References
Akalin, Altuna, Matthias Kormaksson, Sheng Li, Francine E Garrett-Bakelman, Maria E Figueroa, Ari Melnick, and Christopher E Mason. 2012. “methylKit: A Comprehensive r Package for the Analysis of Genome-Wide DNA Methylation Profiles.” Genome Biology 13 (10): R87. https://genomebiology.biomedcentral.com/articles/10.1186/gb-2012-13-10-r87.
“Alex’s Lemonade Training Modules.” 2022. https://github.com/AlexsLemonade/training-modules.
Alföldi, Jessica, and Kerstin Lindblad-Toh. 2013. “Comparative Genomics as a Tool to Understand Evolution and Disease.” Genome Research 23 (7): 1063–68. https://doi.org/10.1101/gr.157503.113.
AlJanahi, Aisha A., Mark Danielsen, and Cynthia E. Dunbar. 2018. “An Introduction to the Analysis of Single-Cell RNA-Sequencing Data.” Molecular Therapy - Methods & Clinical Development 10 (September): 189–96. https://doi.org/10.1016/j.omtm.2018.07.003.
Alonge, Michael, Ludivine Lebeigle, Melanie Kirsche, Katie Jenike, Shujun Ou, Sergey Aganezov, Xingang Wang, Zachary B. Lippman, Michael C. Schatz, and Sebastian Soyk. 2022. “Automated Assembly Scaffolding Using RagTag Elevates a New Tomato System for High-Throughput Genome Editing.” Genome Biology 23 (1): 258. https://doi.org/10.1186/s13059-022-02823-7.
ALSF, CCDL for. 2019. “Introduction to Microarray Data.” https://alexslemonade.github.io/refinebio-examples/02-microarray/00-intro-to-microarray.html.
Amezquita, Robert A., Aaron T. L. Lun, Etienne Becht, Vince J. Carey, Lindsay N. Carpp, Ludwig Geistlinger, Federico Marini, et al. 2020. “Orchestrating Single-Cell Analysis with Bioconductor.” Nature Methods 17 (2): 137–45. https://doi.org/10.1038/s41592-019-0654-x.
Andrews, Simon. n.d. “FastQC: A Quality Control Tool for High Throughput Sequence Data.” https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
Angerer, Philipp, Lukas Simon, Sophie Tritschler, F. Alexander Wolf, David Fischer, and Fabian J. Theis. 2017. “Single Cells Make Big Data: New Challenges and Opportunities in Transcriptomics.” Current Opinion in Systems Biology 4 (August): 85–91. https://doi.org/10.1016/j.coisb.2017.07.004.
Audano, Peter A., Arvis Sulovari, Tina A. Graves-Lindsay, Stuart Cantsilieris, Melanie Sorensen, AnneMarie E. Welch, Max L. Dougherty, et al. 2019. “Characterizing the Major Structural Variant Alleles of the Human Genome.” Cell 176 (3): 663–675.e19. https://doi.org/10.1016/j.cell.2018.12.019.
Baran-Gale, Jeanette, Tamir Chandra, and Kristina Kirschner. 2018. “Experimental Design for Single-Cell RNA Sequencing.” Briefings in Functional Genomics 17 (4): 233–39. https://doi.org/10.1093/bfgp/elx035.
Bentley, David R., Shankar Balasubramanian, Harold P. Swerdlow, Geoffrey P. Smith, John Milton, Clive G. Brown, Kevin P. Hall, et al. 2008. “Accurate Whole Human Genome Sequencing Using Reversible Terminator Chemistry.” Nature 456 (7218): 53–59. https://doi.org/10.1038/nature07517.
Bergholtz, Helga, Jodi M Carter, Alessandra Cesano, Maggie Chon U Cheang, Sarah E Church, Prajan Divakar, Christopher A Fuhrman, et al. 2021. “Best Practices for Spatial Profiling for Breast Cancer Research with the GeoMx Digital Spatial Profiler.” Cancers 13 (17): 4456.
Bewicke-Copley, Findlay, Emil Arjun Kumar, Giuseppe Palladino, Koorosh Korfi, and Jun Wang. 2019. “Applications and Analysis of Targeted Genomic Sequencing in Cancer Studies.” Computational and Structural Biotechnology Journal 17: 1348–59. https://doi.org/10.1016/j.csbj.2019.10.004.
