Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

Schneider, Valerie A., Graves-Lindsay, Tina, Howe, Kerstin, Bouk, Nathan, Chen, Hsiu-Chuan, Kitts, Paul A., Murphy, Terence D., Pruitt, Kim D. +30 more·2017·Genome Research

DOI 10.1101/gr.213611.116

Cited by (999)

Items 801–900 of 999

Efficient identification of de novo mutations in family trios: a consensus-based informatic approach
Mariya Shadrina, Özem Kalay, Sinem Demirkaya-Budak, Charles A. LeDuc, Wendy K. Chung, Deniz Turgut, Güngör Budak, Elif Arslan, Vladimir Semenyuk, Brandi N. Davis‐Dusenbery et al. · 2025 · Life Science Alliance
Human adipose tissue gene expression signatures indicate an inflammatory response and retinoic receptor activation under persistent organic pollutants exposure
Tobias Hagemann, Ulrike Elisabeth Rolle-Kampczyk, Kristin A. Schubert, Arne Dietrich, Martin von Bergen�, Matthias Blüher, Anne Hoffmann · 2025 · Environmental Advances
Risk Assessment With Ultra-Low-Pass Whole-Genome Sequencing of Cell-Free DNA for Large B-Cell Lymphoma
Davidson Zhao, Noémie Lang, Ting Liu, Victoria Shelton, Juan Rangel‐Patiño, Inna Y. Gong, Michael Hong, Anthea Travas, Vanessa Murad, Ibrahim Alrekhais et al. · 2025 · JCO Precision Oncology
Remote BV Management via Metagenomic Vaginal Microbiome Testing and Telemedicine
Krystal J. Thomas-White, David Lyttle, Genevieve Olmschenk, Rob Markowitz, Pita Navarro, Kate McLean · 2025 · Microorganisms
In Silico Prediction and Selection of Exon-Skipping Antisense Oligonucleotide Sequences Using eSkip-Finder
Shuntaro Chiba, Yasushi Okuno · 2025 · Methods in molecular biology
Importance of genome reference and population datasets for annotation and prioritization of disease-causing variants in inherited retinal diseases
Stefan T. Stafie, Mark Lindquist, Samuel Kusher-Lenhoff, Kenji Nakamichi, Debarshi Mustafi · 2025 · Ophthalmic Genetics
Gene traffic mediated by transposable elements shaped the dynamic evolution of ancient sex chromosomes of varanid lizard
Zexian Zhu, Jason Dobry, Erik Wapstra, Qi Zhou, Tariq Ezaz · 2025 · Journal of genetics and genomics/Journal of Genetics and Genomics
The AADR Visualizer: an ArcGIS online visualizer for ancient human DNA from the Allen Ancient DNA Resource
Woojung Yi, Elliot Delroba, Beth Zizzamia, Stephanie A. Spera, Melinda A. Yang · 2024 · Bioinformatics Advances
GViNC: an innovative framework for genome graph comparison reveals hidden patterns in the genetic diversity of human populations
Venkatesh Kamaraj, Ayam Gupta, Karthik Raman, Manikandan Narayanan, Himanshu Sinha · 2025 · NAR Genomics and Bioinformatics
Use of the CHM13-T2T genome improves metagenomic analysis by minimizing host DNA contamination
Donglai Liu, Jinjun Hu, Dan Zhang, Shanshan Ren, Lanqing Zhao, Hongyan Gao, Songnian Hu, Sihong Xu, Guanxiang Liang · 2025 · mSystems
Predicting nonsense-mediated mRNA decay from splicing events in sepsis using RNA-sequencing data
Jaewook Shin, Alger M. Fredericks, Brandon E. Armstead, Alfred Ayala, Maya Cohen, William Guy Fairbrother, Mitchell M. Levy, Kwesi K Lillard, Emanuele Raggi, Gerard J. Nau et al. · 2025 · Life Science Alliance
A study of RNA splicing and protein expression in the living human brain
Brian Harris Kopell, Deepak A. Kaji, Lora E. Liharska, Eric Vornholt, Anina N. Lund, Alice Hashemi, Ryan C. Thompson, Jessica Johnson, Nicole Bussola, Esther Cheng et al. · 2025 · PLoS ONE
