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Citations

2024

  • Jin Hee Kim & Jeongsik Kim (2024) Comprehensive analysis of the chloroplast genome and phylogenetic relationships of Sasa quelpaertensis Nakai, Mitochondrial DNA Part B, 9:1, 88-93, DOI: 10.1080/23802359.2023.2301017
  • genomic and transcriptomic insight into the evolution and breeding of turfgrass species, poa annua and bouteloua dactyloides. Thesis. Christopher W. Benson. https://etda.libraries.psu.edu/files/final_submissions/29057 WGSCoveragePlotter
  • Functional benefit of CRISPR/Cas9-induced allele deletion for RYR1 dominant mutation Mathilde Beaufils, Margaux Melka, Julie Brocard, Clement Benoit, Nagi Debbah, Kamel Mamchaoui, Norma B. Romero, Anne Frédérique Dalmas-Laurent, Susana Quijano-Roy, Julien Fauré, John Rendu, Isabelle Marty doi: https://doi.org/10.1101/2024.01.24.576997
  • Epigenomic profiling of active regulatory elements by enrichment of unmodified CpG dinucleotides. https://www.biorxiv.org/content/biorxiv/early/2024/02/16/2024.02.16.575381.full.pdf
  • Malena Daich Varela, Elena Schiff, Samantha Malka, Genevieve Wright, Omar A. Mahroo, Andrew R. Webster, Michel Michaelides, Gavin Arno; PHYH c.678+5G>T Leads to In-Frame Exon Skipping and Is Associated With Attenuated Refsum Disease. Invest. Ophthalmol. Vis. Sci. 2024;65(2):38. https://doi.org/10.1167/iovs.65.2.38. Biostar214299
  • Imprinted X chromosome inactivation at the gamete-to-embryo transition. Chunyao Wei & al. Published:March 07, 2024 Molecular Cell DOI:https://doi.org/10.1016/j.molcel.2024.02.013
  • Investigating the potential of single-cell DNA methylation data to detect allele-specific methylation and imprinting. Nicholas D. Johnson, David J. Cutler, Karen N. Conneely , 2024 DOI:https://doi.org/10.1016/j.ajhg.2024.02.009
  • Erik McShane, Mary Couvillion, Robert Ietswaart, Gyan Prakash, Brendan M. Smalec, Iliana Soto, Autum R. Baxter-Koenigs, Karine Choquet, L. Stirling Churchman, A kinetic dichotomy between mitochondrial and nuclear gene expression processes, Molecular Cell, 2024, , ISSN 1097-2765, https://doi.org/10.1016/j.molcel.2024.02.028. (https://www.sciencedirect.com/science/article/pii/S1097276524001709) SamFixCigar
  • Pauly R, Alexander Feltus F. Simplified detection of genetic background admixture using artificial intelligence. Clin Genet. 2024 Apr 1. doi: 10.1111/cge.14527. Epub ahead of print. PMID: 38561851.
