Volume 23, issue 1, December 2022
271 articles in this issue
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scGWAS: landscape of trait-cell type associations by integrating single-cell transcriptomics-wide and genome-wide association studies
Authors (first, second and last of 5)
- Peilin Jia
- Ruifeng Hu
- Zhongming Zhao
- Content type: Research
- Open Access
- Published: 17 October 2022
- Article: 220
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iDNA-ABF: multi-scale deep biological language learning model for the interpretable prediction of DNA methylations
Authors (first, second and last of 12)
- Junru Jin
- Yingying Yu
- Leyi Wei
- Content type: Method
- Open Access
- Published: 17 October 2022
- Article: 219
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Evaluation of cell-cell interaction methods by integrating single-cell RNA sequencing data with spatial information
Authors
- Zhaoyang Liu
- Dongqing Sun
- Chenfei Wang
- Content type: Research
- Open Access
- Published: 17 October 2022
- Article: 218
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Global early replication disrupts gene expression and chromatin conformation in a single cell cycle
Authors (first, second and last of 4)
- Miguel M. Santos
- Mark C. Johnson
- Philip Zegerman
- Content type: Research
- Open Access
- Published: 17 October 2022
- Article: 217
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Local CpG density affects the trajectory and variance of age-associated DNA methylation changes
Authors (first, second and last of 17)
- Jonathan Higham
- Lyndsay Kerr
- Duncan Sproul
- Content type: Research
- Open Access
- Published: 17 October 2022
- Article: 216
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Evolutionary dynamics of pseudoautosomal region 1 in humans and great apes
Authors
- Juraj Bergman
- Mikkel Heide Schierup
- Content type: Research
- Open Access
- Published: 17 October 2022
- Article: 215
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Dissemination of circulating tumor cells at night: role of sleep or circadian rhythm?
Authors
- Yves Dauvilliers
- Frédéric Thomas
- Catherine Alix-Panabières
- Content type: Editorial
- Open Access
- Published: 14 October 2022
- Article: 214
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Author Correction: Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG
Authors (first, second and last of 6)
- Zhana Duren
- Fengge Chang
- Wing Hung Wong
- Content type: Author Correction
- Open Access
- Published: 13 October 2022
- Article: 213
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A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes
Authors (first, second and last of 10)
- Jon G. Sanders
- Weiwei Yan
- Andrew H. Moeller
- Content type: Method
- Open Access
- Published: 12 October 2022
- Article: 212
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Enhanced mitochondrial DNA editing in mice using nuclear-exported TALE-linked deaminases and nucleases
Authors (first, second and last of 8)
- Seonghyun Lee
- Hyunji Lee
- Jin-Soo Kim
- Content type: Short Report
- Open Access
- Published: 12 October 2022
- Article: 211
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PCA outperforms popular hidden variable inference methods for molecular QTL mapping
Authors (first, second and last of 5)
- Heather J. Zhou
- Lei Li
- Jingyi Jessica Li
- Content type: Research
- Open Access
- Published: 11 October 2022
- Article: 210
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KAGE: fast alignment-free graph-based genotyping of SNPs and short indels
Authors
- Ivar Grytten
- Knut Dagestad Rand
- Geir Kjetil Sandve
- Content type: Method
- Open Access
- Published: 04 October 2022
- Article: 209
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Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin
Authors (first, second and last of 10)
- Siyuan Ma
- Dmitry Shungin
- Curtis Huttenhower
- Content type: Method
- Open Access
- Published: 03 October 2022
- Article: 208
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H3K18 lactylation marks tissue-specific active enhancers
Authors (first, second and last of 13)
- Eva Galle
- Chee-Wai Wong
- Ferdinand von Meyenn
- Content type: Research
- Open Access
- Published: 03 October 2022
- Article: 207
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MBD5 and MBD6 stabilize the BAP1 complex and promote BAP1-dependent cancer
Authors (first, second and last of 4)
- Natsumi Tsuboyama
- Aileen Patricia Szczepanski
- Lu Wang
- Content type: Research
- Open Access
- Published: 30 September 2022
- Article: 206
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Widespread false gene gains caused by duplication errors in genome assemblies
Authors (first, second and last of 12)
- Byung June Ko
- Chul Lee
- Heebal Kim
- Content type: Research
- Open Access
- Published: 27 September 2022
- Article: 205
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False gene and chromosome losses in genome assemblies caused by GC content variation and repeats
Authors (first, second and last of 19)
