Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis
Cited by (172)
Items 101–172 of 172
- AnnoGen: annotating genome-wide pragmatic featuresQuanhu Sheng, Hui Yu, Olufunmilola Oyebamiji, Jiandong Wang, Dan‐Qian Chen, Scott A. Ness, Ying‐Yong Zhao, Yan Ping Guo · 2020 · Bioinformatics
- Features of Functional Human GenesHelena B. Cooper, Paul P. Gardner · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
- TD-COF: A new method for detecting tandem duplications in next generation sequencing dataDaicong Jia, Jinxin Dong, Hua Jiang, Zuyao Zhao, Xilong Jiang · 2024 · SoftwareX
- Efficient RNA nucleotide encoding enhances the accurate prediction of ac4C modificationsNa Li, Xiao Wang, Ming Zeng, Feng Cao, Ke Qiu, Jianbo Qiao · 2025 · Methods
- Impact of the inaccessible genome on genotype imputation and genome-wide association studiesEva König, Jonathan S. Mitchell, Michele Filosi, Christian Fuchsberger · 2024 · Human Molecular Genetics
- Genome-wide capture sequencing to detect hepatitis C virus at the end of antiviral therapyPeng Peng, Yanjuan Xu, Michael W. Fried, Adrian M. Di Bisceglie, Xiaofeng Fan · 2020 · BMC Infectious Diseases
- CNS: Application of Dynamic Resource Allocation Based on 5G Communication in Technology Innovation of Complex High-Tech IndustriesYunsheng Wang, Shujiang Yu · 2021 · International Journal of Cooperative Information Systems
- Transcript selection for the genetic diagnosis of KIF12-associated progressive familial intrahepatic cholestasisYe Cheng, Yiqiong Zhang, Bing-Xuan Wei, Lian Chen, Qinghe Xing, Jian‐She Wang · 2023 · Gastroenterology report
- Personalized oncology in pheochromocytomas and paragangliomas: integrating genetic analysis with machine learningAbida Abida, Abdullah Rzgallah Alzahrani, Hayaa M. Alhuthali, Afnan Alkathiri, Ruba Omar M. Almaghrabi, Jawaher Mohammad Alshehri, Syed Mohammed Basheeruddin Asdaq, Mohd Imran · 2024 · Medical Oncology
- Systematic detection of brain protein-coding genes under positive selection during primate evolution and their roles in cognitionGuillaume Dumas, Simon Malesys, Thomas Bourgeron · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
- AirLift: A Fast and Comprehensive Technique for Translating Alignments between Reference GenomesJeremie S. Kim, Can Fırtına, Meryem Banu Cavlak, Damla Senol Cali, Mohammed Alser, Nastaran Hajinazar, Can Alkan, Onur Mutlu · 2019 · arXiv (Cornell University)
- [Acute mountain sickness and Menière disease].Hendrik P. Verschuur, Jean‐Paul Richalet, Christian Rathat, Bruno Frachet · 1993 · PubMed
- Laboratory considerations for GRCh37 to GRCh38 reference genome transition: A laboratory quality assurance bulletin of the American College of Medical Genetics and Genomics (ACMG)Vimla S. Aggarwal, Saurav Guha, Matthew S. Lebo, Kyle Retterer, Curt Scharfe, Lora Jh Bean · 2025 · Genetics in Medicine Open
- Resolving structural variations missed by short-read sequencing uncovers their pathogenicityCaroline Schluth‐Bolard, Laïla El Khattabi, Pierre‐Antoine Rollat‐Farnier, Nicolas Chatron, Marion Beaumont, Nicolas Reynaud, Kévin Uguen, Flavie Diguet, Audrey Labalme, Claire Bardel et al. · 2025 · Journal of Medical Genetics
- Tutorial for variant interrogation in tumor samplesRiley J. Arseneau, Leah K. MacLean, Jeanette E. Boudreau, Daniel Gaston · 2026 · PLoS Computational Biology