Bolyen, Evan, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian C Abnet, Gabriel A Al-Ghalith, Harriet Alexander, et al. 2019. “Reproducible, Interactive, Scalable and Extensible Microbiome Data Science Using QIIME 2.” Nat. Biotechnol. 37 (8): 852–57.
Booth, Michael J, Tobias W B Ost, Dario Beraldi, Neil M Bell, Miguel R Branco, Wolf Reik, and Shankar Balasubramanian. 2013. “Oxidative Bisulfite Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine.” Nature Protocols 8 (10): 1841–51. https://doi.org/10.1038/nprot.2013.115.
Bray, Nicolas L, Harold Pimentel, Páll Melsted, and Lior Pachter. 2016. “Near-Optimal Probabilistic RNA-Seq Quantification.” Nature Biotechnology 34 (5): 525–27. https://www.nature.com/articles/nbt.3519.
Brüning, Ralf Schulze, Lukas Tombor, Marcel H. Schulz, Stefanie Dimmeler, and David John. 2021. “Comparative Analysis of Common Alignment Tools for Single Cell RNA Sequencing.” bioRxiv. https://doi.org/10.1101/2021.02.15.430948.
Byrska-Bishop, Marta, Uday S. Evani, Xuefang Zhao, Anna O. Basile, Haley J. Abel, Allison A. Regier, André Corvelo, et al. 2022. “High-Coverage Whole-Genome Sequencing of the Expanded 1000 Genomes Project Cohort Including 602 Trios.” Cell 185 (18): 3426–3440.e19. https://doi.org/10.1016/j.cell.2022.08.004.
Caporaso, J Gregory, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D Bushman, Elizabeth K Costello, Noah Fierer, et al. 2010. “QIIME Allows Analysis of High-Throughput Community Sequencing Data.” Nat. Methods 7 (5): 335–36.
Clark, Michael J, Rui Chen, Hugo Y K Lam, Konrad J Karczewski, Rong Chen, Ghia Euskirchen, Atul J Butte, and Michael Snyder. 2011. “Performance Comparison of Exome DNA Sequencing Technologies.” Nature Biotechnology 29 (10): 908–14. https://doi.org/10.1038/nbt.1975.
Conesa, Ana, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michał Wojciech Szcześniak, et al. 2016. “A Survey of Best Practices for RNA-Seq Data Analysis.” Genome Biology 17 (1). https://doi.org/10.1186/s13059-016-0881-8.
Core, Leighton J, Joshua J Waterfall, and John T Lis. 2008. “Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters.” Science 322 (5909): 1845–48.
De Pasquale, Elisa, and Sandrine Dudoit. 2019. “DoubletDecon: Deconvoluting Doublets from Single-Cell RNA-Sequencing Data.” Cell Reports 29 (6): 1718–1727. e8. https://www.sciencedirect.com/science/article/pii/S2211124719312860.
Dobin, Alexander, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, and Thomas R Gingeras. 2013. “STAR: Ultrafast Universal RNA-Seq Aligner.” Bioinformatics 29 (1): 15–21. https://academic.oup.com/bioinformatics/article/29/1/15/272537.
Dries, Ruben, Jiaji Chen, Natalie Del Rossi, Mohammed Muzamil Khan, Adriana Sistig, and Guo-Cheng Yuan. 2021. “Advances in Spatial Transcriptomic Data Analysis.” Genome Research 31 (10): 1706–18.
Eichler, Evan E. 2019. “Genetic Variation, Comparative Genomics, and the Diagnosis of Disease.” The New England Journal of Medicine 381 (1): 64–74. https://doi.org/10.1056/NEJMra1809315.
Ermini, Luca, and Patrick Driguez. 2024. “The Application of Long-Read Sequencing to Cancer.” Cancers 16 (77): 1275. https://doi.org/10.3390/cancers16071275.
Feng, Hui, and Karen N Conneely. 2016. “Differential Methylation Analysis for BS-Seq Data Under General Experimental Design.” Bioinformatics 32 (2): 289–91. https://pubmed.ncbi.nlm.nih.gov/26819470/.