  • Hervé J, Haurogné K, Allard M, Sourice S, Lindenbaum P, Bach JM, Lieubeau B. Spontaneous Akt2 deficiency in a colony of NOD mice exhibiting early diabetes. Sci Rep. 2024 Apr 20;14(1):9100. doi: 10.1038/s41598-024-60021-w. PMID: 38643275; PMCID: PMC11032318. vcffilterjdk
  • Baudic M, Murata H, Bosada FM, Melo US, Aizawa T, Lindenbaum P, van der Maarel LE, Guedon A, Baron E, Fremy E, Foucal A, Ishikawa T, Ushinohama H, Jurgens SJ, Choi SH, Kyndt F, Le Scouarnec S, Wakker V, Thollet A, Rajalu A, Takaki T, Ohno S, Shimizu W, Horie M, Kimura T, Ellinor PT, Petit F, Dulac Y, Bru P, Boland A, Deleuze JF, Redon R, Le Marec H, Le Tourneau T, Gourraud JB, Yoshida Y, Makita N, Vieyres C, Makiyama T, Mundlos S, Christoffels VM, Probst V, Schott JJ, Barc J. TAD boundary deletion causes PITX2-related cardiac electrical and structural defects. Nat Commun. 2024 Apr 20;15(1):3380. doi: 10.1038/s41467-024-47739-x. PMID: 38643172; PMCID: PMC11032321. lowresbamtoraster
  • Pauly, R., Johnson, L., Feltus, F.A. et al. Enrichment of a subset of Neanderthal polymorphisms in autistic probands and siblings. Mol Psychiatry (2024). https://doi.org/10.1038/s41380-024-02593-7
  • Marshall VA, Cornejo Castro EM, Goodman CA, Labo N, Liu I, Fisher NC, et al. (2024) Sequencing of Kaposi’s Sarcoma Herpesvirus (KSHV) genomes from persons of diverse ethnicities and provenances with KSHV-associated diseases demonstrate multiple infections, novel polymorphisms, and low intra-host variance. PLoS Pathog 20(7): e1012338. https://doi.org/10.1371/journal.ppat.1012338 msa2vcf
  • Sigeman, H., Downing, P.A., Zhang, H. et al. The rate of W chromosome degeneration across multiple avian neo-sex chromosomes. Sci Rep 14, 16548 (2024). https://doi.org/10.1038/s41598-024-66470-7 bamstats04
  • Heczko, L., Liška, V., Vyčítal, O. et al. Targeted panel sequencing of pharmacogenes and oncodrivers in colorectal cancer patients reveals genes with prognostic significance. Hum Genomics 18, 83 (2024). https://doi.org/10.1186/s40246-024-00644-2 vcfpolyx
  • Gilbert, Melissa A., Keefer, Jadhav, Tanaya, Antfolk, Daniel, Ming, Qianqian, Valente, Nicolette, Shaw, Grace Tzun, Sottolano, Christopher J., Matwijec, Grace, Luca, Vincent C., Loomes, Kathleen M., Rajagopalan, Ramakrishnan, Hayeck, Tristan J., Spinner, Nancy B. " Functional characterization of 2,832 JAG1 variants supports reclassification for Alagille syndrome and improves guidance for clinical variant interpretation" doi: 10.1016/j.ajhg.2024.06.011, 10.1016/j.ajhg.2024.06.011, The American Journal of Human Genetics, The American Journal of Human Genetics, Elsevier, 0002, doi: 10.1016/j.ajhg.2024.06.011, https://doi.org/10.1016/j.ajhg.2024.06.011

