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 601–700 of 999

Increasing circulating levels of Tenascin C in response to the Wingate anaerobic test
Ola Ekström, Kristoffer Ström, Bilal Ahmad Mir, Esa Laurila, Ylva Wessman, Mikko Lehtovirta, Karl‐Fredrik Eriksson, Ola Hansson · 2023 · Clinical Physiology and Functional Imaging
The anti-leprosy drug clofazimine reduces polyQ toxicity through activation of PPARγ
Xuexin Li, Ivó H. Hernández, Seda Koyuncu, Balázs Kis, Maria Häggblad, Louise Lidemalm, Anna Anoir Abbas, Bendegúz Sramkó, Anikó Göblös, Lars Brautigam et al. · 2024 · EBioMedicine
Genome-wide association study reveals a locus in ADARB2 for complete freedom from headache in Danish Blood Donors
Isa Amalie Olofsson, Ragnar P. Kristjansson, Ida Callesen, Olafur B. Davidsson, Bendik Slagsvold Winsvold, Henrik Hjalgrim, Sisse Rye Ostrowski, Christian Erikstrup, Mie Topholm Bruun, Ole Birger Pedersen et al. · 2024 · Communications Biology
Innovative approach for high-throughput exploiting sex-specific markers in Japanese parrotfishOplegnathus fasciatus
Yongshuang Xiao, Zhizhong Xiao, Lin Liu, Yuting Ma, Haixia Zhao, Yanduo Wu, Jinwei Huang, Pingrui Xu, Jing Liu, Jun Li · 2024 · GigaScience
VUStruct: A compute pipeline for high throughput and personalized structural biology
Christopher W. Moth, Jonathan H. Sheehan, Abdullah Al Mamun, R. Michael Sivley, Alican Gulsevin, David C. Rinker, Zenab F. Mchaourab, Undiagnosed Diseases Network, John A. Capra, Jens Meiler · 2026 · PLoS Computational Biology
ChIP provides 10-fold microbial DNA enrichment from tissue while minimizing bias
Shrikant Subhash Bhute, Jon G. Sanders, Se Jin Song, Sydney Lavoie, Austin D.-E. Swafford, Caitlin Guccione, Lucas Patel, Antonio Gonzalez, Michelle G. Rooks, Rob D. Knight et al. · 2025 · Molecular Biology Reports
Mudas de Mimosa caesalpiniaefolia Benth (Leguminosae: Mimosoideae) cultivadas em substratos orgânicos
José Israel Pinheiro, Lucas de Sousa Oliveira, Alfredo Mendonça de Sousa, Kaio Gráculo Vieira Garcia, Luan Alves Lima · 2018 · Revista Verde de Agroecologia e Desenvolvimento Sustentável
New de novo assembly of the Atlantic bottlenose dolphin ( Tursiops truncatus ) improves genome completeness and provides haplotype phasing
Karine A. Viaud‐Martinez, Cindy Lawley, Milmer Martinez Vergara, Gil Ben-Zvi, Tammy Biniashvili, Kobi Baruch, Judy St. Leger, Jennie M. Le, Aparna Natarajan, Marlem Rivera et al. · 2019 · GigaScience
KmerKeys: a web resource for searching indexed genome assemblies and variants
Dmitri S. Pavlichin, HoJoon Lee, Stephanie Greer, Susan M. Grimes, Tsachy Weissman, Hanlee P. Ji · 2022 · Nucleic Acids Research
Meta-analyses of host metagenomes from colorectal cancer patients reveal strong relationship between colorectal cancer-associated species
Manuel Adrian Riveros Escalona, Joice de Faria Poloni, Mathias J. Krause, Márcio Dorn · 2023 · Molecular Omics
Standing in the canine precision medicine knowledge gap: Improving annotation of canine cancer genomic biomarkers through systematic comparative analysis of human cancer mutations in COSMIC
Sharadha Sakthikumar, Salvatore J. Facista, Derick B. Whitley, Sara Ann Byron, Zeeshan Ansar Ahmed, Manisha Warrier, Zhanyang Zhu, Esther Chon, Kathryn Banovich, David Haworth et al. · 2023 · Veterinary and Comparative Oncology
The value of primary transcripts to the clinical and non‐clinical genomics community: Survey results and roadmap for improvements
Joannella Morales, Aoife McMahon, Jane E. Loveland, Emily H. Perry, Adam Frankish, Sarah E Hunt, Irina M. Armean, Paul Flicek, Fiona M Cunningham · 2021 · Molecular Genetics & Genomic Medicine