- Juwan Kim
- Chul Lee
- Erich D. Jarvis
- Content type: Research
- Open Access
- Published: 27 September 2022
- Article: 204
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Whole-genome sequencing reveals the genetic mechanisms of domestication in classical inbred mice
Authors (first, second and last of 22)
- Ming Liu
- Caixia Yu
- Zhibin Zhang
- Content type: Research
- Open Access
- Published: 26 September 2022
- Article: 203
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Single-cell multi-omics profiling links dynamic DNA methylation to cell fate decisions during mouse early organogenesis
Authors (first, second and last of 9)
- Stephen J. Clark
- Ricard Argelaguet
- Wolf Reik
- Content type: Research
- Open Access
- Published: 26 September 2022
- Article: 202
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Parental genomes segregate into distinct blastomeres during multipolar zygotic divisions leading to mixoploid and chimeric blastocysts
Authors (first, second and last of 14)
- Tine De Coster
- Heleen Masset
- Joris Robert Vermeesch
- Content type: Research
- Open Access
- Published: 03 October 2022
- Article: 201
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Repeated turnovers keep sex chromosomes young in willows
Authors (first, second and last of 18)
- Deyan Wang
- Yiling Li
- Tao Ma
- Content type: Research
- Open Access
- Published: 23 September 2022
- Article: 200
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Genomics and epigenetics guided identification of tissue-specific genomic safe harbors
Authors (first, second and last of 8)
- Dewan Shrestha
- Aishee Bag
- Yong Cheng
- Content type: Research
- Open Access
- Published: 21 September 2022
- Article: 199
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Author Correction: Towards accurate and reliable resolution of structural variants for clinical diagnosis
Authors (first, second and last of 6)
- Zhichao Liu
- Ruth Roberts
- Weida Tong
- Content type: Author Correction
- Open Access
- Published: 20 September 2022
- Article: 198
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DNA methylation underpins the epigenomic landscape regulating genome transcription in Arabidopsis
Authors (first, second and last of 7)
- Lun Zhao
- Qiangwei Zhou
- Jian-Kang Zhu
- Content type: Research
- Open Access
- Published: 20 September 2022
- Article: 197
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Genetic regulation of RNA splicing in human pancreatic islets
Authors (first, second and last of 20)
- Goutham Atla
- Silvia Bonà s-Guarch
- Jorge Ferrer
- Content type: Research
- Open Access
- Published: 15 September 2022
- Article: 196
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Comprehensive and scalable quantification of splicing differences with MntJULiP
Authors
- Guangyu Yang
- Sarven Sabunciyan
- Liliana Florea
- Content type: Method
- Open Access
- Published: 14 September 2022
- Article: 195
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Testing the generalizability of ancestry-specific polygenic risk scores to predict prostate cancer in sub-Saharan Africa
Authors (first, second and last of 48)
- Michelle S. Kim
- Daphne Naidoo
- Joseph Lachance
- Content type: Research
- Open Access
- Published: 13 September 2022
- Article: 194
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Control of immediate early gene expression by CPEB4-repressor complex-mediated mRNA degradation
Authors (first, second and last of 6)
- Fabian Poetz
- Svetlana Lebedeva
- Georg Stoecklin
- Content type: Research
- Open Access
- Published: 12 September 2022
- Article: 193
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Comparative analyses of vertebrate CPEB proteins define two subfamilies with coordinated yet distinct functions in post-transcriptional gene regulation
Authors (first, second and last of 11)
- Berta Duran-Arqué
- Manuel Cañete
- Raúl Mendez
- Content type: Research
- Open Access
- Published: 12 September 2022
- Article: 192
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Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP
Authors (first, second and last of 5)
- Klara Kuret
- Aram Gustav Amalietti
- Jernej Ule
- Content type: Research
- Open Access
- Published: 09 September 2022
- Article: 191
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Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2
Authors (first, second and last of 4)
- Jamshed Khan
- Marek Kokot
- Rob Patro
- Content type: Method
- Open Access
- Published: 08 September 2022
- Article: 190
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Abnormal molecular signatures of inflammation, energy metabolism, and vesicle biology in human Huntington disease peripheral tissues
Authors (first, second and last of 15)
- Andreas Neueder
- Kerstin Kojer
- Michael Orth
- Content type: Research
- Open Access
- Published: 07 September 2022
- Article: 189
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Genomic insights into the evolutionary history and diversification of bulb traits in garlic
Authors (first, second and last of 30)
