Josipa Lipovac
@jlipovac.bsky.social
PhD student at FER, University of Zagreb | Bioinformatics | Metagenome analysis | Genome assembly
Pinned
Josipa Lipovac
@jlipovac.bsky.social
· May 16
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
🔗https://www.biorxiv.org/content/10.1101/2025.05.12.653324v1
1/9
Reposted by Josipa Lipovac
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
#HumanGenomics #Pangenomes #ReferenceGenomes
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.
www.nature.com
November 4, 2025 at 12:28 PM
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
#HumanGenomics #Pangenomes #ReferenceGenomes
Reposted by Josipa Lipovac
Reposted by Josipa Lipovac
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/...
👉 Preprint www.biorxiv.org/content/10.1...
👉 Github github.com/rolandfaure/...
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 ...
www.biorxiv.org
October 3, 2025 at 2:51 PM
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/...
👉 Preprint www.biorxiv.org/content/10.1...
👉 Github github.com/rolandfaure/...
Reposted by Josipa Lipovac
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]
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 ...
www.biorxiv.org
September 22, 2025 at 5:01 PM
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]
Reposted by Josipa Lipovac
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)
Computing average nucleotide identity (ANI) is neither conceptually nor computationally trivial. Its definition has evolved over years, with different meanings and assumptions (1/5)
September 21, 2025 at 3:26 PM
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)
Computing average nucleotide identity (ANI) is neither conceptually nor computationally trivial. Its definition has evolved over years, with different meanings and assumptions (1/5)
Reposted by Josipa Lipovac
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...
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...
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.
www.nature.com
September 10, 2025 at 9:12 AM
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...
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...
Reposted by Josipa Lipovac
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
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
High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1
September 7, 2025 at 11:35 PM
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
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
Reposted by Josipa Lipovac
🌎👩🔬 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...
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
September 3, 2025 at 8:39 AM
🌎👩🔬 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...
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
Reposted by Josipa Lipovac
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.
PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.
August 15, 2025 at 4:33 PM
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.
PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.
Proud to share our work on the first complete genome of an Indian individual - now on bioRxiv! 😄
Happy to present the first complete genome of an Indian individual biorxiv.org/content/10.1.... Joint effort by @astar-gis.bsky.social, FER, and partners, with support from the Singapore NPM programme!
Joint effort with JJ Liu Lab!
Prasad Sarashetti and
@jlipovac.bsky.social
as co-first authors.
Joint effort with JJ Liu Lab!
Prasad Sarashetti and
@jlipovac.bsky.social
as co-first authors.
A Complete Telomere-to-Telomere Diploid Reference Genome for Indian Population
Human reference genomes have been instrumental in advancing genomic and biomedical research, but South and Southeast Asian populations are underrepresented, despite accounting for a large proportion o...
biorxiv.org
July 20, 2025 at 9:19 AM
Proud to share our work on the first complete genome of an Indian individual - now on bioRxiv! 😄
Reposted by Josipa Lipovac
Campolina: A Deep Neural Framework for Accurate Segmentation of Nanopore Signals https://www.biorxiv.org/content/10.1101/2025.07.08.663658v1
July 11, 2025 at 2:47 PM
Campolina: A Deep Neural Framework for Accurate Segmentation of Nanopore Signals https://www.biorxiv.org/content/10.1101/2025.07.08.663658v1
Reposted by Josipa Lipovac
📜 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
May 27, 2025 at 12:06 PM
📜 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
Reposted by Josipa Lipovac
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...
www.biorxiv.org/content/10.1...
May 16, 2025 at 7:16 AM
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...
www.biorxiv.org/content/10.1...
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
🔗https://www.biorxiv.org/content/10.1101/2025.05.12.653324v1
1/9
May 16, 2025 at 8:37 AM
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
🔗https://www.biorxiv.org/content/10.1101/2025.05.12.653324v1
1/9
Reposted by Josipa Lipovac
High-quality metagenome assembly from nanopore reads with nanoMDBG https://www.biorxiv.org/content/10.1101/2025.04.22.649928v1
April 25, 2025 at 12:46 AM
High-quality metagenome assembly from nanopore reads with nanoMDBG https://www.biorxiv.org/content/10.1101/2025.04.22.649928v1
Reposted by Josipa Lipovac
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/
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/
April 11, 2025 at 3:01 PM
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/
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/
Reposted by Josipa Lipovac
"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
www.biorxiv.org/content/10.1...
from Ryan Wick&co
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...
www.biorxiv.org
February 28, 2025 at 3:47 PM
"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
www.biorxiv.org/content/10.1...
from Ryan Wick&co
Reposted by Josipa Lipovac
🚨 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)
📅 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)
February 10, 2025 at 9:35 AM
🚨 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)
📅 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)
Reposted by Josipa Lipovac
🚨 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
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
January 3, 2025 at 2:49 PM
🚨 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
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
Reposted by Josipa Lipovac
🚀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👇
December 19, 2024 at 2:21 PM
🚀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👇
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
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
December 19, 2024 at 2:29 PM
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
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