References

Abdelaal, Tamim, Lieke Michielsen, Davy Cats, Dylan Hoogduin, Hailiang Mei, Marcel JT Reinders, and Ahmed Mahfouz. 2019. “A Comparison of Automatic Cell Identification Methods for Single-Cell RNA Sequencing Data.” Genome Biology 20 (1): 1–19.
Adams, Levi, Min Kyung Song, Yoshiaki Tanaka, and Yoon-Seong Kim. 2022. “Single-Nuclei Paired Multiomic Analysis of Young, Aged, and Parkinson’s Disease Human Midbrain Reveals Age-and Disease-Associated Glial Changes and Their Contribution to Parkinson’s Disease.” MedRxiv, 2022–01.
Ahlmann-Eltze, Constantin, and Wolfgang Huber. 2023. “Comparison of Transformations for Single-Cell RNA-Seq Data.” Nature Methods, 1–8.
Aibar, Sara, Carmen Bravo González-Blas, Thomas Moerman, Vân Anh Huynh-Thu, Hana Imrichova, Gert Hulselmans, Florian Rambow, et al. 2017. “SCENIC: Single-Cell Regulatory Network Inference and Clustering.” Nature Methods 14 (11): 1083–86.
Almeida, Nathalia, Matthew WH Chung, Elena M Drudi, Elise N Engquist, Eva Hamrud, Abigail Isaacson, Victoria SK Tsang, Fiona M Watt, and Francesca M Spagnoli. 2021. “Employing Core Regulatory Circuits to Define Cell Identity.” The EMBO Journal 40 (10): e106785.
Almet, Axel A, Zixuan Cang, Suoqin Jin, and Qing Nie. 2021. “The Landscape of Cell–Cell Communication Through Single-Cell Transcriptomics.” Current Opinion in Systems Biology 26: 12–23.
Alquicira-Hernandez, Jose, Anuja Sathe, Hanlee P Ji, Quan Nguyen, and Joseph E Powell. 2019. “scPred: Accurate Supervised Method for Cell-Type Classification from Single-Cell RNA-Seq Data.” Genome Biology 20: 1–17.
Ancheta, Sarah, Leah Dorman, Guillaume Le Treut, Abel Gurung, Loic Alain Royer, Alejandro Granados, and Merlin Lange. 2024. “Challenges and Progress in RNA Velocity: Comparative Analysis Across Multiple Biological Contexts.” bioRxiv, 2024–06.
Andreatta, Massimo, and Santiago J Carmona. 2021. “UCell: Robust and Scalable Single-Cell Gene Signature Scoring.” Computational and Structural Biotechnology Journal 19: 3796–98.
Arabi, Tarek Ziad, Aliyah Abdulmohsen Alabdulqader, Belal Nedal Sabbah, and Abderrahman Ouban. 2023. “Brain-Inhabiting Bacteria and Neurodegenerative Diseases: The ‘Brain Microbiome’ Theory.” Frontiers in Aging Neuroscience 15: 1240945.
Argelaguet, Ricard, Anna SE Cuomo, Oliver Stegle, and John C Marioni. 2021. “Computational Principles and Challenges in Single-Cell Data Integration.” Nature Biotechnology 39 (10): 1202–15.
Armingol, Erick, Adam Officer, Olivier Harismendy, and Nathan E Lewis. 2021. “Deciphering Cell–Cell Interactions and Communication from Gene Expression.” Nature Reviews Genetics 22 (2): 71–88.
Arora, Ankita, Raeann Goering, Hei Yong G Lo, Joelle Lo, Charlie Moffatt, and J Matthew Taliaferro. 2022. “The Role of Alternative Polyadenylation in the Regulation of Subcellular RNA Localization.” Frontiers in Genetics 12: 818668.
Arora, Sanjeev, Wei Hu, and Pravesh K Kothari. 2018. “An Analysis of the t-Sne Algorithm for Data Visualization.” In Conference on Learning Theory, 1455–62. PMLR.
Ashouri, Arghavan, Chufan Zhang, and Federico Gaiti. 2023. “Decoding Cancer Evolution: Integrating Genetic and Non-Genetic Insights.” Genes 14 (10): 1856.
Ashuach, Tal, Mariano I Gabitto, Rohan V Koodli, Giuseppe-Antonio Saldi, Michael I Jordan, and Nir Yosef. 2023. “MultiVI: Deep Generative Model for the Integration of Multimodal Data.” Nature Methods, 1–10.
Ashuach, Tal, Daniel A Reidenbach, Adam Gayoso, and Nir Yosef. 2022. “PeakVI: A Deep Generative Model for Single-Cell Chromatin Accessibility Analysis.” Cell Reports Methods 2 (3).
Avsec, Žiga, Vikram Agarwal, Daniel Visentin, Joseph R Ledsam, Agnieszka Grabska-Barwinska, Kyle R Taylor, Yannis Assael, John Jumper, Pushmeet Kohli, and David R Kelley. 2021. “Effective Gene Expression Prediction from Sequence by Integrating Long-Range Interactions.” Nature Methods 18 (10): 1196–1203.
Badia-i-Mompel, Pau, Lorna Wessels, Sophia Müller-Dott, Rémi Trimbour, Ricardo O Ramirez Flores, Ricard Argelaguet, and Julio Saez-Rodriguez. 2023. “Gene Regulatory Network Inference in the Era of Single-Cell Multi-Omics.” Nature Reviews Genetics 24 (11): 739–54.
Bae, Taejeong, Liana Fasching, Yifan Wang, Joo Heon Shin, Milovan Suvakov, Yeongjun Jang, Scott Norton, et al. 2022. “Analysis of Somatic Mutations in 131 Human Brains Reveals Aging-Associated Hypermutability.” Science 377 (6605): 511–17.
Ballouz, Sara, Alexander Dobin, and Jesse A Gillis. 2019. “Is It Time to Change the Reference Genome?” Genome Biology 20 (1): 1–9.
Baran, Yael, Akhiad Bercovich, Arnau Sebe-Pedros, Yaniv Lubling, Amir Giladi, Elad Chomsky, Zohar Meir, Michael Hoichman, Aviezer Lifshitz, and Amos Tanay. 2019. “MetaCell: Analysis of Single-Cell RNA-Seq Data Using k-Nn Graph Partitions.” Genome Biology 20 (1): 1–19.
Barry, Ciarrah, Junxi Liu, Rebecca Richmond, Martin K Rutter, Deborah A Lawlor, Frank Dudbridge, and Jack Bowden. 2021. “Exploiting Collider Bias to Apply Two-Sample Summary Data Mendelian Randomization Methods to One-Sample Individual Level Data.” PLoS Genetics 17 (8): e1009703.
Barry, Timothy, Kathryn Roeder, and Eugene Katsevich. 2024. “Exponential Family Measurement Error Models for Single-Cell CRISPR Screens.” Biostatistics 25 (4): 1254–72.
Barry, Timothy, Xuran Wang, John A Morris, Kathryn Roeder, and Eugene Katsevich. 2021. SCEPTRE Improves Calibration and Sensitivity in Single-Cell CRISPR Screen Analysis.” Genome Biology 22 (1): 1–19.
Becht, Etienne, Leland McInnes, John Healy, Charles-Antoine Dutertre, Immanuel WH Kwok, Lai Guan Ng, Florent Ginhoux, and Evan W Newell. 2019. “Dimensionality Reduction for Visualizing Single-Cell Data Using UMAP.” Nature Biotechnology 37 (1): 38.
Benjamini, Yoav, and Daniel Yekutieli. 2001. “The Control of the False Discovery Rate in Multiple Testing Under Dependency.” Annals of Statistics, 1165–88.
Benner, Christian, Chris CA Spencer, Aki S Havulinna, Veikko Salomaa, Samuli Ripatti, and Matti Pirinen. 2016. “FINEMAP: Efficient Variable Selection Using Summary Data from Genome-Wide Association Studies.” Bioinformatics 32 (10): 1493–1501.
Bilous, Mariia, Léonard Hérault, Aurélie AG Gabriel, Matei Teleman, and David Gfeller. 2024. “Building and Analyzing Metacells in Single-Cell Genomics Data.” Molecular Systems Biology, 1–23.
Blanco, Enrique, Mar González-Ramı́rez, Anna Alcaine-Colet, Sergi Aranda, and Luciano Di Croce. 2020. “The Bivalent Genome: Characterization, Structure, and Regulation.” Trends in Genetics 36 (2): 118–31.
Bock, Christoph, Paul Datlinger, Florence Chardon, Matthew A Coelho, Matthew B Dong, Keith A Lawson, Tian Lu, et al. 2022. “High-Content CRISPR Screening.” Nature Reviews Methods Primers 2 (1): 1–23.
Bouzid, Hind, Julia A Belk, Max Jan, Yanyan Qi, Chloé Sarnowski, Sara Wirth, Lisa Ma, et al. 2023. “Clonal Hematopoiesis Is Associated with Protection from Alzheimer’s Disease.” Nature Medicine 29 (7): 1662–70.
Boyeau, Pierre, Jeffrey Regier, Adam Gayoso, Michael I Jordan, Romain Lopez, and Nir Yosef. 2023. “An Empirical Bayes Method for Differential Expression Analysis of Single Cells with Deep Generative Models.” Proceedings of the National Academy of Sciences 120 (21): e2209124120.
Bravo González-Blas, Carmen, Seppe De Winter, Gert Hulselmans, Nikolai Hecker, Irina Matetovici, Valerie Christiaens, Suresh Poovathingal, Jasper Wouters, Sara Aibar, and Stein Aerts. 2023. SCENIC+: Single-Cell Multiomic Inference of Enhancers and Gene Regulatory Networks.” Nature Methods 20 (9): 1355–67.
Bruggeman-Everts, Fieke. 2008. “Using Mouse Models to Identify the Molecular Mechanisms Mediating Gene by Environment Interactions in Depressive Illness.” PhD thesis. https://www.researchgate.net/publication/233413663_Using_mouse_models_to_identify_the_molecular_mechanisms_mediating_gene_by_environment_interactions_in_depressive_illness.
Buccitelli, Christopher, and Matthias Selbach. 2020. “mRNAs, Proteins and the Emerging Principles of Gene Expression Control.” Nature Reviews Genetics 21 (10): 630–44.
Buenrostro, Jason D, Beijing Wu, Howard Y Chang, and William J Greenleaf. 2015. “ATAC-Seq: A Method for Assaying Chromatin Accessibility Genome-Wide.” Current Protocols in Molecular Biology 109 (1): 21–29.
Burgess, Stephen, and Simon G Thompson. 2017. “Interpreting Findings from Mendelian Randomization Using the MR-Egger Method.” European Journal of Epidemiology 32: 377–89.
Butler, Andrew, Paul Hoffman, Peter Smibert, Efthymia Papalexi, and Rahul Satija. 2018. “Integrating Single-Cell Transcriptomic Data Across Different Conditions, Technologies, and Species.” Nature Biotechnology 36 (5): 411–20.
Cai, T Tony, and Rong Ma. 2022. “Theoretical Foundations of t-Sne for Visualizing High-Dimensional Clustered Data.” Journal of Machine Learning Research 23 (301): 1–54.
Cang, Zixuan, Yanxiang Zhao, Axel A Almet, Adam Stabell, Raul Ramos, Maksim V Plikus, Scott X Atwood, and Qing Nie. 2023. “Screening Cell-Cell Communication in Spatial Transcriptomics via Collective Optimal Transport.” Nature Methods, 1–11.
