Articles

Single-cell ATAC-seq signal extraction and enhancement with SCATE

Single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) is the state-of-the-art technology for analyzing genome-wide regulatory landscapes in single cells. Single-cell ATAC-seq data are ...

Authors: Zhicheng Ji, Weiqiang Zhou, Wenpin Hou and Hongkai Ji

Quantile normalization of single-cell RNA-seq read counts without unique molecular identifiers

Single-cell RNA-seq (scRNA-seq) profiles gene expression of individual cells. Unique molecular identifiers (UMIs) remove duplicates in read counts resulting from polymerase chain reaction, a major source of no...

Authors: F. William Townes and Rafael A. Irizarry

Genomic analysis of the domestication and post-Spanish conquest evolution of the llama and alpaca

Despite their regional economic importance and being increasingly reared globally, the origins and evolution of the llama and alpaca remain poorly understood. Here we report reference genomes for the llama, an...

Authors: Ruiwen Fan, Zhongru Gu, Xuanmin Guang, Juan Carlos Marín, Valeria Varas, Benito A. González, Jane C. Wheeler, Yafei Hu, Erli Li, Xiaohui Sun, Xukui Yang, Chi Zhang, Wenjun Gao, Junping He, Kasper Munch, Russel Corbett-Detig…

Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II, and Pol III

The relationship between transcription and the 3D chromatin structure is debated. Multiple studies have shown that transcription affects global Cohesin binding and 3D genome structures. However, several other ...

Authors: Yongpeng Jiang, Jie Huang, Kehuan Lun, Boyuan Li, Haonan Zheng, Yuanjun Li, Rong Zhou, Wenjia Duan, Chenlu Wang, Yuanqing Feng, Hong Yao, Cheng Li and Xiong Ji

Analysis of endothelial-to-haematopoietic transition at the single cell level identifies cell cycle regulation as a driver of differentiation

Haematopoietic stem cells (HSCs) first arise during development in the aorta-gonad-mesonephros (AGM) region of the embryo from a population of haemogenic endothelial cells which undergo endothelial-to-haematop...

Authors: Giovanni Canu, Emmanouil Athanasiadis, Rodrigo A. Grandy, Jose Garcia-Bernardo, Paulina M. Strzelecka, Ludovic Vallier, Daniel Ortmann and Ana Cvejic

Identification of cell type-specific methylation signals in bulk whole genome bisulfite sequencing data

The traditional approach to studying the epigenetic mechanism CpG methylation in tissue samples is to identify regions of concordant differential methylation spanning multiple CpG sites (differentially methyla...

Authors: C. Anthony Scott, Jack D. Duryea, Harry MacKay, Maria S. Baker, Eleonora Laritsky, Chathura J. Gunasekara, Cristian Coarfa and Robert A. Waterland

Computational inference of cancer-specific vulnerabilities in clinical samples

Systematic in vitro loss-of-function screens provide valuable resources that can facilitate the discovery of drugs targeting cancer vulnerabilities.

Authors: Kiwon Jang, Min Ji Park, Jae Soon Park, Haeun Hwangbo, Min Kyung Sung, Sinae Kim, Jaeyun Jung, Jong Won Lee, Sei-Hyun Ahn, Suhwan Chang and Jung Kyoon Choi

Allele-specific DNA methylation is increased in cancers and its dense mapping in normal plus neoplastic cells increases the yield of disease-associated regulatory SNPs

Mapping of allele-specific DNA methylation (ASM) can be a post-GWAS strategy for localizing regulatory sequence polymorphisms (rSNPs). The advantages of this approach, and the mechanisms underlying ASM in norm...

Authors: Catherine Do, Emmanuel L. P. Dumont, Martha Salas, Angelica Castano, Huthayfa Mujahed, Leonel Maldonado, Arunjot Singh, Sonia C. DaSilva-Arnold, Govind Bhagat, Soren Lehman, Angela M. Christiano, Subha Madhavan, Peter L. Nagy, Peter H. R. Green, Rena Feinman, Cornelia Trimble…

Sustainable agriculture in the era of omics: knowledge-driven crop breeding

Authors: Qing Li and Jianbing Yan

Single-cell transcriptome and antigen-immunoglobin analysis reveals the diversity of B cells in non-small cell lung cancer

Malignant transformation and progression of cancer are driven by the co-evolution of cancer cells and their dysregulated tumor microenvironment (TME). Recent studies on immunotherapy demonstrate the efficacy i...

