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  1. We propose a statistical framework ISLET to infer individual-specific and cell-type-specific transcriptome reference panels. ISLET models the repeatedly measured bulk gene expression data, to optimize the usag...

    Authors: Hao Feng, Guanqun Meng, Tong Lin, Hemang Parikh, Yue Pan, Ziyi Li, Jeffrey Krischer and Qian Li
    Citation: Genome Biology 2023 24:174
  2. The appearance of Slavs in East-Central Europe has been the subject of an over 200-year debate driven by two conflicting hypotheses. The first assumes that Slavs came to the territory of contemporary Poland no...

    Authors: Ireneusz Stolarek, Michal Zenczak, Luiza Handschuh, Anna Juras, Malgorzata Marcinkowska-Swojak, Anna Spinek, Artur Dębski, Marzena Matla, Hanna Kóčka-Krenz, Janusz Piontek and Marek Figlerowicz
    Citation: Genome Biology 2023 24:173
  3. Metachromatic leukodystrophy (MLD) is a lysosomal storage disorder caused by mutations in the arylsulfatase A gene (ARSA) and categorized into three subtypes according to age of onset. The functional effect of mo...

    Authors: Marena Trinidad, Xinying Hong, Steven Froelich, Jessica Daiker, James Sacco, Hong Phuc Nguyen, Madelynn Campagna, Dean Suhr, Teryn Suhr, Jonathan H. LeBowitz, Michael H. Gelb and Wyatt T. Clark
    Citation: Genome Biology 2023 24:172
  4. Although long-read RNA-seq is increasingly applied to characterize full-length transcripts it can also enable detection of nucleotide variants, such as genetic mutations or RNA editing sites, which is signific...

    Authors: Zhiheng Liu, Giovanni Quinones-Valdez, Ting Fu, Elaine Huang, Mudra Choudhury, Fairlie Reese, Ali Mortazavi and Xinshu Xiao
    Citation: Genome Biology 2023 24:171
  5. Structural variant (SV) calling belongs to the standard tools of modern bioinformatics for identifying and describing alterations in genomes. Initially, this work presents several complex genomic rearrangement...

    Authors: Markus Schmidt and Arne Kutzner
    Citation: Genome Biology 2023 24:170
  6. Sequence alignments are the foundations of life science research, but most innovation so far focuses on optimal alignments, while information derived from suboptimal solutions is ignored. We argue that one opt...

    Authors: Andreas Grigorjew, Artur Gynter, Fernando H. C. Dias, Benjamin Buchfink, Hajk-Georg Drost and Alexandru I. Tomescu
    Citation: Genome Biology 2023 24:168
  7. In this manuscript, we introduce and benchmark Mandalorion v4.1 for the identification and quantification of full-length transcriptome sequencing reads. It further improves upon the already strong performance ...

    Authors: Roger Volden, Kayla D. Schimke, Ashley Byrne, Danilo Dubocanin, Matthew Adams and Christopher Vollmers
    Citation: Genome Biology 2023 24:167
  8. The oocyte-to-embryo transition (OET) converts terminally differentiated gametes into a totipotent embryo and is critically controlled by maternal mRNAs and proteins, while the genome is silent until zygotic g...

    Authors: Hongmei Zhang, Shuyan Ji, Ke Zhang, Yuling Chen, Jia Ming, Feng Kong, Lijuan Wang, Shun Wang, Zhuoning Zou, Zhuqing Xiong, Kai Xu, Zili Lin, Bo Huang, Ling Liu, Qiang Fan, Suoqin Jin…
    Citation: Genome Biology 2023 24:166
  9. Detecting allelic imbalance at the isoform level requires accounting for inferential uncertainty, caused by multi-mapping of RNA-seq reads. Our proposed method, SEESAW, uses Salmon and Swish to offer analysis ...

    Authors: Euphy Y. Wu, Noor P. Singh, Kwangbom Choi, Mohsen Zakeri, Matthew Vincent, Gary A. Churchill, Cheryl L. Ackert-Bicknell, Rob Patro and Michael I. Love
    Citation: Genome Biology 2023 24:165
  10. DNA methylation signatures are usually based on multivariate approaches that require hundreds of sites for predictions. Here, we propose a computational framework named CimpleG for the detection of small CpG m...

