Explanipedia

An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation Open

Jill E. Moore, Henry Pratt, Kaili Fan, Nishigandha Phalke, Jonathan Fisher , et al. · 2024

Mammalian genomes contain millions of regulatory elements that control the complex patterns of gene expression. Previously, The ENCODE consortium mapped biochemical signals across many cell types and tissues and integrated these data to de…

A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex Open

Louise A. Huuki-Myers, Abby Spangler, Nicholas J. Eagles, Kelsey D. Montgomery, Sang Ho Kwon , et al. · 2024

The molecular organization of the human neocortex historically has been studied in the context of its histological layers. However, emerging spatial transcriptomic technologies have enabled unbiased identification of transcriptionally defi…

Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain Open

Cindy Wen, Michael Margolis, Rujia Dai, Pan Zhang, Pawel F. Przytycki , et al. · 2024

Neuropsychiatric genome-wide association studies (GWASs), including those for autism spectrum disorder and schizophrenia, show strong enrichment for regulatory elements in the developing brain. However, prioritizing risk genes and mechanis…

Single-cell genomics and regulatory networks for 388 human brains Open

Prashant S. Emani, Jason Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell , et al. · 2024

Single-cell genomics is a powerful tool for studying heterogeneous tissues such as the brain. Yet little is understood about how genetic variants influence cell-level gene expression. Addressing this, we uniformly processed single-nuclei, …

Massively parallel characterization of regulatory elements in the developing human cortex Open

Chengyu Deng, Sean Whalen, Marilyn Steyert, Ryan Ziffra, Pawel F. Przytycki , et al. · 2024

Nucleotide changes in gene regulatory elements are important determinants of neuronal development and diseases. Using massively parallel reporter assays in primary human cells from mid-gestation cortex and cerebral organoids, we interrogat…

Single-cell genomics and regulatory networks for 388 human brains Open

Prashant S. Emani, Jason J. Liu, Declan Clarke, Matthew L. Jensen, Jonathan Warrell , et al. · 2024

Single-cell genomics is a powerful tool for studying heterogeneous tissues such as the brain. Yet, little is understood about how genetic variants influence cell-level gene expression. Addressing this, we uniformly processed single-nuclei,…

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models Open

Joel Rozowsky, Jiahao Gao, Beatrice Borsari, Yucheng Yang, Timur R. Galeev , et al. · 2023

Understanding how genetic variants impact molecular phenotypes is a key goal of functional genomics, currently hindered by reliance on a single haploid reference genome. Here, we present the EN-TEx resource of 1,635 open-access datasets fr…

Structure and Multi-Center Bonding: From Atomic Clusters to Solid Phase Materials Open

Timur R. Galeev · 2021

The work presented in this dissertation has been focused on structure, stability, electronic properties, and chemical bonding of atomic clusters and solid-state compounds. The common thread was development of chemically intuitive models an…

Multi-tissue integrative analysis of personal epigenomes Open

Joel Rozowsky, Jörg Drenkow, Yucheng Yang, Gamze Gürsoy, Timur R. Galeev , et al. · 2021

Evaluating the impact of genetic variants on transcriptional regulation is a central goal in biological science that has been constrained by reliance on a single reference genome. To address this, we constructed phased, diploid genomes for…

An integrative ENCODE resource for cancer genomics Open

Jing Zhang, Donghoon Lee, Vineet K. Dhiman, Peng Jiang, Jie Xu , et al. · 2020

An integrative ENCODE resource for cancer genomics Open

Jing Zhang, Donghoon Lee, Vineet K. Dhiman, Peng Jiang, Jie Xu , et al. · 2019

ENCODE comprises thousands of functional genomics datasets, and the encyclopedia covers hundreds of cell types, providing a universal annotation for genome interpretation. However, for particular applications, it may be advantageous to use…

Multi-platform discovery of haplotype-resolved structural variation in human genomes Open

Mark Chaisson, Ashley D. Sanders, Xuefang Zhao, Ankit Malhotra, David Porubskỳ , et al. · 2019

exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids Open

Oscar Murillo, William Thistlethwaite, Joel Rozowsky, Sai Lakshmi Subramanian, Rocco Lucero , et al. · 2019