Theoretical characterisation of strand cross-correlation in ChIP-seq
Hayato Anzawa, Hitoshi Yamagata, Kengo Kinoshita · 2020 · BMC Bioinformatics
Skip-mers: increasing entropy and sensitivity to detect conserved genic regions with simple cyclic q-grams
Bernardo Clavijo, Gonzalo Garcia Accinelli, Luis Yanes, Katie Barr, Jonathan Wright · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
Microbial contaminants cataloged as novel human sequences in recent human pan-genomes
Mosè Manni, Evgeny M. Zdobnov · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
A powerful HUPAN on a pan-genome study: significance and perspectives
Yingyan Yu, Chaochun Wei · 2020 · Cancer Biology and Medicine
Unsupervised analysis of multi-experiment transcriptomic patterns with SegRNA identifies unannotated transcripts
Mickaël Mendez, Michelle S. Scott, Michael M. Hoffman · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
A roadmap to mammalian oral microbiome evolution with dental calculus
Jaelle C. Brealey, Henrique G. Leitão, Tom van der Valk, Wenbo Xu, Katia Bougiouri, Love Dalén, Katerina Guschanski · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
Genetic dietary adaptation in Neandertal, Denisovan and Sapiens revealed by gene copy number variation
Riccardo Vicedomini, Niccolò Righetti, Lélia Polit, Silvana Condémi, Laura Longo, Alessandra Carbone · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
Lossless Indexing with Counting de Bruijn Graphs
Mikhail Karasikov, Harun Mustafa, Gunnar Rätsch, André Kahles · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
Characterizing the genetic polymorphisms in 370 challenging medically relevant genes using long-read sequencing data from 41 human individuals among 19 global populations
Yanfeng Ji, Jiao Gong, Fritz Joachim Sedlazeck, Shaohua Fan · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
Haploinsufficiency of phosphodiesterase 10A activates PI3K/AKT signaling independent of PTEN to induce an aggressive glioma phenotype
Nicholas Nuechterlein, Allison Shelbourn, Frank Szulzewsky, Sonali Arora, Michelle Casad, Siobhan S. Pattwell, Leyre Merino-Galán, Erik P. Sulman, Sumaita Arowa, Neriah Alvinez et al. · 2024 · Genes & Development
In-Storage Read-Centric Seed Location Filtering Using 3D-NAND Flash for Genome Sequence Analysis
You-Kai Zheng, Ming‐Liang Wei, Hsiang-Yun Cheng, Chia-Lin Yang, Ming-Hsiang Tsai, C.H. Chien, Yuan-Hao Zhong, Po-Hao Tseng, Hsiang-Pang Li · 2025 · Asia and South Pacific Design Automation Conference (ASP-DAC)
Primary keratinocyte model of actinic keratosis reveals UV-induced DNA damage accumulation and persistent IFN signaling
Leonardo Elsbroek, Katja Reuschlein, Syrus Karsai, Anna Geueke, Mareike von Petersdorff, Martina Bresch, Volker Steinkraus, Peter Weisenseel, Peter Wolf, Marc Winnefeld et al. · 2025 · Journal of Investigative Dermatology
Cross-sectional comparative shotgun metagenomic analysis of the subgingival resistome in healthy subjects and patients with periodontitis from four countries
Alexandre Arredondo, G. Àlvarez, Sergio Isabal, Wim Teughels, Isabelle Laleman, M. J. Contreras, Lorena Isbej, Enrique Huapaya, Gerardo Mendoza, Carolina Mor et al. · 2026 · Journal of Oral Microbiology
Learning Micro-C from Hi-C with diffusion models
Tong Liu, Hao Zhu, Zheng Wang · 2024 · PLoS Computational Biology
Leveraging Multi-Tissue, Single-Cell Atlases as Tools to Elucidate Shared Mechanisms of Immune-Mediated Inflammatory Diseases
Anthony K. McLean, Gary Reynolds, Arthur G. Pratt · 2024 · Biomedicines
