to 2032, strengthening research that is collaborative, bold and forward-looking.
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Christophe Dessimoz @dessimoz.bsky.social · 27/09/2026
ISMB is ranked A in CORE largely thanks to @yannponty.bsky.social ‘s tireless efforts. I believe ECCB could/should also be ranked A considering the scientific committee’s qualifications, acceptance rate etc. But it takes a lot of work to do the advocacy….
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Sina Majidian @sinamajidian.bsky.social · 27/09/2026
I'm surprised to see ECCB is ranked C in the CORE ranking! Good for ISMB, which is ranked A. No ranking for ACM-BCB! portal.core.edu.au/conf-ranks/?...
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Human Pangenome Reference Consortium @humanpangenome.bsky.social · 24/09/2026
Shredtools is making it easier to explore regions across a pangenome by quickly finding matching genomic regions across hundreds of genomes. The tool can identify a gene region across 476 human genomes in approximately half a second.  Read more: www.biorxiv.org/content/10.6...
biorxiv.org
Navigating the pangenome coordinate system with Shredtools
Existing notions of pangenome coordinates rely on hard-to-compute multiple sequence alignments. On the other hand, pangenome-wide exact unique matches (multi-MUMs) can be computed efficiently, and rep...
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Reposted by Sina Majidian
Antoine Limasset @npmalfoy.bsky.social · 24/09/2026
Yet another example of "So much to do, so little time"
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Megan Dennis @mydennis.bsky.social · 14/02/2025
A little late on this, but finally got around to reading this review on genome assembly. Found it both comprehensive and accessible. Made it recommended reading for members of the lab and the genomics grad students I am teaching. www.nature.com/articles/s41...
nature.com
Genome assembly in the telomere-to-telomere era - Nature Reviews Genetics
In this Review, Li and Durbin discuss how to generate telomere-to-telomere assemblies for large haploid or diploid genomes using currently available data types and algorithms, and outline remaining ch...
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Joe Hanly @hanliconius.bsky.social · 22/09/2026
I hate to do this with real data, but this is a persistent data vis issue in chromosome synteny riparian plots that we Need to get better at. Left, a synteny plot published today. Right, a rearranged version with exactly the same gross arrangement but with reordered chromosomes:
chromosome synteny riparian plot in which every chromosome has crossing lineschromosome synteny plot in which no chromosomes have crossing lines. The underlying structure is identical.
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Dr. Makenzie Mabry @makenziemabryphd.bsky.social · 23/09/2026
📢 Call for abstracts! PAG 34 is coming to San Diego JAN 8–12 2027! 🧬🌱 We’re organizing five interconnected sessions: • Domestication Genomics • Ancient DNA • Comparative Genomics – Animals • One Health Hologenomics • Wildlife Genomics Submit your abstract by *October 9*: forms.gle/EgwFCVyxaf7R...
forms.gle
PAG 2027 Abstract Submission: Ancient DNA, Domestication Genomics, Comparative Genomics of Animals, Wildlife Genomics, One Health Hologenomics
****DEADLINE: FRIDAY OCTOBER 9, 2026**** This is the abstract submission form for the following PAG 34 workshops: Paleogenomics and Degraded DNA Domestication Genomics Comparative Genomics of Animals...
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Nick Loman @pathogenomenick.bsky.social · 22/09/2026
Folks - if you're interested in how machine learning/AI can be used for microbial genomics, microbiome and metagenomics studies - please join us for a workshop in Birmingham on Thursday 8th October organised with CLIMB & NVIDIA. www.climb.ac.uk/blog/2026/09...
climb.ac.uk
Call for Applications: GPU-Accelerated Computing for Microbiome and Metagenomic Research · CLIMB
CLIMB is a cloud computing infrastructure for microbial bioinformatics — notebook servers, shared storage and reproducible workflows for genomics, metagenomics and pathogen surveillance researchers ac...
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Sina Majidian @sinamajidian.bsky.social · 22/09/2026
RSHash: a fast and space-efficient hash table for k-mers doi.org/10.1093/bioi...
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Sina Majidian @sinamajidian.bsky.social · 22/09/2026
Keep calm and be transparent: advice from scientists who retracted their papers www.nature.com/articles/d41...
nature.com
Keep calm and be transparent: advice from scientists who retracted their papers
Retractions correct the scientific record, but they have stigma attached to them. Some in the research community want that to change.
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Reposted by Sina Majidian
Johannes Cairns @jcairns.bsky.social · 05/09/2026
New pre-print out where we used machine learning to predict multi-strain bacterial growth curves from components. More than two strains improved prediction only a little, suggesting a weak role for higher-order interactions in this system: www.biorxiv.org/content/10.6...
biorxiv.org
How far can microbial monocultures predict growth in multi-strain communities?