2023

  • Varani AM, Silva SR, Lopes S, Barbosa JBF, Oliveira D, Corrêa MA, Moraes AP, Miranda VFO, Prosdocimi F. 2022. The complete organellar genomes of the entheogenic plant Psychotria viridis (Rubiaceae), a main component of the ayahuasca brew. PeerJ 10:e14114 https://doi.org/10.7717/peerj.14114 wgscoverageplotter
  • Vinicius A.C & al. Comparative analyses of Theobroma cacao and T. grandiflorum mitogenomes reveal conserved gene content embedded within complex and plastic structures". Gene Volume 849 2023 .https://doi.org/10.1016/j.gene.2022.146904.
  • Pol32, an accessory subunit of DNA polymerase delta, plays an essential role in genome stability and pathogenesis of Candida albicans. Shraddheya Kumar Patel & al. Gut Microbes. https://doi.org/10.1080/19490976.2022.2163840 2023. vcfpolyx
  • Cho, C.H., Park, S.I., Huang, TY. et al. Genome-wide signatures of adaptation to extreme environments in red algae. Nat Commun 14, 10 (2023). https://doi.org/10.1038/s41467-022-35566-x WGSCoveragePlotter
  • Integrative proteogenomics using ProteomeGenerator2 Nathaniel Kwok, Zita Aretz, Sumiko Takao, Zheng Ser, Paolo Cifani, Alex Kentsis bioRxiv 2023.01.04.522774; doi: https://doi.org/10.1101/2023.01.04.522774
  • Sasimol Udomruk, Areerak Phanphaisarn, Thanat Kanthawang, Apiwat Sangphukieo, Songphon Sutthitthasakul, Siripong Tongjai, Pimpisa Teeyakasem, Patcharawadee Thongkumkoon, Santhasiri Orrapin, Sutpirat Moonmuang, Jeerawan Klangjorhor, Arnat Pasena, Pathacha Suksakit, Sivamoke Dissook, Pitithat Puranachot, Jongkolnee Settakorn, Tonapha Pusadee, Dumnoensun Pruksakorn, Parunya Chaiyawat; Characterization of Cell-free DNA Size Distribution in Osteosarcoma Patients. Clin Cancer Res 2023; https://doi.org/10.1158/1078-0432.CCR-22-2912
  • Rare coding variants in CTSO, a potential new actor of arterial remodeling, are associated to familial intracranial aneurysm Milène Freneau, Raphaël Blanchet, Sandro Benichi, Mary-Adel Mrad, Surya Prakash Rao Batta, Marc Rio, Stéphanie Bonnaud, Pierre Lindenbaum, Fabien Laporte, Stéphane Cuenot, Jean-François Deleuze, Christian Dina, Stéphanie Chatel, Emmanuelle Bourcereau, Solène Jouan, ICAN Study Group, Hubert Desal, Anne-Clémence Vion, Romain Bourcier, Gervaise Loirand, Richard Redon medRxiv 2023.01.31.23285168; doi: https://doi.org/10.1101/2023.01.31.23285168
  • Horizontal gene transfer and CRISPR targeting drive phage-bacterial host interactions and co-evolution in pink berry marine microbial aggregates James C. Kosmopoulos, Danielle E. Campbell, Rachel J. Whitaker, Elizabeth G. Wilbanks bioRxiv 2023.02.06.527410; doi: https://doi.org/10.1101/2023.02.06.527410
  • Rhys T. White, Martina Jelocnik, Natalie Klukowski, Md. Hakimul Haque, Subir Sarker. The first genomic insight into Chlamydia psittaci sequence type (ST)24 from a healthy captive psittacine host in Australia demonstrates evolutionary proximity with strains from psittacine, human, and equine hosts. Veterinary Microbiology, Volume 280, 2023, 109704, ISSN 0378-1135. https://doi.org/10.1016/j.vetmic.2023.109704.
  • Benjamin McClinton, Christopher M. Watson, Laura A. Crinnion, Martin McKibbin, Manir Ali, Chris F. Inglehearn, Carmel Toomes, Haplotyping Using Long-Range PCR and Nanopore Sequencing of Phase Variants; Lessons Learned From the ABCA4 Locus, Laboratory Investigation, 2023, 100160, ISSN 0023-6837 (biostar214299)
  • Xiao Shu, Chenyang Huang, Tengwei Li, Jie Cao, Jianzhao Liu,.a6A-seq: N6-allyladenosine-based cellular messenger RNA metabolic labelling and sequencing,.Fundamental Research,.2023,.,.ISSN 2667-3258,.https://doi.org/10.1016/j.fmre.2023.04.010..(https://www.sciencedirect.com/science/article/pii/S2667325823001267). sam2tsv
