KC Maharana
@iamkcm.bsky.social
Reposted by KC Maharana
GenDiS3 database: census on prevalence of protein domain superfamilies of known structure in the entire sequence database https://www.biorxiv.org/content/10.1101/2025.03.14.643262v1
March 17, 2025 at 6:46 PM
GenDiS3 database: census on prevalence of protein domain superfamilies of known structure in the entire sequence database https://www.biorxiv.org/content/10.1101/2025.03.14.643262v1
Reposted by KC Maharana
Anyone else having issues actually accessing the pdfs on @biorxivpreprint.bsky.social ? E.g. this one : www.biorxiv.org/content/10.1...
A simple way to find related sequences with position-specific probabilities
One way to understand biology is by finding genetic sequences that are related to each other. Often, a family of related sequences has position-varying probabilities of substitutions, insertions, and ...
www.biorxiv.org
March 17, 2025 at 2:09 PM
Anyone else having issues actually accessing the pdfs on @biorxivpreprint.bsky.social ? E.g. this one : www.biorxiv.org/content/10.1...
Reposted by KC Maharana
Pleased to see our latest paper out in Acta Cryst D (journals.iucr.org/d/issues/202...). It describes Slice'N'Dice, software for splitting up an AlphaFold model (or any structure actually) in a variety of ways, and then placing it with Molecular Replacement or directly into a cryo-EM map.
Slice'N'Dice: maximizing the value of predicted models for structural biologists
Recent advancements in computational structural modelling have provided structural biologists with access to high-quality predictions that can be used to aid experimental structure determination. Slic...
journals.iucr.org
March 6, 2025 at 9:04 AM
Pleased to see our latest paper out in Acta Cryst D (journals.iucr.org/d/issues/202...). It describes Slice'N'Dice, software for splitting up an AlphaFold model (or any structure actually) in a variety of ways, and then placing it with Molecular Replacement or directly into a cryo-EM map.
Reposted by KC Maharana
AI as an accelerator for defining new problems that transcends boundaries biodatamining.biomedcentral.com/articles/10.... #science #research #artificialintelligence
AI as an accelerator for defining new problems that transcends boundaries - BioData Mining
Interdisciplinary, transdisciplinary, convergence, and No-Boundary Thinking (NBT) research are methodology and technology-agnostic approaches to problem solving. The focus is on defining problems info...
biodatamining.biomedcentral.com
February 25, 2025 at 2:08 PM
AI as an accelerator for defining new problems that transcends boundaries biodatamining.biomedcentral.com/articles/10.... #science #research #artificialintelligence
Reposted by KC Maharana
In our latest review, we explore 12 deep-learning tools for metagenomic analysis, covering their strengths, limitations, and key applications. We hope it serves as both a resource and inspiration for new ways to analyze metagenomic data. Great work by Eli Levy Karin!
📄 doi.org/10.1093/nsr/...
📄 doi.org/10.1093/nsr/...
February 22, 2025 at 5:47 AM
In our latest review, we explore 12 deep-learning tools for metagenomic analysis, covering their strengths, limitations, and key applications. We hope it serves as both a resource and inspiration for new ways to analyze metagenomic data. Great work by Eli Levy Karin!
📄 doi.org/10.1093/nsr/...
📄 doi.org/10.1093/nsr/...
Reposted by KC Maharana
Setting new boundaries of 16S rRNA gene identity for prokaryotic taxonomy www.biorxiv.org/content/10.1... #jcampubs
Setting new boundaries of 16S rRNA gene identity for prokaryotic taxonomy
The 16S ribosomal RNA (rRNA) gene is frequently sequenced to classify prokaryotes and identify new taxa. If sequences from two strains share less than ~99% identity, the strains are usually classified...
www.biorxiv.org
February 5, 2025 at 2:33 PM
Setting new boundaries of 16S rRNA gene identity for prokaryotic taxonomy www.biorxiv.org/content/10.1... #jcampubs
Reposted by KC Maharana
A batch of cowpea seeds — better known as lobia in Hindi or thattapayaru in Tamil — have successfully sprouted in space, days after they were taken into orbit by an Indian Space Research Organisation mission.
www.thehindu.com/sci-tech/sci...
www.thehindu.com/sci-tech/sci...