Frost, Dr Amy. 2022. “Constitutional (Germline) Vs Somatic (Tumour) Variants.” NHS. https://www.genomicseducation.hee.nhs.uk/genotes/knowledge-hub/constitutional-germline-vs-somatic-tumour-variants/.
Gershman, Ariel, Quinn Hauck, Morag Dick, Jerrica M. Jamison, Michael Tassia, Xabier Agirrezabala, Saad Muhammad, et al. 2023. “Genomic Insights into Metabolic Flux in Hummingbirds.” Genome Research 33 (5): 703–14. https://doi.org/10.1101/gr.276779.122.
Gershman, Ariel, Michael E. G. Sauria, Xavi Guitart, Mitchell R. Vollger, Paul W. Hook, Savannah J. Hoyt, Miten Jain, et al. 2022. “Epigenetic Patterns in a Complete Human Genome.” Science 376 (6588): eabj5089. https://doi.org/10.1126/science.abj5089.
Ghavi-Helm, Yad, Aleksander Jankowski, Sascha Meiers, Rebecca R Viales, Jan O Korbel, and Eileen EM Furlong. 2019. “Highly Rearranged Chromosomes Reveal Uncoupling Between Genome Topology and Gene Expression.” Nature Genetics 51 (8): 1272–82.
Govindarajan, Rajeshwar, Jeyapradha Duraiyan, Karunakaran Kaliyappan, and Murugesan Palanisamy. 2012. “Microarray and Its Applications.” Journal of Pharmacy & Bioallied Sciences 4 (Suppl 2): S310–12. https://doi.org/10.4103/0975-7406.100283.
Guilliams, Martin, Johnny Bonnardel, Birthe Haest, Bart Vanderborght, Camille Wagner, Anneleen Remmerie, Anna Bujko, et al. 2022. “Spatial Proteogenomics Reveals Distinct and Evolutionarily Conserved Hepatic Macrophage Niches.” Cell 185 (2): 379–96.
Hadfield, James. 2016. https://bitesizebio.com/13542/what-everyone-should-know-about-rna-seq/.
Hafemeister, Christoph, and Rahul Satija. 2019. “Normalization and Variance Stabilization of Single-Cell RNA-Seq Data Using Regularized Negative Binomial Regression.” Genome Biology 20 (1): 296.
Hansen, Kasper D., Steven E. Brenner, and Sandrine Dudoit. 2010. “Biases in Illumina Transcriptome Sequencing Caused by Random Hexamer Priming.” Nucleic Acids Research 38 (12): e131. https://doi.org/10.1093/nar/gkq224.
He, Shanshan, Ruchir Bhatt, Carl Brown, Emily A Brown, Derek L Buhr, Kan Chantranuvatana, Patrick Danaher, et al. 2022. “High-Plex Imaging of RNA and Proteins at Subcellular Resolution in Fixed Tissue by Spatial Molecular Imaging.” Nature Biotechnology 40 (12): 1794–1806.
He, Xiaoyu, Shanyu Chen, Ruilin Li, Xinyin Han, Zhipeng He, Danyang Yuan, Shuying Zhang, Xiaohong Duan, and Beifang Niu. 2020. “Comprehensive Fundamental Somatic Variant Calling and Quality Management Strategies for Human Cancer Genomes.” Briefings in Bioinformatics 22 (3). https://doi.org/10.1093/bib/bbaa083.
Heinz, S, Christopher Benner, Nathanael Spann, Eric Bertolino, Yen Ching Lin, Petra Laslo, Jia Cheng, et al. 2010. “Simple Combinations of Lineage-Determining Transcription Factors Prime Cis-Regulatory Elements Required for Macrophage and b Cell Identities.” Molecular Cell 38 (4): 576–89. https://pubmed.ncbi.nlm.nih.gov/20513432/.
Hindorff, Lucia A., Praveen Sethupathy, Heather A. Junkins, Erin M. Ramos, Jayashri P. Mehta, Francis S. Collins, and Teri A. Manolio. 2009. “Potential Etiologic and Functional Implications of Genome-Wide Association Loci for Human Diseases and Traits.” Proceedings of the National Academy of Sciences 106 (23): 9362–67. https://doi.org/10.1073/pnas.0903103106.