Metagenomic next-generation sequencing reveals respiratory flora distribution in COVID-19
Chong Wang, Shuo Yang, Qi Liu, Hongchao Liu, He Wang, Sisi Ma, Jing Li, Liyan Cui · 2025 · Scientific Reports
De novo assembly of an admixed South African genome and its clinical application to genetic susceptibility to tuberculosis
Anel Sparks, Yolandi Swart, Craig John Kinnear, Gian D van der Spuy, Gerard C. Tromp, Brigitte Glanzmann, Marlo Möller · 2025 · Aspects of Molecular Medicine
Exploring the role of genetic variants in susceptibility to autoimmune Diseases: A molecular genetics approach
Fatemah Salem Basingab · 2025 · Human Immunology
THRAISE: An automated and reproducible web platform for RNA-seq analysis
Hyeon Ho Heo, Soo Jong Um · 2025 · Molecules and Cells
GrafGen: distance-based inference of population ancestry for Helicobacter pylori genomes
William Wheeler, Difei Wang, Isaac Zhao, Filipa F. Vale, Yumi Jin, Charles S. Rabkin · 2025 · BMC Bioinformatics
Combination Hormonal Drug Therapy Inhibits In Vitro Growth of Adult Ovarian Granulosa Tumor Cells
Rebekah Summey, Marissa Iden, Shirng-Wern Tsaih, Rachel Schmidt, Deepak Parashar, Shunping Wang, Janet Sue Rader, Elizabeth E. Hopp · 2025 · Cancer Investigation
Associations of FTO and CLOCK Genetic Variants with Emotional Eating and Reward-Related Appetite Regulation Among Healthy Young Adult Males: An Exploratory Secondary Analysis
Julie E. Brown, Christopher P. Hedges, Lindsay Dudley Plank, Andrea Jane Braakhuis · 2026 · Nutrients
Introgressed mitochondrial fragments from archaic hominins alter nuclear genome function in modern humans
Qiong Zhu, Jinning Zhang, Weichen Zhou, Shen-Ao Liang, Shengmiao Wang, Xinyu Cai, Fuyuan Li, Jin Li, Guojie Zhang, Huijuan Feng et al. · 2026 · Science Advances
Household environmental characteristics influence the house dust metagenome
Isabella Gamez, Farnaz Fouladi, Antonio Gonzalez, James M. Ward, Ziyue Wang, Laura E. Beane Freeman, Alison A. Motsinger‐Reif, Shyamal Peddada, Rob D. Knight, Mikyeong Lee et al. · 2026 · Environmental Research
Community assembly modeling of the microbiome within Barrett’s esophagus and esophageal adenocarcinoma
Caitlin Guccione, I. Sfiligoi, Antonio Gonzalez, Justin P. Shaffer, Mariya Kazachkova, Yuhan Weng, Daniel McDonald, Shailja C. Shah, Samuel S. Minot, Thomas G. Paulson et al. · 2026 · BMC Genomics
Pangenome-guided sequence assembly via binary optimization
Josh Cudby, James Bonfield, Chenxi Zhou, Richard Michael Durbin, Sergii Strelchuk · 2026 · Briefings in Bioinformatics
A spatiotemporal transcriptomic atlas of porcine (Sus scrofa) female early gonadal development
Pengcheng He, Wenzhe Xia, Tianzhi Chen, Yaxuan Yan, Dengfeng Gao, Yadi Teng, Ting Zhao, Xinze Chen, Zhiqiang Feng, Runbo Li et al. · 2026 · Communications Biology
Syrah: a pipeline to maximize spatial transcriptomics data output
Carolyn E. Brewster, Frederick G Mann, Blair W. Benham-Pyle, Alejandro Sánchez Alvarado · 2026 · G3 Genes Genomes Genetics
Explicit dynamic cross-strand interactions for DNA sequence language modelling
Cheng Yang, Liu Y, Lei Ling, Yang Liu, F. H. Li, Changjian Chen, Long Wang, Feng Yu, Liang Qiao, Xiangxiang Zeng et al. · 2026 · Nature Machine Intelligence
A longitudinal study of CLDN5 DNA methylation and PTSD
Alessandra R. Grillo, Sara Wallander, Beth M. McCormick, Xiang Zhao, Mark W. Logue, Mark W. Miller, Erika J. Wolf · 2026 · Journal of Behavioral Medicine
