Table of Contents

Molecular and genetic landscapes of retina and brain microglia in neurodegenerative diseases

• Khang Ma and
• Rinki Ratnapriya

• Abstract
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APOBEC3A drives deaminase mutagenesis in human gastric epithelium

• Yohan An,
• Ji-Hyun Lee,
• Joonoh Lim,
• Jeonghwan Youk,
• Seongyeol Park,
• Ji-Hyung Park,
• Kijong Yi,
• Taewoo Kim,
• Chang Hyun Nam,
• Won Hee Lee,
• Soo A Oh,
• Yoo Jin Bae,
• Thomas M. Klompstra,
• Haeun Lee,
• Jinju Han,
• Junehwak Lee,
• Jung Woo Park,
• Jie-Hyun Kim,
• Hyunki Kim,
• Hugo Snippert,
• Bon-Kyoung Koo,
• and Young Seok Ju

• Abstract
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Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations

• Xiu Fan,
• Qili Qian,
• Wenran Li,
• Tianzi Liu,
• Changqing Zeng,
• Peilin Jia,
• Huandong Lin,
• Xin Gao,
• Li Jin,
• Mingfeng Xia,
• Sijia Wang,
• and Fan Liu

• Abstract
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Widespread specific intron retention events in nuclear RNA complexes identified by sedimentation analysis of pluripotent cellular extracts

• Isabela T. Pereira,
• Izabela Mamede,
• Paulo P. Amaral,
• Gloria R. Franco,
• and John L. Rinn

• Abstract
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H3K27 and H3K9 methylation mask potential CTCF binding sites to maintain 3D genome integrity

• Kei Fukuda,
• Chikako Shimura,
• and Yoichi Shinkai

• Abstract
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Mapping multitissue regulatory variants reveals a liver-centric coexpression network associated with duck egg-laying performance

• Yang Xi,
• Jingjing Qi,
• Zhao Yang,
• Yutian Zeng,
• Huicong Zhang,
• Qiuyu Tao,
• Mengru Xu,
• Anqi Huang,
• Shenqiang Hu,
• Chunchun Han,
• Lili Bai,
• Jiwei Hu,
• Jiwen Wang,
• Liang Li,
• Lingzhao Fang,
• and Hehe Liu

• Abstract
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Intergenic accumulation of RNA polymerase II maintains the potential for swift transcriptional restart upon release from quiescence

• Manuela Baquero Pérez,
• Gertjan Laenen,
• Isabelle Loïodice,
• Mickaël Garnier,
• Ugo Szachnowski,
• Antonin Morillon,
• Myriam Ruault,
• and Angela Taddei

• Abstract
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Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus

• Mari B. Gornitzka,
• Egil Røsjø,
• Uddalok Jana,
• Easton E. Ford,
• Alan Tourancheau,
• William D. Lees,
• Zachary Vanwinkle,
• Melissa L. Smith,
• Corey T. Watson,
• and Andreas Lossius

• Abstract
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FocalSV enables target region–based structural variant assembly and refinement using single-molecule long-read sequencing data

• Can Luo,
• Zimeng Jamie Zhou,
• Yichen Henry Liu,
• and Xin Maizie Zhou

• Abstract
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Unveiling the functional fate of duplicated genes through expression profiling and structural analysis

• Alex Warwick Vesztrocy,
• Natasha Glover,
• Paul D. Thomas,
• Christophe Dessimoz,
• and Irene Julca

• Abstract
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Efficient integration of spatial omics data for joint domain detection, matching, and alignment with stMSA

• Han Shu,
• Jing Chen,
• Chang Xu,
• Jialu Hu,
• Yongtian Wang,
• Jiajie Peng,
• Qinghua Jiang,
• Xuequn Shang,
• and Tao Wang

• Abstract
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Deciphering context-specific gene programs from single-cell and spatial transcriptomics data with DeCEP

• Lin Li,
• Xianbin Su,
• and Ze-Guang Han

• Abstract
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Recalibrating differential gene expression by genetic dosage variance prioritizes functionally relevant genes

• Philipp Rentzsch,
• Aaron Kollotzek,
• Kaushik Ram Ganapathy,
• Pejman Mohammadi,
• and Tuuli Lappalainen

• Abstract
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Tree-based differential testing using inferential uncertainty for RNA-seq

• Noor Pratap Singh,
• Euphy Y. Wu,
• Jason Fan,
• Michael I. Love,
• and Rob Patro

• Abstract
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Multicondition and multimodal temporal profile inference during mouse embryonic development

• Ran Zhang,
• Chengxiang Qiu,
• Galina N. Filippova,
• Gang Li,
• Jay Shendure,
• Jean-Philippe Vert,
• Xinxian Deng,
• William Stafford Noble,
• and Christine M. Disteche

• Abstract
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Analyzing the large and complex SFARI autism cohort data using the Genotypes and Phenotypes in Families (GPF) platform

• Liubomir Chorbadjiev,
• Murat Cokol,
• Zohar Weinstein,
• Kevin Shi,
• Christopher Fleisch,
• Nikolay Dimitrov,
• Svetlin Mladenov,
• Ivo Todorov,
• Iordan Ivanov,
• Simon Xu,
• Steven Ford,
• Yoon-ha Lee,
• Boris Yamrom,
• Steven Marks,
• Adriana Munoz,
• Alex Lash,
• Natalia Volfovsky,
• and Ivan Iossifov

• Abstract
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Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival

• Marina Athanasouli,
• Tobias Loschko,
• and Christian Rödelsperger

• Abstract
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Corrigendum: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes

• Ran Li,
• Mian Gong,
• Xinmiao Zhang,
• Fei Wang,
• Zhenyu Liu,
• Lei Zhang,
• Qimeng Yang,
• Yuan Xu,
• Mengsi Xu,
• Huanhuan Zhang,
• Yunfeng Zhang,
• Xuelei Dai,
• Yuanpeng Gao,
• Zhuangbiao Zhang,
• Wenwen Fang,
• Yuta Yang,
• Weiwei Fu,
• Chunna Cao,
• Peng Yang,
• Zeinab Amiri Ghanatsaman,
• Niloufar Jafarpour Negari,
• Hojjat Asadollahpour Nanaei,
• Xiangpeng Yue,
• Yuxuan Song,
• Xianyong Lan,
• Weidong Deng,
• Xihong Wang,
• Chuanying Pan,
• Ruidong Xiang,
• Eveline M. Ibeagha-Awemu,
• Pat (J.S.) Heslop-Harrison,
• Benjamin D. Rosen,
• Johannes A. Lenstra,
• Shangquan Gan,
• and Yu Jiang

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