Cannoodt, Robrecht, Wouter Saelens, Louise Deconinck, and Yvan Saeys. 2021. “Spearheading Future Omics Analyses Using Dyngen, a Multi-Modal Simulator of Single Cells.” Nature Communications 12 (1): 3942.
Cao, Kai, Yiguang Hong, and Lin Wan. 2022. “Manifold Alignment for Heterogeneous Single-Cell Multi-Omics Data Integration Using Pamona.” Bioinformatics 38 (1): 211–19.
Cao, Yingying, Simo Kitanovski, Ralf Küppers, and Daniel Hoffmann. 2021. “UMI or Not UMI, That Is the Question for scRNA-Seq Zero-Inflation.” Nature Biotechnology, 1–2.
Cao, Zhi-Jie, and Ge Gao. 2022. “Multi-Omics Single-Cell Data Integration and Regulatory Inference with Graph-Linked Embedding.” Nature Biotechnology 40 (10): 1458–66.
Carbonetto, Peter, Abhishek Sarkar, Zihao Wang, and Matthew Stephens. 2021. “Non-Negative Matrix Factorization Algorithms Greatly Improve Topic Model Fits.” arXiv Preprint arXiv:2105.13440.
Cha, Junha, and Insuk Lee. 2020. “Single-Cell Network Biology for Resolving Cellular Heterogeneity in Human Diseases.” Experimental & Molecular Medicine 52 (11): 1798–808.
Chan, Michelle M, Zachary D Smith, Stefanie Grosswendt, Helene Kretzmer, Thomas M Norman, Britt Adamson, Marco Jost, et al. 2019. “Molecular Recording of Mammalian Embryogenesis.” Nature 570 (7759): 77–82.
Chang, Lei, Yang Xie, Brett Taylor, Zhaoning Wang, Jiachen Sun, Ethan J Armand, Shreya Mishra, et al. 2024. “Droplet Hi-c Enables Scalable, Single-Cell Profiling of Chromatin Architecture in Heterogeneous Tissues.” Nature Biotechnology, 1–14.
Chari, Tara, and Lior Pachter. 2023. “The Specious Art of Single-Cell Genomics.” PLOS Computational Biology 19 (8): e1011288.
Chen, Huidong, Jayoung Ryu, Michael E Vinyard, Adam Lerer, and Luca Pinello. 2024. “SIMBA: Single-Cell Embedding Along with Features.” Nature Methods 21 (6): 1003–13.
Chen, J, and WA Weiss. 2015. “Alternative Splicing in Cancer: Implications for Biology and Therapy.” Oncogene 34 (1): 1–14.
Chen, Kok Hao, Alistair N Boettiger, Jeffrey R Moffitt, Siyuan Wang, and Xiaowei Zhuang. 2015. “Spatially Resolved, Highly Multiplexed RNA Profiling in Single Cells.” Science 348 (6233): aaa6090.
Chen, Shuxiao, Bokai Zhu, Sijia Huang, John W Hickey, Kevin Z Lin, Michael Snyder, William J Greenleaf, Garry P Nolan, Nancy R Zhang, and Zongming Ma. 2024. “Integration of Spatial and Single-Cell Data Across Modalities with Weakly Linked Features.” Nature Biotechnology 42 (7): 1096–106.
Chen, Wenan, Yan Li, John Easton, David Finkelstein, Gang Wu, and Xiang Chen. 2018. UMI-Count Modeling and Differential Expression Analysis for Single-Cell RNA Sequencing.” Genome Biology 19 (1): 70.
Chen, Xin, Li Tai Fang, Zhong Chen, Wanqiu Chen, Bin Zhu, Hongjin Wu, Malcom Moos Jr, et al. 2024. “A Benchmarking Study of Copy Number Variation Inference Methods Using Single-Cell RNA-Sequencing Data.” bioRxiv, 2024–09.
Cheng, Junyun, Gaole Lin, Tianhao Wang, Yunzhu Wang, Wenbo Guo, Jie Liao, Penghui Yang, et al. 2023. “Massively Parallel CRISPR-Based Genetic Perturbation Screening at Single-Cell Resolution.” Advanced Science 10 (4): 2204484.
Chintalaphani, Sanjog R, Sandy S Pineda, Ira W Deveson, and Kishore R Kumar. 2021. “An Update on the Neurological Short Tandem Repeat Expansion Disorders and the Emergence of Long-Read Sequencing Diagnostics.” Acta Neuropathologica Communications 9 (1): 98.
Claringbould, Annique, and Judith B Zaugg. 2021. “Enhancers in Disease: Molecular Basis and Emerging Treatment Strategies.” Trends in Molecular Medicine 27 (11): 1060–73.
Clifton, Kalen, Manjari Anant, Gohta Aihara, Lyla Atta, Osagie K Aimiuwu, Justus M Kebschull, Michael I Miller, Daniel Tward, and Jean Fan. 2023. “STalign: Alignment of Spatial Transcriptomics Data Using Diffeomorphic Metric Mapping.” Nature Communications 14 (1): 8123.
Cobos, Francisco Avila, Mohammad Javad Najaf Panah, Jessica Epps, Xiaochen Long, Tsz-Kwong Man, Hua-Sheng Chiu, Elad Chomsky, et al. 2023. “Effective Methods for Bulk RNA-Seq Deconvolution Using scnRNA-Seq Transcriptomes.” Genome Biology 24 (1): 177.
Concordet, Jean-Paul, and Maximilian Haeussler. 2018. “CRISPOR: Intuitive Guide Selection for CRISPR/Cas9 Genome Editing Experiments and Screens.” Nucleic Acids Research 46 (W1): W242–45.
Dal Molin, Alessandra, Giacomo Baruzzo, and Barbara Di Camillo. 2017. “Single-Cell RNA-Sequencing: Assessment of Differential Expression Analysis Methods.” Frontiers in Genetics 8: 62.
Das, Samarendra, Anil Rai, and Shesh N Rai. 2022. “Differential Expression Analysis of Single-Cell Rna-Seq Data: Current Statistical Approaches and Outstanding Challenges.” Entropy 24 (7): 995.
Datlinger, Paul, André F Rendeiro, Christian Schmidl, Thomas Krausgruber, Peter Traxler, Johanna Klughammer, Linda C Schuster, Amelie Kuchler, Donat Alpar, and Christoph Bock. 2017. “Pooled CRISPR Screening with Single-Cell Transcriptome Readout.” Nature Methods 14 (3): 297–301.
Demetci, Pinar, Rebecca Santorella, Björn Sandstede, William Stafford Noble, and Ritambhara Singh. 2022. “SCOT: Single-Cell Multi-Omics Alignment with Optimal Transport.” Journal of Computational Biology 29 (1): 3–18.
Denisenko, Elena, Belinda B Guo, Matthew Jones, Rui Hou, Leanne De Kock, Timo Lassmann, Daniel Poppe, et al. 2020. “Systematic Assessment of Tissue Dissociation and Storage Biases in Single-Cell and Single-Nucleus RNA-Seq Workflows.” Genome Biology 21 (1): 1–25.
Ding, Jiarui, Xian Adiconis, Sean K Simmons, Monika S Kowalczyk, Cynthia C Hession, Nemanja D Marjanovic, Travis K Hughes, et al. 2020. “Systematic Comparison of Single-Cell and Single-Nucleus RNA-Sequencing Methods.” Nature Biotechnology 38 (6): 737–46.
Dinh, Laurent, Jascha Sohl-Dickstein, and Samy Bengio. 2016. “Density Estimation Using Real Nvp.” arXiv Preprint arXiv:1605.08803.
Dixit, Atray, Oren Parnas, Biyu Li, Jenny Chen, Charles P Fulco, Livnat Jerby-Arnon, Nemanja D Marjanovic, et al. 2016. “Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.” Cell 167 (7): 1853–66.
Dong, Xiao, Lei Zhang, Xiaoxiao Hao, Tao Wang, and Jan Vijg. 2020. “SCCNV: A Software Tool for Identifying Copy Number Variation from Single-Cell Whole-Genome Sequencing.” Frontiers in Genetics 11: 505441.
Doss, Rose M, Susana Lopez-Ignacio, Anna Dischler, Laurel Hiatt, Harriet Dashnow, Martin W Breuss, and Caroline M Dias. 2025. “Mosaicism in Short Tandem Repeat Disorders: A Clinical Perspective.” Genes 16 (2): 216.
Duan, Honglin, Tao Cheng, and Hui Cheng. 2023. “Spatially Resolved Transcriptomics: Advances and Applications.” Blood Science 5 (1): 1–14.
Ea, Vuthy, Marie-Odile Baudement, Annick Lesne, and Thierry Forné. 2015. “Contribution of Topological Domains and Loop Formation to 3D Chromatin Organization.” Genes 6 (3): 734–50.
Edrisi, Mohammadamin, Xiru Huang, Huw A Ogilvie, and Luay Nakhleh. 2023. “Accurate Integration of Single-Cell DNA and RNA for Analyzing Intratumor Heterogeneity Using MaCroDNA.” Nature Communications 14 (1): 8262.
Efremova, Mirjana, Miquel Vento-Tormo, Sarah A Teichmann, and Roser Vento-Tormo. 2020. “CellPhoneDB: Inferring Cell–Cell Communication from Combined Expression of Multi-Subunit Ligand–Receptor Complexes.” Nature Protocols 15 (4): 1484–1506.
Efron, Bradley, and Robert Tibshirani. 2002. “Empirical Bayes Methods and False Discovery Rates for Microarrays.” Genetic Epidemiology 23 (1): 70–86.
Eisenstein, Michael. 2020. “The Secret Life of Cells.” Nature Methods 17: 7–10.
Elhaik, Eran. 2022. “Principal Component Analyses (PCA)-Based Findings in Population Genetic Studies Are Highly Biased and Must Be Reevaluated.” Scientific Reports 12 (1): 14683.
Ergen, Can, Galen Xing, Chenling Xu, Martin Kim, Michael Jayasuriya, Erin McGeever, Angela Oliveira Pisco, Aaron Streets, and Nir Yosef. 2024. “Consensus Prediction of Cell Type Labels in Single-Cell Data with popV.” Nature Genetics, 1–8.
Erickson, Andrew, Mengxiao He, Emelie Berglund, Maja Marklund, Reza Mirzazadeh, Niklas Schultz, Linda Kvastad, et al. 2022. “Spatially Resolved Clonal Copy Number Alterations in Benign and Malignant Tissue.” Nature 608 (7922): 360–67.
Esposito, Roberta, Núria Bosch, Andrés Lanzós, Taisia Polidori, Carlos Pulido-Quetglas, and Rory Johnson. 2019. “Hacking the Cancer Genome: Profiling Therapeutically Actionable Long Non-Coding RNAs Using CRISPR-Cas9 Screening.” Cancer Cell 35 (4): 545–57.
Fang, Weixiang, Claire M Bell, Abel Sapirstein, Soichiro Asami, Kathleen Leeper, Donald J Zack, Hongkai Ji, and Reza Kalhor. 2022. “Quantitative Fate Mapping: A General Framework for Analyzing Progenitor State Dynamics via Retrospective Lineage Barcoding.” Cell 185 (24): 4604–20.
Feng, Jean, William S DeWitt III, Aaron McKenna, Noah Simon, Amy D Willis, and Frederick A Matsen IV. 2021. “Estimation of Cell Lineage Trees by Maximum-Likelihood Phylogenetics.” The Annals of Applied Statistics 15 (1): 343–62.