Authors: Jian Chen, Yun Tan, Fenghuan Sun, Likun Hou, Chi Zhang, Tao Ge, Huansha Yu, Chunxiao Wu, Yuming Zhu, Liang Duan, Liang Wu, Nan Song, Liping Zhang, Wei Zhang, Di Wang, Chang Chen…

Approaches for integrating heterogeneous RNA-seq data reveal cross-talk between microbes and genes in asthmatic patients

Sputum induction is a non-invasive method to evaluate the airway environment, particularly for asthma. RNA sequencing (RNA-seq) of sputum samples can be challenging to interpret due to the complex and heteroge...

Authors: Daniel Spakowicz, Shaoke Lou, Brian Barron, Jose L. Gomez, Tianxiao Li, Qing Liu, Nicole Grant, Xiting Yan, Rebecca Hoyd, George Weinstock, Geoffrey L. Chupp and Mark Gerstein

Enhanced Integrated Gradients: improving interpretability of deep learning models using splicing codes as a case study

Despite the success and fast adaptation of deep learning models in biomedical domains, their lack of interpretability remains an issue. Here, we introduce Enhanced Integrated Gradients (EIG), a method to ident...

Authors: Anupama Jha, Joseph K. Aicher, Matthew R. Gazzara, Deependra Singh and Yoseph Barash

instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder

Hi-C exploits contact frequencies between pairs of loci to bridge and order contigs during genome assembly, resulting in chromosome-level assemblies. Because few robust programs are available for this type of ...

Authors: Lyam Baudry, Nadège Guiglielmoni, Hervé Marie-Nelly, Alexandre Cormier, Martial Marbouty, Komlan Avia, Yann Loe Mie, Olivier Godfroy, Lieven Sterck, J. Mark Cock, Christophe Zimmer, Susana M. Coelho and Romain Koszul

The two languages of science

Authors: Itai Yanai and Martin Lercher

KAML: improving genomic prediction accuracy of complex traits using machine learning determined parameters

Advances in high-throughput sequencing technologies have reduced the cost of genotyping dramatically and led to genomic prediction being widely used in animal and plant breeding, and increasingly in human gene...

Authors: Lilin Yin, Haohao Zhang, Xiang Zhou, Xiaohui Yuan, Shuhong Zhao, Xinyun Li and Xiaolei Liu

Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics

At least 50% of patients with suspected Mendelian disorders remain undiagnosed after whole-exome sequencing (WES), and the extent to which non-coding variants that are not captured by WES contribute to this fr...

Authors: Sateesh Maddirevula, Hiroyuki Kuwahara, Nour Ewida, Hanan E. Shamseldin, Nisha Patel, Fatema Alzahrani, Tarfa AlSheddi, Eman AlObeid, Mona Alenazi, Hessa S. Alsaif, Maha Alqahtani, Maha AlAli, Hatoon Al Ali, Rana Helaby, Niema Ibrahim, Firdous Abdulwahab…

Removal of H2Aub1 by ubiquitin-specific proteases 12 and 13 is required for stable Polycomb-mediated gene repression in Arabidopsis

Stable gene repression is essential for normal growth and development. Polycomb repressive complexes 1 and 2 (PRC1&2) are involved in this process by establishing monoubiquitination of histone 2A (H2Aub1) and ...

Authors: Lejon E. M. Kralemann, Shujing Liu, Minerva S. Trejo-Arellano, Rafael Muñoz-Viana, Claudia Köhler and Lars Hennig

3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize

Maize ears and tassels are two separate types of inflorescence which are initiated by similar developmental processes but gradually develop distinct architectures. However, coordinated trans and cis regulation of...

Authors: Yonghao Sun, Liang Dong, Ying Zhang, Da Lin, Weize Xu, Changxiong Ke, Linqian Han, Lulu Deng, Guoliang Li, David Jackson, Xingwang Li and Fang Yang

Repeat-induced point mutation in Neurospora crassa causes the highest known mutation rate and mutational burden of any cellular life

Repeat-induced point (RIP) mutation in Neurospora crassa degrades transposable elements by targeting repeats with C→T mutations. Whether RIP affects core genomic sequence in important ways is unknown.

Authors: Long Wang, Yingying Sun, Xiaoguang Sun, Luyao Yu, Lan Xue, Zhen He, Ju Huang, Dacheng Tian, Laurence D. Hurst and Sihai Yang

SWISS: multiplexed orthogonal genome editing in plants with a Cas9 nickase and engineered CRISPR RNA scaffolds

We describe here a CRISPR simultaneous and wide-editing induced by a single system (SWISS), in which RNA aptamers engineered in crRNA scaffold recruit their cognate binding proteins fused with cytidine deamina...