CyCoNP lncRNA establishes cis and trans RNA–RNA interactions to supervise neuron physiology
Fabio Desideri, Alessandro Grazzi, Michela Lisi, Adriano Setti, Tiziana Santini, Alessio Colantoni, Gabriele Proietti, Andrea Carvelli, Gian Gaetano Tartaglia, Monica Ballarino et al. · 2024 · Nucleic Acids Research
Genetic Insights into Brain Morphology: a Genome-Wide Association Study of Cortical Thickness and T1-Weighted MRI Gray Matter-White Matter Intensity Contrast
Nicholas J. Kim, Nahian F. Chowdhury, Kenneth H. Buetow, Paul M. Thompson, Andrei Irimia A · 2025 · Neuroinformatics
CHAS infers cell type-specific signatures in bulk brain histone acetylation studies of neurological and psychiatric disorders
Kitty B. Murphy, Yuqian Ye, Maria Tsalenchuk, Alexi Nott, Sarah J. Marzi · 2025 · Cell Reports Methods
De novo assembly of plasmodium interspersed repeat (pir) genes from Plasmodium vivax RNAseq data suggests geographic conservation of sub-family transcription
Timothy S. Little, Deirdre Cunningham, George K. Christophides, Adam James Reid, Jean Langhorne · 2025 · BMC Genomics
T2T-CHM13 versus hg38: accurate identification of immunoglobulin isotypes from scRNA-seq requires a genome reference matched for ancestry
Junli Nie, Julie Tellier, Ilariya Tarasova, Stephen L. Nutt, Gordon K. Smyth · 2025 · NAR Genomics and Bioinformatics
Characterisation of the Historic Demographic Decline of the British European Polecat Population
Rebecca Shaw, Jenny MacPherson, Andrew C. Kitchener, Graham Etherington, Wilfried Haerty · 2025 · Molecular Ecology
Fecal microbiomes from healthy adult consumers of fruits and vegetables exhibit fiber- and donor-specific fermentation: “5 a day” is not enough
Sarah E Blecksmith, Karen M. Kalanetra, Cheng-Yu Weng, Christopher Suarez, Irnayuli R. Sitepu, Yirui Tang, Shawn Ehlers Cheang, Sophia Jiang, Karina Cernioglo, Karla Damian-Medina et al. · 2025 · Food & Function
Chromatin remodeling restrains oncogenic functions in prostate cancer
Valentina Rosti, Giovanni Lembo, Cristiano Petrini, Francesca Gorini, Roberto Quadri, Chiara Cordiglieri, Margherita Mutarelli, Elisa Salviato, Elisabetta Casari, Emanuele Di Patrizio Soldateschi et al. · 2025 · Nature Communications
Sugar beet long-read reference assembly of genotype KWS2320
Juliane C. Dohm, Thomas Holzweber, Raphaela Pensch, Heinz Himmelbauer · 2025 · NAR Genomics and Bioinformatics
Antimicrobial resistance is widespread among intestinal and extra-intestinal Bacteroides fragilis strains
Marvic Carrillo Terrazas, Renee E. Oles, Luke R. Loomis, Chia-Yun Hsu, Adriana Vasquez Ayala, Michael Hweemoon Lee, Mousumi Paulchakrabarti, David T. Pride, Biswa Choudhury, Victor Nizet et al. · 2025 · Infection and Immunity
Comparative Genomics and Phylogenomics of the Mustelinae Lineage (Mustelidae, Carnivora)
Azamat Totikov, Andrey A. Tomarovsky, Polina L. Perelman, Tatiana Bulyonkova, Natalia A. Serdyukova, Aliya R. Yakupova, David W. Mohr, Daniel W. Förster, Jürke Grau, Violetta R. Beklemisheva et al. · 2026 · Genome Biology and Evolution
Empiric azithromycin alters the upper respiratory microbiome and resistome without anti-inflammatory benefit in COVID-19
Abigail Leigh Glascock, Cole P. Maguire, Hoang Van Phan, Emily Lydon, Joanna M. D. Schaenman, Carolyn S. Calfee, Esther Melamed, John R. Greenland, David Brian Corry, Farrah Kheradmand et al. · 2026 · Nature Microbiology
Gene-level gut microbiome signatures as predictive biomarkers for response to immune checkpoint inhibitors across multiple cancer types