Figiel, Sandy, Anthony Bates, David A Braun, Renu Eapen, Markus Eckstein, Brandon J Manley, Matthew I Milowsky, et al. 2024. “Clinical Implications of Basic Research: Exploring the Transformative Potential of Spatial’omics in Uro-Oncology.” European Urology.
Fleck, Jonas Simon, Sophie Martina Johanna Jansen, Damian Wollny, Fides Zenk, Makiko Seimiya, Akanksha Jain, Ryoko Okamoto, et al. 2023. “Inferring and Perturbing Cell Fate Regulomes in Human Brain Organoids.” Nature 621 (7978): 365–72.
Fornes, Oriol, Jaime A Castro-Mondragon, Aziz Khan, Robin Van der Lee, Xi Zhang, Phillip A Richmond, Bhavi P Modi, et al. 2020. “JASPAR 2020: Update of the Open-Access Database of Transcription Factor Binding Profiles.” Nucleic Acids Research 48 (D1): D87–92.
Fotsing, Stephanie Feupe, Jonathan Margoliash, Catherine Wang, Shubham Saini, Richard Yanicky, Sharona Shleizer-Burko, Alon Goren, and Melissa Gymrek. 2019. “The Impact of Short Tandem Repeat Variation on Gene Expression.” Nature Genetics 51 (11): 1652–59.
Fu, Aikun, Bingqing Yao, Tingting Dong, and Shang Cai. 2023. “Emerging Roles of Intratumor Microbiota in Cancer Metastasis.” Trends in Cell Biology 33 (7): 583–93.
Gabbutt, Calum, Ryan O. Schenck, Daniel J. Weisenberger, Christopher Kimberley, Alison Berner, Jacob Househam, Eszter Lakatos, et al. 2022. “Fluctuating Methylation Clocks for Cell Lineage Tracing at High Temporal Resolution in Human Tissues.” Nature Biotechnology 40 (5): 720–30.
Gao, Ruli, Shanshan Bai, Ying C Henderson, Yiyun Lin, Aislyn Schalck, Yun Yan, Tapsi Kumar, et al. 2021. “Delineating Copy Number and Clonal Substructure in Human Tumors from Single-Cell Transcriptomes.” Nature Biotechnology 39 (5): 599–608.
Garbulowski, Mateusz, Thomas Hillerton, Daniel Morgan, Deniz Seçilmiş, Lisbet Sonnhammer, Andreas Tjärnberg, Torbjörn EM Nordling, and Erik LL Sonnhammer. 2024. “GeneSPIDER2: Large Scale GRN Simulation and Benchmarking with Perturbed Single-Cell Data.” NAR Genomics and Bioinformatics 6 (3): lqae121.
Garg, Shilpa. 2021. “Computational Methods for Chromosome-Scale Haplotype Reconstruction.” Genome Biology 22 (1): 101.
Garrison, Erik, and Gabor Marth. 2012. “Haplotype-Based Variant Detection from Short-Read Sequencing.” arXiv Preprint arXiv:1207.3907.
Gasperini, Molly, Andrew J Hill, José L McFaline-Figueroa, Beth Martin, Seungsoo Kim, Melissa D Zhang, Dana Jackson, et al. 2019. “A Genome-Wide Framework for Mapping Gene Regulation via Cellular Genetic Screens.” Cell 176 (1): 377–90.
Gauba, Kavya, Shruti Gupta, Jyoti Shekhawat, Praveen Sharma, Dharmveer Yadav, and Mithu Banerjee. 2021. “Immunomodulation by Epigenome Alterations in Mycobacterium Tuberculosis Infection.” Tuberculosis 128: 102077.
Gawad, Charles, Winston Koh, and Stephen R Quake. 2016. “Single-Cell Genome Sequencing: Current State of the Science.” Nature Reviews Genetics 17 (3): 175–88.
Ge, Tian, Chia-Yen Chen, Yang Ni, Yen-Chen Anne Feng, and Jordan W Smoller. 2019. “Polygenic Prediction via Bayesian Regression and Continuous Shrinkage Priors.” Nature Communications 10 (1): 1776.
Ghojogh, Benyamin, Ali Ghodsi, Fakhri Karray, and Mark Crowley. 2021. “Factor Analysis, Probabilistic Principal Component Analysis, Variational Inference, and Variational Autoencoder: Tutorial and Survey.” arXiv Preprint arXiv:2101.00734.
Glancy, Eleanor, Natalie Choy, and Melanie A Eckersley-Maslin. 2024. “Bivalent Chromatin: A Developmental Balancing Act Tipped in Cancer.” Biochemical Society Transactions 52 (1): 217–29.
Gohil, Satyen H, J Bryan Iorgulescu, David A Braun, Derin B Keskin, and Kenneth J Livak. 2021. “Applying High-Dimensional Single-Cell Technologies to the Analysis of Cancer Immunotherapy.” Nature Reviews Clinical Oncology 18 (4): 244–56.
Golub, Todd R, Donna K Slonim, Pablo Tamayo, Christine Huard, Michelle Gaasenbeek, Jill P Mesirov, Hilary Coller, et al. 1999. “Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring.” Science 286 (5439): 531–37.
Gong, Boying, Yun Zhou, and Elizabeth Purdom. 2021. “Cobolt: Integrative Analysis of Multimodal Single-Cell Sequencing Data.” Genome Biology 22: 1–21.
Gordeeva, Veronika, Elena Sharova, Konstantin Babalyan, Rinat Sultanov, Vadim M Govorun, and Georgij Arapidi. 2021. “Benchmarking Germline CNV Calling Tools from Exome Sequencing Data.” Scientific Reports 11 (1): 14416.
Grishkevich, Vladislav, and Itai Yanai. 2014. “Gene Length and Expression Level Shape Genomic Novelties.” Genome Research 24 (9): 1497–1503.
Gulati, Gunsagar S, Shaheen S Sikandar, Daniel J Wesche, Anoop Manjunath, Anjan Bharadwaj, Mark J Berger, Francisco Ilagan, et al. 2020. “Single-Cell Transcriptional Diversity Is a Hallmark of Developmental Potential.” Science 367 (6476): 405–11.
Gupta, Chirag, Jielin Xu, Ting Jin, Saniya Khullar, Xiaoyu Liu, Sayali Alatkar, Feixiong Cheng, and Daifeng Wang. 2022. “Single-Cell Network Biology Characterizes Cell Type Gene Regulation for Drug Repurposing and Phenotype Prediction in Alzheimer’s Disease.” PLOS Computational Biology 18 (7): e1010287.
Habib, Naomi. 2007. Analysis of DNA Motifs Based on a Novel Motif Comparison Method. Hebrew University of Jerusalem.
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): 1–15.
Haghverdi, Laleh, Florian Buettner, and Fabian J Theis. 2015. “Diffusion Maps for High-Dimensional Single-Cell Analysis of Differentiation Data.” Bioinformatics 31 (18): 2989–98.
Haghverdi, Laleh, Aaron TL Lun, Michael D Morgan, and John C Marioni. 2018. “Batch Effects in Single-Cell RNA-Sequencing Data Are Corrected by Matching Mutual Nearest Neighbors.” Nature Biotechnology 36 (5): 421–27.
Hamma, Tomoko, and Adrian R Ferré-D’Amaré. 2006. “Pseudouridine Synthases.” Chemistry & Biology 13 (11): 1125–35.
Hannan, Anthony J. 2018. “Tandem Repeats Mediating Genetic Plasticity in Health and Disease.” Nature Reviews Genetics 19 (5): 286–98.
Hansson, Oskar, Kaj Blennow, Henrik Zetterberg, and Jeffrey Dage. 2023. “Blood Biomarkers for Alzheimer’s Disease in Clinical Practice and Trials.” Nature Aging 3 (5): 506–19.
Hao, Yuhan, Stephanie Hao, Erica Andersen-Nissen, William M Mauck, Shiwei Zheng, Andrew Butler, Maddie Jane Lee, et al. 2021. “Integrated Analysis of Multimodal Single-Cell Data.” Cell 184 (13): 3573–87.
Hård, Joanna, Jeff E Mold, Jesper Eisfeldt, Christian Tellgren-Roth, Susana Häggqvist, Ignas Bunikis, Orlando Contreras-Lopez, et al. 2023. “Long-Read Whole-Genome Analysis of Human Single Cells.” Nature Communications 14 (1): 5164.
Hartman, Austin, and Rahul Satija. 2024. “Comparative Analysis of Multiplexed in Situ Gene Expression Profiling Technologies.” bioRxiv, 2024–01.
Hartwig, Fernando Pires, Neil Martin Davies, Gibran Hemani, and George Davey Smith. 2016. “Two-Sample Mendelian Randomization: Avoiding the Downsides of a Powerful, Widely Applicable but Potentially Fallible Technique.” International Journal of Epidemiology. Oxford University Press.
He, Liang, Jose Davila-Velderrain, Tomokazu S Sumida, David A Hafler, Manolis Kellis, and Alexander M Kulminski. 2021. NEBULA Is a Fast Negative Binomial Mixed Model for Differential or Co-Expression Analysis of Large-Scale Multi-Subject Single-Cell Data.” Communications Biology 4 (1): 629.
He, Siyu, Yinuo Jin, Achille Nazaret, Lingting Shi, Xueer Chen, Sham Rampersaud, Bahawar S Dhillon, et al. 2024. “Starfysh Integrates Spatial Transcriptomic and Histologic Data to Reveal Heterogeneous Tumor–Immune Hubs.” Nature Biotechnology, 1–13.
He, Zihuai, Linxi Liu, Michael E Belloy, Yann Le Guen, Aaron Sossin, Xiaoxia Liu, Xinran Qi, et al. 2022. “GhostKnockoff Inference Empowers Identification of Putative Causal Variants in Genome-Wide Association Studies.” Nature Communications 13 (1): 7209.
Heinz, Sven, Christopher Benner, Nathanael Spann, Eric Bertolino, Yin C Lin, Peter Laslo, Jason X Cheng, Cornelis Murre, Harinder Singh, and Christopher K Glass. 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.
Hernández-Beeftink, Tamara, Beatriz Guillen-Guio, Jesús Villar, and Carlos Flores. 2019. “Genomics and the Acute Respiratory Distress Syndrome: Current and Future Directions.” International Journal of Molecular Sciences 20 (16): 4004.
Hernando-Herraez, Irene, Brendan Evano, Thomas Stubbs, Pierre-Henri Commere, Marc Jan Bonder, Stephen Clark, Simon Andrews, Shahragim Tajbakhsh, and Wolf Reik. 2019. “Ageing Affects DNA Methylation Drift and Transcriptional Cell-to-Cell Variability in Mouse Muscle Stem Cells.” Nature Communications 10 (1): 4361.
Heumos, Lukas, Anna C Schaar, Christopher Lance, Anastasia Litinetskaya, Felix Drost, Luke Zappia, Malte D Lücken, et al. 2023. “Best Practices for Single-Cell Analysis Across Modalities.” Nature Reviews Genetics 24 (8): 550–72.
Hormozdiari, Farhad, Emrah Kostem, Eun Yong Kang, Bogdan Pasaniuc, and Eleazar Eskin. 2014. “Identifying Causal Variants at Loci with Multiple Signals of Association.” In Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, 610–11.
