SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes

Cited by (161)

Items 101–161 of 161

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2. B cell stimulation changes the structure and higher-order organization of the inactive X chromosome
   Isabel Sierra, Natalie E. Toothacre, Robin H. van der Weide, Claudia D. Lovell, Son C. Nguyen, R. Jordan Barnett, Ashley L. Cook, Han-Seul Ryu, Sarah Pyfrom, Harrison Wang et al. · 2025 · Cell Reports
3. Allele‐specificcis‐regulatory methylation of the gene for vasoactive intestinal peptide in white‐throated sparrows
   Mackenzie R. Prichard, Kathleen E. Grogan, Jennifer R. Merritt, Jessica T. Root, Donna L. Maney · 2022 · Genes Brain & Behavior
4. Allelic chromatin structure precedes imprinted expression of Kcnk9 during neurogenesis
   Daniel Loftus, Bongmin Bae, Courtney Michelle Whilden, Amanda J. Whipple · 2023 · Genes & Development
5. Master transcription-factor binding sites constitute the core of early replication control elements
   Jesse L. Turner, Laura Hinojosa-Gonzalez, Takayo Sasaki, Satoshi Uchino, Athanasios E Vouzas, Mariella S Soto, Abhijit Chakraborty, Karen E. Alexander, Cheryl A. Fitch, Amber N. Brown et al. · 2025 · The EMBO Journal
6. Single-cell dynamics of genome-nucleolus interactions captured by nucleolar laser microdissection (NoLMseq)
   Kaivalya Walavalkar, Shivani Gupta, Jelena Kresoja‐Rakic, Mathieu Raingeval, Chiara Mungo, Philip D. Rubin, Raffaella Santoro · 2025 · Nature Communications
7. Single-mitosis dissection of acute and chronic DNA mutagenesis and repair
   Paul Adrian Ginno, Helena Borgers, Christina Ernst, Anja Schneider, Mikaela Behm, Sarah J. Aitken, Martin S. Taylor, Duncan T. Odom · 2024 · Nature Genetics
8. Mixed Patterns of Intergenerational DNA Methylation Inheritance in Acropora
   Christopher R. Peterson, Carly B. Scott, Rashin Ghaffari, Groves Dixon, Mikhail V. Matz · 2024 · Molecular Biology and Evolution
9. Maternal SMCHD1 controls both imprinted Xist expression and imprinted X chromosome inactivation
   Iromi Wanigasuriya, Sarah Kinkel, Tamara J Beck · 2022 · Epigenetics & Chromatin
10. Cellular reprogramming is driven by widespread rewiring of promoter-enhancer interactions
    Miao Wang, Bing He, Yueling Hao, Divyaa Srinivasan, Jatin Shrinet, Peter Fraser · 2023 · BMC Biology
11. Chromatin targeting of the RNF12/RLIM E3 ubiquitin ligase controls transcriptional responses
    Carmen Espejo-Serrano, Catriona Aitken, Beatrice F. Tan, Danielle G. May, Rachel J. Chrisopulos, Kyle J. Roux, Jeroen Demmers, Samuel G. Mackintosh, Joost H. Gribnau, Francisco Bustos et al. · 2024 · Life Science Alliance
12. X-linked deletion of Crossfirre, Firre, and Dxz4 in vivo uncovers diverse phenotypes and combinatorial effects on autosomes
    Tim P. Hasenbein, Sarah Hoelzl, Zachary D. Smith et al. · 2024 · Nature Communications
13. Acquired sperm hypomethylation by gestational arsenic exposure is re-established in both the paternal and maternal genomes of post-epigenetic reprogramming embryos
    Keiko Nohara, Takehiro Suzuki, Kazuyuki Okamura, Tomoko Kawai, Kazuhiko Nakabayashi · 2025 · Epigenetics & Chromatin
14. Characterization of genetic‐origin‐dependent monoallelic expression in mouse embryonic stem cells
    Hiroaki Ohishi, Wan Kin Au Yeung, Motoko Unoki, Kenji Ichiyanagi, Kei Fukuda, Shoji Maenohara, Kenjiro Shirane, Hatsune Chiba, Takashi Sado, Hiroyuki Sasaki · 2019 · Genes to Cells
15. The chemical reprogramming of unipotent adult germ cells towards authentic pluripotency and de novo establishment of imprinting
    Chen Yuhan, Jiansen Lu, Yanwen Xu, Yaping Huang, Dazhuang Wang, Peiling Liang, Shaofang Ren, Xuesong Hu, Yewen Qin, Wei Ke et al. · 2022 · Protein & Cell