Previous research in microbes successfully predicted biculture growth based on monoculture growth curves. Still, the usual model-based approach does not seem to extend to communities involving more th...
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Reposted by Sina Majidian
Johannes Cairns @jcairns.bsky.social · 17/09/2026
Happy that our article found a nice outlet in ISME J @isme-microbes.bsky.social. Advance article now available at: academic.oup.com/ismej/advanc...
academic.oup.com
Eco-evolutionary dynamics and environmental detoxification jointly shape bacterial community response to antibiotic perturbation
Abstract. Microbial communities frequently encounter recurrent antibiotic disturbance, yet how ecological, evolutionary, and environmental processes jointl
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Niema Moshiri @niema.net · 17/09/2026
My department is hiring an Assistant Professor! Come join us at @ucsandiego.bsky.social Computer Science & Engineering! Beautiful city, awesome colleagues, delicious tacos 😄 apol-recruit.ucsd.edu/JPF04649
apol-recruit.ucsd.edu
Assistant Professor - CSE
University of California, San Diego is hiring. Apply now!
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Rowan Kuminski @rowankuminski.bsky.social · 17/09/2026
⚠️Please share!⚠️ We are recruiting participants to complete a written interview for a PhD chapter on linguistic experiences of ecologists from Catalonia. Participants do not need to currently reside in Catalonia and can participate in Catalan, Spanish, and/or English. Thank you! 🪶🕷️🌲🐡🍄 #ecology
A white background with the words "Are you a Catalan ecologist?" at the top in black and red, adn underneath the text "If you are a professional ecologist from Catalonia and would be willing to do a written interview about your linguistic experiences, please contact Rowan Kuminski at r01tk22@abdn.ac.uk", and underneath in yellow it says "Gràcies!". In the background are transparent digital images of a shearwater and an oak leaf.
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Janani Durairaj (Jay) @ninjani.bsky.social · 16/09/2026
The PhD and Postdoc application links are now live! Come join me at UNIL to work on deep learning for protein structure, interactions & design. pickybinders.org#open-positions
career5.successfactors.eu
Career Opportunities: PhD student position in deep learning for enzyme structure & catalysis (22980)
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Sina Majidian @sinamajidian.bsky.social · 15/09/2026
Forecasting viral evolution from phylogenetic trees doi.org/10.64898/2026.08.27.741102
Overview of data, training, and evaluation for antiGen.
(A) The goal of antiGen is to predict future mutations to viral proteins based on available genomic surveillance data at present. Mutation forecasts can be applied towards proactive vaccine and antibody design, potentially avoiding future outbreaks. (B) antiGen is a machine learning method trained on pandemic-scale phylogenetic trees annotated with inferred mutations along each branch. These mutation-annotated trees are partitioned into training and testing examples, each consisting of a past genotype together with the set of substitutions to have altered that genotype. antiGen then learns the probability of each possible mutation being the next to emerge, conditional on the starting sequence, using a likelihood-based training objective. (C) We evaluate antiGen several ways: its ability to predict the next mutation(s) to affect a given query sequence, to forecast which mutations will occur in future population-wide genomic surveillance data, and to propose mutations that remain compatible with pseudovirus infectivity in experimental validation. (D) We use antiGen to study the evolution of four key viral proteins: the SARS-CoV-2 spike protein (PDB 6X79), the influenza hemagglutinin protein (PDB 2YP2), the respiratory syncytial virus fusion protein (PDB 5TDL), and the dengue virus envelope protein (PDB 4UTC).Figure 2
State-of-the-art performance for SARS-CoV-2 mutation forecasting.
(A) Definition of next-mutation recall for a single testing example; overall recall is then calculated by averaging the recall across all testing examples. (B, C) Next-mutation-recall-by-quantile curves based on all mutations and de novo mutations (mutations never seen in training data), respectively. antiGen is shown together with the best-performing model from each of the following three categories: DMS experiments, models that train on genomic surveillance data up through the train-test cutoff, and pre-pandemic data alone. (D, E)
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RECOMB Conference Series @recombconf.bsky.social · 15/09/2026
#RECOMB2027 is now accepting submissions and we'd love to see your best work! 📌 Abstract registration: October 28 📌 Full paper submission: November 4 📜More info: recomb.org/recomb2027/c...
recomb.org
Call for Papers
RECOMB 2027
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Reposted by Sina Majidian
Nature Biotechnology @natbiotech.nature.com · 14/09/2026
The SciLifeLab PULSE entrepreneurial model: accelerating drug discovery by bridging academia and industry - @scilifelab.se www.nature.com/articles/s41...
nature.com
The SciLifeLab PULSE entrepreneurial model: accelerating drug discovery by bridging academia and industry - Nature Biotechnology
A scalable blueprint for postdoctoral training embeds entrepreneurial venture mechanics and industry mobility directly into academic infrastructure to cultivate ‘T-shaped’ scientific leaders.