    Authors: Tiago Maié, Marco Schmidt, Myriam Erz, Wolfgang Wagner and Ivan G. Costa
    Citation: Genome Biology 2023 24:161
  11. Small nucleolar RNAs (snoRNAs) are abundant noncoding RNAs best known for their involvement in ribosomal RNA maturation. In mammals, most expressed snoRNAs are embedded in introns of longer genes and produced ...

    Authors: Danny Bergeron, Laurence Faucher-Giguère, Ann-Kathrin Emmerichs, Karine Choquet, Kristina Sungeun Song, Gabrielle Deschamps-Francoeur, Étienne Fafard-Couture, Andrea Rivera, Sonia Couture, L. Stirling Churchman, Florian Heyd, Sherif Abou Elela and Michelle S. Scott
    Citation: Genome Biology 2023 24:160
  12. Intestinal barrier dysfunction plays a central role in the pathological onset of Crohn’s disease. We identify the cadherin superfamily member protocadherin 20 (PCDH20) as a crucial factor in Crohn’s disease. H...

    Authors: Shanshan Huang, Zhuo Xie, Jing Han, Huiling Wang, Guang Yang, Manying Li, Gaoshi Zhou, Ying Wang, Lixuan Li, Li Li, Zhirong Zeng, Jun Yu, Minhu Chen and Shenghong Zhang
    Citation: Genome Biology 2023 24:159
  13. The first telomere-to-telomere (T2T) human genome assembly (T2T-CHM13) release is a milestone in human genomics. The T2T-CHM13 genome assembly extends our understanding of telomeres, centromeres, segmental dup...

    Authors: Xiangyu Yang, Xuankai Wang, Yawen Zou, Shilong Zhang, Manying Xia, Lianting Fu, Mitchell R. Vollger, Nae-Chyun Chen, Dylan J. Taylor, William T. Harvey, Glennis A. Logsdon, Dan Meng, Junfeng Shi, Rajiv C. McCoy, Michael C. Schatz, Weidong Li…
    Citation: Genome Biology 2023 24:157
  14. Sequencing has revealed hundreds of millions of human genetic variants, and continued efforts will only add to this variant avalanche. Insufficient information exists to interpret the effects of most variants,...

    Authors: Douglas M. Fowler, David J. Adams, Anna L. Gloyn, William C. Hahn, Debora S. Marks, Lara A. Muffley, James T. Neal, Frederick P. Roth, Alan F. Rubin, Lea M. Starita and Matthew E. Hurles
    Citation: Genome Biology 2023 24:147
  15. Prime editing is limited by low efficiency in plants. Here, we develop an upgraded engineered plant prime editor in hexaploid wheat, ePPEplus, by introducing a V223A substitution into reverse transcriptase in ...

    Authors: Pei Ni, Yidi Zhao, Ximeng Zhou, Zehua Liu, Zhengwei Huang, Zhongfu Ni, Qixin Sun and Yuan Zong
    Citation: Genome Biology 2023 24:156
  16. The ring-shaped cohesin complex is an important factor for the formation of chromatin loops and topologically associating domains (TADs) by loop extrusion. However, the regulation of association between cohesi...

    Authors: Yuao Sun, Xin Xu, Wenxue Zhao, Yu Zhang, Keyang Chen, Yongzheng Li, Xiaotian Wang, Mengling Zhang, Boxin Xue, Wanting Yu, Yingping Hou, Chaobin Wang, Wei Xie, Cheng Li, Daochun Kong, Shu Wang…
    Citation: Genome Biology 2023 24:155
  17. Deep learning models such as convolutional neural networks (CNNs) excel in genomic tasks but lack interpretability. We introduce ExplaiNN, which combines the expressiveness of CNNs with the interpretability of...

    Authors: Gherman Novakovsky, Oriol Fornes, Manu Saraswat, Sara Mostafavi and Wyeth W. Wasserman
    Citation: Genome Biology 2023 24:154
  18. A large-scale application of the “stacked modeling” approach for chromatin state discovery previously provides a single “universal” chromatin state annotation of the human genome based jointly on data from many c...

    Authors: Ha Vu and Jason Ernst
    Citation: Genome Biology 2023 24:153
  19. Platelets and erythrocytes constitute over 95% of all hematopoietic stem cell output. However, the clonal dynamics of HSC contribution to these lineages remains largely unexplored.