Hou, Wenpin, Zhicheng Ji, Zeyu Chen, E John Wherry, Stephanie C Hicks, and Hongkai Ji. 2023. “A Statistical Framework for Differential Pseudotime Analysis with Multiple Single-Cell RNA-Seq Samples.” Nature Communications 14 (1): 7286.
Hou, Wenpin, Zhicheng Ji, Hongkai Ji, and Stephanie C Hicks. 2020. “A Systematic Evaluation of Single-Cell RNA-Sequencing Imputation Methods.” Genome Biology 21 (1): 1–30.
Hu, Zhirui, Pawel F Przytycki, and Katherine S Pollard. 2024. “CellWalker2: Multi-Omic Discovery of Hierarchical Cell Type Relationships and Their Associations with Genomic Annotations.” bioRxiv.
Huang, Haiyang, Yingfan Wang, Cynthia Rudin, and Edward P Browne. 2022. “Towards a Comprehensive Evaluation of Dimension Reduction Methods for Transcriptomic Data Visualization.” Communications Biology 5 (1): 719.
Ito, Shinsuke, Nando Dulal Das, Takashi Umehara, and Haruhiko Koseki. 2022. “Factors and Mechanisms That Influence Chromatin-Mediated Enhancer–Promoter Interactions and Transcriptional Regulation.” Cancers 14 (21): 5404.
Jaakkola, Maria K, Fatemeh Seyednasrollah, Arfa Mehmood, and Laura L Elo. 2017. “Comparison of Methods to Detect Differentially Expressed Genes Between Single-Cell Populations.” Briefings in Bioinformatics 18 (5): 735–43.
Jaiswal, Siddhartha, Pierre Fontanillas, Jason Flannick, Alisa Manning, Peter V Grauman, Brenton G Mar, R Coleman Lindsley, et al. 2014. “Age-Related Clonal Hematopoiesis Associated with Adverse Outcomes.” New England Journal of Medicine 371 (26): 2488–98.
Jiang, Ruochen, Tianyi Sun, Dongyuan Song, and Jingyi Jessica Li. 2022. “Statistics or Biology: The Zero-Inflation Controversy about scRNA-Seq Data.” Genome Biology 23 (1): 31.
Jiang, Yuchao, Nancy R Zhang, and Mingyao Li. 2017. “SCALE: Modeling Allele-Specific Gene Expression by Single-Cell RNA Sequencing.” Genome Biology 18: 1–15.
Jin, Suoqin, Christian F Guerrero-Juarez, Lihua Zhang, Ivan Chang, Raul Ramos, Chen-Hsiang Kuan, Peggy Myung, Maksim V Plikus, and Qing Nie. 2021. “Inference and Analysis of Cell-Cell Communication Using CellChat.” Nature Communications 12 (1): 1088.
Johnson, Eric M, William Kath, and Madhav Mani. 2022. EMBEDR: Distinguishing Signal from Noise in Single-Cell Omics Data.” Patterns 3 (3).
Jones, Matthew G, Alex Khodaverdian, Jeffrey J Quinn, Michelle M Chan, Jeffrey A Hussmann, Robert Wang, Chenling Xu, Jonathan S Weissman, and Nir Yosef. 2020. “Inference of Single-Cell Phylogenies from Lineage Tracing Data Using Cassiopeia.” Genome Biology 21 (1): 1–27.
Jones, Matthew G, Dian Yang, and Jonathan S Weissman. 2023. “New Tools for Lineage Tracing in Cancer in Vivo.”
Jumper, John, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, et al. 2021. “Highly Accurate Protein Structure Prediction with AlphaFold.” Nature 596 (7873): 583–89.
Junttila, Sini, Joahnnes Smolander, and Laura L Elo. 2022. “Benchmarking Methods for Detecting Differential States Between Conditions from Multi-Subject Single-Cell RNA-Seq Data.” Briefings in Bioinformatics 23 (5): bbac286.
Karamveer, and Yasin Uzun. 2024. “Approaches for Benchmarking Single-Cell Gene Regulatory Network Methods.” Bioinformatics and Biology Insights 18: 11779322241287120.
Kaufmann, Tom L, Marina Petkovic, Thomas BK Watkins, Emma C Colliver, Sofya Laskina, Nisha Thapa, Darlan C Minussi, et al. 2022. “MEDICC2: Whole-Genome Doubling Aware Copy-Number Phylogenies for Cancer Evolution.” Genome Biology 23 (1): 241.
Kennedy, Hannah L, Lisa Dinkler, Martin A Kennedy, Cynthia M Bulik, and Jennifer Jordan. 2022. “How Genetic Analysis May Contribute to the Understanding of Avoidant/Restrictive Food Intake Disorder (ARFID).” Journal of Eating Disorders 10 (1): 53.
Kent, JT, John Bibby, and KV Mardia. 1979. Multivariate Analysis. Academic Press Amsterdam.
Kepchia, Devin, Ling Huang, Richard Dargusch, Robert A Rissman, Maxim N Shokhirev, Wolfgang Fischer, and David Schubert. 2020. “Diverse Proteins Aggregate in Mild Cognitive Impairment and Alzheimer’s Disease Brain.” Alzheimer’s Research & Therapy 12: 1–20.
Khan, Faiza Shafique, Farhan Goher, Dapeng Zhang, Peng Shi, Zhiying Li, Yin Min Htwe, and Yong Wang. 2022. “Is CRISPR/Cas9 a Way Forward to Fast-Track Genetic Improvement in Commercial Palms? Prospects and Limits.” Frontiers in Plant Science 13: 1042828.
Kharchenko, Peter V, Lev Silberstein, and David T Scadden. 2014. “Bayesian Approach to Single-Cell Differential Expression Analysis.” Nature Methods 11 (7): 740.
Khatri, Robin, and Stefan Bonn. 2022. “Uncertainty Estimation for Single-Cell Label Transfer.” In Conformal and Probabilistic Prediction with Applications, 109–28. PMLR.
Kiessling, Paul, and Christoph Kuppe. 2024. “Spatial Multi-Omics: Novel Tools to Study the Complexity of Cardiovascular Diseases.” Genome Medicine 16 (1): 14.
Kim, Daniel, Andy Tran, Hani Jieun Kim, Yingxin Lin, Jean Yee Hwa Yang, and Pengyi Yang. 2023. “Gene Regulatory Network Reconstruction: Harnessing the Power of Single-Cell Multi-Omic Data.” NPJ Systems Biology and Applications 9 (1): 51.
Kim, Mirang, and Joseph Costello. 2017. DNA Methylation: An Epigenetic Mark of Cellular Memory.” Experimental & Molecular Medicine 49 (4): e322–22.
Kim, Tae Hyun, Xiang Zhou, and Mengjie Chen. 2020. “Demystifying ‘Drop-Outs’ in Single-Cell UMI Data.” Genome Biology 21 (1): 196.
Kim, Yoon-Seob, Jinyong Choi, and Sug Hyung Lee. 2023. “Single-Cell and Spatial Sequencing Application in Pathology.” Journal of Pathology and Translational Medicine 57 (1): 43–51.
Kobyzev, Ivan, Simon JD Prince, and Marcus A Brubaker. 2020. “Normalizing Flows: An Introduction and Review of Current Methods.” IEEE Transactions on Pattern Analysis and Machine Intelligence 43 (11): 3964–79.
Korsunsky, Ilya, Nghia Millard, Jean Fan, Kamil Slowikowski, Fan Zhang, Kevin Wei, Yuriy Baglaenko, Michael Brenner, Po-ru Loh, and Soumya Raychaudhuri. 2019. “Fast, Sensitive and Accurate Integration of Single-Cell Data with Harmony.” Nature Methods, 1–8.
Kosicki, Michael, Felicity Allen, Frances Steward, Kärt Tomberg, Yangyang Pan, and Allan Bradley. 2022. “Cas9-Induced Large Deletions and Small Indels Are Controlled in a Convergent Fashion.” Nature Communications 13 (1): 3422.
Kuhn, Maria, António J Santinha, and Randall J Platt. 2021. “Moving from in Vitro to in Vivo CRISPR Screens.” Gene and Genome Editing 2: 100008.
Kunkle, Brian W, Benjamin Grenier-Boley, Rebecca Sims, Joshua C Bis, Vincent Damotte, Adam C Naj, Anne Boland, et al. 2019. “Genetic Meta-Analysis of Diagnosed Alzheimer’s Disease Identifies New Risk Loci and Implicates aβ, Tau, Immunity and Lipid Processing.” Nature Genetics 51 (3): 414–30.
La Manno, Gioele, Ruslan Soldatov, Amit Zeisel, Emelie Braun, Hannah Hochgerner, Viktor Petukhov, Katja Lidschreiber, et al. 2018. RNA Velocity of Single Cells.” Nature 560 (7719): 494–98.
Lahnemann, David, Johannes Koster, Ewa Szczurek, Davis J McCarthy, Stephanie C Hicks, Mark D Robinson, Catalina A Vallejos, et al. 2020. “Eleven Grand Challenges in Single-Cell Data Science.” Genome Biology 21 (1): 1–35.
Lance, Christopher, Malte D Luecken, Daniel B Burkhardt, Robrecht Cannoodt, Pia Rautenstrauch, Anna Laddach, Aidyn Ubingazhibov, et al. 2022. “Multimodal Single Cell Data Integration Challenge: Results and Lessons Learned.” BioRxiv, 2022–04.
Lause, Jan, Philipp Berens, and Dmitry Kobak. 2021. “Analytic Pearson Residuals for Normalization of Single-Cell RNA-Seq UMI Data.” Genome Biology 22: 1–20.
———. 2024. “The Art of Seeing the Elephant in the Room: 2D Embeddings of Single-Cell Data Do Make Sense.” bioRxiv.
Leblanc, Francis JA, and Guillaume Lettre. 2023. “Major Cell-Types in Multiomic Single-Nucleus Datasets Impact Statistical Modeling of Links Between Regulatory Sequences and Target Genes.” Scientific Reports 13 (1): 3924.
Lee, Colin YC, James McCaffrey, Dominic McGovern, and Menna R Clatworthy. 2024. “Profiling Immune Cell Tissue Niches in the Spatial-Omics Era.” Journal of Allergy and Clinical Immunology.
Lei, Yalan, Rong Tang, Jin Xu, Wei Wang, Bo Zhang, Jiang Liu, Xianjun Yu, and Si Shi. 2021. “Applications of Single-Cell Sequencing in Cancer Research: Progress and Perspectives.” Journal of Hematology & Oncology 14 (1): 91.
Leiz, Janna, Maria Rutkiewicz, Carmen Birchmeier, Udo Heinemann, and Kai M Schmidt-Ott. 2021. “Technologies for Profiling the Impact of Genomic Variants on Transcription Factor Binding.” Medizinische Genetik 33 (2): 147–55.
Leung, Szi Kay, Aaron R Jeffries, Isabel Castanho, Ben T Jordan, Karen Moore, Jonathan P Davies, Emma L Dempster, et al. 2021. “Full-Length Transcript Sequencing of Human and Mouse Cerebral Cortex Identifies Widespread Isoform Diversity and Alternative Splicing.” Cell Reports 37 (7).
Li, Haoyang, Yingxin Lin, Wenjia He, Wenkai Han, Xiaopeng Xu, Chencheng Xu, Elva Gao, Hongyu Zhao, and Xin Gao. 2024. “SANTO: A Coarse-to-Fine Alignment and Stitching Method for Spatial Omics.” Nature Communications 15 (1): 6048.
