Sina Majidian
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sinamajidian.bsky.social
Sina Majidian
@sinamajidian.bsky.social
1.3K followers 1.6K following 130 posts
On the academic job market | How are species compared to one another across different genomic regions? Postdoc at Langmead Lab, Johns Hopkins | Comparative #genomics at scale | Formerly at UNIL/SIB/WUR | sinamajidian.github.io
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sinamajidian.bsky.social
Sina Majidian @sinamajidian.bsky.social · Jan 3
FastOMA is out now in Nature Methods 🎉: nature.com/articles/s41592-024-02552-8 A new orthology inference algorithm that scales linearly and is highly accurate. FastOMA can process all >2000 eukaryotic UniProt ref proteomes <24 hours 🚀. Try it out github.com/DessimozLab/fastoma @dessimoz.bsky.social
FastOMA retains OMA’s high precision accuracy and even improves upon it in terms of recall, positioning it on the Pareto frontier of orthology inference methods. FastOMA is not only fast but also accurate. a, QfO benchmar, agreement with SwissTree reference phylogeny covering manually curated gene trees. The error bars indicate 95% confidence intervals comparing FastOMA with EnsemblCompara, Domainoid, OrthoMCL, Ortholnspector, sonicparanoid, PANTHER, OrthoFinder, Hieranoid26 and the OMA family including OMA pairs, OMA groups and OMA GETHOGs (graph-based efficient technique for HOGs). c) A computation time comparison of FastOMA and state-of-the-art alternatives. https://www.nature.com/articles/s41592-024-02552-8
Reposted by Sina Majidian
sedlazeck.bsky.social
From coffee-fueled coding marathons ☕ to new genomics tools: Our 2024 #Hackathon paper is out in @f1000publishing.bsky.social !
Huge thanks to everyone world wide who joined the @bcmhgsc.bsky.social madness 🎉
🔗 f1000research.com/articles/14-...
@gregor-research.bsky.social @smahtnetwrk.bsky.social
November 10, 2025 at 2:25 PM
Reposted by Sina Majidian
Thank you folks for your feedback on our survey about Hash functions in genomic sequence analysis. We've updated the paper and you can see the new version here: tinyurl.com/4kk9ccmt.
September 25, 2025 at 1:21 PM
Reposted by Sina Majidian
gamfeldt.bsky.social
Opportunity!
Anybody knows of young marine ecologists (within 7 years from earned PhD) that would like to come to Gothenburg, Sweden, for a nationally funded Assistant Professorship? It is highly competitive but well funded. (1) of (3)
November 10, 2025 at 9:32 AM
sinamajidian.bsky.social
Specificity, length and luck drive gene rankings in association studies
nature.com/articles/s41586-025-09703-7
a,b, Schematics of GWAS (a) and LoF burden tests (b). c, Each cell is a genome-wide significant gene according to LoF burden tests, ordered by significance (most significant (top) to least significant (bottom)). Genes are coloured by the rank of the locus that contains the gene according to GWAS or are coloured black if they are not contained in any genome-wide significant locus. Across 151 traits with at least one burden hit and one GWAS hit, 74.6% (1,382 out of 1,852) of genome-wide significant burden test hits fall within a GWAS locus. Trait abbreviations are defined in Supplementary Table 1. d, Minimum LoF burden test P values for any gene overlapping a genome-wide significant GWAS locus plotted against the minimum GWAS P value within that locus (n = 382 loci). e, The genomic region surrounding NPR2. GWAS P values of approximately independent genome-wide significant GWAS hits (top), and the location of genes coloured by LoF burden test P values (bottom) are shown. f, Similar to panel e but for the genomic region surrounding HHIP. a, A cartoon of two genes that affect a trait under study. The widths of the arrows represent the relative effect sizes. Gene 1 is more trait specific, but gene 2 is more trait important. b, Formal definitions of trait importance and trait specificity for genes in the context of LoF burden tests.