- The SMN locus in the T2T era: Structure, gene conversion, and clinical implicationsDemi Gommers, Maria M Zwartkruis, W. Ludo van der Pol, Ewout J. N. Groen, Gijs W van Haaften · 2026 · Trends in Genetics
- Research on Cancer Molecular Typing Based on High-Throughput Sequencing TechnologyWei Dan · 2021 · Computational and Mathematical Methods in Medicine · Retracted
- StableLift: Optimized Germline and Somatic Variant Detection Across Genome BuildsNicholas K. Wang, Nicholas Wiltsie, Helena K. Winata, Sorel T. Fitz‐Gibbon, Alfredo E. Gonzalez, Nicole Zeltser, Raag Agrawal, Jieun Oh, Jaron Arbet, Yash Patel et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- Exome and genome sequencing for diagnosing patients with suspected rare genetic diseaseGo Hun Seo, Hane Lee · 2023 · Journal of genetic medicine
- Congenital enteropathy caused by ezrin deficiencyGeorg Friedrich Vogel, Katharina MC Klee, Arzu Meltem Demir, Dorota Garczarczyk‐Asim, Michael W. Hess, Lukas Alfons Huber, Thomas M. Müller, Andreas Janecke · 2025 · Human Genetics
- Transcriptomic profiling and biomarker discovery in pre-eclampsia: An integrated approach leveraging WGCNA and LASSO with ROC validationTamil Barathi Palanisamy, Mohanapriya Arumugam · 2025 · Computational Biology and Chemistry
- Importance of genome reference and population datasets for annotation and prioritization of disease-causing variants in inherited retinal diseasesStefan T. Stafie, Mark Lindquist, Samuel Kusher-Lenhoff, Kenji Nakamichi, Debarshi Mustafi · 2025 · Ophthalmic Genetics
- Thymidylate synthase inhibitory drugs induce p53-dependent pathways differentlyEszter Holub, Milda Blanka Szajkó, Anna Felföldi, Beáta G. Vértessy, Angéla Békési · 2026 · PLoS ONE
- ACSL4-associated lipid metabolism is a distinct therapeutic vulnerability in KMT2A-rearranged acute myeloid leukemiaSilvia Schäfer, Elahe Rahimian, Lola Schmitz-Hübsch, Mehak Shaikh, Silke Brilloff, Vida Kufrin, Sandra Küchler, Maria Fedorova, Natalie Kusebauch, Zhixu Ni et al. · 2026 · Cell Reports
- VDJ-Insights: simplifying the annotation of genomic immunoglobulin and T cell receptor regionsSusan Ott, Ngoc Giang Le, Sayed J Mohammadi, Jesse Mittertreiner, Erica M. Pasini, Ronald E. Bontrop, Natasja G. de Groot, Jesse Bruijnesteijn · 2026 · Bioinformatics
- Multi-ancestry genome-wide association study in all of Us for primary open-angle glaucomaKiana Tavakoli, Bonnie B. Huang, Tara Mirmira, Nichole Ma, Robert Neal Weinreb, Sally L. Baxter · 2026 · Scientific Reports
- Targeting intra‐tumoral heterogeneity of human brain tumors with in vivo imaging: A roadmap for imaging genomics from multiparametric MR signalsJason G. Parker, Mahsa Servati, Emily E. Diller, Sha Cao, Chang Yueh Ho, Robert M. Lober, Aaron Cohen‐Gadol · 2022 · Medical Physics
- Personalized medicine: the role of sequencing technologies in diagnostics, prediction and selection of treatment of monogenous and multifactorial diseasesO. Glotov, A. Chernov, Michael Fedyakov, V. Larionova, A. Zaretsky, M. Donnikov, A. Glotov · 2022 · Biological Communications
- Computational Tools for Genomics Data AnalysisThanh-Truong Pham, Nhat Le Bui, Chi-Dung Trinh, Duc Thuan Nguyen, Dinh‐Toi Chu · 2024 · Springer eBooks