Systematic analysis of homozygous autosomal copy number losses in exomes improves diagnostic yield and uncovers ultra-rare recessive disorders
Ankur Chaurasia, Anju Shukla, Shruti Pande, Greeshma Purushothama, Akhil Kanathay Ashokan, Purvi Majethia, Namanpreet Kaur, Priyanka Upadhyai, Neha Quadri, Gandham SriLakshmi Bhavani et al. · 2026 · European Journal of Human Genetics
Comparative genomic analysis of Bacteroides fragilis from intestinal and extra-intestinal sites
Renee E. Oles, Marvic Carrillo Terrazas, Luke R. Loomis, Simone Zuffa, Maxwell Neal, Chia-Yun Hsu, Adriana Vasquez Ayala, Caitlin Tribelhorn, Pedro Belda‐Ferre, Jianshu Zhao et al. · 2026 · Microbiology Spectrum
MZF1-mediated GAPDH overexpression drives glycolytic reprogramming and neuroendocrine progression in advanced prostate cancer
Wang Liu, Lily He, Cuncong Zhong, Yuzhuo Wang, da zhang, Moben Mirza, Benyi Li · 2026 · Drug Resistance Updates
Single-Cell Transcriptome Analysis Reveals IRF1-Driven Epithelial States and Glycosaminoglycan–Glycolysis Coupling in Cisplatin-Resistant HGSOC
贾朝阳, Wenjing Pan, Xibo Zhao, Lianxiu Li, Wenhua Tan · 2026 · Cancer Informatics
Long-read sequencing reveals pre-meiotic gene conversion in sperm
Regev Schweiger, S. Y. Lee, Chenxi Zhou, Tsun-Po Yang, Stacy Li, Rashesh Sanghvi, Matthew D. C. Neville, Katie Smith, Kirsty Roberts, Ayrun Nessa et al. · 2026 · Nature
Exploratory study on blood and urine transcriptomes for identifying miRNA biomarkers in pediatric febrile bacterial and viral infections
Tatjana Kiseļova, Baiba Vilne, Gunda Zvigule-Neidere, Dace Gardovska · 2026 · Scientific Reports
Assessing Hardy-Weinberg equilibrium in T2T-aligned 1000 genomes project
Elika Garg, Jaffa Romain, Lei Sun, Andrew D. Paterson · 2026 · PLoS Genetics
GenomeLandscaper: Landscape analysis of genome-fingerprints maps assessing chromosome architecture
Hannan Ai, Yuncan Ai, Fanmei Meng · 2018 · Scientific Reports
SRAMM: Short Read Alignment Mapping Metrics
Alvin Chon, Xiaoqiu Huang · 2021 · International Journal on Bioinformatics & Biosciences
Classification of Single Cell Types using Small Sets of Expressed Genes: Comparative Analysis of Supervised Machine Learning Methods
Aleksandar N. Veljković, Mirjana M. Maljković, Nenad S. Mitić, Saša N. Malkov, Minjie Lyu, Xin Hui Lin, Marek T. Michalewicz, Guanglan Zhang, Vladimir Brusić · 2021 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
LT1, an ONT long-read-based assembly scaffolded with Hi-C data and polished with short reads
Hui-Su Kim, Asta Blažytė, Sungwon Jeon, Changhan Yoon, Yeonkyung Kim, Changjae Kim, Dan M Bolser, Ji-Hye Ahn, Jeremy S. Edwards, Jong Bhak · 2022 · Gigabyte
Position-Defined CpG Islands Provide Complete Co-methylation Indexing for Human Genes
Ming Xiao, Rui-Ying Yin, Pengbo Gao, Jun Myoung Yu, Fubo Ma, Zichun Dai, Le Zhang · 2022 · Lecture notes in computer science
A Practical Analysis of Techniques for Minting Genetic Information as NFTs in Blockchain Technology
Marco Radovancovici, Darius Galiş, Ciprian Pungilă · 2022 · International Symposium on Symbolic and Numeric Algorithms for Scientific Computing (SYNASC)
Optimizing Variant Calling for Human Genome Analysis: A Comprehensive Pipeline Approach
Miguel M. Pinheiro, Jorge Miguel Silva, José Luís Oliveira · 2023 · Lecture notes in computer science