Li, Jingyi Jessica, Heather J Zhou, Peter J Bickel, and Xin Tong. 2024. “Dissecting Gene Expression Heterogeneity: Generalized Pearson Correlation Squares and the k-Lines Clustering Algorithm.” Journal of the American Statistical Association, 1–14.
Li, Lei, Yumei Li, Xudong Zou, Fuduan Peng, Ya Cui, Eric J Wagner, and Wei Li. 2022. “Population-Scale Genetic Control of Alternative Polyadenylation and Its Association with Human Diseases.” Quantitative Biology 10 (1): 44–54.
Li, Xintao, Shi Peng, Bo Guan, Songwen Chen, Genqing Zhou, Yong Wei, Chao Gong, et al. 2021. “Genetically Determined Inflammatory Biomarkers and the Risk of Heart Failure: A Mendelian Randomization Study.” Frontiers in Cardiovascular Medicine 8: 734400.
Li, Yumei, Xinzhou Ge, Fanglue Peng, Wei Li, and Jingyi Jessica Li. 2022. “Exaggerated False Positives by Popular Differential Expression Methods When Analyzing Human Population Samples.” Genome Biology 23 (1): 1–13.
Li, Zhuoxuan, Tianjie Wang, Pentao Liu, and Yuanhua Huang. 2023. “SpatialDM for Rapid Identification of Spatially Co-Expressed Ligand–Receptor and Revealing Cell–Cell Communication Patterns.” Nature Communications 14 (1): 3995.
Li, Zizhang, Wenjing Yang, Peng Wu, Yuyan Shan, Xiaoyu Zhang, Feng Chen, Junnan Yang, and Jian-Rong Yang. 2024. “Reconstructing Cell Lineage Trees with Genomic Barcoding: Approaches and Applications.” Journal of Genetics and Genomics 51 (1): 35–47.
Liao, Jie, Xiaoyan Lu, Xin Shao, Ling Zhu, and Xiaohui Fan. 2021. “Uncovering an Organ’s Molecular Architecture at Single-Cell Resolution by Spatially Resolved Transcriptomics.” Trends in Biotechnology 39 (1): 43–58.
Lim, Jongsu, Chanho Park, Minjae Kim, Hyukhee Kim, Junil Kim, and Dong-Sung Lee. 2024. “Advances in Single-Cell Omics and Multiomics for High-Resolution Molecular Profiling.” Experimental & Molecular Medicine 56 (3): 515–26.
Lin, Kevin Z, Yixuan Qiu, and Kathryn Roeder. 2022. eSVD: Cohort-Level Differential Expression in Multi-Individual Single-Cell RNA-Seq Data Using Exponential-Family Embeddings.” (In Preparation).
———. 2024. eSVD-DE: Cohort-Wide Differential Expression in Single-Cell RNA-Seq Data Using Exponential-Family Embeddings.” BMC Bioinformatics 25 (1): 113.
Lin, Xueqiu, Yanxia Liu, Shuai Liu, Xiang Zhu, Lingling Wu, Yanyu Zhu, Dehua Zhao, et al. 2022. “Nested Epistasis Enhancer Networks for Robust Genome Regulation.” Science 377 (6610): 1077–85.
Liu, Hanqing, Jingtian Zhou, Wei Tian, Chongyuan Luo, Anna Bartlett, Andrew Aldridge, Jacinta Lucero, et al. 2021. DNA Methylation Atlas of the Mouse Brain at Single-Cell Resolution.” Nature 598 (7879): 120–28.
Liu, Jiayi, Anat Kreimer, and Wei Vivian Li. 2023. “Differential Variability Analysis of Single-Cell Gene Expression Data.” Briefings in Bioinformatics 24 (5): bbad294.
Liu, Ning, Wai Yee Low, Hamid Alinejad-Rokny, Stephen Pederson, Timothy Sadlon, Simon Barry, and James Breen. 2021. “Seeing the Forest Through the Trees: Prioritising Potentially Functional Interactions from Hi-c.” Epigenetics & Chromatin 14 (1): 41.
Liu, Yunqing, Jiayi Zhao, Taylor S Adams, Ningya Wang, Jonas C Schupp, Weimiao Wu, John E McDonough, et al. 2023. iDESC: Identifying Differential Expression in Single-Cell RNA Sequencing Data with Multiple Subjects.” BMC Bioinformatics 24 (1): 318.
Loers, Jens Uwe, and Vanessa Vermeirssen. 2024. “A Single-Cell Multimodal View on Gene Regulatory Network Inference from Transcriptomics and Chromatin Accessibility Data.” Briefings in Bioinformatics 25 (5): bbae382.
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.
Lopes, Inês, Gulam Altab, Priyanka Raina, and JoãO Pedro De Magalhães. 2021. “Gene Size Matters: An Analysis of Gene Length in the Human Genome.” Frontiers in Genetics 12: 559998.
Lopez, Romain, Jeffrey Regier, Michael B Cole, Michael I Jordan, and Nir Yosef. 2018. “Deep Generative Modeling for Single-Cell Transcriptomics.” Nature Methods 15 (12): 1053.
Lotfollahi, Mohammad, Mohsen Naghipourfar, Malte D Luecken, Matin Khajavi, Maren Büttner, Marco Wagenstetter, Žiga Avsec, et al. 2022. “Mapping Single-Cell Data to Reference Atlases by Transfer Learning.” Nature Biotechnology 40 (1): 121–30.
Lotfollahi, Mohammad, F Alexander Wolf, and Fabian J Theis. 2019. “scGen Predicts Single-Cell Perturbation Responses.” Nature Methods 16 (8): 715–21.
Love, Michael I, Wolfgang Huber, and Simon Anders. 2014. “Moderated Estimation of Fold Change and Dispersion for RNA-Seq Data with DESeq2.” Genome Biology 15 (12): 550.
Lu, Bingxin. 2025. “Cancer Phylogenetic Inference Using Copy Number Alterations Detected from DNA Sequencing Data.” Cancer Pathogenesis and Therapy 3 (01): 16–29.
Luecken, Malte D, Maren Büttner, Kridsadakorn Chaichoompu, Anna Danese, Marta Interlandi, Michaela F Müller, Daniel C Strobl, et al. 2022. “Benchmarking Atlas-Level Data Integration in Single-Cell Genomics.” Nature Methods 19 (1): 41–50.
Luecken, Malte D, and Fabian J Theis. 2019. “Current Best Practices in Single-Cell RNA-Seq Analysis: A Tutorial.” Molecular Systems Biology 15 (6): e8746.
Ma, Rong, Eric D Sun, David Donoho, and James Zou. 2024. “Principled and Interpretable Alignability Testing and Integration of Single-Cell Data.” Proceedings of the National Academy of Sciences 121 (10): e2313719121.
Ma, Sai, Bing Zhang, Lindsay M LaFave, Andrew S Earl, Zachary Chiang, Yan Hu, Jiarui Ding, et al. 2020. “Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin.” Cell 183 (4): 1103–16.
Ma, Ying, Shiquan Sun, Xuequn Shang, Evan T Keller, Mengjie Chen, and Xiang Zhou. 2020. “Integrative Differential Expression and Gene Set Enrichment Analysis Using Summary Statistics for scRNA-Seq Studies.” Nature Communications 11 (1): 1–13.
Macrae, Trisha A, Julie Fothergill-Robinson, and Miguel Ramalho-Santos. 2023. “Regulation, Functions and Transmission of Bivalent Chromatin During Mammalian Development.” Nature Reviews Molecular Cell Biology 24 (1): 6–26.
Maden, Sean K, Sang Ho Kwon, Louise A Huuki-Myers, Leonardo Collado-Torres, Stephanie C Hicks, and Kristen R Maynard. 2023. “Challenges and Opportunities to Computationally Deconvolve Heterogeneous Tissue with Varying Cell Sizes Using Single-Cell RNA-Sequencing Datasets.” Genome Biology 24 (1): 288.
Mai, Jialin, Mingming Lu, Qianwen Gao, Jingyao Zeng, and Jingfa Xiao. 2023. “Transcriptome-Wide Association Studies: Recent Advances in Methods, Applications and Available Databases.” Communications Biology 6 (1): 899.
Mansisidor, Andrés R, and Viviana I Risca. 2022. “Chromatin Accessibility: Methods, Mechanisms, and Biological Insights.” Nucleus 13 (1): 238–78.
Mao, Yanfei, Jose Ramon Botella, and Jian-Kang Zhu. 2017. “Heritability of Targeted Gene Modifications Induced by Plant-Optimized CRISPR Systems.” Cellular and Molecular Life Sciences 74 (6): 1075–93.
Marine, Jean-Christophe, Sarah-Jane Dawson, and Mark A Dawson. 2020. “Non-Genetic Mechanisms of Therapeutic Resistance in Cancer.” Nature Reviews Cancer 20 (12): 743–56.
Martens, Laura D, David S Fischer, Vicente A Yépez, Fabian J Theis, and Julien Gagneur. 2024. “Modeling Fragment Counts Improves Single-Cell ATAC-Seq Analysis.” Nature Methods 21 (1): 28–31.
Martignano, Filippo, Uday Munagala, Stefania Crucitta, Alessandra Mingrino, Roberto Semeraro, Marzia Del Re, Iacopo Petrini, Alberto Magi, and Silvestro G Conticello. 2021. “Nanopore Sequencing from Liquid Biopsy: Analysis of Copy Number Variations from Cell-Free DNA of Lung Cancer Patients.” Molecular Cancer 20: 1–6.
Martin, Alicia R, Masahiro Kanai, Yoichiro Kamatani, Yukinori Okada, Benjamin M Neale, and Mark J Daly. 2019. “Clinical Use of Current Polygenic Risk Scores May Exacerbate Health Disparities.” Nature Genetics 51 (4): 584–91.
Masood, Daniall, Luyao Ren, Cu Nguyen, Francesco G Brundu, Lily Zheng, Yongmei Zhao, Erich Jaeger, et al. 2024. “Evaluation of Somatic Copy Number Variation Detection by NGS Technologies and Bioinformatics Tools on a Hyper-Diploid Cancer Genome.” Genome Biology 25 (1): 163.
Mattick, John S, Paulo P Amaral, Piero Carninci, Susan Carpenter, Howard Y Chang, Ling-Ling Chen, Runsheng Chen, et al. 2023. “Long Non-Coding RNAs: Definitions, Functions, Challenges and Recommendations.” Nature Reviews Molecular Cell Biology 24 (6): 430–47.
McGinnis, Christopher S, Lyndsay M Murrow, and Zev J Gartner. 2019. “DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors.” Cell Systems 8 (4): 329–37.
McKenna, Aaron, Matthew Hanna, Eric Banks, Andrey Sivachenko, Kristian Cibulskis, Andrew Kernytsky, Kiran Garimella, et al. 2010. “The Genome Analysis Toolkit: A MapReduce Framework for Analyzing Next-Generation DNA Sequencing Data.” Genome Research 20 (9): 1297–1303.
McLean, Cory Y, Dave Bristor, Michael Hiller, Shoa L Clarke, Bruce T Schaar, Craig B Lowe, Aaron M Wenger, and Gill Bejerano. 2010. “GREAT Improves Functional Interpretation of Cis-Regulatory Regions.” Nature Biotechnology 28 (5): 495–501.
McVey, Mitch, and Sang Eun Lee. 2008. “MMEJ Repair of Double-Strand Breaks (Director’s Cut): Deleted Sequences and Alternative Endings.” Trends in Genetics 24 (11): 529–38.
