Citation List

More than 900 publications citing the Sentieon Software. Click below categories to see list.

Genetic Disease
 
Tumor Sequencing
 
Agrigenomics
 
Population Sequencing
 
Multi-omics
 
Gene Editing
 
Other Topics
 

Genetic Disease

Kumar, A., Im, K., Banjevic, M. et al. Whole-genome risk prediction of common diseases in human preimplantation embryos. Nat Med 28, 513–516 (2022). https://doi.org/10.1038/s41591-022-01735-0

Wu, D., Zheng, Y., Li, Y. et al. Exploring the molecular and clinical spectrum of COVID-19-related acute necrotizing encephalopathy in three pediatric cases. J Hum Genet 68, 769–775 (2023). https://doi.org/10.1038/s10038-023-01171-z

Badla, B.A., Hanifa, M.S., Jain, R. et al. Genetic determinants of severe COVID-19 in young Asian and Middle Eastern patients: a case series. Sci Rep 13, 20294 (2023). https://doi.org/10.1038/s41598-023-47718-0

Feng, X., Ping, J., Gao, S. et al. Novel JAG1 variants leading to Alagille syndrome in two Chinese cases. Sci Rep 14, 1812 (2024). https://doi.org/10.1038/s41598-024-52357-0

Garrison, M.A., Jang, Y., Bae, T. et al. Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases. Sci Data 10, 813 (2023). https://doi.org/10.1038/s41597-023-02645-7

Simeone, C.A., Wilkerson, J.L., Poss, A.M. et al. A dominant negative ADIPOQ mutation in a diabetic family with renal disease, hypoadiponectinemia, and hyperceramidemia. npj Genom. Med. 7, 43 (2022). https://doi.org/10.1038/s41525-022-00314-z

Greer, S.U., Chen, J., Ogmundsdottir, M.H. et al. Germline variants of ATG7 in familial cholangiocarcinoma alter autophagy and p62. Sci Rep 12, 10333 (2022). https://doi.org/10.1038/s41598-022-13569-4

Yang, G., Ullah, H.M.A., Parker, E. et al. Neurite outgrowth deficits caused by rare PLXNB1 mutation in pediatric bipolar disorder. Mol Psychiatry 28, 2525–2539 (2023). https://doi.org/10.1038/s41380-023-02035-w

Zhao, J., Zhang, S., Jiang, Y. et al. Mutation analysis of the WFS1 gene in a Chinese family with autosomal-dominant non-syndrome deafness. Sci Rep 12, 22180 (2022). https://doi.org/10.1038/s41598-022-26850-3

Raphael Carapito et al. ,Identification of driver genes for critical forms of COVID-19 in a deeply phenotyped young patient cohort.Sci. Transl. Med.14,eabj7521(2022).DOI:10.1126/scitranslmed.abj7521

Guan Ning Lin et al. ,De novo mutations identified by whole-genome sequencing implicate chromatin modifications in obsessive-compulsive disorder.Sci. Adv.8,eabi6180(2022).DOI:10.1126/sciadv.abi6180

Kimura et al., 2022, Cell 185, 4216–4232 October 27, 2022 ª 2022 Elsevier Inc. https://doi.org/10.1016/j.cell.2022.09.031

Expended List

Tumor Sequencing

Markowski, M.C., Taplin, ME., Aggarwal, R. et al. Bipolar androgen therapy plus nivolumab for patients with metastatic castration-resistant prostate cancer: the COMBAT phase II trial. Nat Commun 15, 14 (2024). https://doi.org/10.1038/s41467-023-44514-2

Vo, J.N., Wu, YM., Mishler, J. et al. The genetic heterogeneity and drug resistance mechanisms of relapsed refractory multiple myeloma. Nat Commun 13, 3750 (2022). https://doi.org/10.1038/s41467-022-31430-0

Noviello, T.M.R., Di Giacomo, A.M., Caruso, F.P. et al. Guadecitabine plus ipilimumab in unresectable melanoma: five-year follow-up and integrated multi-omic analysis in the phase 1b NIBIT-M4 trial. Nat Commun 14, 5914 (2023). https://doi.org/10.1038/s41467-023-40994-4