SUZ domain–containing proteins have multiple effects on nonsense-mediated decay target transcripts
Mathias Halbout, Marina Bury, Aoife Hanet, Isabelle Gerin, Julie Graff, Theo Killian, Laurent Gatto, Didier Vertommen, Guido T. Bommer · 2023 · Journal of Biological Chemistry
Differential Gene Expression Associated with Idiopathic Epilepsy in Belgian Shepherd Dogs
Nathan Kinsey, Janelle M. Belanger, Anita M. Oberbauer · 2024 · Genes
Association of lactose intake and lactase persistence genotype with microbial taxa and function in healthy multi-ethnic U.S. adults
Yirui Tang, Andrew S. Oliver, Zeynep Alkan, Ian F. Korf, Liping Huang, Mary E. Kable, Danielle G. Lemay · 2025 · Food & Function
Genome-wide screening of pharmacogenomic biomarkers in jordanian patients with genetic disorders
Yazun Bashir Jarrar, Nancy Hakooz, Dina Abu Hashem, Mariam Homsi, Sufyan Ali Ajeen, Maher Al Ghedan, Rania Almasri, Amnah Y. Bdier, Mohammed Al‐Raqad · 2025 · The Pharmacogenomics Journal
cfGWAS reveal genetic basis of cell-free DNA end motifs
Huanhuan Zhu, Yan Zhang, Linxuan Li, Shuang Zeng, Xinyi Zhang, Ying Lin, Rijing Ou, Lin Wang, Xiameizi Li, Yu Wang et al. · 2026 · Nature Communications
Meta-analysis of Gene Expression in Neurodegenerative Diseases Reveals Patterns in GABA Synthesis and Heat Stress Pathways
Abdulahad Bayraktar, Tuğba Önal-Süzek, Barış Ethem Süzek, Ömür Baysal · 2019 · arXiv (Cornell University)
AIDE: annotation-assisted isoform discovery with high precision
Shan Li, Shan Li, Xin Tong, Ling Deng, Hubing Shi, Wei Vivian Li · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
IMDSVs: An integrated method based on machine learning and deep learning of calling structural variations from long-read data
Yaoxian Lv, Lei Cai, Jingyang Gao · 2021 · International Conference on Computer Science & Education (ICCSE)
Chromatin-bound protein colocalization analysis using bedGraph2Cluster and PanChIP
Hanjun Lee, Ioannis Sanidas, Nicholas J. Dyson, Michael S. Lawrence · 2023 · STAR Protocols
Practical universal k -mer sets for minimizer schemes
Dan DeBlasio, Fiyinfoluwa Gbosibo, Carl Kingsford, Guillaume Marçais · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
Population Structure, Stratification and Introgression of Human Structural Variation
Mohamed A. Almarri, Anders Bergström, Javier Prado-Martinez, Fengtang Yang, Beiyuan Fu, Alistair S. Dunham, Yuan Chen, Matthew E. Hurles, Chris Tyler-Smith, Yali Xue · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
Complex networks of miRNA-transcription factors mediate gene dosage compensation in aneuploid cancer
ManSai Acón, Guillermo Oviedo, Edwin Baéz, Gloriana Vásquez-Vargas, Jose Andres Guevara-Coto, Andrés Segura-Castillo, Francisco Siles-Canales, Steve Quirós-Barrantes, Pedro Mendes, Rodrigo Antonio Mora-Rodríguez · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
Semi-supervised segmentation and genome annotation
Rachel C.W. Chan, Matthew McNeil, Eric G. Roberts, Mickaël Mendez, Maxwell W. Libbrecht, Michael M. Hoffman · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
Design and implementation of an intelligent framework for supporting evidence-based treatment recommendations in precision oncology
Frank P. Y. Lin · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
Longest Order Conserved Exemplar Subsequences