- Ningyang Li
- Xueyu Zhang
- Touming Liu
- Content type: Research
- Open Access
- Published: 07 September 2022
- Article: 188
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The histone modification reader ZCWPW1 promotes double-strand break repair by regulating cross-talk of histone modifications and chromatin accessibility at meiotic hotspots
Authors (first, second and last of 8)
- Shenli Yuan
- Tao Huang
- Zi-Jiang Chen
- Content type: Research
- Open Access
- Published: 06 September 2022
- Article: 187
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Integrating temporal single-cell gene expression modalities for trajectory inference and disease prediction
Authors
- Jolene S. Ranek
- Natalie Stanley
- Jeremy E. Purvis
- Content type: Research
- Open Access
- Published: 05 September 2022
- Article: 186
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CTCF and cohesin promote focal detachment of DNA from the nuclear lamina
Authors (first, second and last of 6)
- Tom van Schaik
- Ning Qing Liu
- Bas van Steensel
- Content type: Research
- Open Access
- Published: 01 September 2022
- Article: 185
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MIRTH: Metabolite Imputation via Rank-Transformation and Harmonization
Authors (first, second and last of 6)
- Benjamin A. Freeman
- Sophie Jaro
- Ed Reznik
- Content type: Method
- Open Access
- Published: 01 September 2022
- Article: 184
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Prediction of evolutionary constraint by genomic annotations improves functional prioritization of genomic variants in maize
Authors
- Guillaume P. Ramstein
- Edward S. Buckler
- Content type: Research
- Open Access
- Published: 01 September 2022
- Article: 183
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Multiple genome alignment in the telomere-to-telomere assembly era
Authors (first, second and last of 5)
- Bryce Kille
- Advait Balaji
- Todd J. Treangen
- Content type: Review
- Open Access
- Published: 29 August 2022
- Article: 182
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The Arabidopsis APOLO and human UPAT sequence-unrelated long noncoding RNAs can modulate DNA and histone methylation machineries in plants
Authors (first, second and last of 14)
- Camille Fonouni-Farde
- Aurélie Christ
- Federico Ariel
- Content type: Research
- Open Access
- Published: 29 August 2022
- Article: 181
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Identifying and correcting repeat-calling errors in nanopore sequencing of telomeres
Authors (first, second and last of 4)
- Kar-Tong Tan
- Michael K. Slevin
- Heng Li
- Content type: Short Report
- Open Access
- Published: 26 August 2022
- Article: 180
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What puzzle are you in?
Authors
- Itai Yanai
- Martin J. Lercher
- Content type: Editorial
- Open Access
- Published: 25 August 2022
- Article: 179
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A pan-Zea genome map for enhancing maize improvement
Authors (first, second and last of 13)
- Songtao Gui
- Wenjie Wei
- Jianbing Yan
- Content type: Research
- Open Access
- Published: 23 August 2022
- Article: 178
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Human dyskerin binds to cytoplasmic H/ACA-box-containing transcripts affecting nuclear hormone receptor dependence
Authors (first, second and last of 12)
- Federico Zacchini
- Giulia Venturi
- Lorenzo Montanaro
- Content type: Research
- Open Access
- Published: 22 August 2022
- Article: 177
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Comparative transcriptome in large-scale human and cattle populations
Authors (first, second and last of 26)
- Yuelin Yao
- Shuli Liu
- Albert Tenesa
- Content type: Research
- Open Access
- Published: 22 August 2022
- Article: 176
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PerSVade: personalized structural variant detection in any species of interest
Authors
- Miquel Àngel Schikora-Tamarit
- Toni Gabaldón
- Content type: Software
- Open Access
- Published: 16 August 2022
- Article: 175
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BindVAE: Dirichlet variational autoencoders for de novo motif discovery from accessible chromatin
Authors (first, second and last of 4)
- Meghana Kshirsagar
- Han Yuan
- Christina Leslie
- Content type: Method
- Open Access
- Published: 15 August 2022
- Article: 174
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Single-cell diploid Hi-C reveals the role of spatial aggregations in complex rearrangements and KMT2A fusions in leukemia
Authors (first, second and last of 9)
- Zhihao Xing
- Huirong Mai
- Feiqiu Wen
- Content type: Research
- Open Access
- Published: 09 August 2022
- Article: 173
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The recombination landscape of the Khoe-San likely represents the upper limits of recombination divergence in humans
Authors (first, second and last of 8)
- Gerald van Eeden
- Caitlin Uren
- Marlo Möller
- Content type: Research
- Open Access
- Published: 09 August 2022
- Article: 172