Hu, Jian, Xiangjie Li, Kyle Coleman, Amelia Schroeder, Nan Ma, David J Irwin, Edward B Lee, Russell T Shinohara, and Mingyao Li. 2021. “SpaGCN: Integrating Gene Expression, Spatial Location and Histology to Identify Spatial Domains and Spatially Variable Genes by Graph Convolutional Network.” Nature Methods 18 (11): 1342–51.
Hunter, Miranda V, Reuben Moncada, Joshua M Weiss, Itai Yanai, and Richard M White. 2021. “Spatially Resolved Transcriptomics Reveals the Architecture of the Tumor-Microenvironment Interface.” Nature Communications 12 (1): 6278.
Hwang, Kyu-Baek, In-Hee Lee, Honglan Li, Dhong-Geon Won, Carles Hernandez-Ferrer, Jose Alberto Negron, and Sek Won Kong. 2019. “Comparative Analysis of Whole-Genome Sequencing Pipelines to Minimize False Negative Findings.” Scientific Reports 9 (1). https://doi.org/10.1038/s41598-019-39108-2.
Kaya-Okur, Hicran S, Suzanna J Wu, Catherine A Codomo, Emily S Pledger, Timothy D Bryson, and Jorja G Henikoff. 2019. “CUT&tag for Efficient Epigenomic Profiling of Small Samples and Single Cells.” Nature Communications 10 (1): 1930.
Kellis, Manolis, Barbara Wold, Michael P. Snyder, Bradley E. Bernstein, Anshul Kundaje, Georgi K. Marinov, Lucas D. Ward, et al. 2014. “Defining Functional DNA Elements in the Human Genome.” Proceedings of the National Academy of Sciences 111 (17): 6131–38. https://doi.org/10.1073/pnas.1318948111.
Kim, Daehwan, Ben Langmead, and Steven L Salzberg. 2015. “HISAT: A Fast Spliced Aligner with Low Memory Requirements.” Nature Methods 12 (4): 357–60. https://www.nature.com/articles/nmeth.3317.
Kochmanski, Joseph, Candace Savonen, and Alison I. Bernstein. 2019 10. https://doi.org/10.3389/fgene.2019.00801.
Krueger, Felix, and Simon R Andrews. n.d. “Trim Galore!: A Wrapper Tool Around Cutadapt and FastQC to Consistently Apply Quality and Adapter Trimming to FastQ Files.” https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/.
Lafzi, Atefeh, Catia Moutinho, Simone Picelli, and Holger Heyn. 2018. “Tutorial: Guidelines for the Experimental Design of Single-Cell RNA Sequencing Studies.” Nature Protocols 13 (12): 2742–57. https://doi.org/10.1038/s41596-018-0073-y.
Langmead, Ben, and Steven L Salzberg. 2012. “Fast Gapped-Read Alignment with Bowtie 2.” Nature Methods 9 (4): 357–59. https://www.nature.com/articles/nmeth.1923.
Li, Heng, and Richard Durbin. 2024. “Genome Assembly in the Telomere-to-Telomere Era.” Nature Reviews Genetics, April, 1–13. https://doi.org/10.1038/s41576-024-00718-w.
Liu, Yi, Kimberly D Siegmund, Peter W Laird, and Benjamin P Berman. 2019. “Bismark: A Flexible Aligner and Methylation Caller for Bisulfite-Seq Applications.” Bioinformatics 36 (22-23): 5280–82. https://academic.oup.com/bioinformatics/article/27/11/1571/216956.
Longo, Sophia K, Margaret G Guo, Andrew L Ji, and Paul A Khavari. 2021. “Integrating Single-Cell and Spatial Transcriptomics to Elucidate Intercellular Tissue Dynamics.” Nature Reviews Genetics 22 (10): 627–44.
Love, Michael I., John B. Hogenesch, and Rafael A. Irizarry. 2016. “Modeling of RNA-Seq Fragment Sequence Bias Reduces Systematic Errors in Transcript Abundance Estimation.” Nature Biotechnology 34 (12): 1287–91. https://doi.org/10.1038/nbt.3682.
Love, Mike. 2016. “RNA-Seq Fragment Sequence Bias.” Mike Love’s Blog. https://mikelove.wordpress.com/2016/09/26/rna-seq-fragment-sequence-bias/.