Fengyun Zhang, Kaimiao Hu, Changming Sun, Ruibing Chen, Guangjian Ni, Xiaofeng Liu, Leyi Wei, Ran Su · 2026 · Gut Microbes
Using Apache Spark on genome assembly for scalable overlap-graph reduction
Alexander J. Paul, Dylan Lawrence, Myoungkyu Song, Seung–Hwan Lim, Chongle Pan, Tae-Hyuk Ahn · 2019 · Human Genomics
A consensus‑based ensemble approach to improve transcriptome assembly
Adam Voshall, Sairam Behera, Li, Xiangjun, Xiaohong Yu, Kushagra Kapil, Jitender S. Deogun, John Shanklin, Edgar B. Cahoon, Etsuko N. Moriyama · 2021 · Lincoln (University of Nebraska)
Development and application of a computable genotype model in the GA4GH Variation Representation Specification
Wesley Goar, Lawrence J. Babb, Srikar Chamala, Melissa Cline, Robert R. Freimuth, Reece K. Hart, Kori Kuzma, Jennifer Lee, Tristan H. Nelson, Andreas Prlić et al. · 2022 · Pacific Symposium on Biocomputing (PSB)
PCGIMA: developing the web server for human position-defined CpG islands methylation analysis
Ming Xiao, Yi Qun Xiao, Jun Myoung Yu, Le Zhang · 2024 · Frontiers in Genetics
Genomic tumor evolution dictates human medulloblastoma progression
Yana Ruchiy, Ιωάννα Τσέα, Efthalia Preka, Bronte Manouk Verhoeven, Thale Kristin Olsen, Shenglin Mei, Indranil Sinha, Klas Blomgren, Lena-Maria Carlson, Cecilia H. Dyberg et al. · 2024 · Neuro-Oncology Advances
Detection and Characterization of Clonal Hematopoiesis
Benjamin Nick Locher, Pelle Löwe, Friederike Christen, Frédérik Damm · 2024 · Methods in molecular biology
Identification and characterization of Faecalibacterium prophages rich in diversity-generating retroelements
Anastasia A. Gulyaeva, Lei Liu, Sanzhima Garmaeva, Marloes Kruk, Rinse Karel Weersma, Hermie J. M. Harmsen, Alexandra Zhernakova · 2024 · Microbiology Spectrum
De Novo Genome Assembly for an Endangered Lemur Using Portable Nanopore Sequencing in Rural Madagascar
Lindsey Hauff, Noa Elosmie Rasoanaivo, Andriamahery Razafindrakoto, Hajanirina Noëline Ravelonjanahary, Patricia Chapple Wright, Rindra Rakotoarivony, Christina M. Bergey · 2025 · Ecology and Evolution
Chromosome-length genome assembly of the stone marten (Martes foina, Mustelidae): A new view on one of the cornerstones in carnivore cytogenetics
Andrey A. Tomarovsky, Ruqayya Khan, Olga Dudchenko, Azamat Totikov, Natalia A. Serdyukova, David Weisz, Nadejda V Vorobieva, Tatiana Bulyonkova, Alexei V. Abramov, Wenhui Nie et al. · 2025 · Journal of Heredity
Genome Sequencing of Rare Disease Patients Through the Korean Regional Rare Disease Diagnostic Support Program
Rin Khang, Hane Lee, Jihye Kim, Dongseok Moon, Seokhui Jang, Eugene Lee, Yongjun Song, Seung Woo Ryu, Sohyun Lee, Heonjong Han et al. · 2025 · Human Mutation
The Karnataka Individual Genome Project expands the human reference landscape to include South Asia
Apoorva Ganesh, Anisha Mhatre, Yash Chindarkar, Moushmi Goswami, Prakruti Mishra, Aditya Sharma, Manjushri Kalpande, Febina Ravindran, Subhashini Srinivasan, Bibha Choudhary · 2025 · Human Genetics and Genomics Advances
Reframing analytical validation in preimplantation genetic testing: phase 1
Mina Popovic, Emily L. Mounts, Chaim Jalas, Richard Thomas Scott · 2025 · Fertility and Sterility
Medium levels of transcription and replication related chromosomal instability are associated with poor clinical outcome
Ataaillah Benhaddou, Laëtitia Gaston, Gaëlle Pérot, Nelly Desplat, Laura Leroy, Sophie Le Guellec, Mohamed Ben Haddou, Philippe Rochaix, Thibaud Valentin, Gwénaël Ferron et al. · 2021 · Scientific Reports
Isolation and Genomic Analysis of Single Circulating Tumor Cell Using Human Telomerase Reverse Transcriptase and Desmoglein‐2