Martinez-Monleon, A., Kryh Öberg, H., Gaarder, J. et al. Amplification of CDK4 and MDM2: a detailed study of a high-risk neuroblastoma subgroup. Sci Rep 12, 12420 (2022). https://doi.org/10.1038/s41598-022-16455-1

Lin, M., Zhang, XL., You, R. et al. Evolutionary route of nasopharyngeal carcinoma metastasis and its clinical significance. Nat Commun 14, 610 (2023). https://doi.org/10.1038/s41467-023-35995-2

Magen, A., Hamon, P., Fiaschi, N. et al. Intratumoral dendritic cell–CD4+ T helper cell niches enable CD8+ T cell differentiation following PD-1 blockade in hepatocellular carcinoma. Nat Med 29, 1389–1399 (2023). https://doi.org/10.1038/s41591-023-02345-0

Sakamoto, Y., Miyake, S., Oka, M. et al. Phasing analysis of lung cancer genomes using a long read sequencer. Nat Commun 13, 3464 (2022). https://doi.org/10.1038/s41467-022-31133-6

Puig-Saus, C., Sennino, B., Peng, S. et al. Neoantigen-targeted CD8+ T cell responses with PD-1 blockade therapy. Nature 615, 697–704 (2023). https://doi.org/10.1038/s41586-023-05787-1

McLaughlin, R.T., Asthana, M., Di Meo, M. et al. Fast, accurate, and racially unbiased pan-cancer tumor-only variant calling with tabular machine learning. npj Precis. Onc. 7, 4 (2023). https://doi.org/10.1038/s41698-022-00340-1

Walentynowicz et al., 2023, Cell Reports 42, 112235 March 28, 2023 ª 2023 The Author(s). https://doi.org/10.1016/j.celrep.2023.112235

Frank et al., 2022, Cell Reports Medicine 3, 100815 November 15, 2022 ª 2022 The Author(s). https://doi.org/10.1016/j.xcrm.2022.100815

Tan et al., 2023, Cell Reports Medicine 4, 101335 December 19, 2023 ª 2023 The Author(s). https://doi.org/10.1016/j.xcrm.2023.101335

Expended List

Agrigenomics

You, J., Liu, Z., Qi, Z. et al. Regulatory controls of duplicated gene expression during fiber development in allotetraploid cotton. Nat Genet 55, 1987–1997 (2023). https://doi.org/10.1038/s41588-023-01530-8

Liu, F., Zhao, J., Sun, H. et al. Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation. Nat Commun 14, 5487 (2023). https://doi.org/10.1038/s41467-023-41251-4

Ding, YM., Pang, XX., Cao, Y. et al. Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes. Nat Commun 14, 617 (2023). https://doi.org/10.1038/s41467-023-36247-z

Ouyang, J., Zheng, S., Huang, M. et al. Chromosome-level genome and population genomics reveal evolutionary characteristics and conservation status of Chinese indigenous geese. Commun Biol 5, 1191 (2022). https://doi.org/10.1038/s42003-022-04125-x

Zhao, P., Gu, L., Gao, Y. et al. Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits. Commun Biol 6, 894 (2023). https://doi.org/10.1038/s42003-023-05234-x

Jia, Z., Gao, P., Yin, F. et al. Asymmetric gene expression in grain development of reciprocal crosses between tetraploid and hexaploid wheats. Commun Biol 5, 1412 (2022). https://doi.org/10.1038/s42003-022-04374-w

Liu, Y., Wang, S., Li, L. et al. The Cycas genome and the early evolution of seed plants. Nat. Plants 8, 389–401 (2022). https://doi.org/10.1038/s41477-022-01129-7

Erik D. Enbody et al. ,Community-wide genome sequencing reveals 30 years of Darwin’s finch evolution.Science381,eadf6218(2023).DOI:10.1126/science.adf6218

Carl-Johan Rubin et al. ,Rapid adaptive radiation of Darwin’s finches depends on ancestral genetic modules.Sci. Adv.8,eabm5982(2022).DOI:10.1126/sciadv.abm5982

Niu et al., 2022, Cell 185, 204–217 January 6, 2022 ª 2021 The Authors. Published by Elsevier Inc. https://doi.org/10.1016/j.cell.2021.12.006