Shu Zhang, Lianrong Pu, Runmin Yang, Luli Wang, Daming Zhu, Haitao Jiang · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
Repetitive DNA Sequences
Andrew G. Clark, Barbash, Daniel A., Lower, Sarah E., Dion-Coté, Anne-Marie · 2020 · MDPI eBooks
Trio-binned genomes of the woodrats Neotoma bryanti and N. lepida reveal novel gene islands and rapid copy number evolution of xenobiotic metabolizing cytochrome p450 genes
Robert Greenhalgh, Matthew L. Holding, Teri J. Orr, James Henderson, Thomas Lee Parchman, Marjorie D. Matocq, Michael D. Shapiro, M. Denise Dearing · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
Accelerating Genome Sequence Analysis via Efficient Hardware/Algorithm Co-Design
Damla Senol Cali · 2021 · arXiv (Cornell University)
Interrogating Genomic Data in the Phylogenetic Placement of Treeshrews Reveals Potential Sources of Conflict
Alexander Knyshov, Yana Hrytsenko, Robert Literman, Rachel S. Schwartz · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
Faculty Opinions recommendation of Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.
Steven L. Salzberg · 2019 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
Faculty Opinions recommendation of Nanopore sequencing and assembly of a human genome with ultra-long reads.
Roderic Guigó · 2018 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
Study of HLA Allele Frequencies Associated with Autoimmune Diseases in the Population of the Russian Federation
Polina N. Kazakova, Nadezhda V. Smirnova, Митрофанов Сергей Игоревич, Шпакова Татьяна Андреевна, Liliya A. Golubnikova, Konstantin S. Grammatikati, Фролова Лидия Владимировна, Ekaterina U. Oleynikova, Pavel U. Zemsky, А. А. Васильева et al. · 2022 · SSRN Electronic Journal
Deriving genetic codes for molecular phenotypes from first principles
Salil S. Bhate, Anna Seigal, Juan Caicedo · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
KaryoCreate: a new CRISPR-based technology to generate chromosome-specific aneuploidy by targeting human centromeres
Nazario Bosco, Aleah Goldberg, Adam F. Johnson, Xin Zhao, Joseph C. Mays, Pan Cheng, Joy J. Bianchi, Cecilia Toscani, Lizabeth Katsnelson, Dania Annuar et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
ShinyGAStool: A user-friendly tool for candidate gene association studies
Thomas J. Hoffmann, Christine A. Miaskowski, Kord M. Kober · 2022 · SoftwareX
Integrative single-cell characterization of frugivory adaptations in the bat kidney and pancreas
Wei E. Gordon, Seungbyn Baek, Hai P. Nguyen, Yien–Ming Kuo, Rachael Bradley, Alexander V. Galazyuk, Insuk Lee, Melissa R. Ingala, Nancy B. Simmons, Tony Schountz et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
Telomere-to-Telomere Assembly Improves Host Reads Removal in Metagenomic High-Throughput Sequencing of Human Samples
Lei Wang, Guoning Xing · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
GWAS of cataract in Puerto Ricans identifies a novel large-effect variant in ITGA6
Jingchunzi Shi, Jared O’Connell, Barry Hicks, Wei Wang, Katarzyna Bryc, Brady Jennifer J, Vladimir Vacic, Will Freyman, Noura S. Abul‐Husn, Adam Auton et al. · 2023 · medRxiv
Random forest classifiers trained on simulated data enable accurate short read-based genotyping of structural variants in the alpha globin region at Chr16p13.3