- Evaluating reproductive carrier screening using biotinidase deficiency as a model: Variants identified, variant rates, and managementPETER A. BENN, Yang Wang, Josie Gray, E. Dugan, Mark Hajjar, Brittany Prigmore, Vivienne Souter, Barry Wolf · 2024 · Genetics in Medicine
- Qualitative Comparison of Selected Indel Detection Methods for RNA-Seq DataTamara Slosarek, Milena Kraus, Matthieu-P. Schapranow, Erwin Boettinger · 2019 · Lecture notes in computer science
- Quality control of large genome datasetsMax Robinson, Arpita Joshi, Ansh Vidyarthi, Mary Maccoun, Sanjay Rangavajjhala, Gustavo Glusman · 2022 · Human Genetics and Genomics Advances
- The Regulatory Mendelian Mutation score for GRCh38Lusiné Nazaretyan, Martin Kircher, Max Schubach · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
- Malignant A-to-I RNA editing by ADAR1 drives T-cell acute lymphoblastic leukemia relapse via attenuating dsRNA sensingJessica Pham, Jane Marie Isquith, Maria Rivera, Haoran Zhang, Qingchem Zhou, Roman Šášik, Adam Mark, Wenxue Ma, Frida Holm, Kathleen M Fisch et al. · 2023 · Research Square
- Human ribomes reveal DNA-embedded ribonucleotides as a new type of epigenetic markDeepali L. Kundnani, Taehwan Yang, Tejasvi Channagiri, Penghao Xu, Yeunsoo Lee, Mo Sun, Francisco Martinez-Figueroa, Supreet Randhawa, Ashlesha Gogate, Youngkyu Jeon et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- The Impact of Variant Calling on Substitution Mutational Signature InferenceZichen Jiang, Jessica N. Au, Mariya Kazachkova, Marcos Díaz-Gay, Raviteja Vangara, Ludmil B. Alexandrov · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Insights into the human demographic history of africa through whole-genome sequence analysisSerra Vidal, Gérard · 2018 · LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas)
- Quality control of large genome datasets using genome fingerprintsMax Robinson, Arpita Joshi, Ansh Vidyarthi, Mary Maccoun, Sanjay Rangavajjhala, Gustavo Glusman · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
- 4q-D4Z4 chromatin architecture regulates the transcription of muscle atrophic genes in FSHDAlice Cortesi, Matthieu Pesant, Shruti Sinha, Federica Marasca, Eleonora Sala, Francesco Gregoretti, Laura Antonelli, Gennaro Oliva, Chiara Chiereghin, Giulia Soldà et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
- Fundamentals of Drug Metabolism and Pharmacogenomics Within a Learning Healthcare System Workflow PerspectiveMatthew K. Breitenstein, Erin Lynn Crowgey · 2019 · Health informatics
- Transcriptomic data integration for precision medicine in leukemiaAshwini Kumar · 2019 · Työväentutkimus Vuosikirja
- Lost in Translation: The Pitfalls of Ensembl Gene Annotations Between Human Genome Assemblies and Their Impact on DiagnosticsMohammed O. E. Abdallah, Mahmoud Koko, Raj Ramesar · 2020 · Research Square
- Ancient Migrations - The first complete genome assembly, annotation and variants of the Zoroastrian-Parsi community of IndiaNaseer Pasha, Kashyap Krishnasamy, Nagarajan Naveenkumar, Seshank Mutya, Bhavika Mam, Kouser Sonnekhan, Chellappa Gopalakrishnan, Renuka Jain, Villoo Morawala‐Patell · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