November 9, 2025 at 12:52 PM
Reposted by Sina Majidian
mnguyen667.bsky.social
Finally on BlueSky, and happy to have had the opportunity to give a talk at Genome Informatics!
sinamajidian.bsky.social Sina Majidian @sinamajidian.bsky.social · 6d
Matthew Nguyen delivered a great talk on "Refining Kraken2 long-read taxonomic classifications using convolutional neural networks"
November 8, 2025 at 5:27 PM
Reposted by Sina Majidian
vikramshivakumar.bsky.social
Really excited to see our new work in scaling Mumemto to any size pangenome published in Genome Research this morning. And right on cue with the great opportunity to present this work at #GI2025 this week.
genomeresearch.bsky.social Genome Research @genomeresearch.bsky.social · 6d
#GI2025 Vikram Shivakumar from Ben Langmead's lab (@benlangmead.bsky.social) presents "MumemtoM - partitioned Multi-MUM finding for scalable pangenomics ". Now published in Genome Research @genomeresearch.bsky.social. Read full text here ➡️ tinyurl.com/Genome-Res-2...
November 7, 2025 at 9:29 PM
sinamajidian.bsky.social
Third day of Genome Informatics #GI2025 began with an exciting session on “AI, ML and Integrative Genomics” chaired by Irene Kaplow & Thomas Pierrot.
The first talk, by Irene Kaplow, focused on Challenges in Predicting Enhancer Activity Differences Between Species
doi.org/10.1186/s12864-022-08450-7
OCR Ortholog Open Chromatin Status Prediction Framework Overview. a We trained a convolutional neural network (CNN) for predicting brain open chromatin using sequences underlying brain open chromatin region (OCR) orthologs in a small number of species and used the CNN to predict brain OCR ortholog open chromatin status across the species in the Zoonomia Consortium. Specifically, we used the sequences underlying the orthologs for which we have brain open chromatin data to train a CNN for predicting open chromatin. Then, we used the CNN to predict the probability of brain open chromatin for all brain OCR orthologs; predictions are illustrated on the right. Animals for which we do not have open chromatin data are in dark gray instead of black to indicate that their brain open chromatin is imputed. While we cannot evaluate the accuracy of most of our predictions, obtaining open chromatin data from most tissues in most species is infeasible, so predictions might be the best OCR annotations that we can obtain. b To demonstrate that our models can accurately predict whether sequence differences between species are associated with open chromatin differences, in addition to the evaluations described in previous work [57], we evaluated our performance on species-specific open chromatin for a species not used in model training and clade-specific open and closed chromatin for clades not used in model training. Since such regions often comprise a minority of OCR orthologs, models could obtain good overall performance while obtaining poor performance on such regions. We also evaluated our performance on tissue-specific open and closed chromatin for a tissue not used in model training, where we expect models to predict 0 if model learns sequence signatures related to the tissue used in training. c Full mouse test set and lineage-specific OCR accuracy evaluations for mouse sequence-only brain model, illustrating that, even for the best of these models,
November 7, 2025 at 2:28 PM
Reposted by Sina Majidian
genomeresearch.bsky.social
#GI2025 Mile Sikic @msikic.bsky.social presents "Geometric deep learning framework for de novo genome assembly" Now published in GenomeResearch @genomeresearch.bsky.social Full text here ➡️ tinyurl.com/Genome-Res-2...
November 6, 2025 at 10:33 PM
sinamajidian.bsky.social
Second day of Genome Informatics #GI2025 began with the session “Genome Assembly and Sequence Algorithms" Yun William Yu presented “Average-case Analysis of Seed-Chain-Extend under Random Mutations"
genome.cshlp.org/content/33/7/1175
providing theoretical guarantees for the popular seed-chain-extend
Abstract: Seed-chain-extend with k-mer seeds is a powerful heuristic technique for sequence alignment used by modern sequence aligners. Although effective in practice for both runtime and accuracy, theoretical guarantees on the resulting alignment do not exist for seed-chain-extend. In this work, we give the first rigorous bounds for the efficacy of seed-chain-extend with k-mers in expectation. Assume we are given a random nucleotide sequence of length ∼n that is indexed (or seeded) and a mutated substring of length ∼m ≤ n with mutation rate θ < 0.206. We prove that we can find a k = Θ(log n) for the k-mer size such that the expected runtime of seed-chain-extend under optimal linear-gap cost chaining and quadratic time gap extension is O(mn^f(θ) log n), where f(θ) < 2.43 · θ holds as a loose bound. The alignment also turns out to be good; we prove that more than 1-o(sqrt(1/m)) fraction of the homologous bases is recoverable under an optimal chain. We also show that our bounds work when k-mers are sketched, that is, only a subset of all k-mers is selected, and that sketching reduces chaining time without increasing alignment time or decreasing accuracy too much, justifying the effectiveness of sketching as a practical speedup in sequence alignment. We verify our results in simulation and on real noisy long-read data and show that our theoretical runtimes can predict real runtimes accurately. We conjecture that our bounds can be improved further, and in particular, f(θ) can be further reduced.