16. Sequence and parent-of-origin dependent m6A contribute to allele-specific gene expression
    Ying Zhang, Zeyu Zhang, Hong-Xuan Chen, Chao Liu, Biao-Di Liu, Ye-Lin Lan, Ying-Yuan Xie, Tao Chen, Shaobo Chen, Guihai Feng et al. · 2025 · The EMBO Journal
17. Zfp57 Exerts Maternal and Sexually Dimorphic Effects on Genomic Imprinting
    Zhen Xu, Jiajia Shi, Yu Zhang, Yuhan Liu, Junzheng Zhao, Qian Chen, Chenglin Song, Shuhui Geng, Wei Xie, Feizhen Wu et al. · 2022 · Frontiers in Cell and Developmental Biology
18. Reconstruction of diploid higher-order human 3D genome interactions from noisy Pore-C data using Dip3D
    Ying Chen, Zhuobin Lin, Shaokai Wang, Bo Ming Wu, Longjian Niu, Jiayong Zhong, Yimeng Sun, Zhenxian Zheng, Xin Bai, Luo-Ran Liu et al. · 2025 · Nature Structural & Molecular Biology
19. Insertion of short L1 sequences generates inter-strain histone acetylation differences in the mouse
    Beverly Ann G. Boyboy, Kenji Ichiyanagi · 2024 · Mobile DNA
20. Concert: Genome-wide prediction of sequence elements that modulate DNA replication timing
    Yang Yang, Yuchuan Wang, Yang Zhang, Jian Ma · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
21. Epigenetic reprogramming of imprinting at meiosis
    Sean Akira Montgomery, Frédéric Berger · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
22. Linking STRs/SNPs and DNA methylation using massively parallel sequencing for potential forensic applications
    Laura Schmelzer, Jerry Hoogenboom, Jana Naue · 2025 · International Journal of Legal Medicine
23. CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers
    Osamu Maruyama, Yinuo Li, Hiroki Narita, Hidehiro Toh, Wan Kin Au Yeung, Hiroyuki Sasaki · 2022 · BMC Bioinformatics
24. Functional genomics in primary T cells and monocytes identifies mechanisms by which genetic susceptibility loci influence systemic sclerosis risk
    David González‐Serna, Chenfu Shi, Martin Kerick, Jenny Hankinson, James Ding, Amanda McGovern, Mauro Tutino, Gonzalo Villanueva Martin, Norberto Ortego‐Centeno, José Luís Callejas-Rubio et al. · 2022 · medRxiv
25. Transcription can be sufficient, but is not necessary, to advance replication timing
    Athanasios E Vouzas, Takayo Sasaki, Juan Carlos Rivera‐Mulia, Jesse L. Turner, Amber N. Brown, Karen E. Alexander, Laura Brueckner, Bas van Steensel, David M. Gilbert · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
26. SETDB1 and HUSH modulate Xist RNA levels during establishment of X chromosome inactivation
    Mafalda R. Almeida, Guifeng Wei, Adam D. Cawte, Tatyana B. Nesterova, Neil Brockdorff · 2026 · Nature Communications
27. MC profiling: a novel approach to analyze DNA methylation heterogeneity in genome-wide bisulfite sequencing data
    Giulia De Riso, Antonella Sarnataro, Giovanni Scala, Mariella Cuomo, Rosa Della Monica, Stefano Amente, Lorenzo Chiariotti, Gennaro Miele, Sergio Cocozza · 2022 · NAR Genomics and Bioinformatics
28. Genetic polymorphisms lead to major, locus-specific, variation in piRNA production in mouse
    Eduard Casas, Adrià Mitjavila-Ventura, Pío Sierra, Cristina Moreta-Moraleda, Judith Cebrià, Ilaria Panzeri, John Andrew Pospisilik, Josep C. Jiménez‐Chillarón, Sonia Vanina Forcales, Tanya Vavouri · 2025 · The EMBO Journal
29. X-chromosome upregulation operates on a gene-by-gene basis at RNA and protein levels
    Ryan Allsop, Jeffrey Boeren, Beatrice F. Tan et al. · 2025 · Nature Communications
30. Specific genomic targeting of the RNF12/RLIM E3 ubiquitin ligase selectively programmes developmental transcription
    Carmen Espejo-Serrano, Catriona Aitken, Beatrice F. Tan, Danielle G. May, Rachel J. Chrisopulos, Kyle J. Roux, Samuel G. Mackintosh, Joost H. Gribnau, Francisco Bustos, Cristina Gontan et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
