Social Media Ideas for Encode Project

Garbage Goodbye: In Blow to Junk RNA, “Majority” of Transcription Not “Background Noise”

A 2026 paper reports on an AI trained on genomic data, including data from a 2024 paper, enabling it to predict when transcription would be initiated. Source

Decima predicts gene expression at single-cell resolution

RNA sequencing from more than 22 million cells trained a model that predicts cell-type-specific gene expression and noncoding variant...

The Zygote Code and Other Mysteries

As development progresses, each cell is directed to unique use of its DNA files by the epigenetic system, which sits above the DNA. Source

D&D‑seq Uses Base Editing to Map DNA–Protein Interactions in Single Cells

D&D‑seq uses a base editor–nanobody fusion to record DNA–protein contacts at single‑cell resolution. The method maps transcription factor and chromatin-remodeling proteins. The...

New effort will get genome sequences for entire Endangered Species list

Colossal Biosciences will be biobanking tissues from all of them as well.

A Surprising Discovery Challenges What Scientists Thought DNA Methylation Was For

DNA carries the instructions for life, but additional molecular systems help determine how those instructions are used. New research in a sea anemone reveals an unexpected role for...

Epigenome Is Biology’s Second Revolution

Thomas Woodward compares the epigenetic system to a supercomputer where information is written everywhere — on the hardware, the screen, and even the keys. Source

Time resolved DNA barcodes enable dynamic information storage and encryption

DNA temporal barcodes encode information through chromatographic readout and reveal encrypted messages only after a molecular key reconstructs the correct tags.

CIPHER: An end-to-end framework for designing optimized aggregated spatial transcriptomics experiments

by Zachary Hemminger, Haley De Ocampo, Fangming Xie, Zhiqian Zhai, Jingyi Jessica Li, Roy Wollman Motivation Most imaging-based spatial transcriptomics methods measure individual g...

A Hormone Cell Atlas maps the human endocrine system at cellular resolution

RNA sequencing powers a comprehensive Hormone Cell Atlas that maps hormone producing and hormone receiving cells across the human body at single cell resolution...

New RNA interaction atlas expands understanding of gene regulation

RNA sequencing and new computational tools enabled construction of a large RNA interactome atlas linking RNA-binding proteins, RNA interactions, and gene regulation...

NIH’s All of Us Research Program is now the largest integrated genomics and health database in the world

RNA sequencing joins genomic, proteomic, and clinical data in the expanded NIH All of Us database, creating an unprecedented resource for precision medicine research...

Paper in Cell Reports “Paradigm Shift” Against TEs as “Genomic Parasites or Junk DNA”

This language is remarkable coming from a journal often considered the third most important in the world for biology. Source

Boosting Genomic Equity: Africa’s National Genome Projects

In recent years, the global scientific community has increasingly recognized the critical need to address disparities in genomic research representation. A groundbreaking new publi...

DeepMethylation: A deep learning framework for tissue-specific DNA methylation prediction and functional variant annotat...

by Wenran Li, Shijia Yu, Yingyu Cheng, Sijia Wang DNA methylation is a key epigenetic modification that regulates gene expression and plays a vital role in cell differentiation, d...

Scientists Unlock Hidden DNA From 1,300-Year-Old Manuscripts

Historic parchments may hold genetic clues that can be studied without harming the manuscripts. Scientists have shown that it is possible to collect cellular material from historic...

First use of precision editing reveals role of master gene

Scientists have, for the first time, used an extremely precise genome editing technique called base editing to study gene function in human embryos.

DNA Uncovers Hidden Biodiversity Loss in Ontario Streams, Introducing a Powerful New Tool for Freshwater Monitoring

In a compelling breakthrough for freshwater biodiversity monitoring, researchers have demonstrated that environmental DNA (eDNA) metabarcoding offers a transformative leap over tra...

New Book: Epigenome Is the Genome’s Sophisticated Dance Partner

The book was published yesterday and is already Amazon's #1 bestseller in genetics. Source

A breakthrough single-cell method for mapping DNA-protein interactions

New single-cell method maps protein-DNA interactions, revealing gene regulation changes and advancing multi-omics studies of health and disease.

Ancestral Genomes

scFAIR Consortium – a decentralized hub for single-cell RNA-Seq data standardization and unification

A new consortium framework improves how RNA sequencing datasets are standardized, annotated, and shared, enabling more reliable integration and reuse of single-cell transcriptomic...

BINSEQ: A family of high-performance binary formats for nucleotide sequences

by Noam Teyssier, Alexander Dobin Modern genomics produces billions of sequencing records per run, which are typically stored as gzip-compressed FASTQ files. While this format is...

HELIX – a scalable model for predicting context-dependent regulation of RNA splicing and isoform usage

RNA sequencing combined with deep learning enabled HELIX to predict tissue-specific splicing patterns, transcript isoforms, and patient-specific splicing changes in cancer...