  • The Mitoribosome. Methods in Molecular Biology. https://doi.org/10.1007/978-1-0716-3171-3 Biostar84452
  • N. Mamoozadeh, C. Goldsworthy, L. Miller, N. Peterson, M. Meek, Sources of coaster brook trout (Salvelinus fontinalis) revealed by genomic analysis of brook trout populations along Minnesota's shoreline with Lake Superior, Journal of Great Lakes Research, 2023, , ISSN 0380-1330, https://doi.org/10.1016/j.jglr.2023.06.005. (https://www.sciencedirect.com/science/article/pii/S0380133023001351) VcfFilterJdk
  • "Inferences of Local Genetic Adaptation from Palaeolithic Hunter Gatherers" Dean James Cornish . Thesis. https://discovery.ucl.ac.uk/id/eprint/10170497/1/Cornish_Thesis_MPhil.pdf VcfAncestralAllele
  • Tretter, C., de Andrade Krätzig, N., Pecoraro, M. et al. Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification. Nat Commun 14, 4632 (2023). https://doi.org/10.1038/s41467-023-39570-7 FindAllCoverageAtPosition
  • Pawar, H., Rymbekova, A., Cuadros-Espinoza, S. et al. Ghost admixture in eastern gorillas. Nat Ecol Evol (2023). https://doi.org/10.1038/s41559-023-02145-2
  • "Key innovation triggers widespread radiation of the genus Medicago". Zhipeng Liu & al. https://doi.org/10.21203/rs.3.rs-3181566/v1 bamstats05
  • Rhys T. White. A discovery down under: decoding the draft genome sequence of Pantoea stewartii from Australia’s Critically Endangered western ground parrot/kyloring (Pezoporus flaviventris). https://doi.org/10.1099/mgen.0.001101 . Microbial Genomics Vol9 Issue 9. wgscoverageplotter
  • Huang, Y., Li, L., An, G. et al. Single-cell multi-omics sequencing of human spermatogenesis reveals a DNA demethylation event associated with male meiotic recombination. Nat Cell Biol (2023). https://doi.org/10.1038/s41556-023-01232-7
  • Xu, Z., Sziraki, A., Lee, J. et al. Dissecting key regulators of transcriptome kinetics through scalable single-cell RNA profiling of pooled CRISPR screens. Nat Biotechnol (2023). https://doi.org/10.1038/s41587-023-01948-9 sam2tsv
  • Shinde SS, Sharma A and Vijay N (2023) Decoding the fibromelanosis locus complex chromosomal rearrangement of black-bone chicken: genetic differentiation, selective sweeps and protein-coding changes in Kadaknath chicken. Front. Genet. 14:1180658. doi: 10.3389/fgene.2023.1180658 biostar214299
  • Braton & al (2023) HIVepsilon-seq—scalable characterization of intact persistent proviral HIV reservoirs in women. Virology. https://doi.org/10.1128/jvi.00705-23 SAM2tsv
  • Ansari, Nadia et al. Environmental surveillance for COVID-19 using SARS-CoV-2 RNA concentration in wastewater – a study in District East, Karachi, Pakistan The Lancet Regional Health - Southeast Asia, Volume 0, Issue 0, 100299. https://doi.org/10.1016/j.lansea.2023.100299
  • Yu-Qian Qin, Chu-Yun Yang, Ze-Long Nie, Jun Wen, Ying Meng,.Phylogenomics and divergence pattern of Polygonatum (Asparagaceae: Polygonateae) in the north temperate region,.Molecular Phylogenetics and Evolution,.2023,.107962,.ISSN 1055-7903,.https://doi.org/10.1016/j.ympev.2023.107962. msa2vcf
  • Heczko, L., Hlaváč, V., Holý, P. et al. Prognostic potential of whole exome sequencing in the clinical management of metachronous colorectal cancer liver metastases. Cancer Cell Int 23, 295 (2023). https://doi.org/10.1186/s12935-023-03135-x vcfpolyx
  • Kaylee J Watson & al. Common analysis of direct RNA sequencinG CUrrently leads to misidentification of m5/C at GCU motifs . 10.26508/lsa.202302201 .
  • Hany U, Watson CM, Liu L, et al. Novel Ameloblastin Variants, Contrasting Amelogenesis Imperfecta Phenotypes. Journal of Dental Research. 2023;0(0). doi:10.1177/00220345231203694 Biostar214299