31. Gene-specific reactivation of X-linked genes upon Xist loss is linked to the chromatin states in extraembryonic endoderm and epiblast stem cells
    Maniteja Arava, S Majumdar, LS Sowjanya · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
32. ASET: an end-to-end pipeline for quantification and visualization of allele specific expression
    Wei-Sheng Wu, K. Shedden, C. Vincenz, Chris Gates, Beverly Strassmann · 2025 · BMC Bioinformatics
33. Long-read sequencing disentangles isoform complexity at allele-specific loci
    Lison Lemoine, Sarah Hoelzl, Tim P. Hasenbein · 2025 · Scientific Reports
34. Polycomb repressive-deubiquitinase complex safeguards oocyte epigenome and female fertility by restraining Polycomb activity
    Jinwen Kang, Peiyao Liu, Shoko Ichimura, Lauryn Cook, Mengwen Hu, Satoshi H. Namekawa, Zhiyuan Chen · 2026 · Nature Communications
35. Machine learning on alignment features for parent-of-origin classification of simulated hybrid RNA-seq
    Jason Rafe Miller, Donald Adjeroh · 2024 · BMC Bioinformatics
36. Genome-wide profiling of the epigenetic landscape of histone variant TH2B in murine oocytes and pre-implantation embryos
    Isha Singh, Priyanka P. Parte · 2024 · Reproduction
37. Xmas ESC: A new female embryonic stem cell system that reveals the BAF complex as a key regulator of the establishment of X chromosome inactivation
    Andrew Keniry, Natasha Jansz, Linden J. Gearing, Iromi Wanigasuriya, Joseph Chen, Christian Maximilian Nefzger, Peter F. Hickey, Quentin A. Gouil, Joy J. Liu, Kelsey A. Breslin et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
38. Integrated analysis of Xist upregulation and gene silencing at the onset of random X-chromosome inactivation at high temporal and allelic resolution
    Guido Pacini, Ilona Dunkel, Norbert Mages, Verena Mutzel, Bernd Timmermann, Annalisa Marsico, Edda G. Schulz · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
39. Identification of cis Elements for Spatio-temporal Control of DNA Replication
    Jiao Sima, Abhijit Chakraborty, Vishnu Dileep, Marco Michalski, Juan Carlos Rivera‐Mulia, Claudia Trevilla‐García, Kyle N. Klein, Daniel A. Bartlett, Brian K. Washburn, Michelle T. Paulsen et al. · 2018 · SSRN Electronic Journal
40. Deletion of Xist upstream sequences alters TAD interactions and leads to defects in Xist coating and expression
    S Majumdar, Lakshmi Sowjanya Bammidi, HC Naik, Avinchal, Runumi Baro, A Kalita, N Sundarraj, GS Bariha, Dimple Notani, Srimonta Gayen · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
41. High-resolution diploid 3D genome reconstruction using Pore-C data
    Ying Chen, Zhuobin Lin, Shaokai Wang, Bo Ming Wu, Longjian Niu, Jiayong Zhong, Yimeng Sun, Xin Bai, Luo-Ran Liu, Wei Xie et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
42. Multi-omics analysis in primary T cells elucidates mechanisms behind disease associated genetic loci
    Gisela Orozco, Chenfu Shi, Danyun Zhao, Stefano Rossi, Antonios Frantzeskos, James Ding, Carlo Ferrazzano, Charlotte Wynn, Ryan Malcolm Hum, Ellie Richards et al. · 2023 · Research Square
43. NF-κB Signaling is Required for X-Chromosome Inactivation Maintenance Following T cell Activation
    Katherine S. Forsyth, Natalie E. Toothacre, Nikhil Jiwrajka, Amanda M. Driscoll, Lindsey A. Shallberg, Charlotte Cunningham‐Rundles, Sara Barmettler, Jocelyn R. Farmer, James W. Verbsky, John M. Routes et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
44. Selective interaction of the protein SMCHD1 with specific chromatin regions is governed by the loading factor LRIF1 and SMCHD1 ATPase activity