Nancy Fisher Hansen, Xunde Wang, Mickias B. Tegegn, Zhi Liu, Mateus Henrique Gouveia, Gracelyn Hill, Jennifer Lin, Temiloluwa Okulosubo, Daniel Shriner, Swee Lay Thein et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
Genes in Humans and Mice: Insights from Deep learning of 777K Bulk Transcriptomes
Zheng Su, Mingyan Fang, Andrei Smolnikov, Fatemeh Vafaee, Marcel E. Dinger, Emily C. Oates · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
Multiomic foundations of human prefrontal cortex tissue function
Brian Harris Kopell, Deepak A. Kaji, Lora E. Liharska, Eric Vornholt, Alissa A. Valentine, Anina N. Lund, Alice Hashemi, Ryan C. Thompson, Terry M. Lohrenz, Jessica Johnson et al. · 2024 · medRxiv
Enhanced Gut Microbiome Capacity for Amino Acid Metabolism is associated with Peanut Oral Immunotherapy Failure
Mustafa Özçam, Din L. Lin, Chhedi Lal Gupta, Allison Li, Lisa M. Wheatley, Carolyn Baloh, Srinath Sanda, Stacie M. Jones, Susan V. Lynch · 2024 · medRxiv
cfGWAS reveal genetic basis of cell-free DNA features
Huanhuan Zhu, Yan Zhang, Shuang Zeng, Linxuan Li, Rijing Ou, Xinyi Zhang, Yu Lin, Ying H. Lin, Chuang Xu, Lin Wang et al. · 2024 · medRxiv
Re-calibration of flow cytometry standards for plant genome size estimation
Abhishek Soni, Robert James Henry · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
Large complex structural rearrangements in human genomes harbor cryptic structures
Peter A. Audano, Carolyn A. Paisie, Christine R. Beck · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
Homo Sapiens Chromosomal Location Ontology: A Framework for Genomic Data in Biomedical Knowledge Graphs
Taha Mohseni Ahooyi, Benjamin J. Stear, J. Alan Simmons, Chris Nemarich, Jonathan C. Silverstein, Deanne M. Taylor · 2025 · Scientific Data
Computational modeling of human genetic variants in mice
Kexin Dong, Samuel I. Gould, Minghang Li, Francisco J. Sánchez Rivera · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
Cellular Diversity, Immune Crosstalk, and Genomic Alterations in Light Chain Amyloidosis
Ankita Srivastava, Romika Kumari, Juho Jalmari Miettinen, Minna H. Suvela, Klara Acs, Sini Luoma, Caroline Akemi Heckman · 2025 · medRxiv
Mapping the causal chain from genetic risk variants to lipid dysmetabolism in Parkinson’s disease
Ruth B. De-Paula, Jonggeol Kim, Hervé Rhinn, Hiba Saade, Fatima I. Chavez, Téah Segura, Maria Valeria Lozano, Michelle Etoundi, Karla Silos, Viktoriya Korchina et al. · 2025 · medRxiv
Telomere-to-Telomere Accurate and Gapless Korean Standard Reference Genome
Jihun Bhak, Yoonsung Kwon, Dong-Hyun Shin, Kyungwhan An, H. Alex Choi, Sang Soo Park, Changhan Yoon, Yookyung Christy Choi, Hyomin Lee, Daeui Park et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
Revisiting the lineages of the Cohanim using data from next-generation sequencing
J. Lipson, Simcha Gershon Bohrer, S. Cohen-Weinstein, L. Cooper, Dolev Revivo, Laura Staetsky, Paul Andrew Maier, Göran Runfeldt, Karl L. Skorecki · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
A full-length mtDNA dataset for studying genetic variations across generations and complex family structures
Yanan Liu, Qi Yang, Yujia Xuan, Jinyuan Zhao, Anqi Chen, Suhua Zhang · 2026 · Scientific Data
Minipoa: A minimizer-based method for fast and memory-efficient partial order alignment
Haodong Liu, Pinglu Zhang, Yanming Wei, Qinzhong Tian, Yixiao Zhai, Quan Zou, Mengting Niu · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