2022

  • blastn2snp : Guo, Y., Betzen, B., Salcedo, A. et al. Population genomics of Puccinia graminis f.sp. tritici highlights the role of admixture in the origin of virulent wheat rust races. Nat Commun 13, 6287 (2022). https://doi.org/10.1038/s41467-022-34050-w
  • Han, W., Liu, L., Wang, J. et al. Ancient homomorphy of molluscan sex chromosomes sustained by reversible sex-biased genes and sex determiner translocation. Nat Ecol Evol (2022). https://doi.org/10.1038/s41559-022-01898-6
  • A long noncoding RNA promotes parasite differentiation in African trypanosomes. Fabien GueganK & al. Sci. Adv., 8 (24), eabn2706. • DOI: 10.1126/sciadv.abn2706 ( biostar84452 ).
  • Baaijens, J.A., Zulli, A., Ott, I.M. et al. Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques. Genome Biol 23, 236 (2022). https://doi.org/10.1186/s13059-022-02805-9 ( biostar84452 )
  • Xi, L., Sun, Y., Xu, T., Wang, Z., Chiu, M. Y., Plouviez, S., Jollivet, D., & Qiu, J.-W. (2022). Phylogenetic divergence and population genetics of the hydrothermal vent annelid genus Hesiolyra along the East Pacific Rise: Reappraisal using multi-locus data. Diversity and Distributions, 00, 1–15. https://doi.org/10.1111/ddi.13653 (msa2vcf)
  • Garsed, D.W., Pandey, A., Fereday, S. et al. The genomic and immune landscape of long-term survivors of high-grade serous ovarian cancer. Nat Genet (2022). https://doi.org/10.1038/s41588-022-01230-9 (samviewwithmate)
  • McLaughlin, Jessica. Why are there so many birds in the tropics: using comparative approaches to investigate the confluence of landscape, ecology, and genome in the generation of Neotropical avian diversity https://shareok.org/handle/11244/336942
  • Fine structure and transcription dynamics of bread wheat ribosomal DNA loci deciphered by a multi-omics approach. Z Tulpova & al. 2022. The Plante Genome. https://doi.org/10.1002/tpg2.20191
  • Varani AM, Silva SR, Lopes S, Barbosa JBF, Oliveira D, Corrêa MA, Moraes AP, Miranda VFO, Prosdocimi F. 2022. The complete organellar genomes of the entheogenic plant Psychotria viridis (Rubiaceae), a main component of the ayahuasca brew. PeerJ 10:e14114 https://doi.org/10.7717/peerj.14114
  • Watson CM, Jackson L, Crinnion LA, et al. Long-read sequencing to resolve the parent of origin of a de novo pathogenic UBE3A variant. Journal of Medical Genetics Published Online First: 12 April 2022. doi: 10.1136/jmedgenet-2021-108314
  • Distinct genetic determinants and mechanisms of SARS-CoV-2 resistance to remdesivir .Laura J. Stevens, Andrea J. Pruijssers, Hery W. Lee, Calvin J. Gordon, Egor P. Tchesnokov, Jennifer Gribble, Amelia S. George, Tia M. Hughes, Xiaotao Lu, Jiani Li, Jason K. Perry, Danielle P. Porter, Tomas Cihlar, Timothy P. Sheahan, Ralph S. Baric, Matthias Götte, Mark R. Denison bioRxiv 2022.01.25.477724; doi: https://doi.org/10.1101/2022.01.25.477724
  • Cappelletti E, Piras FM, Sola L, Santagostino M, Abdelgadir WA, Raimondi E, Lescai F, Nergadze SG, Giulotto E. Robertsonian fusion and centromere repositioning contributed to the formation of satellite-free centromeres during the evolution of zebras. Mol Biol Evol. 2022 Jul 26:msac162. doi: 10.1093/molbev/msac162. Epub ahead of print. PMID: 35881460.
  • High-throughput Detection of T-DNA Insertion Sites for Multiple Transgenes in Complex Genomes. Edwards & al. Research Square. https://doi.org/10.21203/rs.3.rs-1325310/v1

2021

  • Yang & al. "Sequencing 5-Formyluracil in Genomic DNA at Single-Base Resolution" (2021) Analytical Chemistry doi: 10.1021/acs.analchem.1c03339" Nat Genet. 2014 Feb 2. doi: 10.1038/ng.2892." +
  • "Burden of Cardiomyopathic Genetic Variation in Lethal Pediatric Myocarditis". Amy R. Kontorovich & al. 6 Jul 2021 https://doi.org/10.1161/CIRCGEN.121.003426Circulation: Genomic and Precision Medicine. 2021;0 Biostar154220
  • Reciprocal allopolyploid grasses (Festuca × Lolium) display stable patterns of genome dominance . Marek Glombik & al. 2021. The plant journal. doi:10.1111/tpj.15375
  • Lado, S. & al. Innate and Adaptive Immune Genes Associated with MERS-CoV Infection in Dromedaries. Cells 2021, 10, 1291. https://doi.org/10.3390/cells10061291
  • Anatomy, transcription dynamics and evolution of wheat ribosomal RNA loci deciphered by a multi-omics approach. https://doi.org/10.1101/2020.08.29.273623

