19 papers · ranked by Valyu relevance
Avinash M Veerappa, M Jordan Rowley, Angela Maggio, Laura Beaudry + 5 more
'Dale Hawkins' 'Allen Kim' 'Sahil Sethi' 'Paul L Sorgen' 'Chittibabu Guda'] Title: Abstract Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) generates genome-wide chromatin accessibility profiles, providing valuable insights into epigenetic gene regulation at both pooled-cell and…
Islem Toumi, Laurent Lecam, Pierre-François Roux
Assay for transposase-accessible chromatin using sequencing (ATAC-seq) is a cornerstone for epigenomic profiling, yet its potential for genomic characterization remains poorly explored. Here, we systematically benchmarked bulk ATAC-seq against whole-genome sequencing (WGS) to assess its capacity for detecting small…
Shaopeng Liu, Daofeng Li, Cheng Lyu, Paul M. Gontarz + 4 more
Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) is a technique widely used to investigate genome-wide chromatin accessibility. The recently published Omni-ATAC-seq protocol substantially improves the signal/noise ratio and reduces the input cell number. High-quality data are…
Mayur Divate, Edwin Cheung
Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) is a powerful genomic technology that is used for the global mapping and analysis of open chromatin regions. However, for users to process and analyze such data they either have to use a number of complicated bioinformatic tools or…
Ya Cui, Jason Sheng Li, Wei Li
Underlying the regulation of mammalian gene expression at the level of transcription is the structure and modifications of chromatin. Understanding the twisting structures of DNA wrapped around histones and their higher-level ordering allows us to peek into a vast regulatory landscape. Looking closer, the physical…
Avantika Lal, Zachary D. Chiang, Nikolai Yakovenko, Fabiana M. Duarte + 2 more
We introduce AtacWorks (https://github.com/clara-genomics/AtacWorks), a method to denoise and identify accessible chromatin regions from low-coverage or low-quality ATAC-seq data. AtacWorks uses a deep neural network to learn a mapping between noisy ATAC-seq data and corresponding higher-coverage or higher-quality…
Shaopeng Liu, Daofeng Li, Cheng Lyu, Paul Gontarz + 4 more
ATAC-seq is a technique widely used to investigate genome-wide chromatin accessibility. The recently published Omni-ATAC-seq protocol substantially improves the signal/noise ratio and reduces the input cell number. High-quality data are critical to ensure accurate analysis. Several tools have been developed for…
Yu Zhao, Xianwen Zhang, Zhenhua Song, Danian Wei + 5 more
'Wei Chen' 'Guodong Sun' 'Weiying Ma' 'Kebing Chen'] Assay for transposase-accessible chromatin using sequencing (ATAC-seq) is associated with significant progress in biological research and has attracted increasing attention. However, the impact of ATAC-seq on cancer biology has not been objectively analyzed. We…
Zeeshan Ahmed, Duygu Ucar, Alistair Forrest
Assay for Transposase Accessible Chromatin (ATAC-seq) is an open chromatin profiling assay that is adapted to interrogate chromatin accessibility from small cell numbers. ATAC-seq surmounted a major technical barrier and enabled epigenome profiling of clinical samples. With this advancement in technology, we are now…
Fan Gao, Lior Pachter
The primary tool currently used to pre-process 10X Chromium single-cell ATAC-seq data is Cell Ranger, which can take very long to run on standard datasets. To facilitate rapid pre-processing that enables reproducible workflows, we present a suite of tools called scATAK for pre-processing single-cell ATAC-seq data that…
Ionut Sebastian Mihai, Sarang Chafle, Johan Henriksson
Single-cell analysis is currently one of the most high-resolution techniques to study biology. The large complex datasets that have been generated have spurred numerous developments in computational biology, in particular the use of advanced statistics and machine learning. This review attempts to explain the deeper…
Wuming Gong, Nikita Dsouza, Daniel J. Garry
Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) reveals chromatin accessibility across the genome. Currently, no method specifically detects differential chromatin accessibility. Here, SeATAC uses a conditional variational autoencoder model to learn the latent representation of ATAC-seq V-plots…
Aslihan Karabacak Calviello, Antje Hirsekorn, Ricardo Wurmus, Dilmurat Yusuf + 1 more
DNase-seq and ATAC-seq are broadly used methods to assay open chromatin regions genome-wide. The single nucleotide resolution of DNase-seq has been further exploited to infer transcription factor binding sites (TFBS) in regulatory regions via footprinting. Recent studies have demonstrated the sequence bias of DNase I…
Lei Huang, Lei Xiong, Na Sun, Zunpeng Liu + 2 more
generation and analysis Authors: ['Lei Huang' 'Lei Xiong' 'Na Sun' 'Zunpeng Liu' 'Ka‐Chun Wong' 'Manolis Kellis'] The rapid advancement of single-cell ATAC sequencing (scATAC-seq) technologies holds great promise for investigating the heterogeneity of epigenetic landscapes at the cellular level. The amplification…
Lopamudra Dey
Chromatin regulators can alter transcriptional programs by modifying the accessibility of regulatory DNA elements. Understanding how regulatory sequences differ between wild-type (WT) and knockout (KO) conditions is crucial for deciphering transcriptional control. Here, we applied a convolutional neural network…
Azusa Tanaka, Yasuhiro Ishitsuka, Hiroki Ohta, Norihiro Takenouchi + 7 more
'Masanori Nakagawa' 'Ki‐Ryang Koh' 'Chiho Onishi' 'Hiromitsu Tanaka' 'Akihiro Fujimoto' 'Jun‐ichirou Yasunaga' 'Masao Matsuoka'] Human T-cell leukemia virus type 1 (HTLV-1) causes adult T-cell leukemia (ATL) and HTLV-1-associated myelopathy (HAM) after a long latent period in a fraction of infected individuals. These…
Orsolya Lapohos, Gregory J. Fonseca, Amin Emad
Sequence-to-expression models have gained popularity in the past decade, enabling prediction of gene expression from genomic sequence alone. However, these models typically do not take into account chromatin accessibility, a major factor limiting gene regulation. We hypothesized that supplying accessibility as an input…
Authors not listed
Molecular mechanisms governing initiation steps of the assembly of thousands of endogenous multi-protein complexes (EMCs) remain incompletely understood. Here, multiple lines of observations are reported reflecting the biological functions-aligned initiation sequence of hybrid assembly pathways (HAPs) of EMCs. HAPs…
Xuesong Wang, Zhigang Hu, Tingyang Yu, Ruijie Wang + 4 more
Alignment and Integration Authors: ['Xuesong Wang' 'Zhigang Hu' 'Tingyang Yu' 'Ruijie Wang' 'Yumeng Wei' 'Juan Shu' 'Jianzhu Ma' 'Yu Li'] Muilti-modality data are ubiquitous in biology, especially that we have entered the multi-omics era, when we can measure the same biological object (cell) from different aspects…