Luecken, Malte D, and Fabian J Theis. 2019. “Current Best Practices in Single‐cell RNA‐seq Analysis: A Tutorial.” Molecular Systems Biology 15 (6). https://doi.org/10.15252/msb.20188746.
Lyubetskaya, Anna, Brian Rabe, Andrew Fisher, Anne Lewin, Isaac Neuhaus, Constance Brett, Todd Brett, et al. 2022. “Assessment of Spatial Transcriptomics for Oncology Discovery.” Cell Reports Methods 2 (11).
Mantione, K. J., R. M. Kream, H. Kuzelova, R. Ptacek, J. Raboch, J. M. Samuel, and G. B. Stefano. 2014. “Comparing Bioinformatic Gene Expression Profiling Methods: Microarray and RNA-Seq.” Medical Science Monitor Basic Research 20 (August): 138–42. https://doi.org/10.12659/MSMBR.892101.
McGinnis, Christopher S, Lillian M Murrow, and Zev J Gartner. 2020. “DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors.” Cell Systems 8 (4): 329–337. e4. https://pubmed.ncbi.nlm.nih.gov/30954475/.
Miller, Jeremiah, Aleksey V Zimin, and Andrew Gordus. 2023. “Chromosome-Level Genome and the Identification of Sex Chromosomes in Uloborus Diversus.” GigaScience 12 (January): giad002. https://doi.org/10.1093/gigascience/giad002.
Naj, Adam C., Honghuang Lin, Badri N. Vardarajan, Simon White, Daniel Lancour, Yiyi Ma, Michael Schmidt, et al. 2019. “Quality Control and Integration of Genotypes from Two Calling Pipelines for Whole Genome Sequence Data in the Alzheimers Disease Sequencing Project.” Genomics 111 (4): 808–18. https://doi.org/10.1016/j.ygeno.2018.05.004.
NHGRI. 2022. “Genomic Data Science.” https://www.genome.gov/about-genomics/fact-sheets/Genomic-Data-Science.
———. 2024. “Genome.” https://www.genome.gov/genetics-glossary/Genome.
Nurk, Sergey, Sergey Koren, Arang Rhie, Mikko Rautiainen, Andrey V. Bzikadze, Alla Mikheenko, Mitchell R. Vollger, et al. 2022. “The Complete Sequence of a Human Genome.” Science 376 (6588): 44–53. https://doi.org/10.1126/science.abj6987.
Ospina, Oscar, Alex Soupir, and Brooke L Fridley. 2023. “A Primer on Preprocessing, Visualization, Clustering, and Phenotyping of Barcode-Based Spatial Transcriptomics Data.” In Statistical Genomics, 115–40. Springer.
Park, Daeun, and Kyoung-Jae Won. 2018. “Gene Expression Profiling by GRO-Seq in Single Cells.” Methods in Molecular Biology (Clifton, N.J.) 1722: 1–15.
Patro, Rob, Geet Duggal, Michael I Love, Rafael A Irizarry, and Carl Kingsford. 2017. “Salmon Provides Fast and Bias-Aware Quantification of Transcript Expression.” Nature Methods 14 (4): 417–19. https://pubmed.ncbi.nlm.nih.gov/28263959/.
Pearson, William R. 2013. “An Introduction to Sequence Similarity (‘Homology’) Searching.” Current Protocols in Bioinformatics 42 (1). https://doi.org/10.1002/0471250953.bi0301s42.
Pepke, Shirley, Barbara Wold, and Ali Mortazavi. 2009. “Computation for ChIP-Seq and RNA-Seq Studies.” Nature Methods 6 (11 0): S22–32. https://doi.org/10.1038/nmeth.1371.
Qiu, Xiaojie, Qi Mao, Ying Tang, Li Wang, Raghav Chawla, Hannah A. Pliner, and Cole Trapnell. 2017. “Reversed Graph Embedding Resolves Complex Single-Cell Trajectories.” Nature Methods 14 (10): 979–82. https://doi.org/10.1038/nmeth.4402.
Ramı́rez, Fidel, Devon P Ryan, Bjørn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S Richter, Steffen Heyne, et al. 2016. “deepTools2: A Next Generation Web Server for Deep-Sequencing Data Analysis.” Nucleic Acids Research 44 (W1): W160–65.