Jae Won Song, Jungyo Suh, Seok Won Lee, Jung Ki Yoo, Uijeong Lee, Jang Hee Han, Cheol Hun Kwak, Minyong Kang, Yi Rang Kim, Chang Wook Jeong et al. · 2022 · Small Methods
Whole Exome Sequencing Reveals Genetic Variants in HLA Class II Genes Associated With Transplant-free Survival of Indeterminate Acute Liver Failure
Tsung-Jen Liao, Bohu Pan, Huixiao Hong, Paul Hideyo Hayashi, Jody A. Rule, Daniel R. Ganger, William M. Lee, Jorge L. Rakela, Minjun Chen · 2022 · Clinical and Translational Gastroenterology
HPV genotyping by L1 amplicon sequencing of archived invasive cervical cancer samples: a pilot study
Charles Warden, Preetam A. Cholli, Hanjun Qin, Chao Guo, Yafan Wang, Chetan Kancharla, Angelique M. Russell, Sylvana Salvatierra, Lorraine Z. Mutsvunguma, Kerin K. Higa et al. · 2022 · Infectious Agents and Cancer
The many genomes of Parkinson's disease
Haydeh Payami · 2022 · International review of neurobiology
Sketching and sampling approaches for fast and accurate long read classification
Arun Das, Michael C. Schatz · 2022 · BMC Bioinformatics
HELIOS: High-speed sequence alignment in optics
Ehsan Maleki, Saeedeh Akbari Rokn Abadi, Somayyeh Koohi · 2022 · PLoS Computational Biology
GENEMASK: Fast Pretraining of Gene Sequences to Enable Few-Shot Learning
Soumyadeep Roy, Jonas Wallat, Sowmya S. Sundaram, Wolfgang Nejdl, Niloy Ganguly · 2023 · Frontiers in artificial intelligence and applications
Molecular and Metabolic Analysis of Arsenic-Exposed Humanized AS3MT Mice
Jenna E. Todero, Christelle Douillet, Alexandria J. Shumway, Beverly H. Koller, Matt Kanke, Daryl J. Phuong, Miroslav Stýblo, Praveen Sethupathy · 2023 · Environmental Health Perspectives
Automated Design of Efficient Search Schemes for Lossless Approximate Pattern Matching
Luca Renders, Lore Depuydt, Sven Rahmann, Jan Fostier · 2024 · Lecture notes in computer science
AnnoGen: annotating genome-wide pragmatic features
Quanhu Sheng, Hui Yu, Olufunmilola Oyebamiji, Jiandong Wang, Dan‐Qian Chen, Scott A. Ness, Ying‐Yong Zhao, Yan Ping Guo · 2020 · Bioinformatics
The potential presence of the highly similar paralogue gene KCNE1B blurs the genetic basis of KCNE1-LQTS patients
Malena P. Pantou, Polyxeni Gourzi, Dimitrios Degiannis · 2019 · European Journal of Human Genetics
Novel sequencing technologies and bioinformatic tools for deciphering the non-coding genome
Jana Marie Schwarz, Richard Lüpken, Dominik Seelow, Birte Kehr · 2021 · Medizinische Genetik
How well can we create phased, diploid, human genomes?: An assessment of FALCON-Unzip phasing using a human trio
Arkarachai Fungtammasan, Brett T. Hannigan · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
Pooled analysis of radiation hybrids identifies loci for growth and drug action in mammalian cells
Arshad H. Khan, Andy Lin, Richard T. Wang, Joshua S. Bloom, Kenneth L. Lange, Desmond Smith · 2020 · Genome Research
Population-specific genome graphs improve high-throughput sequencing data analysis: A case study on the Pan-African genome
Huseyin Serhat Tetikol, Kübra Narcı, Deniz Turgut, Güngör Budak, Özem Kalay, Elif Arslan, Sinem Demirkaya-Budak, Alexey Dolgoborodov, Amit Jain, Duygu Kabakci-Zorlu et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
Acute COVID-19 gene-expression profiles show multiple etiologies of long-term sequelae
Ryan C. Thompson, Nicole W. Simons, Lillian Wilkins, Esther Cheng, Diane Marie Del Valle, Gabriel E. Hoffman, Brian Fennessy, Konstantinos Mouskas, Nancy J. Francoeur, Jessica Johnson et al. · 2021 · medRxiv