    Authors: Edyta E. Wojtowicz, Jayna J. Mistry, Vladimir Uzun, Charlotte Hellmich, Anita Scoones, Desmond W. Chin, Laura M. Kettyle, Francesca Grasso, Allegra M. Lord, David J. Wright, Graham J. Etherington, Petter S. Woll, Mirjam E. Belderbos, Kristian M. Bowles, Claus Nerlov, Wilfried Haerty…
    Citation: Genome Biology 2023 24:152
  20. Human papillomavirus (HPV) drives almost all cervical cancers and up to 70% of head and neck cancers. Frequent integration into the host genome occurs predominantly in tumorigenic types of HPV. We hypothesize ...

    Authors: Mehran Karimzadeh, Christopher Arlidge, Ariana Rostami, Mathieu Lupien, Scott V. Bratman and Michael M. Hoffman
    Citation: Genome Biology 2023 24:142
  21. The pathophysiological causes of kidney disease are not fully understood. Here we show that the integration of genome-wide genetic, transcriptomic, and proteomic association studies can nominate causal determi...

    Authors: Pascal Schlosser, Jingning Zhang, Hongbo Liu, Aditya L. Surapaneni, Eugene P. Rhee, Dan E. Arking, Bing Yu, Eric Boerwinkle, Paul A. Welling, Nilanjan Chatterjee, Katalin Susztak, Josef Coresh and Morgan E. Grams
    Citation: Genome Biology 2023 24:150
  22. Variability of gene expression due to stochasticity of transcription or variation of extrinsic signals, termed biological noise, is a potential driving force of cellular differentiation. Utilizing single-cell ...

    Authors: Reyna Edith Rosales-Alvarez, Jasmin Rettkowski, Josip Stefan Herman, Gabrijela Dumbović, Nina Cabezas-Wallscheid and Dominic Grün
    Citation: Genome Biology 2023 24:148
  23. The efficiency of homology-directed repair (HDR) plays a crucial role in the development of animal models and gene therapy. We demonstrate that microhomology-mediated end-joining (MMEJ) constitutes a substanti...

    Authors: Hongyu Chen, Xingchen Liu, Lanxin Li, Qingtong Tan, Shiyan Li, Li Li, Chunyang Li, Jiqiang Fu, Yong Lu, Yan Wang, Yidi Sun, Zhen-Ge Luo, Zongyang Lu, Qiang Sun and Zhen Liu
    Citation: Genome Biology 2023 24:146
  24. The CRISPR/Cas12a and CRISPR/Cas13d systems are widely used for fundamental research and hold great potential for future clinical applications. However, the short half-life of guide RNAs (gRNAs), particularly ...

    Authors: Xin Zhang, Xinlong Wang, Jie Lv, Hongxin Huang, Jiahong Wang, Ma Zhuo, Zhihong Tan, Guanjie Huang, Jiawei Liu, Yuchen Liu, Mengrao Li, Qixiao Lin, Lian Li, Shufeng Ma, Tao Huang, Ying Lin…
    Citation: Genome Biology 2023 24:145
  25. Phylogenetic trees based on copy number profiles from multiple samples of a patient are helpful to understand cancer evolution. Here, we develop a new maximum likelihood method, CNETML, to infer phylogenies fr...

    Authors: Bingxin Lu, Kit Curtius, Trevor A. Graham, Ziheng Yang and Chris P. Barnes
    Citation: Genome Biology 2023 24:144
  26. Seed oil content is an important agronomic trait of Brassica napus (B. napus), and metabolites are considered as the bridge between genotype and phenotype for physical traits.

    Authors: Long Li, Zhitao Tian, Jie Chen, Zengdong Tan, Yuting Zhang, Hu Zhao, Xiaowei Wu, Xuan Yao, Weiwei Wen, Wei Chen and Liang Guo
    Citation: Genome Biology 2023 24:141
  27. In droplet-based single-cell and single-nucleus RNA-seq experiments, not all reads associated with one cell barcode originate from the encapsulated cell. Such background noise is attributed to spillage from ce...

    Authors: Philipp Janssen, Zane Kliesmete, Beate Vieth, Xian Adiconis, Sean Simmons, Jamie Marshall, Cristin McCabe, Holger Heyn, Joshua Z. Levin, Wolfgang Enard and Ines Hellmann
    Citation: Genome Biology 2023 24:140
  28. The Bovine Pangenome Consortium (BPC) is an international collaboration dedicated to the assembly of cattle genomes to develop a more complete representation of cattle genomic diversity. The goal of the BPC is...