The Extracellular RNA Communication Consortium: Establishing Foundational Knowledge and Technologies for Extracellular RNA Research Open

Saumya Das, K. Mark Ansel, Markus Bitzer, Xandra O. Breakefield, Alain Charest , et al. · 2019

exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling Open

Joel Rozowsky, Robert R. Kitchen, Jonathan J. Park, Timur R. Galeev, James A. Diao , et al. · 2019

Small RNA sequencing has been widely adopted to study the diversity of extracellular RNAs (exRNAs) in biofluids; however, the analysis of exRNA samples can be challenging: they are vulnerable to contamination and artifacts from different i…

Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci Open

Robert C. Altshuler, Vitor Onuchic, Eugene Lurie, Ivenise Carrero, Piotr Pawliczek , et al. · 2018

To assess the impact of genetic variation in regulatory loci on human health, we constructed a high-resolution map of allelic imbalances in DNA methylation, histone marks, and gene transcription in 71 epigenomes from 36 distinct cell and t…

Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci Open

Vitor Onuchic, Eugene Lurie, Ivenise Carrero, Piotr Pawliczek, Ronak Y. Patel , et al. · 2018

Dissecting the epigenomic footprint Genome-wide epigenetic marks regulate gene expression, but the amount and function of variability in these marks are poorly understood. Working with human-derived samples, Onuchic et al. examined disease…

FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods Open

Timothy Becker, Wan‐Ping Lee, Joseph F. Leone, Qihui Zhu, Chengsheng Zhang , et al. · 2018

Additional file 5: of FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods Open

Timothy Becker, Wan‐Ping Lee, Joseph F. Leone, Qihui Zhu, Chengsheng Zhang , et al. · 2018

This file contains Table S5. (XLSX 145 kb)

Additional file 2: of FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods Open

Timothy Becker, Wan‐Ping Lee, Joseph F. Leone, Qihui Zhu, Chengsheng Zhang , et al. · 2018

Shell script used for population SV calling using GenomeSTRiP. (SH 10 kb)

Dirac cones in two-dimensional borane Open

Miguel Martínez-Canales, Timur R. Galeev, Alexander I. Boldyrev, Chris J. Pickard · 2017

We introduce two-dimensional borane, a single-layered material of BH stoichiometry, with promising electronic properties. We show that, according to density functional theory calculations, two-dimensional borane is semimetallic, with two s…

Multi-platform discovery of haplotype-resolved structural variation in human genomes Open

Mark Chaisson, Ashley D. Sanders, Xuefang Zhao, Ankit Malhotra, David Porubskỳ , et al. · 2017

The incomplete identification of structural variants (SVs) from whole-genome sequencing data limits studies of human genetic diversity and disease association. Here, we apply a suite of long-read, short-read, and strand-specific sequencing…

Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development Open

Karolina Elżbieta Kaczor‐Urbanowicz, Yong Kim, Feng Li, Timur R. Galeev, Rob R Kitchen , et al. · 2017

Motivation Analysis of RNA sequencing (RNA-Seq) data in human saliva is challenging. Lack of standardization and unification of the bioinformatic procedures undermines saliva‘s diagnostic potential. Thus, it motivated us to perform this st…

Correction: Corrigendum: Diverse human extracellular RNAs are widely detected in human plasma Open

Jane E. Freedman, Mark Gerstein, Eric Mick, Joel Rozowsky, Daniel Levy , et al. · 2016

Nature Communications 7: Article number: 11106 (2016); Published: 26 April 2016; Updated: 3 June 2016 The original version of this Article contained an error in the spelling of the author Milka Koupenova, which was incorrectly given as Mil…

Diverse human extracellular RNAs are widely detected in human plasma Open

Jane E. Freedman, Mark Gerstein, Eric Mick, Joel Rozowsky, Daniel Levy , et al. · 2016

A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals Open

Jieming Chen, Joel Rozowsky, Timur R. Galeev, Arif Harmanci, Robert R. Kitchen , et al. · 2016

Reads meet rotamers: structural biology in the age of deep sequencing Open

Anurag Sethi, Declan Clarke, Jieming Chen, Sushant Kumar, Timur R. Galeev , et al. · 2015

Timur R. Galeev YOU? Author Swipe