2019

  • Robust mapping of polyadenylated and non-polyadenylated RNA 3’-ends at nucleotide resolution by 3́end sequencing 23 May 2019. Roy & al. Methods. https://doi.org/10.1016/j.ymeth.2019.05.016
  • Han Ming Gan & al. , Genomic evidence of neo-sex chromosomes in the eastern yellow robin, GigaScience, Volume 8, Issue 9, September 2019, giz111, https://doi.org/10.1093/gigascience/giz111
  • "Blood transcriptome analysis in a buck-ewe hybrid and its parents" Falker-Gieske, C., Knorr, C. & Tetens, J. Blood transcriptome analysis in a buck-ewe hybrid and its parents. Sci Rep 9, 17492 (2019) doi:10.1038/s41598-019-53901-z
  • "Accurate detection of m6A RNA modifications in native RNA sequences" Huanle Liu, Oguzhan Begik, Morghan C Lucas, Christopher E Mason, Schraga Schwartz, John S Mattick, Martin A Smith, Eva Maria Novoa bioRxiv 525741; doi: https://doi.org/10.1101/525741
  • Ashley Byrne, Megan A Supple, Roger Volden, Kristin L Laidre, Beth Shapiro, Christopher Vollmers" bioRxiv 527978; doi: https://doi.org/10.1101/527978

2018

  • 'Pleiotropic effects of regulatory variation in tan result in correlation of two pigmentation traits in Drosophila melanogaster'. 2018. Molecular Ecology. Lukas Endler, Jean‐Michel Gibert, Viola Nolte, Christian Schlotterer. doi: 10.1111/mec.14781
  • Molly M McDonough, Lillian D Parker, Nancy Rotzel McInerney, Michael G Campana, Jesus E Maldonado; Performance of commonly requested destructive museum samples for mammalian genomic studies, Journal of Mammalogy, , gyy080, https://doi.org/10.1093/jmammal/gyy080

2017

  • Suppl. material of: "The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology". http://genome.cshlp.org/content/27/11/1916.short Gardner et al. Genome Res. 2017. 27: 1916-1929
  • 'Differential distribution of Neandertal genomic signatures in human mitochondrial haplogroups'. 2017. Renata C Ferreira, Camila R Rodrigues, James R Broach, View ORCID ProfileMarcelo RS Briones. doi: https://doi.org/10.1101/190363
  • "Direct Head-to-Head Evaluation of Recombinant Adeno-associated Viral Vectors Manufactured in Human versus Insect Cells". Kondratov & al. Molecular Therapy. https://doi.org/10.1016/j.ymthe.2017.08.003.
  • "High-Throughput Identification of Genetic Variation Impact on pre-mRNA Splicing Efficiency". Scott I Adamson, Lijun Zhan, Brenton R Graveley. doi: https://doi.org/10.1101/191122.

2015

  • Yi-Jyun Luo, Noriyuki Satoh, Kazuyoshi Endo, Mitochondrial gene order variation in the brachiopod Lingula anatina and its implications for mitochondrial evolution in lophotrochozoans, Marine Genomics, Volume 24, Part 1, 2015, Pages 31-40, ISSN 1874-7787, https://doi.org/10.1016/j.margen.2015.08.005 (SAM4WebLogo)

2014

  • Ding Z, Mangino M, Aviv A, Spector T, Durbin R; UK10K Consortium. Estimating telomere length from whole genome sequence data. Nucleic Acids Res. 2014;42(9):e75. doi:10.1093/nar/gku181
  • "Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements" . McCoy RC, Taylor RW, Blauwkamp TA, Kelley JL, Kertesz M, et al. (2014) Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements. PLoS ONE 9(9): e106689. doi: 10.1371/journal.pone.0106689 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0106689