Miao, Zhen, Benjamin D Humphreys, Andrew P McMahon, and Junhyong Kim. 2021. “Multiomics Integration in the Age of Million Single Cell Data.” Nature Reviews Nephrology 17 (11): 710–24.
Miao, Zhen, and Junhyong Kim. 2024. “Uniform Quantification of Single-Nucleus ATAC-Seq Data with Paired-Insertion Counting (PIC) and a Model-Based Insertion Rate Estimator.” Nature Methods 21 (1): 32–36.
Michielsen, Lieke, Mohammad Lotfollahi, Daniel Strobl, Lisa Sikkema, Marcel JT Reinders, Fabian J Theis, and Ahmed Mahfouz. 2023. “Single-Cell Reference Mapping to Construct and Extend Cell-Type Hierarchies.” NAR Genomics and Bioinformatics 5 (3): lqad070.
Mignone, Flavio, Carmela Gissi, Sabino Liuni, and Graziano Pesole. 2002. “Untranslated Regions of mRNAs.” Genome Biology 3: 1–10.
Mihaylova, M, R Staneva, D Toncheva, M Pancheva, and S Hadjidekova. 2017. “Benign, Pathogenic and Copy Number Variations of Unknown Clinical Significance in Patients with Congenital Malformations and Developmental Delay.” Balkan Journal of Medical Genetics: BJMG 20 (1): 5.
Milholland, Brandon, Xiao Dong, Lei Zhang, Xiaoxiao Hao, Yousin Suh, and Jan Vijg. 2017. “Differences Between Germline and Somatic Mutation Rates in Humans and Mice.” Nature Communications 8 (1): 15183.
Moerman, Thomas, Sara Aibar Santos, Carmen Bravo González-Blas, Jaak Simm, Yves Moreau, Jan Aerts, and Stein Aerts. 2019. “GRNBoost2 and Arboreto: Efficient and Scalable Inference of Gene Regulatory Networks.” Bioinformatics 35 (12): 2159–61.
Moffitt, Jeffrey R, Dhananjay Bambah-Mukku, Stephen W Eichhorn, Eric Vaughn, Karthik Shekhar, Julio D Perez, Nimrod D Rubinstein, et al. 2018. “Molecular, Spatial, and Functional Single-Cell Profiling of the Hypothalamic Preoptic Region.” Science 362 (6416): eaau5324.
Mölbert, Carla, and Laleh Haghverdi. 2023. “Adjustments to the Reference Dataset Design Improve Cell Type Label Transfer.” Frontiers in Bioinformatics 3: 1150099.
Mubeen, Sarah, Alpha Tom Kodamullil, Martin Hofmann-Apitius, and Daniel Domingo-Fernández. 2022. “On the Influence of Several Factors on Pathway Enrichment Analysis.” Briefings in Bioinformatics 23 (3): bbac143.
Myers, Matthew A, Gryte Satas, and Benjamin J Raphael. 2019. “CALDER: Inferring Phylogenetic Trees from Longitudinal Tumor Samples.” Cell Systems 8 (6): 514–22.
Neufeld, Anna, Lucy L Gao, Joshua Popp, Alexis Battle, and Daniela Witten. 2022. “Inference After Latent Variable Estimation for Single-Cell RNA Sequencing Data.” arXiv Preprint arXiv:2207.00554.
Ng, Bernard, William Casazza, Nam Hee Kim, Chendi Wang, Farnush Farhadi, Shinya Tasaki, David A Bennett, Philip L De Jager, Christopher Gaiteri, and Sara Mostafavi. 2021. “Cascading Epigenomic Analysis for Identifying Disease Genes from the Regulatory Landscape of GWAS Variants.” PLoS Genetics 17 (11): e1009918.
Ng, Bernard, Charles C White, Hans-Ulrich Klein, Solveig K Sieberts, Cristin McCabe, Ellis Patrick, Jishu Xu, et al. 2017. “An xQTL Map Integrates the Genetic Architecture of the Human Brain’s Transcriptome and Epigenome.” Nature Neuroscience 20 (10): 1418–26.
Nguyen, Hai CT, Bukyung Baik, Sora Yoon, Taesung Park, and Dougu Nam. 2023. “Benchmarking Integration of Single-Cell Differential Expression.” Nature Communications 14 (1): 1570.
Nguyen, Hung, Ha Nguyen, Duc Tran, Sorin Draghici, and Tin Nguyen. 2024. “Fourteen Years of Cellular Deconvolution: Methodology, Applications, Technical Evaluation and Outstanding Challenges.” Nucleic Acids Research 52 (9): 4761–83.
Niazi, Sarfaraz K. 2023. “RNA Therapeutics: A Healthcare Paradigm Shift.” Biomedicines 11 (5): 1275.
Novembre, John, Toby Johnson, Katarzyna Bryc, Zoltán Kutalik, Adam R Boyko, Adam Auton, Amit Indap, et al. 2008. “Genes Mirror Geography Within Europe.” Nature 456 (7218): 98–101.
Pan, Bohu, Rebecca Kusko, Wenming Xiao, Yuanting Zheng, Zhichao Liu, Chunlin Xiao, Sugunadevi Sakkiah, et al. 2019. “Similarities and Differences Between Variants Called with Human Reference Genome HG19 or HG38.” BMC Bioinformatics 20 (2): 17–29.
Park, Han-Eol, Song Hyun Jo, Rosalind H Lee, Christian P Macks, Taeyun Ku, Jihwan Park, Chung Whan Lee, Junho K Hur, and Chang Ho Sohn. 2023. “Spatial Transcriptomics: Technical Aspects of Recent Developments and Their Applications in Neuroscience and Cancer Research.” Advanced Science 10 (16): 2206939.
Peng, Minshi, Brie Wamsley, Andrew G Elkins, Daniel M Geschwind, Yuting Wei, and Kathryn Roeder. 2021. “Cell Type Hierarchy Reconstruction via Reconciliation of Multi-Resolution Cluster Tree.” bioRxiv.
Pratapa, Aditya, Amogh P Jalihal, Jeffrey N Law, Aditya Bharadwaj, and TM Murali. 2020. “Benchmarking Algorithms for Gene Regulatory Network Inference from Single-Cell Transcriptomic Data.” Nature Methods 17 (2): 147–54.
Prater, Katherine E, and Kevin Z Lin. 2024. “All the Single Cells: Single-Cell Transcriptomics/Epigenomics Experimental Design and Analysis Considerations for Glial Biologists.” Glia.
Privé, Florian, Julyan Arbel, and Bjarni J Vilhjálmsson. 2020. “LDpred2: Better, Faster, Stronger.” Bioinformatics 36 (22-23): 5424–31.
Qian, Kun, Shiwei Fu, Hongwei Li, and Wei Vivian Li. 2022. “scINSIGHT for Interpreting Single-Cell Gene Expression from Biologically Heterogeneous Data.” Genome Biology 23 (1): 1–23.
Rademacher, Anne, Alik Huseynov, Michele Bortolomeazzi, Sina Jasmin Wille, Sabrina Schumacher, Pooja Sant, Denise Keitel, et al. 2024. “Comparison of Spatial Transcriptomics Technologies Using Tumor Cryosections.” bioRxiv, 2024–04.
Risso, Davide, John Ngai, Terence P Speed, and Sandrine Dudoit. 2014. “Normalization of RNA-Seq Data Using Factor Analysis of Control Genes or Samples.” Nature Biotechnology 32 (9): 896–902.
Robinson, Mark D, and Gordon K Smyth. 2007. “Moderated Statistical Tests for Assessing Differences in Tag Abundance.” Bioinformatics 23 (21): 2881–87.
Robles-Espinoza, Carla Daniela, Pejman Mohammadi, Ximena Bonilla, and Maria Gutierrez-Arcelus. 2021. “Allele-Specific Expression: Applications in Cancer and Technical Considerations.” Current Opinion in Genetics & Development 66: 10–19.
Rusilowicz-Jones, Emma V, Sylvie Urbé, and Michael J Clague. 2022. “Protein Degradation on the Global Scale.” Molecular Cell 82 (8): 1414–23.
Saelens, Wouter, Robrecht Cannoodt, Helena Todorov, and Yvan Saeys. 2019. “A Comparison of Single-Cell Trajectory Inference Methods.” Nature Biotechnology 37 (5): 547–54.
Salzberg, Steven L. 2018. “Open Questions: How Many Genes Do We Have?” BMC Biology 16 (1): 94.
Sanderson, Eleanor, M Maria Glymour, Michael V Holmes, Hyunseung Kang, Jean Morrison, Marcus R Munafò, Tom Palmer, et al. 2022. “Mendelian Randomization.” Nature Reviews Methods Primers 2 (1): 6.
Sarkar, Abhishek, and Matthew Stephens. 2021. “Separating Measurement and Expression Models Clarifies Confusion in Single Cell RNA-Seq Analysis.” Nature Genetics 53 (6): 770–77.
Sasse, Alexander, Bernard Ng, Anna E Spiro, Shinya Tasaki, David A Bennett, Christopher Gaiteri, Philip L De Jager, Maria Chikina, and Sara Mostafavi. 2023. “Benchmarking of Deep Neural Networks for Predicting Personal Gene Expression from DNA Sequence Highlights Shortcomings.” Nature Genetics 55 (12): 2060–64.
Sato, Yuma, Shumpei Watanabe, Yoshinari Fukuda, Takao Hashiguchi, Yusuke Yanagi, and Shinji Ohno. 2018. “Cell-to-Cell Measles Virus Spread Between Human Neurons Is Dependent on Hemagglutinin and Hyperfusogenic Fusion Protein.” Journal of Virology 92 (6): 10–1128.
Saunders, Lauren M, Sanjay R Srivatsan, Madeleine Duran, Michael W Dorrity, Brent Ewing, Tor H Linbo, Jay Shendure, et al. 2023. “Embryo-Scale Reverse Genetics at Single-Cell Resolution.” Nature 623 (7988): 782–91.
Schaff, Dylan L, Aria J Fasse, Phoebe E White, Robert J Vander Velde, and Sydney M Shaffer. 2024. “Clonal Differences Underlie Variable Responses to Sequential and Prolonged Treatment.” Cell Systems 15 (3): 213–26.
Schefzik, Roman, Julian Flesch, and Angela Goncalves. 2021. “Fast Identification of Differential Distributions in Single-Cell RNA-Sequencing Data with waddR.” Bioinformatics 37 (19): 3204–11.
Schep, Alicia N, Beijing 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.
Schnitzler, Gavin R, Helen Kang, Shi Fang, Ramcharan S Angom, Vivian S Lee-Kim, X Rosa Ma, Ronghao Zhou, et al. 2024. “Convergence of Coronary Artery Disease Genes onto Endothelial Cell Programs.” Nature 626 (8000): 799–807.
Schott, Marie, Daniel León-Periñán, Elena Splendiani, Leon Strenger, Jan Robin Licha, Tancredi Massimo Pentimalli, Simon Schallenberg, et al. 2024. “Open-ST: High-Resolution Spatial Transcriptomics in 3D.” Cell 187 (15): 3953–72.
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.
Shalek, Alex K, and Mikael Benson. 2017. “Single-Cell Analyses to Tailor Treatments.” Science Translational Medicine 9 (408): eaan4730.