Shao et al., 2023, Cell 186, 1279–1294 March 16, 2023 ª 2023 The Author(s). Published by Elsevier Inc. https://doi.org/10.1016/j.cell.2023.02.005

Expended List

Population Sequencing

Zhao, Q., Wang, F., Chen, YX. et al. Comprehensive profiling of 1015 patients’ exomes reveals genomic-clinical associations in colorectal cancer. Nat Commun 13, 2342 (2022). https://doi.org/10.1038/s41467-022-30062-8

Erwin, G.S., Gürsoy, G., Al-Abri, R. et al. Recurrent repeat expansions in human cancer genomes. Nature 613, 96–102 (2023). https://doi.org/10.1038/s41586-022-05515-1

Cheng, S., Xu, Z., Bian, S. et al. The STROMICS genome study: deep whole-genome sequencing and analysis of 10K Chinese patients with ischemic stroke reveal complex genetic and phenotypic interplay. Cell Discov 9, 75 (2023). https://doi.org/10.1038/s41421-023-00582-8

Han, S., DiBlasi, E., Monson, E.T. et al. Whole-genome sequencing analysis of suicide deaths integrating brain-regulatory eQTLs data to identify risk loci and genes. Mol Psychiatry 28, 3909–3919 (2023). https://doi.org/10.1038/s41380-023-02282-x

Jaya Shankar, A., Jadhao, S., Hoy, W. et al. Pharmacogenomic analysis of a genetically distinct Indigenous population. Pharmacogenomics J 22, 100–108 (2022). https://doi.org/10.1038/s41397-021-00262-4

Nagasaki, M., Sekiya, Y., Asakura, A. et al. Design and implementation of a hybrid cloud system for large-scale human genomic research. Hum Genome Var 10, 6 (2023). https://doi.org/10.1038/s41439-023-00231-2

Chang, D., Hunkapiller, J., Bhangale, T. et al. A whole genome sequencing study of moderate to severe asthma identifies a lung function locus associated with asthma risk. Sci Rep 12, 5574 (2022). https://doi.org/10.1038/s41598-022-09447-8

Expended List

Multi-omics

Zhao, S., Chen, DP., Fu, T. et al. Single-cell morphological and topological atlas reveals the ecosystem diversity of human breast cancer. Nat Commun 14, 6796 (2023). https://doi.org/10.1038/s41467-023-42504-y

Zheng, Y., Liu, Y., Yang, J. et al. Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials. Nat Biotechnol (2023). https://doi.org/10.1038/s41587-023-01934-1

Liao, Z., Zhang, J., Sun, S. et al. Reprogramming mechanism dissection and trophoblast replacement application in monkey somatic cell nuclear transfer. Nat Commun 15, 5 (2024). https://doi.org/10.1038/s41467-023-43985-7

Hu, L.S., D’Angelo, F., Weiskittel, T.M. et al. Integrated molecular and multiparametric MRI mapping of high-grade glioma identifies regional biologic signatures. Nat Commun 14, 6066 (2023). https://doi.org/10.1038/s41467-023-41559-1

Zhang, F., Zhang, Q., Zhu, J. et al. Integrated proteogenomic characterization across major histological types of pituitary neuroendocrine tumors. Cell Res 32, 1047–1067 (2022). https://doi.org/10.1038/s41422-022-00736-5

Shi, X., Sun, Y., Shen, C. et al. Integrated proteogenomic characterization of medullary thyroid carcinoma. Cell Discov 8, 120 (2022). https://doi.org/10.1038/s41421-022-00479-y

Chen, Q., Liu, Y., Gao, Y. et al. A comprehensive genomic and transcriptomic dataset of triple-negative breast cancers. Sci Data 9, 587 (2022). https://doi.org/10.1038/s41597-022-01681-z

Baxi, E.G., Thompson, T., Li, J. et al. Answer ALS, a large-scale resource for sporadic and familial ALS combining clinical and multi-omics data from induced pluripotent cell lines. Nat Neurosci 25, 226–237 (2022). https://doi.org/10.1038/s41593-021-01006-0

Guan-Hua Su et al. ,Radiogenomic-based multiomic analysis reveals imaging intratumor heterogeneity phenotypes and therapeutic targets.Sci. Adv.9,eadf0837(2023).DOI:10.1126/sciadv.adf0837