- GABOLA: A Reliable Gap-Filling Strategy for de novo Chromosome-Level AssemblyWei‐Hsuan Chuang, Hsueh-Chien Raymond Cheng, Yu-Jung Chang, Pao-Yin Fu, Yichen Huang, Ping-Heng Hsieha, Shu‐Hwa Chen, Chung-Yen Lina, Jan-Ming Ho · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
- Genetic diversity and population structure within Botswana: association with HIV-1 infectionPrisca K. Thami · 2021 · Open University of Cape Town (University of Cape Town)
- Assessment of accuracy in identifying structural variants using third-generation sequencing for breast cancer in the absence of gold standardQianqian Song, Taobo Hu, Baosheng Liang, Zhen Zhang, Liu Yang, Jinbo Wu, Jin Xia Zhao, Mengping Long, Sheng Lian, Xiaodan Fan et al. · 2022 · Research Square
- ADAR1 drives stemness of leukemia initiating cells in T-cell acute lymphoblastic leukemia via attenuating immunogenic dsRNA sensingJessica Pham, Jane Marie Isquith, Maria Rivera, Haoran Zhang, Qingchem Zhou, Roman Šášik, Adam Mark, Wenxue Ma, Frida Holm, Kathleen M Fisch et al. · 2023 · Research Square
- Lost in translation: the pitfalls of Ensembl gene annotations between human genome assemblies and their impact on diagnosticsMohammed O. E. Abdallah, Mahmoud Koko, Raj Ramesar · 2023 · Expert Review of Molecular Diagnostics
- Genomic approaches to rare disorder diagnosisKristin B. Linscott, Anna Hurst · 2023 · Elsevier eBooks
- Evaluation of Genome Conversion to Genome Reference Consortium Human Build 38 from Human Genome 19Kyoung‐Jin Park, Jong-Ho Park · 2023 · Imsang byeong'ri wa jeongdo gwanri/Journal of laboratory medicine and quality assurance
- Limitations and Enhancements in Genomic Language Models: Dynamic Selection ApproachShibo Qiu · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- Genetic variations and recurrence in stage III Korean colorectal cancer: Insights from tumor-only mutation analysisHajin Jeon, Jong Lyul Lee, Hyeran Shim, Soobok Joe, Iksu Byeon, Chan Wook Kim, Seok‐Byung Lim, In Ja Park, Yong Sik Yoon, Hoang Bao Khanh Chu et al. · 2025 · PLoS ONE
- Selection of microhaplotype loci and development of panel for forensic applicationJing Zhou, Shuai Zhang, Yan Wang, Zhen Lu, Zhangsen Shi, Huayan Zheng, Weizhong Gu, Enping Xu · 2025 · Journal of Forensic Sciences
- Microhaplotype insights into the population structure of seven ethnic minorities in Guizhou, ChinaChangyun Gu, Xiaolan Huang, Qianchong Ran, Zheng Ren, Qiyan Wang, Yubo Liu, Shuaiji Pan, Meiqing Yang, Jingyan Ji, Hongling Zhang et al. · 2025 · Journal of Translational Genetics and Genomics
- Modelling constant and cell-type specific CTCF sites by using Convolutional Neural NetworksEdward Sanders, Simone G. Riva, Emily Georgiades, Matthew D. Baxter, Jim R. Hughes · 2025 · International Joint Conference on Neural Networks (IJCNN)
- Characterizing and decoding ultraconserved regions uncovers their regulatory significance in human brain development and disordersYun Bai, Xuehan Zhang, Xiangting Wang, Meiting Wang, Tao Shen · 2025 · Communications Biology
- Additional file 8 of Investigating the impact of reference assembly choice on genomic analyses in a cattle breedAudald Lloret‐Villas, Meenu Bhati, Naveen Kumar Kadri, Ruedi Fries, Hubert Pausch · 2021 · Figshare
- Additional file 12 of Investigating the impact of reference assembly choice on genomic analyses in a cattle breedAudald Lloret‐Villas, Meenu Bhati, Naveen Kumar Kadri, Ruedi Fries, Hubert Pausch · 2021 · Figshare