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Reposted by Sina Majidian
mitotalks.bsky.social @mitotalks.bsky.social · 13/09/2026
Are you working on mitochondria-related topics? We want to hear from you. MITOchat slots open for applications. Apply here: mitotalks.org Deadline: September 17th, 2026 We want to see the MITOscoence of the future again! Image
mitotalks.org
MITO talks online seminar series | mitochondria
MITOtalks: Online Seminar Series Focusing on Mitochondria
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UCSC Genome Browser @genomebrowser.bsky.social · 10/09/2026
New on hg38: Google DeepMind's AlphaGenome Variant Impact (AVI) scores, all 8.8 billion possible single-base changes. It scores non-coding DNA too, flagging things like the TERT promoter mutations common in cancer. See our news for more: bit.ly/GenomeBrowser...
AVI scores at the TERT locus on hg38, one subtrack per alternate allele. Scores stay high across the highlighted promoter, shown in red as EH38E3622530, and fall to background either side. The two promoter mutations most often seen in cancer sit inside it, beyond the end of every TERT transcript.
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Reposted by Sina Majidian
Yun S. Song @yun-s-song.bsky.social · 09/09/2026
We are thrilled to share that our GPN-Star manuscript is now published and freely available: doi.org/10.1038/s415... (1/n)
doi.org
Predicting genome-wide functional constraints with GPN-Star - Nature
GPN-Star, a genomic language model with a phylogeny-aware architecture for whole-genome alignment data, is shown to be a scalable and flexible tool for genetic variant effect prediction across species...
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Alex Cope, PhD (he/him) @alexcope241.bsky.social · 08/07/2026
If anyone is looking for a postdoc/staff scientist with experience in evolutionary genetics, computational biology/bioinformatics, and/or various omics methods (RNA-seq, Ribo-seq, LC-MS/MS), I'm still looking! (1) doi.org/10.1126/scie... (2) doi.org/10.1073/pnas... (3) doi.org/10.1371/jour...
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ISCB News @iscb.bsky.social · 09/09/2026
🧭 The September ISCB Career Compass is out! We have two featured jobs to check out, a list of what's leaving the Career Center this month, and an article sharing a few things to consider if you’re prepping for an industry interview. Read the full newsletter here: tinyurl.com/yk3dt6vf
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 08/09/2026
A fast method for building phylogenetic trees with millions of sequences and then a model that leverages the tree structure to predict viral protein evolution! @seyonec.bsky.social @claudiadriscoll.bsky.social @garykbrixi.bsky.social @brianhie.bsky.social www.biorxiv.org/content/10.6...
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Maria Sachkova @mariasachkova.bsky.social · 07/09/2026
Lecturer in Bioinformatics job at University of Bristol! www.bristol.ac.uk/jobs/find/de...
bristol.ac.uk
Details | Working at Bristol | University of Bristol
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Jessica Abbott @jessicakabbott.bsky.social · 05/09/2026
Are you a mathematical modeller in ecology and evolution looking for a job? My department has an opening! Please spread the word! lu.varbi.com/en/what:job/...
lu.varbi.com
Senior Lecturer in Computational Biology
Lund University welcomes applicants with different backgrounds and experiences. Gender equality, equal opportunities and diversity are fundamental principles in all parts of the University’s activit
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Open Athena @openathena.ai · 02/09/2026
With the generous support of The Jen-Hsun and Lori Huang Foundation, we have launched the largest live-streamed pretraining run in history, and Marin’s largest model yet: a fully open source 535B total parameter MoE model, with 18T tokens of data. Learn more at: openathena.ai/blog/huang-f...
openathena.ai
Marin's 535 billion parameter model training run launched with support of The Jen-Hsun and Lori Huang Foundation GPU gift
Open Athena announces the launch of Marin's largest training run yet—a 535B parameter large language model—with a generous gift of compute from The Jen-Hsun and Lori Huang Foundation.