Trost et al., 2022, Cell 185, 4409–4427 November 10, 2022 ª 2022 Elsevier Inc. https://doi.org/10.1016/j.cell.2022.10.009

Chowdhury et al., 2023, Cell 186, 3476–3498 August 3, 2023 ª 2023 The Authors. Published by Elsevier Inc. https://doi.org/10.1016/j.cell.2023.07.004

Liu et al., 2023, Cancer Cell 41, 181–195 January 9, 2023 ª 2022 Elsevier Inc. https://doi.org/10.1016/j.ccell.2022.12.004

Li et al., 2022, Cancer Cell 40, 1374–1391 November 14, 2022 ª 2022 The Author(s). Published by Elsevier Inc. https://doi.org/10.1016/j.ccell.2022.10.001

Rosenberg et al., 2023, Cell Reports 42, 112879 August 29, 2023 ª 2023 The Authors. https://doi.org/10.1016/j.celrep.2023.112879

Expended List

Gene Editing

Zhang, S., Song, L., Yuan, B. et al. TadA reprogramming to generate potent miniature base editors with high precision. Nat Commun 14, 413 (2023). https://doi.org/10.1038/s41467-023-36004-2

Kan, Sh., Huang, J.Y., Harb, J. et al. CRISPR-mediated generation and characterization of a Gaa homozygous c.1935C>A (p.D645E) Pompe disease knock-in mouse model recapitulating human infantile onset-Pompe disease. Sci Rep 12, 21576 (2022). https://doi.org/10.1038/s41598-022-25914-8

Huang, J.Y., Kan, SH., Sandfeld, E.K. et al. CRISPR-Cas9 generated Pompe knock-in murine model exhibits early-onset hypertrophic cardiomyopathy and skeletal muscle weakness. Sci Rep 10, 10321 (2020). https://doi.org/10.1038/s41598-020-65259-8

Expended List

Other Topics

Arslan, S., Garcia, F.J., Guo, M. et al. Sequencing by avidity enables high accuracy with low reagent consumption. Nat Biotechnol 42, 132–138 (2024). https://doi.org/10.1038/s41587-023-01750-7

Feng, X., Cheng, H., Portik, D. et al. Metagenome assembly of high-fidelity long reads with hifiasm-meta. Nat Methods 19, 671–674 (2022). https://doi.org/10.1038/s41592-022-01478-3

Wagner, J., Olson, N.D., Harris, L. et al. Curated variation benchmarks for challenging medically relevant autosomal genes. Nat Biotechnol 40, 672–680 (2022). https://doi.org/10.1038/s41587-021-01158-1

Cheng, H., Jarvis, E.D., Fedrigo, O. et al. Haplotype-resolved assembly of diploid genomes without parental data. Nat Biotechnol 40, 1332–1335 (2022). https://doi.org/10.1038/s41587-022-01261-x

Kokot, M., Gudyś, A., Li, H. et al. CoLoRd: compressing long reads. Nat Methods 19, 441–444 (2022). https://doi.org/10.1038/s41592-022-01432-3

Ogasawara, O. Building cloud computing environments for genome analysis in Japan. Hum Genome Var 9, 46 (2022). https://doi.org/10.1038/s41439-022-00223-8

Ren, Y., Kong, Y., Zhou, X. et al. FVC as an adaptive and accurate method for filtering variants from popular NGS analysis pipelines. Commun Biol 5, 975 (2022). https://doi.org/10.1038/s42003-022-03397-7

Martini, P., Sales, G., Diamante, L. et al. BrewerIX enables allelic expression analysis of imprinted and X-linked genes from bulk and single-cell transcriptomes. Commun Biol 5, 146 (2022). https://doi.org/10.1038/s42003-022-03087-4

Olson et al., 2022, Cell Genomics 2, 100129 May 11, 2022 ª 2022 The Author(s). https://doi.org/10.1016/j.xgen.2022.100129

Bolze et al., 2022, Cell Reports Medicine 3, 100564 March 15, 2022 ª 2022 The Author(s). https://doi.org/10.1016/j.xcrm.2022.100564

Expended List

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