ARCH3D: A foundation model for global genome architecture
Nicholas Galioto, Cooper M. Stansbury, Alex Gorodetsky, Indika Rajapakse · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
Whole-genome benchmarking reveals context-specific error rates in the Ultima UG100 and Illumina NovaSeqX Platforms
Oona Shigeno Risse-Adams, Paul Collier, Theodore M. Nelson, Jonathan Foox, Christopher E. Mason · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
Performance Analysis of MEC Approach for Haplotype Assembly
Sina Majidian, Mohammad Hossein Kahaei · 2018 · arXiv (Cornell University)
Investigating the functional roles of microRNA-29b and microRNA-146a in prion diseases
Wenting Zhao · 2018 · Minerva Access (University of Melbourne)
Phasing single DNA molecules with barcode linked sequencing
David Redin · 2018 · KTH Publication Database DiVA (KTH Royal Institute of Technology)
Efficient whole genome haplotyping and single molecule phasing with barcode-linked reads
David Redin, Tobias Frick, Hooman Aghelpasand, Jennifer Theland, Max Käller, Erik Borgström, Remi‐André Olsen, Afshin Ahmadian · 2018 · KTH Publication Database DiVA (KTH Royal Institute of Technology)
Systematic re-annotation of 191 genes associated with early-onset epilepsy unmasks de novo variants linked to Dravet syndrome in novel SCN1A exons
Charles A. Steward, Jolien Roovers, Marie‐Marthe Suner, José M. González, Barbara Uszczyńska-Ratajczak, Dmitri Davidovich Pervouchine, Stephen F. Fitzgerald, Margarida Viola, Hannah Stamberger, Fadi F. Hamdan et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
Analysis of the pattern and trend of human genomic variations in the form of single nucleotide polymorphisms (SNPs) and small insertions and deletions (INDELs)
vinay kumar chundi · 2019 · Brock University Digital Repository (Brock University)
Fundamentals of Drug Metabolism and Pharmacogenomics Within a Learning Healthcare System Workflow Perspective
Matthew K. Breitenstein, Erin Lynn Crowgey · 2019 · Health informatics
Human Reference Genome and a High Contiguity Ethnic Genome AK1
Jina Kim, Joohon Sung, Kyudong Han, Wooseok Lee, Seyoung Mun, Jooyeon Lee, Kunhyung Bahk, Inchul Yang, Young‐Kyung Bae, Changhoon Kim et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
Characterising copy number polymorphisms using next generation sequencing data
Zhiwei Li · 2019 · KTH Publication Database DiVA (KTH Royal Institute of Technology)
Bioinformatics methods and approaches to discover disease variants from DNA sequencing data
Harriet Dashnow · 2019 · Minerva Access (University of Melbourne)
Identification of a Novel Gene, Slc39a8, Encoding Zinc Transporter Specific to Treg Cells by Integrative Bioinformatic Analysis and Its Functional Validation
Dong Woo Ko, Jeesang Yoon, Jung Jin Yang · 2019 · Computational Biology and Bioinformatics
The transcriptome dynamics of single cells during the cell cycle
Daniel Schwabe, Sara Formichetti, Jan Philipp Junker, Martin Falcke, Nikolaus Rajewsky · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
SeAlM: A Query Cache Optimization Technique for Next Generation Sequence Alignment
Evan Stene, Farnoush Banaei‐Kashani · 2019 · IEEE ... International Conference on Data Mining workshops
New Exploration to Identify the Naive T Cell-Specific Gene Using Gene Similarity
Dongwoo Ko, Jung-Jin Yang · 2020 · The Journal of Korean Institute of Information Technology