Shang, Renfu, Seungjae Lee, Gayan Senavirathne, and Eric C Lai. 2023. “microRNAs in Action: Biogenesis, Function and Regulation.” Nature Reviews Genetics 24 (12): 816–33.
Sheth, Maya U, Wei-Lin Qiu, X Rosa Ma, Andreas R Gschwind, Evelyn Jagoda, Anthony S Tan, Hjörleifur Einarsson, et al. 2024. “Mapping Enhancer-Gene Regulatory Interactions from Single-Cell Data.” bioRxiv, 2024–11.
Siersbæk, Rasmus, Songjoon Baek, Atefeh Rabiee, Ronni Nielsen, Sofie Traynor, Nicholas Clark, Albin Sandelin, et al. 2014. “Molecular Architecture of Transcription Factor Hotspots in Early Adipogenesis.” Cell Reports 7 (5): 1434–42.
Siletti, Kimberly, Rebecca Hodge, Alejandro Mossi Albiach, Ka Wai Lee, Song-Lin Ding, Lijuan Hu, Peter Lönnerberg, et al. 2023. “Transcriptomic Diversity of Cell Types Across the Adult Human Brain.” Science 382 (6667): eadd7046.
Silva, Paulo FL da, and Björn Schumacher. 2021. “Principles of the Molecular and Cellular Mechanisms of Aging.” Journal of Investigative Dermatology 141 (4): 951–60.
Singh, Ashish Kumar, Maren Fridtjofsen Olsen, Liss Anne Solberg Lavik, Trine Vold, Finn Drabløs, and Wenche Sjursen. 2021. “Detecting Copy Number Variation in Next Generation Sequencing Data from Diagnostic Gene Panels.” BMC Medical Genomics 14 (1): 214.
Sollier, Etienne, Jack Kuipers, Koichi Takahashi, Niko Beerenwinkel, and Katharina Jahn. 2023. “COMPASS: Joint Copy Number and Mutation Phylogeny Reconstruction from Amplicon Single-Cell Sequencing Data.” Nature Communications 14 (1): 4921.
Song, Dongyuan, Kexin Li, Xinzhou Ge, and Jingyi Jessica Li. 2023. “ClusterDE: A Post-Clustering Differential Expression (DE) Method Robust to False-Positive Inflation Caused by Double Dipping.” Research Square.
Squair, Jordan W, Matthieu Gautier, Claudi Kathe, Mark A Anderson, Nicholas D James, Thomas H Hutson, Rémi Hudelle, et al. 2021. “Confronting False Discoveries in Single-Cell Differential Expression.” Nature Communications 12 (1): 5692.
St. John, Katherine. 2017. “The Shape of Phylogenetic Treespace.” Systematic Biology 66 (1): e83–94.
Statello, Luisa, Chun-Jie Guo, Ling-Ling Chen, and Maite Huarte. 2021. “Gene Regulation by Long Non-Coding RNAs and Its Biological Functions.” Nature Reviews Molecular Cell Biology 22 (2): 96–118.
Steele, Christopher D, Ammal Abbasi, SM Ashiqul Islam, Amy L Bowes, Azhar Khandekar, Kerstin Haase, Shadi Hames-Fathi, et al. 2022. “Signatures of Copy Number Alterations in Human Cancer.” Nature 606 (7916): 984–91.
Stegle, Oliver, Leopold Parts, Richard Durbin, and John Winn. 2010. “A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies.” PLoS Computational Biology 6 (5): e1000770.
Steinbach, Nicole. 2017. PTEN Affects Gene Expression and Histone Modifications and Plays a Role in the Regulation of Transcription. Columbia University.
Stephenson, Emily, Gary Reynolds, Rachel A Botting, Fernando J Calero-Nieto, Michael D Morgan, Zewen Kelvin Tuong, Karsten Bach, et al. 2021. “Single-Cell Multi-Omics Analysis of the Immune Response in COVID-19.” Nature Medicine 27 (5): 904–16.
Stock, Marco, Niclas Popp, Jonathan Fiorentino, and Antonio Scialdone. 2024. “Topological Benchmarking of Algorithms to Infer Gene Regulatory Networks from Single-Cell RNA-Seq Data.” Bioinformatics, btae267.
Street, Kelly, Davide Risso, Russell B Fletcher, Diya Das, John Ngai, Nir Yosef, Elizabeth Purdom, and Sandrine Dudoit. 2018. “Slingshot: Cell Lineage and Pseudotime Inference for Single-Cell Transcriptomics.” BMC Genomics 19 (1): 477.
Stuart, Tim, Andrew Butler, Paul Hoffman, Christoph Hafemeister, Efthymia Papalexi, William M Mauck III, Yuhan Hao, Marlon Stoeckius, Peter Smibert, and Rahul Satija. 2019. “Comprehensive Integration of Single-Cell Data.” Cell 177 (7): 1888–1902.
Subramanian, Aravind, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, et al. 2005. “Gene Set Enrichment Analysis: A Knowledge-Based Approach for Interpreting Genome-Wide Expression Profiles.” Proceedings of the National Academy of Sciences 102 (43): 15545–50.
Svensson, Valentine. 2020. “Droplet scRNA-Seq Is Not Zero-Inflated.” Nature Biotechnology 38 (2): 147–50.
———. 2021. “Reply to: UMI or Not UMI, That Is the Question for scRNA-Seq Zero-Inflation.” Nature Biotechnology 39 (2): 160–60.
Swaminath, Sharmada, and Alistair B Russell. 2024. “The Use of Single-Cell RNA-Seq to Study Heterogeneity at Varying Levels of Virus–Host Interactions.” PLoS Pathogens 20 (1): e1011898.
Sznajder, Łukasz J, and Maurice S Swanson. 2019. “Short Tandem Repeat Expansions and RNA-Mediated Pathogenesis in Myotonic Dystrophy.” International Journal of Molecular Sciences 20 (13): 3365.
Tang, Wenhao, Andreas Christ Sølvsten Jørgensen, Samuel Marguerat, Philipp Thomas, and Vahid Shahrezaei. 2023. “Modelling Capture Efficiency of Single Cell RNA-Sequencing Data Improves Inference of Transcriptome-Wide Burst Kinetics.” bioRxiv, 2023–03.
Tangherloni, Andrea, Simone Spolaor, Leonardo Rundo, Marco S Nobile, Paolo Cazzaniga, Giancarlo Mauri, Pietro Liò, Ivan Merelli, and Daniela Besozzi. 2019. “GenHap: A Novel Computational Method Based on Genetic Algorithms for Haplotype Assembly.” BMC Bioinformatics 20: 1–14.
Tanudisastro, Hope A, Ira W Deveson, Harriet Dashnow, and Daniel G MacArthur. 2024. “Sequencing and Characterizing Short Tandem Repeats in the Human Genome.” Nature Reviews Genetics 25 (7): 460–75.
Taylor, Rebecca C, Sean P Cullen, and Seamus J Martin. 2008. “Apoptosis: Controlled Demolition at the Cellular Level.” Nature Reviews Molecular Cell Biology 9 (3): 231–41.
Teichmann, Sarah, and Mirjana Efremova. 2020. “Method of the Year 2019: Single-Cell Multimodal Omics.” Nature Methods 17 (1): 2020.
Theunissen, Lauren, Thomas Mortier, Yvan Saeys, and Willem Waegeman. 2024. “Uncertainty-Aware Single-Cell Annotation with a Hierarchical Reject Option.” Bioinformatics 40 (3): btae128.
Tibshirani, Robert, Michael Saunders, Saharon Rosset, Ji Zhu, and Keith Knight. 2005. “Sparsity and Smoothness via the Fused Lasso.” Journal of the Royal Statistical Society Series B: Statistical Methodology 67 (1): 91–108.
Tipping, Michael E, and Christopher M Bishop. 1999. “Probabilistic Principal Component Analysis.” Journal of the Royal Statistical Society: Series B (Statistical Methodology) 61 (3): 611–22.
Townes, F William, Stephanie C Hicks, Martin J Aryee, and Rafael A Irizarry. 2019. “Feature Selection and Dimension Reduction for Single-Cell RNA-seq Based on a Multinomial Model.” Genome Biology 20 (1): 1–16.
Traag, Vincent A, Ludo Waltman, and Nees Jan Van Eck. 2019. “From Louvain to Leiden: Guaranteeing Well-Connected Communities.” Scientific Reports 9 (1): 1–12.
Tran, Hoa Thi Nhu, Kok Siong Ang, Marion Chevrier, Xiaomeng Zhang, Nicole Yee Shin Lee, Michelle Goh, and Jinmiao Chen. 2020. “A Benchmark of Batch-Effect Correction Methods for Single-Cell RNA Sequencing Data.” Genome Biology 21 (1): 1–32.
Trapnell, Cole, Davide Cacchiarelli, Jonna Grimsby, Prapti Pokharel, Shuqiang Li, Michael Morse, Niall J Lennon, Kenneth J Livak, Tarjei S Mikkelsen, and John L Rinn. 2014. “The Dynamics and Regulators of Cell Fate Decisions Are Revealed by Pseudotemporal Ordering of Single Cells.” Nature Biotechnology 32 (4): 381.
Trapp, Alexandre, Csaba Kerepesi, and Vadim N Gladyshev. 2021. “Profiling Epigenetic Age in Single Cells.” Nature Aging 1 (12): 1189–1201.
Valecha, Monica, and David Posada. 2022. “Somatic Variant Calling from Single-Cell DNA Sequencing Data.” Computational and Structural Biotechnology Journal 20: 2978–85.
Van Dijk, David, Roshan Sharma, Juozas Nainys, Kristina Yim, Pooja Kathail, Ambrose J Carr, Cassandra Burdziak, et al. 2018. “Recovering Gene Interactions from Single-Cell Data Using Data Diffusion.” Cell 174 (3): 716–29.
VanHorn, Sadie, and Samantha A Morris. 2021. “Next-Generation Lineage Tracing and Fate Mapping to Interrogate Development.” Developmental Cell 56 (1): 7–21.
Verbanck, Marie, Chia-Yen Chen, Benjamin Neale, and Ron Do. 2018. “Detection of Widespread Horizontal Pleiotropy in Causal Relationships Inferred from Mendelian Randomization Between Complex Traits and Diseases.” Nature Genetics 50 (5): 693–98.
Verschoor, Chris P, Alina Lelic, Jonathan L Bramson, and Dawn ME Bowdish. 2015. “An Introduction to Automated Flow Cytometry Gating Tools and Their Implementation.” Frontiers in Immunology 6: 380.
Von Bernhardi, Rommy, Laura Eugenı́n-von Bernhardi, and Jaime Eugenı́n. 2015. “Microglial Cell Dysregulation in Brain Aging and Neurodegeneration.” Frontiers in Aging Neuroscience 7: 124.
Wainberg, Michael, Nasa Sinnott-Armstrong, Nicholas Mancuso, Alvaro N Barbeira, David A Knowles, David Golan, Raili Ermel, et al. 2019. “Opportunities and Challenges for Transcriptome-Wide Association Studies.” Nature Genetics 51 (4): 592–99.
Wall, Jeffrey D, and Jonathan K Pritchard. 2003. “Haplotype Blocks and Linkage Disequilibrium in the Human Genome.” Nature Reviews Genetics 4 (8): 587–97.
Wang, Gao, Abhishek Sarkar, Peter Carbonetto, and Matthew Stephens. 2020. “A Simple New Approach to Variable Selection in Regression, with Application to Genetic Fine Mapping.” Journal of the Royal Statistical Society Series B: Statistical Methodology 82 (5): 1273–1300.