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Sina Majidian @sinamajidian.bsky.social · 02/09/2026
Congratulations to all the ECCB 2026 Awardees! #ECCB2026
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Marc Robinson-Rechavi @marcrr.ecoevo.social.ap.brid.gy · 02/09/2026
Hamed Najafabadi: GHT-Selex: in vitro profiling of TF binding, on genomic fragments instead of synthetic DNA -> allow analysis of genomic information. Results very similar to ChIPseq, with extra info on binding affinity from enrichment cycles. #ECCB2026 doi.org/10.1038/s41592-026-03177-9
nature.com
GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors - Nature Methods
GHT-SELEX—high-throughput SELEX with fragmented genomic DNA—shows that transcription factors can be rather particular about which genomic loci they bind, and that C2H2 zinc finger proteins often engage different fingers at different sites.
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Sina Majidian @sinamajidian.bsky.social · 01/09/2026
Ana Conesa @anaconesa.bsky.social is sharing her scientific journey to a full house at #ECCB2026, from the challenges of being a young PI to the success of BLAST2GO and much more on long read
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Kristoffer Sahlin @ksahlin.bsky.social · 01/09/2026
strobealign v0.18.0 is out, and it's now written in Rust. Handwritten by Marcel, started 2y ago. No LLM involved (yet*). Contributions by Nicolas and Ivan. 1/3
github.com
Release Version 0.18.0 · ksahlin/strobealign
Changes Strobealign has been ported to Rust. The Rust version is at least as fast and accurate as the C++ version. There are currently some regressions due to the port: The Rust version cannot sat...
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OIST (Okinawa Institute of Science and Technology) @oistedu.bsky.social · 02/07/2026
Faculty Positions Open! OIST is now inviting applications for tenure-track assistant professor positions in two broad areas: - Chemistry & Materials Science - Life Sciences & Neuroscience Learn more and apply by October 1st: www.oist.jp/careers/facu... #FacultySearch
Open Faculty Positions at OIST
Image of a modern campus with a blue sea in the background, accompanied by images of scientists at work in the labs. 

Text describes we are looking for faculty in the fields of chemistry & materials science and life sciences & neuroscience.
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Marc Robinson-Rechavi @marcrr.ecoevo.social.ap.brid.gy · 01/09/2026
#ECCB2026 keynote: Anna-Sapfo Malaspinas Different subspecies of Treponemal pallidum are responsible for 4 diseases: syphilis, bejel, yaws and pinta. Paleopathology shows some pre-Colombian evidence of syphilis in the Old World, but it is very uncertain and the conclusions are debated.
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Torsten Schwede @torstenschwede.bsky.social · 31/08/2026
“Don’t wait for somebody else to solve the problem, don’t wait for somebody else to make the case for science.” Jeremy Farrar (WHO) opening keynote “Science in a changing world” at #ECCB2026 on the power of science beyond politics 🧬
Jeremy Farrar WHO opening keynote at ECCB “Science in a changing world”.
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Marc Robinson-Rechavi @marcrr.ecoevo.social.ap.brid.gy · 31/08/2026
Timofey Prodanov: Locityper calls haplotypes if they are already known to exist (i.e., human genome) doi.org/10.1038/s41588-025-02362-4 #ECCB2026
nature.com
Locityper enables targeted genotyping of complex polymorphic genes - Nature Genetics
Locityper is a general-purpose genotyper that can efficiently genotype and analyze a diverse set of genes, such as hyperpolymorphic HLA genes, using both short-read and long-read whole-genome sequencing data.
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Silvia Prieto @silviaprietob.bsky.social · 31/08/2026
Come visit my poster G.54 if you are at #eccb2026 ! 😃 #synteny #GO #animals #genes
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Torsten Schwede @torstenschwede.bsky.social · 31/08/2026
Looking forward to three days full of exciting science and inspiring conversations. #ECCB2026
ECCB 2026 is hosted by SIB in Geneva
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Sina Majidian @sinamajidian.bsky.social · 30/08/2026
It was a great pleasure to co-organise the 9th edition of the Quest for Orthologs consortium event in Lausanne. We had fantastic speakers and great discussions! qfo2026.unil.ch We'll also meet you in ECCB's workshop on orthology on Thursday! #genevalovesdata #eccb2026 #bioinformatics
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Janani Durairaj (Jay) @ninjani.bsky.social · 28/08/2026
Some exciting news: I'm joining the University of Lausanne @unil.bsky.social @dbc-unil.bsky.social as an Assistant Professor next month 🎉 My group will work on context-aware deep learning for protein structure, interaction & design. Postdoc and PhD openings coming soon - keep an eye out!
compare, predict, design
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Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 28/08/2026
I am delighted to announce that The Department of Human Genetics at the University of Utah is continuing a multi-year recruiting initiative for multiple tenure-track faculty positions at the rank of Assistant Professor. Please share and consider applying! utah.peopleadmin.com/postings/208...