- Additional file 5 of Investigating the impact of reference assembly choice on genomic analyses in a cattle breedAudald Lloret‐Villas, Meenu Bhati, Naveen Kumar Kadri, Ruedi Fries, Hubert Pausch · 2021 · Figshare
- Additional file 13 of Investigating the impact of reference assembly choice on genomic analyses in a cattle breedAudald Lloret‐Villas, Meenu Bhati, Naveen Kumar Kadri, Ruedi Fries, Hubert Pausch · 2021 · Figshare
- Next-Generation Sequencing AnalysisDinesh Velayutham, Nismabi A Nisamudheen, Fathima Mohammed, Randa S. Al-Yafei, Puthen Veettil Jithesh · 2025 · Springer handbooks
- TD-TSPS: A hybrid strategy method for TD detection based on two-step progressive segmentationYuxi Zhang, Jinxin Dong, Hua Jiang, Ruchao Du, Ranran Sun · 2026 · SoftwareX
- A comprehensive identification and annotation of mobile LINE-1 retrotransposons across human reference and personal genomesAdriano Ferrasa, Roberto H. Herai · 2026 · Human Gene
- An Efficient Pattern Matching Approach for Compressed Genomic SequencesHan Duan, Chuan Zhi Hu, Zhihong Shen · 2025 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
- Détection d'organismes génétiquement modifiés (OGM) inconnus par analyse statistique de données de séquençage haut débitJulie Hurel · 2020
- Contribution of primate-specific transposable elements to the evolution of inflammation-related enhancersMengliang Ye · 2024 · theses.fr (ABES)
- A Novel 5-bp c.433-1_436delGAGTA (p.Ser145Lysfs*9) Frameshift Deletion in C22orf31 Associated with Global Developmental Delay and Microcephaly in a Saudi Consanguineous FamilyMd. Safayet Hossain, Osama Yousef Muthaffar, Angham Abdulrahman Abdulkareem, Muhammad Imran Naseer · 2026 · Journal of Disability Research
- A Practical Framework for Constructing Population-Specific and Alternate-Contig-Aware Genome References: A case study of VietnamTrang T. H. Tran, Vinh C. Duong, Nam N. Nguyen, Tien M. Pham, Quang T. Vu, Mai Hoang Tran, Tham H. Hoang, Quan Hoang Nguyen, Nguyen Thuy Duong, Nam S. Vo · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
- Human nuclear ribomes reveal DNA-embedded ribonucleotides as epigenetic modulators of transcription-associated DNA supercoilingDeepali L. Kundnani, Yeunsoo Lee, Taehwan Yang, Tyler P. Warner, Francisco Martinez-Figueroa, Tejasvi Channagiri, Penghao Xu, Ryan A. Eckerty, Mo Sun, Supreet Randhawa et al. · 2026 · Cell
- Comprehensive genetic screening of the South African Parkinson's disease study collection using the NeuroBooster arrayKathryn Step, Lusanda Madula, Nicole Kuznetsov, Elizna Maasdorp, Jonathan Ambrose Carr, Riaan van Coller, Marlo Möller, Ignacio Fernandez Mata, Soraya Bardien · 2026 · Clinical Parkinsonism & Related Disorders
- Re-Analysis on GRCh38 with the MANE Select Transcript Resolves Previously Undetected Biallelic ODAD4 Variants in Primary Ciliary DyskinesiaPetra Pennekamp, Marina Praprotnik, Bernd Dworniczak, Heymut Omran, Rim Hjeij · 2026 · Cells
- The average individual genome: a survey of nearly 1 million whole-genome sequencesHarrison I. W. Wright, Robin N. Beaumont, James Fasham, Joseph S. Leslie, V. Kartik Chundru, Timothy S. Hall, Stuart J Cannon, Alistair T. Pagnamenta, Emma L. Baple, Andrew R. Wood et al. · 2026 · Genome Medicine