Rao, Anjali, Dalia Barkley, Gustavo S França, and Itai Yanai. 2021. “Exploring Tissue Architecture Using Spatial Transcriptomics.” Nature 596 (7871): 211–20.
Raredon, Micha Sam Brickman, Junchen Yang, Neeharika Kothapalli, Wesley Lewis, Naftali Kaminski, Laura E Niklason, and Yuval Kluger. 2023. “Comprehensive Visualization of Cell–Cell Interactions in Single-Cell and Spatial Transcriptomics with NICHES.” Bioinformatics 39 (1): btac775.
Ravi, Vidhya M, Paulina Will, Jan Kueckelhaus, Na Sun, Kevin Joseph, Henrike Salié, Lea Vollmer, et al. 2022. “Spatially Resolved Multi-Omics Deciphers Bidirectional Tumor-Host Interdependence in Glioblastoma.” Cancer Cell 40 (6): 639–55.
Rhie, Arang, Sergey Nurk, Monika Cechova, Savannah J. Hoyt, Dylan J. Taylor, Nicolas Altemose, Paul W. Hook, et al. 2023. “The Complete Sequence of a Human y Chromosome.” Nature 621 (7978): 344–54. https://doi.org/10.1038/s41586-023-06457-y.
Schatz, Michael C., Arthur L. Delcher, and Steven L. Salzberg. 2010. “Assembly of Large Genomes Using Second-Generation Sequencing.” Genome Research 20 (9): 1165–73. https://doi.org/10.1101/gr.101360.109.
Schep, Alicia N, Bin Wu, Jason D Buenrostro, and William J Greenleaf. 2017. “chromVAR: Inferring Transcription-Factor-Associated Accessibility from Single-Cell Epigenomic Data.” Nature Methods 14 (10): 975–78. https://www.nature.com/articles/nmeth.4401.
Setty, Manu, Vaidotas Kiseliovas, Jacob Levine, Adam Gayoso, Linas Mazutis, and Dana Pe’er. 2019. “Characterization of Cell Fate Probabilities in Single-Cell Data with Palantir.” Nature Biotechnology 37 (4): 451–60. https://doi.org/10.1038/s41587-019-0068-4.
Sims, David, Ian Sudbery, Nicholas E. Ilott, Andreas Heger, and Chris P. Ponting. 2014. “Sequencing Depth and Coverage: Key Considerations in Genomic Analyses.” Nature Reviews Genetics 15 (2): 121–32. https://doi.org/10.1038/nrg3642.
Sistrom, Mark, Benjamin Evans, Joshua Benoit, Oliver Balmer, Serap Aksoy, and Adalgisa Caccone. 2016. “De Novo Genome Assembly Shows Genome Wide Similarity Between Trypanosoma Brucei Brucei and Trypanosoma Brucei Rhodesiense.” PLOS ONE 11 (2): e0147660. https://doi.org/10.1371/journal.pone.0147660.
Skene, Peter J, and Steven Henikoff. 2017. “An Efficient Targeted Nuclease Strategy for High-Resolution Mapping of DNA Binding Sites.” eLife 6: e21856.
———. 2018. “Targeted DamID (TaDa): A Toolbox for Selective Genome-Wide Profiling of DNA- and Chromatin-Binding Proteins.” Current Protocols in Molecular Biology 122 (1): e82.
Slonim, Donna K., and Itai Yanai. 2009. “Getting Started in Gene Expression Microarray Analysis.” PLOS Computational Biology 5 (10): e1000543. https://doi.org/10.1371/journal.pcbi.1000543.
Smith, Tom. 2015. “Unique Molecular Identifiers – the Problem, the Solution and the Proof.” CGAT. https://cgatoxford.wordpress.com/2015/08/14/unique-molecular-identifiers-the-problem-the-solution-and-the-proof/.
Ståhl, Patrik L, Fredrik Salmén, Sanja Vickovic, Anna Lundmark, José Fernández Navarro, Jens Magnusson, Stefania Giacomello, et al. 2016. “Visualization and Analysis of Gene Expression in Tissue Sections by Spatial Transcriptomics.” Science 353 (6294): 78–82.
Starmer, Josh. 2017. https://www.youtube.com/watch?v=tlf6wYJrwKY.
