Josipa Lipovac
@jlipovac.bsky.social
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PhD student at FER, University of Zagreb | Bioinformatics | Metagenome analysis | Genome assembly
pinned post!
I am happy to share our new preprint introducing MADRe - a pipeline for Metagenomic Assembly-Driven Database Reduction, enabling accurate and computationally efficient strain-level metagenomic classification. 🔗https://www.biorxiv.org/content/10.1101/2025.05.12.653324v1 1/9
6 months ago
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Josipa Lipovac
Ensembl
5 days ago
As new human assemblies become available on
beta.ensembl.org
- which human reference genome will you choose? This article explores the question with insights from Ensembl’s own Fergal Martin -
www.nature.com/articles/s41...
#HumanGenomics
#Pangenomes
#ReferenceGenomes
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Choose your human genome reference wisely - Nature Methods
Scientists can choose between multiple human genome references, and a pangenome reference is coming. Deciding what to use when is not quite straightforward.
https://www.nature.com/articles/s41592-025-02850-9
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Josipa Lipovac
Mile Sikic
5 days ago
🚀 Looking for talented PhD students! Join us in 🇸🇬 Singapore for 1-2 years to push the frontiers of AI for Genomics. Work on: 🧬 Cancer genome reconstruction 🧫 Cancer genome & cell foundation models 💊 RNA drug & mRNA therapeutic design
#AI
#Genomics
#PhD
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Josipa Lipovac
Roland Faure
about 1 month ago
Our preprint on our new metagenomic HiFi assembler Alice is out 🥳 Based on a *new sketching method* (🧵1/6) 👉 Preprint
www.biorxiv.org/content/10.1...
👉 Github
github.com/rolandfaure/...
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Alice: fast and haplotype-aware assembly of high-fidelity reads based on MSR sketching
We introduce Mapping-friendly Sequence Reduction (MSR) sketches, a sketching method for high-fidelity (HiFi) long reads, and Alice, an assembler that operates directly on these sketches. MSR produces ...
https://www.biorxiv.org/content/10.1101/2025.09.29.679204v1
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Josipa Lipovac
Adam Phillippy
about 2 months ago
Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy:
www.biorxiv.org/content/10.1...
🧵[1/14]
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A complete diploid human genome benchmark for personalized genomics
Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...
https://www.biorxiv.org/content/10.1101/2025.09.21.677443v1
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Josipa Lipovac
Sina Majidian
about 2 months ago
Excited to share our EvANI benchmarking workflow, published in Briefings in Bioinformatics
doi.org/10.1093/bib/...
Computing average nucleotide identity (ANI) is neither conceptually nor computationally trivial. Its definition has evolved over years, with different meanings and assumptions (1/5)
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Josipa Lipovac
Zamin Iqbal
2 months ago
Sometimes you meet absolutely incredible bioinfo-magicians. It was a huge privilege when
@shenwei356.bsky.social
joined our group for a year on an
@embl.org
sabbatical. While here, he developed a new way of aligning to millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
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Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology
LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.
https://www.nature.com/articles/s41587-025-02812-8
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Josipa Lipovac
Jim Shaw
2 months ago
Preprint out for myloasm, our new nanopore / HiFi metagenome assembler! Nanopore's getting accurate, but 1. Can this lead to better metagenome assemblies? 2. How, algorithmically, to leverage them? with co-author Max Marin
@mgmarin.bsky.social
, supervised by Heng Li
@lh3lh3.bsky.social
1 / N
add a skeleton here at some point
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Josipa Lipovac
Rayan Chikhi
2 months ago
🌎👩🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵 Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
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Josipa Lipovac
Tami Lieberman
3 months ago
Our high-precision metagenomic strain caller, PHLAME, is now published in Cell Reports!!
www.cell.com/cell-reports...
PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.
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Proud to share our work on the first complete genome of an Indian individual - now on bioRxiv! 😄
add a skeleton here at some point
4 months ago
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Josipa Lipovac
bioRxiv Bioinfo
4 months ago
Campolina: A Deep Neural Framework for Accurate Segmentation of Nanopore Signals
https://www.biorxiv.org/content/10.1101/2025.07.08.663658v1
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Josipa Lipovac
Pierre Peterlongo
6 months ago
📜 Excited to share insights from our recent paper: "Kaminari: a resource-frugal index for approximate colored k-mer queries". The study aims to efficiently identify documents containing a query string, focusing on DNA strings.
www.biorxiv.org/content/10.1...
🧬 🖥️ 1/8
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Josipa Lipovac
Zamin Iqbal
6 months ago
This looks cool from
@jlipovac.bsky.social
! Strain-level metag assignment; first use EM +mapping to shrink your ref db, then do read classification
www.biorxiv.org/content/10.1...
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I am happy to share our new preprint introducing MADRe - a pipeline for Metagenomic Assembly-Driven Database Reduction, enabling accurate and computationally efficient strain-level metagenomic classification. 🔗https://www.biorxiv.org/content/10.1101/2025.05.12.653324v1 1/9
6 months ago
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reposted by
Josipa Lipovac
bioRxiv Bioinfo
7 months ago
High-quality metagenome assembly from nanopore reads with nanoMDBG
https://www.biorxiv.org/content/10.1101/2025.04.22.649928v1
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Josipa Lipovac
Karel Břinda
7 months ago
A decade ago, we had thousands of bacterial genomes. Now, we have millions. How to scale computational methods? Our paper in
@naturemethods.bsky.social
answers this: use evolutionary history to guide compression and search.
rdcu.be/eg4OA
w/
@baym.lol
,
@zaminiqbal.bsky.social
et al. 🧵1/
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Josipa Lipovac
Zamin Iqbal
8 months ago
"benchmarking multiple assembly and variant-calling pipelines....read-based methods consistently achieved high accuracy. Assembly-based approaches performed well in some cases but were highly dependent on assembly quality"
www.biorxiv.org/content/10.1...
from Ryan Wick&co
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Are reads required? High-precision variant calling from bacterial genome assemblies
Accurate nucleotide variant calling is essential in microbial genomics, particularly for outbreak tracking and phylogenetics. This study evaluates variant calls derived from genome assemblies compared...
https://www.biorxiv.org/content/10.1101/2025.02.20.639404v1
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Josipa Lipovac
ICLR Nucleic Acids Workshop
9 months ago
🚨 We have extended the deadline for submissions! 🚨 📅 New deadline: Feb 13, 2025, AoE - so you can finish just in time for Valentine's day 🥰 🔗 More details on our website (link in bio)
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Josipa Lipovac
ICLR Nucleic Acids Workshop
10 months ago
🚨 1 month to go! 🚨 The submission deadline for the AI4NA workshop at
@iclr-conf.bsky.social
is fast approaching! 🧬 ✨ Submissions on OpenReview will open soon—stay tuned! ✨ 🔗 Learn more on our web page (link below 👇)
#AI4NA
#ICLR2025
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Josipa Lipovac
ICLR Nucleic Acids Workshop
11 months ago
🚀Thrilled to be part of ICLR 2025! Join our workshop AI for Nucleic Acids (AI4NA) to explore cutting-edge research and connect with field leaders. Thanks to our organizers and
@iclr-conf.bsky.social
for making this possible. Find the link to the website in our bio! More info below👇
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So our paper is finally out! 🥳 Our findings aim to guide researchers on balancing cost, data, and quality in population-level human genome assembly projects. Check it here:
rdcu.be/d36pr
add a skeleton here at some point
11 months ago
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