Volume 24, issue 1, December 2023
294 articles in this issue
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Utilizing AAV-mediated LEAPER 2.0 for programmable RNA editing in non-human primates and nonsense mutation correction in humanized Hurler syndrome mice
Authors (first, second and last of 16)
- Zongyi Yi
- Yanxia Zhao
- Wensheng Wei
- Content type: Research
- Open Access
- Published: 23 October 2023
- Article: 243
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aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow
Authors (first, second and last of 13)
- Zoé Pochon
- Nora Bergfeldt
- Nikolay Oskolkov
- Content type: Method
- Open Access
- Published: 23 October 2023
- Article: 242
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SPIRAL: integrating and aligning spatially resolved transcriptomics data across different experiments, conditions, and technologies
Authors (first, second and last of 7)
- Tiantian Guo
- Zhiyuan Yuan
- Xiangyu Li
- Content type: Method
- Open Access
- Published: 20 October 2023
- Article: 241
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DIVE: a reference-free statistical approach to diversity-generating and mobile genetic element discovery
Authors
- Jordi Abante
- Peter L. Wang
- Julia Salzman
- Content type: Method
- Open Access
- Published: 20 October 2023
- Article: 240
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Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors
Authors (first, second and last of 8)
- Ariel A. Hippen
- Dalia K. Omran
- Casey S. Greene
- Content type: Research
- Open Access
- Published: 20 October 2023
- Article: 239
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Measuring cell-to-cell expression variability in single-cell RNA-sequencing data: a comparative analysis and applications to B cell aging
Authors (first, second and last of 4)
- Huiwen Zheng
- Jan Vijg
- Jessica Cara Mar
- Content type: Research
- Open Access
- Published: 20 October 2023
- Article: 238
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Dual spatially resolved transcriptomics for human host–pathogen colocalization studies in FFPE tissue sections
Authors (first, second and last of 16)
- Hailey Sounart
- Enikő Lázár
- Stefania Giacomello
- Content type: Method
- Open Access
- Published: 19 October 2023
- Article: 237
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GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership
Authors (first, second and last of 7)
- Peter Carbonetto
- Kaixuan Luo
- Matthew Stephens
- Content type: Method
- Open Access
- Published: 19 October 2023
- Article: 236
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GeneSegNet: a deep learning framework for cell segmentation by integrating gene expression and imaging
Authors (first, second and last of 6)
- Yuxing Wang
- Wenguan Wang
- Zhicheng Ji
- Content type: Method
- Open Access
- Published: 19 October 2023
- Article: 235
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Single-cell metabolic profiling reveals subgroups of primary human hepatocytes with heterogeneous responses to drug challenge
Authors (first, second and last of 4)
- Eva Sanchez-Quant
- Maria Lucia Richter
- Celia Pilar Martinez-Jimenez
- Content type: Research
- Open Access
- Published: 17 October 2023
- Article: 234
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Data-driven identification of total RNA expression genes for estimation of RNA abundance in heterogeneous cell types highlighted in brain tissue
Authors (first, second and last of 7)
- Louise A. Huuki-Myers
- Kelsey D. Montgomery
- Leonardo Collado-Torres
- Content type: Software
- Open Access
- Published: 16 October 2023
- Article: 233
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The evolution and mutational robustness of chromatin accessibility in Drosophila
Authors (first, second and last of 8)
- Samuel Khodursky
- Eric B. Zheng
- Li Zhao
- Content type: Research
- Open Access
- Published: 16 October 2023
- Article: 232
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MalariaSED: a deep learning framework to decipher the regulatory contributions of noncoding variants in malaria parasites
Authors (first, second and last of 16)
- Chengqi Wang
- Yibo Dong
- Xiaoming Liu
- Content type: Method
- Open Access
- Published: 16 October 2023
- Article: 231
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A fast non-parametric test of association for multiple traits
Authors (first, second and last of 4)
- Diego Garrido-MartÃn
- Miquel Calvo
- Roderic Guigó
- Content type: Method
- Open Access
- Published: 12 October 2023
- Article: 230
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The landscape of cell-free mitochondrial DNA in liquid biopsy for cancer detection
Authors (first, second and last of 13)
- Ymke van der Pol
- Norbert Moldovan
- Florent Mouliere
- Content type: Research
- Open Access
- Published: 12 October 2023
- Article: 229
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Robust, scalable, and informative clustering for diverse biological networks
Authors (first, second and last of 8)
- Chris Gaiteri
- David R. Connell
- Shinya Tasaki
- Content type: Method
