Sofie R. Salama

PULSE, a foundation model trained on neural recordings, reveals how disease variants affect network development and how circuits encode information in brain organoids.

HIPPIE is a deep learning model that classifies neurons from electrophysiological recordings by combining self-supervised pretraining and supervised fine-tuning, showing better performance than unsupervised methods.

The paper presents a cloud-based pipeline for analyzing and visualizing neuronal electrophysiology data from HD-MEAs, demonstrating its utility in simplifying data analysis and understanding neural activity.

This paper develops a 3D-printed, servo-actuated microvalve system for automated organoid culture, validated in mouse and human models with comparable viability and gene expression to manual methods.

This study develops a microfluidic platform to induce spatially segregated ventral and dorsal domains in mouse forebrain organoids without fusion, enabling study of tissue regionalization.

The paper characterizes the genetic diversity and regulatory features of human-specific NOTCH2NL duplications using long-read sequencing and organoid models.

The paper presents the first telomere-to-telomere diploid reference genome of the human embryonic stem cell line H9, revealing genomic features and ancestry.

This study uses mouse forebrain organoids to show how variations in cellular composition influence the self-organization of neural circuits, revealing intrinsic principles of forebrain circuit assembly.

This paper introduces an automated in-incubator microscope for long-term live cell imaging, enabling high-frequency, continuous data collection with improved thermal stability and operational reliability.

HMM-Flagger evaluates genome assemblies by detecting structural errors using read coverage modeling, showing improved accuracy in human assemblies.

This study demonstrates goal-directed learning in cortical organoids using a closed-loop electrophysiology framework and artificial reinforcement learning.

This paper introduces a sealed recirculatory system for organoid culture that eliminates the need for CO2 incubators and enables continuous live imaging and metabolic viability.

This paper introduces an automated brain organoid platform with IoT integration for continuous monitoring and control, showing increased neural activity and stable firing rates during automated media exchange.

The paper evaluates the CARE pipeline for identifying druggable targets in pediatric cancers using RNA-Seq data from 33 patients, showing 94% of cases had clinically significant findings.

The paper identifies specialized tRNA-derived small RNAs (tDRs) in early human brain development using cerebral cortex organoids and ARM-seq, revealing dynamic expression patterns and sequence motifs associated with neural-specific tDRs.

The paper identifies cis-acting elements linking alternative splicing to translational control across primate species and shows sequence variation affects polyribosome association.

The paper presents a comprehensive analysis of fully assembled human centromeres, revealing their architecture, variation, and evolutionary dynamics at high resolution.

The paper introduces Piphys, an open-source platform for neural recording that enables remote control and scalability through cloud-based software and low-cost hardware.

The paper evaluates the informativeness of reads in bulk RNA-Seq datasets and recommends using MEND reads for accurate gene expression quantification in pediatric cancer studies.

ProTECT identifies and ranks tumor neoepitopes from raw sequencing data for cancer immunotherapy, outperforming existing tools in efficiency and scalability.

The paper presents an optimized PromethION nanopore sequencing method and new computational tools for efficient human genome assembly, achieving high accuracy and speed.

The UCSC Repeat Browser provides a tool for visualizing and analyzing repeat elements in the genome, enabling the study of evolutionary conflicts across species.

The paper uses chimpanzee cerebral organoids to identify human-specific genes in cortical development and finds increased PI3K/AKT/mTOR activation in human outer radial glia.

The paper identifies human-specific NOTCH2NL genes linked to neurodevelopmental disorders and shows they affect cortical neurogenesis through Notch signaling.