November 6, 2025 at 2:19 PM
sinamajidian.bsky.social
Ben Langmead @benlangmead.bsky.social delivers the official opening for this year's Genome Informatics Conference #GI2025 at Cold Spring Harbor Laboratory.
List of talks and posters: meetings.cshl.edu/abstracts.as...
November 6, 2025 at 12:38 AM
sinamajidian.bsky.social
Excited to be at the Genome Informatics conference #GI2025 in Cold Spring Harbor Laboratory this week! I’ll be sharing my current work on using machine learning to improve the reliability of Metagenomics classification for analzing gut microbiota and soil samples. Let's connect!
November 4, 2025 at 8:51 PM
Reposted by Sina Majidian
pengellab.bsky.social
🐝🦠 New paper: rdcu.be/eOf7A
Phages may drive microbial diversity, yet we often don’t even know how phages & bacteria correlate in nature. Our new study tackles this in the honeybee gut, thanks to the great work of PhD student @malickndiaye.bsky.social at @dmf-unil.bsky.social @fbm-unil.bsky.social
Phage diversity mirrors bacterial strain diversity in the honey bee gut microbiota - Nature Communications
Authors analyse paired viral and bacterial shotgun metagenomics data from individual honeybee guts, revealing modular, nested phage–bacteria networks, with viral diversity mirroring bacterial strain c...
www.nature.com
November 4, 2025 at 8:36 PM
Reposted by Sina Majidian
recombconf.bsky.social
📆 Only 4 days left until the #RECOMB2026 abstract registration deadline!

📌 Authors who register abstracts can update their submissions until November 14.

👉 See submission guidelines: recomb.org/recomb2026/c...
RECOMB 2026 | CALL FOR PAPERS
Call For Papers
recomb.org
November 3, 2025 at 8:44 PM
Reposted by Sina Majidian
genomesevolve.bsky.social
mceb2026.sciencesconf.org
Mathematical and Computational Evolutionary Biology, Crete, 2026 - Sciencesconf.org
Welcome to MCEB 2026
mceb2026.sciencesconf.org
November 3, 2025 at 9:16 PM
Reposted by Sina Majidian
waynemaddison.bsky.social
The end of an era: the Tree of Life Web Project is going dark after 3 decades. Anyone interested in communicating phylogeny online should read David's account of goals, history, and future. @bembidion.bsky.social
subulatepalpomere.com/2025/11/02/t...
The Passing of the Tree of Life Web Project
The Tree of Life Web Project began its journey almost 40 years ago, and was formally announced in early 1996. It has served thousands of pages of information about the evolutionary tree of life and…
subulatepalpomere.com
November 3, 2025 at 3:54 PM
Reposted by Sina Majidian
mohsenzakeri.bsky.social
We’re all so proud of Steven Tan! He’s a super talented undergraduate at JHU. Thanks to the incredible support of @benlangmead.bsky.social, I had the opportunity to help guide this work, and I really loved it. Many thanks also to @sinamajidian.bsky.social for his valuable collaboration and input.
benlangmead.bsky.social Ben Langmead @benlangmead.bsky.social · 13d
Huge congratulations to Steven Tan, a superb undergraduate junior at JHU CS whose first-author paper "Movi Color: fast and accurate taxonomic classification with the move structure" won best paper at ACM-BCB. Please check it out: www.biorxiv.org/content/10.1.... Congrats, Steven!!
Steven Tan accepting ACM-BCB 2025 best paper award
November 2, 2025 at 7:27 PM
Reposted by Sina Majidian
speciationlab.bsky.social
Great new postdoc fellowship for foundational plant research.
If you’re into genetics and genomics of plant reproductive evolution or adaptive convergence (incl in the cool and charismatic nightshades!) I’d be happy to talk about possible projects!
www.simonsfoundation.org/grant/simons...