Tan, Xiao, Andrew Su, Minh Tran, and Quan Nguyen. 2020. “SpaCell: Integrating Tissue Morphology and Spatial Gene Expression to Predict Disease Cells.” Bioinformatics 36 (7): 2293–94.
Tarca, A. L., R. Romero, and S. Draghici. 2006. “Analysis of Microarray Experiments of Gene Expression Profiling.” American Journal of Obstetrics and Gynecology 195 (2): 373–88. https://doi.org/10.1016/j.ajog.2006.07.001.
Taylor, Dylan J., Jordan M. Eizenga, Qiuhui Li, Arun Das, Katharine M. Jenike, Eimear E. Kenny, Karen H. Miga, et al. 2024. “Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References.” Annual Review of Genomics and Human Genetics, April. https://doi.org/10.1146/annurev-genom-021623-081639.
Taylor, James, Svitlana Tyekucheva, David C. King, Ross C. Hardison, Webb Miller, and Francesca Chiaromonte. 2006. “ESPERR: Learning Strong and Weak Signals in Genomic Sequence Alignments to Identify Functional Elements.” Genome Research 16 (12): 1596–1604. https://doi.org/10.1101/gr.4537706.
Tignat-Perrier, Romie, Nathalie Técher, Timothy M Vogel, Catherine Larose, and Aurélien Dommergue. 2022. “Microorganisms Floating Through the Air.” Front. Young Minds 10 (March).
Wang, Nan, Xia Li, Rongshui Wang, and Zhiyong Ding. 2021. “Spatial Transcriptomics and Proteomics Technologies for Deconvoluting the Tumor Microenvironment.” Biotechnology Journal 16 (9): 2100041.
Wang, Xinyi, Axel A Almet, and Qing Nie. 2023. “The Promising Application of Cell-Cell Interaction Analysis in Cancer from Single-Cell and Spatial Transcriptomics.”
“What Is Genetic Diversity and Why Does It Matter?” n.d. Frontiers for Young Minds. https://kids.frontiersin.org/articles/10.3389/frym.2021.656168.
Williams, Cameron G, Hyun Jae Lee, Takahiro Asatsuma, Roser Vento-Tormo, and Ashraful Haque. 2022. “An Introduction to Spatial Transcriptomics for Biomedical Research.” Genome Medicine 14 (1): 1–18.
Wolf, F. Alexander, Fiona K. Hamey, Mireya Plass, Jordi Solana, Joakim S. Dahlin, Berthold Göttgens, Nikolaus Rajewsky, Lukas Simon, and Fabian J. Theis. 2019. “PAGA: Graph Abstraction Reconciles Clustering with Trajectory Inference Through a Topology Preserving Map of Single Cells.” Genome Biology 20 (1): 59. https://doi.org/10.1186/s13059-019-1663-x.
Wolock, Samuel L, Smita Krishnaswamy, and B Jesse Huang. 2019. “Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data.” Cell Systems 8 (4): 281–291. e9. https://pubmed.ncbi.nlm.nih.gov/30954476/.
Wong, Kit Man, Thomas J. Hudson, and John D. McPherson. 2011. “Unraveling the Genetics of Cancer: Genome Sequencing and Beyond.” Annual Review of Genomics and Human Genetics 12 (1): 407–30. https://doi.org/10.1146/annurev-genom-082509-141532.
Wu, Sunny Z, Ghamdan Al-Eryani, Daniel Lee Roden, Simon Junankar, Kate Harvey, Alma Andersson, Aatish Thennavan, et al. 2021. “A Single-Cell and Spatially Resolved Atlas of Human Breast Cancers.” Nature Genetics 53 (9): 1334–47.
Xiao, Chunlin, Zhong Chen, Wanqiu Chen, Cory Padilla, Michael Colgan, Wenjun Wu, Li-Tai Fang, et al. 2022. “Personalized Genome Assembly for Accurate Cancer Somatic Mutation Discovery Using Tumor-Normal Paired Reference Samples.” Genome Biology 23 (1): 237. https://doi.org/10.1186/s13059-022-02803-x.