    Authors: Timothy P. L. Smith, Derek M. Bickhart, Didier Boichard, Amanda J. Chamberlain, Appolinaire Djikeng, Yu Jiang, Wai Y. Low, Hubert Pausch, Sebastian Demyda-Peyrás, James Prendergast, Robert D. Schnabel and Benjamin D. Rosen
    Citation: Genome Biology 2023 24:139
  29. We propose a polynomial algorithm computing a minimum plain-text representation of k-mer sets, as well as an efficient near-minimum greedy heuristic. When compressing read sets of large model organisms or bacteri...

    Authors: Sebastian Schmidt, Shahbaz Khan, Jarno N. Alanko, Giulio E. Pibiri and Alexandru I. Tomescu
    Citation: Genome Biology 2023 24:136
  30. Recent deep learning models that predict the Hi-C contact map from DNA sequence achieve promising accuracy but cannot generalize to new cell types and or even capture differences among training cell types. We ...

    Authors: Rui Yang, Arnav Das, Vianne R. Gao, Alireza Karbalayghareh, William S. Noble, Jeffery A. Bilmes and Christina S. Leslie
    Citation: Genome Biology 2023 24:134
  31. It has been over a decade since the first publication of a method dedicated entirely to mapping long-reads. The distinctive characteristics of long reads resulted in methods moving from the seed-and-extend fra...

    Authors: Kristoffer Sahlin, Thomas Baudeau, Bastien Cazaux and Camille Marchet
    Citation: Genome Biology 2023 24:133
  32. Multiplexed assays of variant effect (MAVE) experimentally measure the effect of large numbers of sequence variants by selective enrichment of sequences with desirable properties followed by quantification by ...

    Authors: Charlotte Soneson, Alexandra M. Bendel, Guillaume Diss and Michael B. Stadler
    Citation: Genome Biology 2023 24:132
  33. Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central...

    Authors: Benjamin Noel, France Denoeud, Alice Rouan, Carol Buitrago-López, Laura Capasso, Julie Poulain, Emilie Boissin, Mélanie Pousse, Corinne Da Silva, Arnaud Couloux, Eric Armstrong, Quentin Carradec, Corinne Cruaud, Karine Labadie, Julie Lê-Hoang, Sylvie Tambutté…
    Citation: Genome Biology 2023 24:123
  34. We present a novel data structure for searching sequences in large databases: the Hierarchical Interleaved Bloom Filter (HIBF). It is extremely fast and space efficient, yet so general that it could serve as t...

    Authors: Svenja Mehringer, Enrico Seiler, Felix Droop, Mitra Darvish, René Rahn, Martin Vingron and Knut Reinert
    Citation: Genome Biology 2023 24:131
  35. Genetic variation influences both chromatin accessibility, assessed in chromatin accessibility quantitative trait loci (caQTL) studies, and gene expression, assessed in expression QTL (eQTL) studies. Genetic v...

    Authors: Nil Aygün, Dan Liang, Wesley L. Crouse, Gregory R. Keele, Michael I. Love and Jason L. Stein
    Citation: Genome Biology 2023 24:130
  36. Transcriptional regulation is a key aspect of environmental stress responses. Heat stress induces transcriptional memory, i.e., sustained induction or enhanced re-induction of transcription, that allows plants...

    Authors: Christian Kappel, Thomas Friedrich, Vicky Oberkofler, Li Jiang, Tim Crawford, Michael Lenhard and Isabel Bäurle
    Citation: Genome Biology 2023 24:129
  37. Therapy resistance in cancer is often driven by a subpopulation of cells that are temporarily arrested in a non-proliferative G0 state, which is difficult to capture and whose mutational drivers remain largely...

    Authors: Anna J. Wiecek, Stephen J. Cutty, Daniel Kornai, Mario Parreno-Centeno, Lucie E. Gourmet, Guidantonio Malagoli Tagliazucchi, Daniel H. Jacobson, Ping Zhang, Lingyun Xiong, Gareth L. Bond, Alexis R. Barr and Maria Secrier
    Citation: Genome Biology 2023 24:128
  38. Understanding the variation between well and poorly adapted cattle breeds to local environments and pathogens is essential for breeding cattle with improved climate and disease-resistant phenotypes. Although c...

    Authors: Jessica Powell, Andrea Talenti, Andressa Fisch, Johanneke D. Hemmink, Edith Paxton, Philip Toye, Isabel Santos, Beatriz R. Ferreira, Tim K. Connelley, Liam J. Morrison and James G. D. Prendergast
    Citation: Genome Biology 2023 24:127

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