    Flavia Constantinescu, Aleksander Szczurek, Tatyana B. Nesterova, Guifeng Wei, Victoria Pustygina, Stephan Uphoff, Adam D. Cawte, Neil Brockdorff · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
45. Tissue-Specific and NF-kappaB-Independent Xist RNA Localization Patterns in Female Intestinal, Blood, and Muscle Progenitors
    Claudia D. Lovell, Isabel Sierra, Emma M. Welter, Donavon Sandoval-Heglund, Ning Li, Ashley Vanderbeck, Christopher J. Lengner, Christoph Lepper, Montserrat C. Anguera · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
46. The causes and consequences of human-specific DNA methylation
    Zhenzhen Ma, Alexander L. Starr, David Gokhman, Hunter B. Fraser · 2026 · eLife
47. Principles of 3D Nucleus Organization and Epigenetic Regulation in Diploid Genome Revealed by Multi-omic Data from Hybrid Mouse
    Zhijun Han, Cui Kairong, Katarzyna Placek, Ni Hong, Chengqi Lin, Wei Chen, Keji Zhao, Wenfei Jin · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
48. Faculty Opinions recommendation of Identifying cis elements for spatiotemporal control of mammalian DNA replication.
    Angela Taddei · 2019 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
49. Allelic chromatin structure primes imprinted expression of Kcnk9 during neurogenesis
    Daniel Loftus, Bongmin Bae, Courtney Michelle Whilden, Amanda J. Whipple · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
50. Comprehensive profiling of transcriptional regulation in cartilage reveals pathogenesis of osteoarthritis
    Wen Tian, Shan-Shan Dong, Feng Jiang, Jun-qi Zhang, Chen Wang, Chang-Yi He, Shou-Ye Hu, Ruo-Han Hao, Huimiao Song, Hui-Wu Gao et al. · 2024 · bioRxiv
51. Read Mapping for Hi-C Analysis
    Simon Thomas Kelly, Kugui Tanaka, Chiaki Hosaka, Satoshi Yuhara · 2024 · Methods in molecular biology
52. Functional mutations in the thyroid-stimulating hormone receptor in natural stickleback populations at sites identical to human disease-causing mutations
    Jun Kitano, Mana Sato, Hiyu Kanbe, Genta Okude, Asano Ishikawa, Yukinori Kazeto, Takashi T Makino · 2025 · BMC Ecology and Evolution
53. A Novel Computational Approach to Transcriptome Mapping in Polyploid Species
    Haifeng Zhang, Yi Zheng, Yajuan Du · 2025 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
54. Exploring the structural and functional dynamics of the X-inactivation centre locus during development
    Rafael Galupa · 2017 · theses.fr (ABES)
55. Analyse de la méthylation de l'ADN par séquençage haut-débit chez la Poule
    Marjorie Mersch · 2018 · theses.fr (ABES)
56. Cis-regulation and natural selection in the evolution of human DNA methylation
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57. Chromatin structure of the inactive X chromosome revealed by in situ cryo-electron tomography
    Jeongyoon Choi, Dimitrios Bellos, Joseph S. Bowness · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
58. Enhancer Tuning by Sequence-Specific Repressors
    Lucia Ichino, Kaelan Brennan, Benjamin J. Mallory, Tomek Swigut, Stephanie C. Bohaczuk, Jaaved Mohammed, Devaraja Gouda Mudeppa, Saman Tabatabaee, Chunyang Ni, Andrew B. Stergachis et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
59. Folate deficiency disrupts key metabolic transitions within the developing neural ectoderm
    Nicolas Dias, Daniel P. Lewinsohn, William N. Colgan, Minming Wang, Yusuke Kijima, JoAnne Villagrana, Tien-Chi Jason Hou, Gokul Gowri, Adelina Chau, Tuğçe Aktaş et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
60. Maternal epigenetic regulation of embryonic patterning in plants
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61. Cis-regulation and natural selection in the evolution of human DNA methylation
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