- Open Access
- Published: 12 October 2023
- Article: 228
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Dynamic DNA methylation turnover in gene bodies is associated with enhanced gene expression plasticity in plants
Authors (first, second and last of 5)
- Clara J. Williams
- Dawei Dai
- Ben P. Williams
- Content type: Research
- Open Access
- Published: 12 October 2023
- Article: 227
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Metagenome-wide analysis uncovers gut microbial signatures and implicates taxon-specific functions in end-stage renal disease
Authors (first, second and last of 47)
- Pan Zhang
- Xifan Wang
- Xiaoqiang Ding
- Content type: Research
- Open Access
- Published: 12 October 2023
- Article: 226
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scIBD: a self-supervised iterative-optimizing model for boosting the detection of heterotypic doublets in single-cell chromatin accessibility data
Authors (first, second and last of 4)
- Wenhao Zhang
- Rui Jiang
- Ying Wang
- Content type: Method
- Open Access
- Published: 09 October 2023
- Article: 225
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Large sample size and nonlinear sparse models outline epistatic effects in inflammatory bowel disease
Authors (first, second and last of 5)
- Nora Verplaetse
- Antoine Passemiers
- Daniele Raimondi
- Content type: Research
- Open Access
- Published: 05 October 2023
- Article: 224
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GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation
Authors (first, second and last of 8)
- Bruno Contreras-Moreira
- Shradha Saraf
- Sarah Dyer
- Content type: Method
- Open Access
- Published: 05 October 2023
- Article: 223
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HycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing
Authors (first, second and last of 7)
- Renmin Han
- Junhai Qi
- Guojun Li
- Content type: Method
- Open Access
- Published: 05 October 2023
- Article: 222
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Genomic variant benchmark: if you cannot measure it, you cannot improve it
Authors (first, second and last of 5)
- Sina Majidian
- Daniel Paiva Agustinho
- Medhat Mahmoud
- Content type: Review
- Open Access
- Published: 05 October 2023
- Article: 221
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MCProj: metacell projection for interpretable and quantitative use of transcriptional atlases
Authors (first, second and last of 6)
- Oren Ben-Kiki
- Akhiad Bercovich
- Amos Tanay
- Content type: Method
- Open Access
- Published: 05 October 2023
- Article: 220
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CEGA: a method for inferring natural selection by comparative population genomic analysis across species
Authors
- Shilei Zhao
- Lianjiang Chi
- Hua Chen
- Content type: Method
- Open Access
- Published: 03 October 2023
- Article: 219
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MBE: model-based enrichment estimation and prediction for differential sequencing data
Authors
- Akosua Busia
- Jennifer Listgarten
- Content type: Method
- Open Access
- Published: 02 October 2023
- Article: 218
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GenArk: towards a million UCSC genome browsers
Authors (first, second and last of 23)
- Hiram Clawson
- Brian T. Lee
- Maximilian Haeussler
- Content type: Short Report
- Open Access
- Published: 02 October 2023
- Article: 217
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A loss-of-function mutation in human Oxidation Resistance 1 disrupts the spatial–temporal regulation of histone arginine methylation in neurodevelopment
Authors (first, second and last of 29)
- Xiaolin Lin
- Wei Wang
- Magnar Bjørås
- Content type: Research
- Open Access
- Published: 29 September 2023
- Article: 216
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Dominance is common in mammals and is associated with trans-acting gene expression and alternative splicing
Authors (first, second and last of 16)
- Leilei Cui
- Bin Yang
- Lusheng Huang
- Content type: Research
- Open Access
- Published: 29 September 2023
- Article: 215
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happi: a hierarchical approach to pangenomics inference
Authors
- Pauline Trinh
- David S. Clausen
- Amy D. Willis
- Content type: Method
- Open Access
- Published: 29 September 2023
- Article: 214
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Dosage compensation of Z sex chromosome genes in avian fibroblast cells
Authors (first, second and last of 12)
- Ruslan Deviatiiarov
- Hiroki Nagai
- Guojun Sheng
- Content type: Short Report
- Open Access
- Published: 20 September 2023
- Article: 213
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DISCERN: deep single-cell expression reconstruction for improved cell clustering and cell subtype and state detection
Authors (first, second and last of 9)
- Fabian Hausmann
- Can Ergen
- Stefan Bonn
- Content type: Research
- Open Access
- Published: 20 September 2023
- Article: 212
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Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment
Authors (first, second and last of 30)