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Simon Olsson @smnlssn.bsky.social · 25/08/2026
Happy to announce this years Structured Learning Workshop, Oct 27–28 at Chalmers, Gothenburg! Exceptional speakers from academia & industry. Limited spots, apply to attend via the waiting list: chalmers.ungapped.io/Events/5f087...
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Katharina Hoff @katharinahoff.bsky.social · 28/08/2026
Off to a new adventure: first, Quest for Orthologs 9 qfo2026.unil.ch, then ECCB eccb2026.org . Exciting!!!
qfo2026.unil.ch
Quest for Orthologs 9
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Gagneur lab @gagneurlab.bsky.social · 27/08/2026
Next week's Kipoi seminar by Michael Vollenweider von ETH Zurich. For once about how to evaluate rather than to model. As important, if not more.
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Sina Majidian @sinamajidian.bsky.social · 26/08/2026
A unicellular relative links aggregative multicellularity to animal origins www.nature.com/articles/s41...
Fig. 4 | Dynamics of gene expression during M. vibrans aggregation time
series. a, The average aggregate area in four biological replicate M. vibrans
monoxenic cultures was used to assess gene expression, taken at 12, 18, 24, 33,
48 and 72 h after inoculation into fresh medium. The coloured circle represents
the final timepoint at which RNA was extracted for that set of replicates. b, The
mean gene expression trends for the eight DEG clusters that arose from
expression profile clustering analysis. c, Schematic of the main groups of genes that increased and decreased in expression across the time series from each
DEG cluster based on gene enrichment analyses. See also Extended Data
Figs. 5–8, Supplementary Figs. 1 and 2 and Supplementary Data 7 and 8. The
constantly increasing and constantly decreasing DEG clusters are also referred
to without ‘constantly’. Fig. 5 | Key animal multicellularity genes are expressed during M. vibrans
aggregation. a, The percentage of DEGs linked to cell adhesion, cell signalling
and transcriptional regulation assigned to the DEG clusters outlined in Fig. 4b
and coloured according to the legend in c. The white numbers indicate
the absolute number of DEGs in each category. b, Overview of Opisthokonta
species relationships and ancestors indicated by coloured circles. c, Schematic
of two M. vibrans cells and heat maps showing the expression patterns of
different categories of genes encoding homologues of multicellularity-related
proteins that are significantly differentially expressed across the aggregation
time series. The bottom row indicates the timepoint; column A denotes the
predicted gene/domain age inferred from previous studies, coloured as in b,
and column C outlines DEG cluster assignment. Mean gene expression values
were calculated across timepoint replicates using normalized and variance-
stabilizing transformed gene counts that were then centred and row-scaled.
Abbreviations of genes, gene families and domain containing proteins: SPT,
spectrin; FSCN, fascin; DRF, diaphanous-related formin; DIA, diaphanous
DRF; MYOX, myosin X; ACTN, alpha actinin; COL4, alpha type IV collagen;
LAMG, laminin G domain; FNII and FNIII, fibronectin type II and type III
domains; FGC, fibrinogen C-terminal domain; ITGA, integrin alpha; ITGB,
integrin beta; ILK, integrin-linked kinase; VIN, alpha-catenin/vinculin family;
TLN, talin; CDH, cadherin domain; CLEC, C-type lectin domain; ERM-merlin,
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Adam Ameur @adameur.bsky.social · 12/02/2026
Save the date! The Long‑Read Sequencing Uppsala Meeting (#LRUA26) is happening Nov 2–4, with a great lineup of invited and selected speakers Stay tuned — registration and abstract submission will open soon🧬🖥️ lrua.se
lrua.se
Long-Read Sequencing Uppsala, November 2–4, 2026
#LRUA26: Empower your research with long-read sequencing technologies and connect with experts, peers, and industry leaders in Uppsala this November.
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Corrie Moreau @corriemoreau.bsky.social · 23/08/2026
📣 📣 📣 UPDATE: The 2026-2027 list of faculty and postdoc positions in ecology and evolutionary biology is out! Be sure to check out this active and helpful community run resource! docs.google.com/spreadsheets...
docs.google.com
ecoevojobs.net 2026-27
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Rui Borges @ruiborges23.bsky.social · 19/08/2026
1/4 Excited to share that our paper "Phylogenetic inference with not-so-rare mutations and tiny organisms" has been accepted in Systematic Biology! 🧬🦠 academic.oup.com/sysbio/artic...
academic.oup.com
Phylogenetic inference with not-so-rare mutations and tiny organisms
Abstract. A common assumption in mathematical models of molecular evolution is that mutations are rare. One example is the boundary mutation assumption, wh
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