Xu, Chang, Xiyun Jin, Songren Wei, Pingping Wang, Meng Luo, Zhaochun Xu, Wenyi Yang, et al. 2022. “DeepST: Identifying Spatial Domains in Spatial Transcriptomics by Deep Learning.” Nucleic Acids Research 50 (22): e131–31.
Yu, Miao, Gary C Hon, Keith E Szulwach, Chun-Xiao Song, Peng Jin, Bing Ren, and Chuan He. 2012. “Tet-Assisted Bisulfite Sequencing of 5-Hydroxymethylcytosine.” Nature Protocols 7 (12): 2159–70. https://doi.org/10.1038/nprot.2012.137.
Yue, Liangchen, Feng Liu, Jiongsong Hu, Pin Yang, Yuxiang Wang, Junguo Dong, Wenjie Shu, Xingxu Huang, and Shengqi Wang. 2023. “A Guidebook of Spatial Transcriptomic Technologies, Data Resources and Analysis Approaches.” Computational and Structural Biotechnology Journal.
Zhang, Cheng-Zhong, and David Pellman. 2022. “Cancer Genomic Rearrangements and Copy Number Alterations from Errors in Cell Division.” Annual Review of Cancer Biology 6 (1): 245–68. https://doi.org/10.1146/annurev-cancerbio-070620-094029.
Zhang, Linlin, Dongsheng Chen, Dongli Song, Xiaoxia Liu, Yanan Zhang, Xun Xu, and Xiangdong Wang. 2022. “Clinical and Translational Values of Spatial Transcriptomics.” Signal Transduction and Targeted Therapy 7 (1): 111.
Zhang, Meng, Stephen W Eichhorn, Brian Zingg, Zizhen Yao, Kaelan Cotter, Hongkui Zeng, Hongwei Dong, and Xiaowei Zhuang. 2021. “Spatially Resolved Cell Atlas of the Mouse Primary Motor Cortex by MERFISH.” Nature 598 (7879): 137–43.
Zhang, Wenqian, Ying Yu, Falk Hertwig, Jean Thierry-Mieg, Wenwei Zhang, Danielle Thierry-Mieg, Jian Wang, et al. 2015. “Comparison of RNA-Seq and Microarray-Based Models for Clinical Endpoint Prediction.” Genome Biology 16 (1). https://doi.org/10.1186/s13059-015-0694-1.
Zhang, Xiannian, Tianqi Li, Feng Liu, Yaqi Chen, Jiacheng Yao, Zeyao Li, Yanyi Huang, and Jianbin Wang. 2019. “Comparative Analysis of Droplet-Based Ultra-High-Throughput Single-Cell RNA-Seq Systems.” Molecular Cell 73 (1): 130–142.e5. https://doi.org/10.1016/j.molcel.2018.10.020.
Zhang, Yong, Tao Liu, Clifford A Meyer, Jie Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, et al. 2008. “Model-Based Analysis of ChIP-Seq (MACS).” Genome Biology 9 (9): R137. https://genomebiology.biomedcentral.com/articles/10.1186/gb-2008-9-9-r137.
Zhao, Peiyao, Jiaqiang Zhu, Ying Ma, and Xiang Zhou. 2022. “Modeling Zero Inflation Is Not Necessary for Spatial Transcriptomics.” Genome Biology 23 (1): 118.
Zheng, Grace XY, Jessica M Terry, Phillip Belgrader, Paul Ryvkin, Zachary W Bent, Ryan Wilson, Solongo B Ziraldo, et al. 2017. “Massively Parallel Digital Transcriptional Profiling of Single Cells.” Nature Communications 8 (1): 1–12. https://www.nature.com/articles/ncomms14049.
Ziegenhain, Christoph, Beate Vieth, Swati Parekh, Björn Reinius, Amy Guillaumet-Adkins, Martha Smets, Heinrich Leonhardt, Holger Heyn, Ines Hellmann, and Wolfgang Enard. 2017. “Comparative Analysis of Single-Cell RNA Sequencing Methods.” Molecular Cell 65 (4): 631–643.e4. https://doi.org/10.1016/j.molcel.2017.01.023.
Ziemann, Mark, Yotam Eren, and Assam El-Osta. 2016. “Gene Name Errors Are Widespread in the Scientific Literature.” Genome Biology 17 (1). https://doi.org/10.1186/s13059-016-1044-7.