January 7, 2025 at 9:04 AM
A batch of cowpea seeds — better known as lobia in Hindi or thattapayaru in Tamil — have successfully sprouted in space, days after they were taken into orbit by an Indian Space Research Organisation mission.
www.thehindu.com/sci-tech/sci...
www.thehindu.com/sci-tech/sci...
Reposted by KC Maharana
We added another 100 citations (total 577) in the latest version of our review on LLMs and agents in chemistry. Take a look!
arxiv.org/abs/2407.01603
arxiv.org/abs/2407.01603
November 18, 2024 at 2:05 AM
We added another 100 citations (total 577) in the latest version of our review on LLMs and agents in chemistry. Take a look!
arxiv.org/abs/2407.01603
arxiv.org/abs/2407.01603
Reposted by KC Maharana
Complete genomes of 152 root commensal bacteria from the model legume Lotus japonicus https://www.biorxiv.org/content/10.1101/2025.01.02.630998v1
January 3, 2025 at 12:34 PM
Complete genomes of 152 root commensal bacteria from the model legume Lotus japonicus https://www.biorxiv.org/content/10.1101/2025.01.02.630998v1
Reposted by KC Maharana
Happy new year
1³+2³+3³+4³+5³+6³+7³+8³+9³
1³+2³+3³+4³+5³+6³+7³+8³+9³
December 31, 2024 at 12:24 PM
Happy new year
1³+2³+3³+4³+5³+6³+7³+8³+9³
1³+2³+3³+4³+5³+6³+7³+8³+9³
Reposted by KC Maharana
CLCNet: a contrastive learning and chromosome-aware network for genomic prediction in plants https://www.biorxiv.org/content/10.1101/2024.12.29.630569v1
December 30, 2024 at 6:33 PM
CLCNet: a contrastive learning and chromosome-aware network for genomic prediction in plants https://www.biorxiv.org/content/10.1101/2024.12.29.630569v1
Reposted by KC Maharana
Vcfexpress: flexible, rapid user-expressions to filter and format VCFs. #VCF #VariantFiltering #RUST @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Vcfexpress: flexible, rapid user-expressions to filter and format VCFs
Motivation Variant Call Format (VCF) files are the standard output format for various software tools that identify genetic variation from DNA sequencing experiments. Downstream analyses require the ab...
www.biorxiv.org
December 22, 2024 at 1:53 PM
Vcfexpress: flexible, rapid user-expressions to filter and format VCFs. #VCF #VariantFiltering #RUST @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by KC Maharana
Prediction confidence scores help #AlphaFold users gauge the reliability of protein structure predictions. 🖥️🧬
But things get more challenging for protein families.
A new method helps improve low confidence predictions within protein families.
academic.oup.com/bioinformati...
But things get more challenging for protein families.
A new method helps improve low confidence predictions within protein families.
academic.oup.com/bioinformati...
December 16, 2024 at 9:28 AM
Prediction confidence scores help #AlphaFold users gauge the reliability of protein structure predictions. 🖥️🧬
But things get more challenging for protein families.
A new method helps improve low confidence predictions within protein families.
academic.oup.com/bioinformati...
But things get more challenging for protein families.
A new method helps improve low confidence predictions within protein families.
academic.oup.com/bioinformati...
Reposted by KC Maharana
‘Dark proteome’ survey reveals thousands of new human genes | Science www.science.org/content/arti...
‘Dark proteome’ survey reveals thousands of new human genes
Database confirms that overlooked segments of the genome code for a multitude of tiny proteins
www.science.org
November 30, 2024 at 12:32 PM
‘Dark proteome’ survey reveals thousands of new human genes | Science www.science.org/content/arti...