- Xiaoting Xia
- Fengwei Zhang
- Ningbo Chen
- Content type: Research
- Open Access
- Published: 18 September 2023
- Article: 211
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Author Correction: Single-cell resolution analysis reveals the preparation for reprogramming the fate of stem cell niche in cotton lateral meristem
Authors (first, second and last of 15)
- Xiangqian Zhu
- Zhongping Xu
- Shuangxia Jin
- Content type: Author Correction
- Open Access
- Published: 18 September 2023
- Article: 210
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Disparities in spatially variable gene calling highlight the need for benchmarking spatial transcriptomics methods
Authors (first, second and last of 7)
- Natalie Charitakis
- Agus Salim
- Mirana Ramialison
- Content type: Short Report
- Open Access
- Published: 18 September 2023
- Article: 209
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ZINBMM: a general mixture model for simultaneous clustering and gene selection using single-cell transcriptomic data
Authors (first, second and last of 4)
- Yang Li
- Mingcong Wu
- Mengyun Wu
- Content type: Method
- Open Access
- Published: 11 September 2023
- Article: 208
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The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees
Authors
- Kenneth A. Barr
- Katherine L. Rhodes
- Yoav Gilad
- Content type: Research
- Open Access
- Published: 11 September 2023
- Article: 207
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Coupling of co-transcriptional splicing and 3’ end Pol II pausing during termination in Arabidopsis
Authors (first, second and last of 6)
- Sixian Zhou
- Fengli Zhao
- Zhe Wu
- Content type: Research
- Open Access
- Published: 11 September 2023
- Article: 206
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PhaseDancer: a novel targeted assembler of segmental duplications unravels the complexity of the human chromosome 2 fusion going from 48 to 46 chromosomes in hominin evolution
Authors (first, second and last of 5)
- Barbara Poszewiecka
- Krzysztof Gogolewski
- Anna Gambin
- Content type: Method
- Open Access
- Published: 11 September 2023
- Article: 205
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COLLAGENE enables privacy-aware federated and collaborative genomic data analysis
Authors (first, second and last of 6)
- Wentao Li
- Miran Kim
- Arif Harmanci
- Content type: Software
- Open Access
- Published: 11 September 2023
- Article: 204
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ChromGene: gene-based modeling of epigenomic data
Authors
- Artur Jaroszewicz
- Jason Ernst
- Content type: Method
- Open Access
- Published: 07 September 2023
- Article: 203
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Quartet protein reference materials and datasets for multi-platform assessment of label-free proteomics
Authors (first, second and last of 19)
- Sha Tian
- Dongdong Zhan
- Chen Ding
- Content type: Research
- Open Access
- Published: 07 September 2023
- Article: 202
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Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method
Authors (first, second and last of 17)
- Ying Yu
- Naixin Zhang
- Yuanting Zheng
- Content type: Research
- Open Access
- Published: 07 September 2023
- Article: 201
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Pervasive under-dominance in gene expression underlying emergent growth trajectories in Arabidopsis thaliana hybrids
Authors (first, second and last of 7)
- Wei Yuan
- Fiona Beitel
- Detlef Weigel
- Content type: Research
- Open Access
- Published: 04 September 2023
- Article: 200
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Single-cell transcriptomics reveals multiple chemoresistant properties in leukemic stem and progenitor cells in pediatric AML
Authors (first, second and last of 22)
- Yongping Zhang
- Shuting Jiang
- Qian-Fei Wang
- Content type: Research
- Open Access
- Published: 31 August 2023
- Article: 199
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A DNA adenine demethylase impairs PRC2-mediated repression of genes marked by a specific chromatin signature
Authors (first, second and last of 13)
- Qingxiao Jia
- Xinran Zhang
- Dao-Xiu Zhou
- Content type: Research
- Open Access
- Published: 30 August 2023
- Article: 198
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Ariadne: synthetic long read deconvolution using assembly graphs
Authors (first, second and last of 7)
- Lauren Mak
- Dmitry Meleshko
- Iman Hajirasouliha
- Content type: Method
- Open Access
- Published: 28 August 2023
- Article: 197
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A high-resolution genotype–phenotype map identifies the TaSPL17 controlling grain number and size in wheat
Authors (first, second and last of 27)
- Yangyang Liu
- Jun Chen
- Zifeng Guo
- Content type: Research
- Open Access
- Published: 28 August 2023
- Article: 196
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SCA: recovering single-cell heterogeneity through information-based dimensionality reduction
Authors
- Benjamin DeMeo
- Bonnie Berger
- Content type: Method
- Open Access
- Published: 25 August 2023
- Article: 195