Authors: Chao Li, Yuan Zong, Shuai Jin, Haocheng Zhu, Dexing Lin, Shengnan Li, Jin-Long Qiu, Yanpeng Wang and Caixia Gao

Dynamic rewiring of the human interactome by interferon signaling

The type I interferon (IFN) response is an ancient pathway that protects cells against viral pathogens by inducing the transcription of hundreds of IFN-stimulated genes. Comprehensive catalogs of IFN-stimulate...

Authors: Craig H. Kerr, Michael A. Skinnider, Daniel D. T. Andrews, Angel M. Madero, Queenie W. T. Chan, R. Greg Stacey, Nikolay Stoynov, Eric Jan and Leonard J. Foster

SURF: integrative analysis of a compendium of RNA-seq and CLIP-seq datasets highlights complex governing of alternative transcriptional regulation by RNA-binding proteins

Advances in high-throughput profiling of RNA-binding proteins (RBPs) have resulted inCLIP-seq datasets coupled with transcriptome profiling by RNA-seq. However, analysis methods that integrate both types of da...

Authors: Fan Chen and Sündüz Keleş

Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes

Glioblastoma (GBM) has one of the worst 5-year survival rates of all cancers. While genomic studies of the disease have been performed, alterations in the non-coding regulatory regions of GBM have largely rema...

Authors: Sharadha Sakthikumar, Ananya Roy, Lulu Haseeb, Mats E. Pettersson, Elisabeth Sundström, Voichita D. Marinescu, Kerstin Lindblad-Toh and Karin Forsberg-Nilsson

Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations

Eubacterium rectale is one of the most prevalent human gut bacteria, but its diversity and population genetics are not well understood because large-scale whole-genome investigations of this microbe have not been...

Authors: Nicolai Karcher, Edoardo Pasolli, Francesco Asnicar, Kun D. Huang, Adrian Tett, Serena Manara, Federica Armanini, Debbie Bain, Sylvia H. Duncan, Petra Louis, Moreno Zolfo, Paolo Manghi, Mireia Valles-Colomer, Roberta Raffaetà, Omar Rota-Stabelli, Maria Carmen Collado…

CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data

An important challenge in pre-processing data from droplet-based single-cell RNA sequencing protocols is distinguishing barcodes associated with real cells from those binding background reads. Existing methods...

Authors: Zijian Ni, Shuyang Chen, Jared Brown and Christina Kendziorski

Direct-seq: programmed gRNA scaffold for streamlined scRNA-seq in CRISPR screen

CRISPR-based genome perturbation provides a new avenue to conveniently change DNA sequences, transcription, and epigenetic modifications in genetic screens. However, it remains challenging to assay the complex...

Authors: Qingkai Song, Ke Ni, Min Liu, Yini Li, Lixia Wang, Yingying Wang, Yingzheng Liu, Zhenxing Yu, Yinyao Qi, Zhike Lu and Lijia Ma

Molecular mechanisms of coronary disease revealed using quantitative trait loci for TCF21 binding, chromatin accessibility, and chromosomal looping

To investigate the epigenetic and transcriptional mechanisms of coronary artery disease (CAD) risk, as well as the functional regulation of chromatin structure and function, we create a catalog of genetic vari...

Authors: Quanyi Zhao, Michael Dacre, Trieu Nguyen, Milos Pjanic, Boxiang Liu, Dharini Iyer, Paul Cheng, Robert Wirka, Juyong Brian Kim, Hunter B. Fraser and Thomas Quertermous

MAUDE: inferring expression changes in sorting-based CRISPR screens

Improved methods are needed to model CRISPR screen data for interrogation of genetic elements that alter reporter gene expression readout. We create MAUDE (Mean Alterations Using Discrete Expression) for quant...

Authors: Carl G. de Boer, John P. Ray, Nir Hacohen and Aviv Regev

Author Correction: Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation

An amendment to this paper has been published and can be accessed via the original article.

Authors: Mayilaadumveettil Nishana, Caryn Ha, Javier Rodriguez-Hernaez, Ali Ranjbaran, Erica Chio, Elphege P. Nora, Sana B. Badri, Andreas Kloetgen, Benoit G. Bruneau, Aristotelis Tsirigos and Jane A. Skok

Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae

The majority of eukaryotic promoters utilize multiple transcription start sites (TSSs). How multiple TSSs are specified at individual promoters across eukaryotes is not understood for most species. In Saccharomyc...