Simons Postdoctoral Fellowships in Plant Biology
Simons Postdoctoral Fellowships in Plant Biology on Simons Foundation
www.simonsfoundation.org
October 14, 2025 at 3:47 PM
sinamajidian.bsky.social
"We have named the package Basset, as an allusion to the extraordinary abilities of these hound dogs to learn a scent that they are subsequently able to detect and pursue."
genome.cshlp.org/content/26/7...
Kelley et al, Genome research 2016.
Figure1. Deep convolutional neural network (CNN) for DNA sequence analysis. Basset predicts the cell-specific functional activity (here DNase I hypersensitivity) of sequences. First, we convert the sequence to a “one hot code” representation, where each position has a four-element vector with one nucleotide's bit set to one. Convolution layers proceed by scanning weight matrices across the input matrix to produce an output matrix with a row for every convolution filter and a column for every position in the input (minus the width of the filter). We apply a rectified linear unit (ReLU) nonlinear transformation to the convolution output and pool by taking the maximum across a window of adjacent positions. The first convolution layer operates directly on the one hot coding of the input sequence, making the convolution filters akin to the common bioinformatics tool position weight matrices. Subsequent convolution layers consider the orientations and spatial distances between patterns recognized in the previous layer. Fully connected layers perform a linear transformation of the input vector and apply a ReLU. The final layer performs a linear transformation to a vector of 164 elements that represents the target cells. A sigmoid nonlinearity maps this vector to the range zero to one, where the elements serve as probability predictions of DNase I hypersensitivity, to be compared via a loss function to the true hypersensitivity vector. https://genome.cshlp.org/content/26/7/990.full
November 1, 2025 at 3:00 AM
Reposted by Sina Majidian
cotoorellana.bsky.social
The average nucleotide identity (ANI) underpins how we map microbial diversity, compare species, and connect genomes to ecology.
I wrote a short piece reflecting on the discovery and significance of this metric (and really enjoyed digging into the context and story behind it!) #microsky 🧬
Average nucleotide identity — the backbone of modern ecological genomics - Nature Reviews Genetics
In this Journal Club, Luis Orellana recalls a 2005 publication by Konstantinidis and Tiedje that introduced average nucleotide identity as a sequence-based metric to determine the relatedness between ...
www.nature.com
October 30, 2025 at 9:11 PM
Reposted by Sina Majidian
guppy-stott.bsky.social
Final committee meeting... DONE. Defending in the first week of April, so if you're looking for postdocs or know someone who is, let me know!
October 29, 2025 at 6:10 PM
Reposted by Sina Majidian
sib.swiss
Join our interdisciplinary online workshop on the Galaxy platform! Nov 6, 2025 | 13:30–16:05 (CET)
Learn how to build reproducible data analysis workflows using Galaxy, a powerful, user-friendly platform. The session is intended for the Swiss rsrch community.
Register forms.gle/Y3vxW1u62FLM...
GALAXY-CH Transdisciplinary Workflows Workshop Registration
Galaxy is a web-based and open-source platform (see e.g. https://usegalaxy.eu/). It shall enable researchers to access and use computational tools and high-performance compute infrastructures easily. ...
forms.gle
October 29, 2025 at 4:19 PM
Reposted by Sina Majidian
sokrypton.org
Is 3D dragging you down? Wish you could instead use the 2D ColabFold representation for all your work? 🤓

Introducing: py2Dmol 🧬

(feedback, suggestions, requests are welcome)
October 29, 2025 at 1:39 AM
Reposted by Sina Majidian
m-correa-m.bsky.social
Hot off the press! Our paper, “Global comparative structural analysis of responses to protein phosphorylation”, is now out in Nature Communications!

www.nature.com/articles/s41...
Global comparative structural analysis of responses to protein phosphorylation - Nature Communications
Phosphorylation is central to protein regulation, yet its structural mechanisms remain poorly understood. Here, the authors conduct a global, systematic analysis of phosphorylated versus non-phosphory...
www.nature.com
October 27, 2025 at 10:29 AM
sinamajidian.bsky.social
It’s a tricky time of year to schedule meetings for international collaborations, some countries have already changed their clocks and ended daylight saving time, while others not. I guess I’ll just have to trust Google Calendar and Doodle to handle the time zone math for me!
October 27, 2025 at 12:51 PM