Overexpressed Malat1 Drives Metastasis through Inflammatory Reprogramming of Lung Adenocarcinoma Microenvironment
Elena Martínez‐Terroba, Fernando J. de Miguel, Vincent Li, Camila Robles-Oteíza, Katerina A. Politi, Jesse R. Zamudio, Nadya Dimitrova · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
Construction and representation of human pangenome graphs
Francesco Andreace, Pierre Lechat, Yoann Dufresne, Rayan Chikhi · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
Hedgehog target genes regulate lipid metabolism to drive basal cell carcinoma and medulloblastoma
Vikas Daggubati, Akshara Vykunta, Abrar Choudhury, Zulekha A. Qadeer, Kanish Mirchia, Olivier Saulnier, Naomi Zakimi, Kelly Marie Hines, Michael Paul, Linyu Wang et al. · 2023 · Research Square
Pangenome graph layout by Path-Guided Stochastic Gradient Descent
Simon Heumos, Andrea Guarracino, Jan-Niklas M. Schmelzle, Jiajie Li, Zhiru Zhang, Jörg Hagmann, Sven Nahnsen, Pjotr Prins, Erik P. Garrison · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
Genetic Diversity and Structural Complexity of the Killer-Cell Immunoglobulin-Like Receptor Gene Complex: A Comprehensive Analysis Using Human Pangenome Assemblies
Tsung-Kai Hung, Wan-Chi Liu, Sheng-Kai Lai, Hui-Wen Chuang, Yi-Che Lee, Hong-Ye Lin, Chia‐Lang Hsu, Chien‐Yu Chen, Ya‐Chien Yang, Jacob Shujui Hsu et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
Full resolution HLA and KIR genes annotation for human genome assemblies
Ying Zhou, Li Song, Heng Li · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
Computational Tools for Studying Genome Structural Variation
Xingyu Chen, Siyu Wei, Chen Sun, Zhihui Yi, Zihan Wang, Yingyi Wu, Jing Xu, Junxian Tao, Haiyan Chen, Mingming Zhang et al. · 2025 · OMICS A Journal of Integrative Biology
Type-2 diabetes epigenetic biomarkers: present status and future directions for global and Indigenous health
Sarah Munns, Alex D. H. Brown, Sam Buckberry · 2025 · Frontiers in Molecular Biosciences
Endoscopic healing in pediatric IBD perpetuates a persistent signature defined by Th17 cells with molecular and microbial drivers of disease
Kolja Siebert, Tim Faro, Nikolai Köhler, Hannes Hoelz, Sebastian Jarosch, Monica Steffi Matchado, Deborah Häcker, Federica De Zen, Mohammad Samer Hajji, Eberhard Lurz et al. · 2025 · Cell Reports Medicine
Shallow shotgun metagenomic sequencing of vaginal microbiomes with the Oxford Nanopore technology enables the reliable determination of vaginal community state types and broad community structures
Enid Graeber, Alona Tysha, Azlan Nisar, Daniel Wind, Werner Mendling, Patrick Finzer, Alexander Dilthey · 2025 · BMC Microbiology
Evaluation of Long-Read RNA Sequencing Procedures for Novel Isoform Identification and Quantification in Human Whole Blood
Hikari Okada, Alessandro Nasti, Yoshio Sakai, Yumie Takeshita, Sadahiro Iwabuchi, Tuyen Thuy Bich Ho, Tomomi Hashiba, Noboru Takata, Takaaki Sato, Takeshi Urabe et al. · 2025 · Genes
Human cytomegalovirus regulates host DNA repair machinery for viral genome integrity
Pierce Longmire, Sebastian Zeltzer, Kristen Zarrella, Olivia Daigle, Marek Svoboda, Justin M. Reitsma, Scott S. Terhune, Carly A. Bobak, Giovanni Bosco, Felicia D. Goodrum · 2025 · Nucleic Acids Research
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 Chavez, Téah Segura, Maria Valeria Lozano, Michelle Etoundi, Karla Silos, Naomi R. Kass et al. · 2026 · Brain
Ecological and Functional Stratification of the Stool Microbiome Predicts Response to Immune Checkpoint Inhibitors across Cancer Types
Vera Orletskaia, Evgenii I. Olekhnovich · 2026 · Computational and Structural Biotechnology Journal