Authors: Chenxi Qiu, Huiyan Jin, Irina Vvedenskaya, Jordi Abante Llenas, Tingting Zhao, Indranil Malik, Alex M. Visbisky, Scott L. Schwartz, Ping Cui, Pavel Čabart, Kang Hoo Han, William K. M. Lai, Richard P. Metz, Charles D. Johnson, Sing-Hoi Sze, B. Franklin Pugh…

The promise and challenge of cancer microbiome research

Many microbial agents have been implicated as contributors to cancer genesis and development, and the search to identify and characterize new cancer-related organisms is ongoing. Modern developments in methodo...

Authors: Sumeed Syed Manzoor, Annemiek Doedens and Michael B. Burns

Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

Single-cell RNA sequencing has been widely adopted to estimate the cellular composition of heterogeneous tissues and obtain transcriptional profiles of individual cells. Multiple approaches for optimal sample ...

Authors: Elena Denisenko, Belinda B. Guo, Matthew Jones, Rui Hou, Leanne de Kock, Timo Lassmann, Daniel Poppe, Olivier Clément, Rebecca K. Simmons, Ryan Lister and Alistair R. R. Forrest

Assembly and annotation of an Ashkenazi human reference genome

Thousands of experiments and studies use the human reference genome as a resource each year. This single reference genome, GRCh38, is a mosaic created from a small number of individuals, representing a very sm...

Authors: Alaina Shumate, Aleksey V. Zimin, Rachel M. Sherman, Daniela Puiu, Justin M. Wagner, Nathan D. Olson, Mihaela Pertea, Marc L. Salit, Justin M. Zook and Steven L. Salzberg

Developmental regulation of canonical and small ORF translation from mRNAs

Ribosomal profiling has revealed the translation of thousands of sequences outside annotated protein-coding genes, including small open reading frames of less than 100 codons, and the translational regulation ...

Authors: Pedro Patraquim, Muhammad Ali Shahzad Mumtaz, José Ignacio Pueyo, Julie Louise Aspden and Juan-Pablo Couso

CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data

To discover driver fusions beyond canonical exon-to-exon chimeric transcripts, we develop CICERO, a local assembly-based algorithm that integrates RNA-seq read support with extensive annotation for candidate r...

Authors: Liqing Tian, Yongjin Li, Michael N. Edmonson, Xin Zhou, Scott Newman, Clay McLeod, Andrew Thrasher, Yu Liu, Bo Tang, Michael C. Rusch, John Easton, Jing Ma, Eric Davis, Austyn Trull, J. Robert Michael, Karol Szlachta…

FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing

Genome replication mapping methods profile cell populations, masking cell-to-cell heterogeneity. Here, we describe FORK-seq, a nanopore sequencing method to map replication of single DNA molecules at 200-nucle...

Authors: Magali Hennion, Jean-Michel Arbona, Laurent Lacroix, Corinne Cruaud, Bertrand Theulot, Benoît Le Tallec, Florence Proux, Xia Wu, Elizaveta Novikova, Stefan Engelen, Arnaud Lemainque, Benjamin Audit and Olivier Hyrien

Personalized and graph genomes reveal missing signal in epigenomic data

Epigenomic studies that use next generation sequencing experiments typically rely on the alignment of reads to a reference sequence. However, because of genetic diversity and the diploid nature of the human ge...

Authors: Cristian Groza, Tony Kwan, Nicole Soranzo, Tomi Pastinen and Guillaume Bourque

Accounting for cell type hierarchy in evaluating single cell RNA-seq clustering

Cell clustering is one of the most common routines in single cell RNA-seq data analyses, for which a number of specialized methods are available. The evaluation of these methods ignores an important biological...

Authors: Zhijin Wu and Hao Wu

Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians

African populations provide a unique opportunity to interrogate host-microbe co-evolution and its impact on adaptive phenotypes due to their genomic, phenotypic, and cultural diversity. We integrate gut microb...

Authors: Meagan A. Rubel, Arwa Abbas, Louis J. Taylor, Andrew Connell, Ceylan Tanes, Kyle Bittinger, Valantine N. Ndze, Julius Y. Fonsah, Eric Ngwang, André Essiane, Charles Fokunang, Alfred K. Njamnshi, Frederic D. Bushman and Sarah A. Tishkoff

Gapless assembly of maize chromosomes using long-read technologies

Creating gapless telomere-to-telomere assemblies of complex genomes is one of the ultimate challenges in genomics. We use two independent assemblies and an optical map-based merging pipeline to produce a maize...

Authors: Jianing Liu, Arun S. Seetharam, Kapeel Chougule, Shujun Ou, Kyle W. Swentowsky, Jonathan I. Gent, Victor Llaca, Margaret R. Woodhouse, Nancy Manchanda, Gernot G. Presting, David A. Kudrna, Magdy Alabady, Candice N. Hirsch, Kevin A. Fengler, Doreen Ware, Todd P. Michael…

RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function

Vertebrate early embryogenesis is initially directed by a set of maternal RNAs and proteins, yet the mechanisms controlling this program remain largely unknown. Recent transcriptome-wide studies on RNA structu...