Novel start codons introduce novel coding sequences in the human genomes
He Zhang, Yang Xie · 2023 · Scientific Reports
Transcriptome driven discovery of novel candidate genes for human neurological disorders in the telomer-to-telomer genome assembly era
Clemens Falker‐Gieske · 2023 · Human Genomics
A Novel Method for Sampling Subgingival Microbiome: A Comparative Metatranscriptomic Study
Diana Demusaj, Ryan Toma, Tanveer Khan, Lan Hu, Guruduth S. Banavar, Momchilo Vuyisich · 2024 · BioTechniques
The genetic regulation of the gastric transcriptome is associated with metabolic and obesity-related traits and diseases
Laura L. Koebbe, Timo Hess, Ann-Sophie Giel, Jessica Bigge, Jan Gehlen, Vitalia Schueller, Michael Geppert, Franz Ludwig Dumoulin, Joerg Heller, Michael Schepke et al. · 2024 · Physiological Genomics
FANCM Gene Variants in a Male Diagnosed with Sertoli Cell-Only Syndrome and Diffuse Astrocytoma
Monika Logara Klarić, Tihana Marić, Lucija Žunić, Lovro Trgovec-Greif, Filip Rokić, Ana Fiolić, Ana Merkler, Davor Ježek, Oliver Vugrek, Antonia Jakovčević et al. · 2024 · Genes
Toward building a comprehensive human pan-genome: The SEN-GENOME project
Amadou Gaye, Andréa Régina Gnilane Sène, Macoura Gadji, A Dème, Aynina Cissé, Rokhaya Ndiaye · 2024 · The American Journal of Human Genetics
Duchenne Muscular Dystrophy in Two Half-Brothers Due to Inherited 306 Kb Inverted Insertion of 10p15.1 into Intron 44 of the Dp427m Transcript of the DMD Gene
Wayne M. Jepsen, Andrew C. Fazenbaker, Keri M. Ramsey, Anna Bonfitto, Marcus Naymik, Bryce Turner, Jennifer Sloan, Nishant R. Tiwari, Saunder M. Bernes, Derek Neilson et al. · 2024 · International Journal of Molecular Sciences
DUBR non-coding RNA regulates gene expression by affecting AP-1 enhancer accessibility
Simone D. Hall, Khoa Tran, Jonathan Zhu, Tong Su, Colleen A. McHugh · 2025 · Functional & Integrative Genomics
Rare predicted loss-of-function and damaging missense variants in CFHR5 associate with protection from age-related macular degeneration
Aaron M. Holleman, Aimée M. Deaton, Rachel A. Hoffing, Lynne Krohn, Philip J. LoGerfo, Paul Nioi, Mollie E. Plekan, Sebastian Akle Serrano, Simina Ticau, Tony E. Walshe et al. · 2025 · The American Journal of Human Genetics
Best practices for improving alignment and variant calling on human sex chromosomes.
A. M. Taravella Oill, S. Plaisier, Tanya N. Phung, M. Wilson · 2026 · American Journal of Human Genetics
Genomes for all
Deanna M. Church · 2018 · Nature Biotechnology
A Protein Composite Neural Scaffold Modulates Astrocyte Migration and Transcriptome Profile
Li Yao, Ryan Brice, Teresa D. Shippy · 2022 · Macromolecular Bioscience
Improving Transcriptome Fidelity Following Synovial Tissue Disaggregation
David L. Boyle, Edward B. Prideaux, Joshua Hillman, Wei Wang, Gary S. Firestein · 2022 · Frontiers in Medicine
Transcriptomic analysis reveals the immune response of human microglia to a soy protein and collagen hybrid bioscaffold
Li Yao, Jacques Blasi, Teresa D. Shippy, Ryan Brice · 2023 · Heliyon
Clarifying CRISPR: Why Repeats Identified in the Human Genome Should Not Be Considered CRISPRs
Murat Buyukyoruk, William S. Henriques, Blake Wiedenheft · 2023 · The CRISPR Journal
Are we genetically literate enough for global precision health?
Ambroise Wonkam · 2023 · The Lancet
hipFG: high-throughput harmonization and integration pipeline for functional genomics data
Jeffrey Cifello, Pavel P. Kuksa, Naveensri Saravanan, Otto Valladares, Li‐San Wang, Yuk Yee Leung · 2023 · Bioinformatics