Authors: Boyang Shi, Jinsong Zhang, Jian Heng, Jing Gong, Ting Zhang, Pan Li, Bao-Fa Sun, Ying Yang, Ning Zhang, Yong-Liang Zhao, Hai-Lin Wang, Feng Liu, Qiangfeng Cliff Zhang and Yun-Gui Yang

tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing

Recent advances in long-read sequencing solve inaccuracies in alternative transcript identification of full-length transcripts in short-read RNA-Seq data, which encourages the development of methods for isofor...

Authors: Lorena de la Fuente, Ángeles Arzalluz-Luque, Manuel Tardáguila, Héctor del Risco, Cristina Martí, Sonia Tarazona, Pedro Salguero, Raymond Scott, Alberto Lerma, Ana Alastrue-Agudo, Pablo Bonilla, Jeremy R. B. Newman, Shunichi Kosugi, Lauren M. McIntyre, Victoria Moreno-Manzano and Ana Conesa

Protection from DNA re-methylation by transcription factors in primordial germ cells and pre-implantation embryos can explain trans-generational epigenetic inheritance

A growing body of evidence suggests that certain epiphenotypes can be passed across generations via both the male and female germlines of mammals. These observations have been difficult to explain owing to a g...

Authors: Isaac Kremsky and Victor G. Corces

BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks

Non-canonical residues, caps, crosslinks, and nicks are important to many functions of DNAs, RNAs, proteins, and complexes. However, we do not fully understand how networks of such non-canonical macromolecules...

Authors: Paul F. Lang, Yassmine Chebaro, Xiaoyue Zheng, John A. P. Sekar, Bilal Shaikh, Darren A. Natale and Jonathan R. Karr

APEC: an accesson-based method for single-cell chromatin accessibility analysis

The development of sequencing technologies has promoted the survey of genome-wide chromatin accessibility at single-cell resolution. However, comprehensive analysis of single-cell epigenomic profiles remains a...

Authors: Bin Li, Young Li, Kun Li, Lianbang Zhu, Qiaoni Yu, Pengfei Cai, Jingwen Fang, Wen Zhang, Pengcheng Du, Chen Jiang, Jun Lin and Kun Qu

Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank

Genomic analyses are sensitive to contamination in public databases caused by incorrectly labeled reference sequences. Here, we describe Conterminator, an efficient method to detect and remove incorrectly labe...

Authors: Martin Steinegger and Steven L. Salzberg

Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study

Positional weight matrix (PWM) is a de facto standard model to describe transcription factor (TF) DNA binding specificities. PWMs inferred from in vivo or in vitro data are stored in many databases and used in...

Authors: Giovanna Ambrosini, Ilya Vorontsov, Dmitry Penzar, Romain Groux, Oriol Fornes, Daria D. Nikolaeva, Benoit Ballester, Jan Grau, Ivo Grosse, Vsevolod Makeev, Ivan Kulakovskiy and Philipp Bucher

Effects of the COVID-19 pandemic on life scientists

Authors: Jan O. Korbel and Oliver Stegle

Sampling time-dependent artifacts in single-cell genomics studies

Robust protocols and automation now enable large-scale single-cell RNA and ATAC sequencing experiments and their application on biobank and clinical cohorts. However, technical biases introduced during sample ...

Authors: Ramon Massoni-Badosa, Giovanni Iacono, Catia Moutinho, Marta Kulis, Núria Palau, Domenica Marchese, Javier Rodríguez-Ubreva, Esteban Ballestar, Gustavo Rodriguez-Esteban, Sara Marsal, Marta Aymerich, Dolors Colomer, Elias Campo, Antonio Julià, José Ignacio Martín-Subero and Holger Heyn

Chromatin topology reorganization and transcription repression by PML-RARα in acute promyeloid leukemia

Acute promyeloid leukemia (APL) is characterized by the oncogenic fusion protein PML-RARα, a major etiological agent in APL. However, the molecular mechanisms underlying the role of PML-RARα in leukemogenesis ...

Authors: Ping Wang, Zhonghui Tang, Byoungkoo Lee, Jacqueline Jufen Zhu, Liuyang Cai, Przemyslaw Szalaj, Simon Zhongyuan Tian, Meizhen Zheng, Dariusz Plewczynski, Xiaoan Ruan, Edison T. Liu, Chia-Lin Wei and Yijun Ruan