Wang, Lingfei, Nikolaos Trasanidis, Ting Wu, Guanlan Dong, Michael Hu, Daniel E Bauer, and Luca Pinello. 2023. “Dictys: Dynamic Gene Regulatory Network Dissects Developmental Continuum with Single-Cell Multiomics.” Nature Methods 20: 1368–78.
Wang, Qingbo S, and Hailiang Huang. 2022. “Methods for Statistical Fine-Mapping and Their Applications to Auto-Immune Diseases.” In Seminars in Immunopathology, 44:101–13. 1. Springer.
Wang, Tao, Yongzhuang Liu, Junpeng Ruan, Xianjun Dong, Yadong Wang, and Jiajie Peng. 2021. “A Pipeline for RNA-Seq Based eQTL Analysis with Automated Quality Control Procedures.” BMC Bioinformatics 22: 1–18.
Wang, Tianyu, Boyang Li, Craig E Nelson, and Sheida Nabavi. 2019. “Comparative Analysis of Differential Gene Expression Analysis Tools for Single-Cell RNA Sequencing Data.” BMC Bioinformatics 20 (1): 1–16.
Wang, Yizhuo, Christopher R Flowers, Michael Wang, Xuelin Huang, and Ziyi Li. 2024. “CASi: A Framework for Cross-Timepoint Analysis of Single-Cell RNA Sequencing Data.” Scientific Reports 14 (1): 10633.
Wang, Yulei, Chih Long Liu, John D Storey, Robert J Tibshirani, Daniel Herschlag, and Patrick O Brown. 2002. “Precision and Functional Specificity in mRNA Decay.” Proceedings of the National Academy of Sciences 99 (9): 5860–65.
Wei, Lai, Derek Lee, Cheuk-Ting Law, Misty Shuo Zhang, Jialing Shen, Don Wai-Ching Chin, Allen Zhang, et al. 2019. “Genome-Wide CRISPR/Cas9 Library Screening Identified PHGDH as a Critical Driver for Sorafenib Resistance in HCC.” Nature Communications 10 (1): 4681.
Weiner, Samson, and Mukul S Bansal. 2025. “DICE: Fast and Accurate Distance-Based Reconstruction of Single-Cell Copy Number Phylogenies.” Life Science Alliance 8 (3).
Weinreb, Caleb, Alejo Rodriguez-Fraticelli, Fernando D Camargo, and Allon M Klein. 2020. “Lineage Tracing on Transcriptional Landscapes Links State to Fate During Differentiation.” Science 367 (6479).
Wen, Lu, Guoqiang Li, Tao Huang, Wei Geng, Hao Pei, Jialiang Yang, Miao Zhu, et al. 2022. “Single-Cell Technologies: From Research to Application.” The Innovation 3 (6).
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): 68.
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.
Wong, Karen HY, Walfred Ma, Chun-Yu Wei, Erh-Chan Yeh, Wan-Jia Lin, Elin HF Wang, Jen-Ping Su, et al. 2020. “Towards a Reference Genome That Captures Global Genetic Diversity.” Nature Communications 11 (1): 5482.
Wright, Shannon E, and Peter K Todd. 2023. “Native Functions of Short Tandem Repeats.” Elife 12: e84043.
Wu, Kevin E, Kathryn E Yost, Howard Y Chang, and James Zou. 2021. BABEL Enables Cross-Modality Translation Between Multiomic Profiles at Single-Cell Resolution.” Proceedings of the National Academy of Sciences 118 (15).
Xi, Nan Miles, and Jingyi Jessica Li. 2021. “Benchmarking Computational Doublet-Detection Methods for Single-Cell RNA Sequencing Data.” Cell Systems 12 (2): 176–94.
Xia, Lucy, Christy Lee, and Jingyi Jessica Li. 2024. “Statistical Method scDEED for Detecting Dubious 2D Single-Cell Embeddings and Optimizing t-SNE and UMAP Hyperparameters.” Nature Communications 15 (1): 1753.
Xie, Fangming, Ethan J Armand, Zizhen Yao, Hanqing Liu, Anna Bartlett, M Margarita Behrens, Yang Eric Li, et al. 2023. “Robust Enhancer-Gene Regulation Identified by Single-Cell Transcriptomes and Epigenomes.” Cell Genomics 3 (7).
Xing, Yue, Alan R Dabney, Xiao Li, Guosong Wang, Clare A Gill, and Claudio Casola. 2020. “SECNVs: A Simulator of Copy Number Variants and Whole-Exome Sequences from Reference Genomes.” Frontiers in Genetics 11: 82.
Xu, Chenling, Romain Lopez, Edouard Mehlman, Jeffrey Regier, Michael I Jordan, and Nir Yosef. 2021. “Probabilistic Harmonization and Annotation of Single-Cell Transcriptomics Data with Deep Generative Models.” Molecular Systems Biology 17 (1): e9620.
Xu, Yang, and Rachel Patton McCord. 2022. “Diagonal Integration of Multimodal Single-Cell Data: Potential Pitfalls and Paths Forward.” Nature Communications 13 (1): 3505.
Yang, Zikun, Chen Wang, Linxi Liu, Atlas Khan, Annie Lee, Badri Vardarajan, Richard Mayeux, Krzysztof Kiryluk, and Iuliana Ionita-Laza. 2023. “CARMA Is a New Bayesian Model for Fine-Mapping in Genome-Wide Association Meta-Analyses.” Nature Genetics 55 (6): 1057–65.
Yao, Douglas, Loic Binan, Jon Bezney, Brooke Simonton, Jahanara Freedman, Chris J Frangieh, Kushal Dey, et al. 2024. “Scalable Genetic Screening for Regulatory Circuits Using Compressed Perturb-Seq.” Nature Biotechnology 42 (8): 1282–95.
Yazar, Seyhan, Jose Alquicira-Hernandez, Kristof Wing, Anne Senabouth, M Grace Gordon, Stacey Andersen, Qinyi Lu, et al. 2022. “Single-Cell eQTL Mapping Identifies Cell Type-Specific Genetic Control of Autoimmune Disease.” Science 376 (6589): eabf3041.
Young, Matthew D, and Sam Behjati. 2020. “SoupX Removes Ambient RNA Contamination from Droplet-Based Single-Cell RNA Sequencing Data.” Gigascience 9 (12): giaa151.
Yu, Hengshi, and Joshua D Welch. 2022. “Perturbnet Predicts Single-Cell Responses to Unseen Chemical and Genetic Perturbations.” BioRxiv, 2022–07.
Yu, Lei, Xinlei Wang, Quanhua Mu, Sindy Sing Ting Tam, Danson Shek Chun Loi, Aden KY Chan, Wai Sang Poon, et al. 2023. “scONE-Seq: A Single-Cell Multi-Omics Method Enables Simultaneous Dissection of Phenotype and Genotype Heterogeneity from Frozen Tumors.” Science Advances 9 (1): eabp8901.
Yu, Lijia, Yue Cao, Jean YH Yang, and Pengyi Yang. 2022. “Benchmarking Clustering Algorithms on Estimating the Number of Cell Types from Single-Cell RNA-Sequencing Data.” Genome Biology 23 (1): 49.
Yuan, Qiuyue, and Zhana Duren. 2024. “Inferring Gene Regulatory Networks from Single-Cell Multiome Data Using Atlas-Scale External Data.” Nature Biotechnology, 1–11.
Zafar, Hamim, Chieh Lin, and Ziv Bar-Joseph. 2020. “Single-Cell Lineage Tracing by Integrating CRISPR-Cas9 Mutations with Transcriptomic Data.” Nature Communications 11 (1): 3055.
Zeng, Hongkui. 2022. “What Is a Cell Type and How to Define It?” Cell 185 (15): 2739–55.
Zhang, Le, Wanyu Bai, Na Yuan, and Zhenglin Du. 2019. “Comprehensively Benchmarking Applications for Detecting Copy Number Variation.” PLoS Computational Biology 15 (5): e1007069.
Zhang, Martin Jinye, Kangcheng Hou, Kushal K Dey, Saori Sakaue, Karthik A Jagadeesh, Kathryn Weinand, Aris Taychameekiatchai, et al. 2022. “Polygenic Enrichment Distinguishes Disease Associations of Individual Cells in Single-Cell RNA-Seq Data.” Nature Genetics 54 (10): 1572–80.
Zhang, Meng, Xingjie Pan, Won Jung, Aaron Halpern, Stephen W Eichhorn, Zhiyun Lei, Limor Cohen, et al. 2023. “A Molecularly Defined and Spatially Resolved Cell Atlas of the Whole Mouse Brain.” bioRxiv, 2023–03.
Zhang, Mengqi, Si Liu, Zhen Miao, Fang Han, Raphael Gottardo, and Wei Sun. 2022. IDEAS: Individual Level Differential Expression Analysis for Single-Cell RNA-Seq Data.” Genome Biology 23 (1): 1–17.
Zhang, Qiuyu, Wenjie Cao, Jiaqi Wang, Yihao Yin, Rui Sun, Zunyi Tian, Yuhan Hu, Yalan Tan, and Ben-gong Zhang. 2024. “Transcriptional Bursting Dynamics in Gene Expression.” Frontiers in Genetics 15: 1451461.
Zhang, Ran, Laetitia Meng-Papaxanthos, Jean-philippe Vert, and William Stafford Noble. 2022. “Multimodal Single-Cell Translation and Alignment with Semi-Supervised Learning.” Journal of Computational Biology 29 (11): 1198–1212.
Zhang, Shixiong, Xiangtao Li, Qiuzhen Lin, and Ka-Chun Wong. 2020. “Review of Single-Cell RNA-Seq Data Clustering for Cell Type Identification and Characterization.” arXiv Preprint arXiv:2001.01006.
Zhang, Xiaoli, Yirui Huang, Yajing Yang, Qi-En Wang, and Lang Li. 2024. “Advancements in Prospective Single-Cell Lineage Barcoding and Their Applications in Research.” Genome Research 34 (12): 2147–62.
Zhang, Xinyuan, Yanqiu Feng, Wufan Chen, Xin Li, Andreia V Faria, Qianjin Feng, and Susumu Mori. 2019. “Linear Registration of Brain Mri Using Knowledge-Based Multiple Intermediator Libraries.” Frontiers in Neuroscience 13: 909.
Zhang, Yifan, Duc Tran, Tin Nguyen, Sergiu M Dascalu, and Frederick C Harris Jr. 2023. “A Robust and Accurate Single-Cell Data Trajectory Inference Method Using Ensemble Pseudotime.” BMC Bioinformatics 24 (1): 55.
Zhang, Ying, and Marc-André Sirard. 2021. “Epigenetic Inheritance of Acquired Traits Through DNA Methylation.” Animal Frontiers 11 (6): 19–27.
Zhang, Yuqing, Giovanni Parmigiani, and W Evan Johnson. 2020. “ComBat-Seq: Batch Effect Adjustment for RNA-Seq Count Data.” NAR Genomics and Bioinformatics 2 (3): lqaa078.
Zhang, Zhaojun, Divij Mathew, Tristan L Lim, Kaishu Mason, Clara Morral Martinez, Sijia Huang, E John Wherry, et al. 2024. “Recovery of Biological Signals Lost in Single-Cell Batch Integration with CellANOVA.” Nature Biotechnology, 1–17.
Zhang, Ziqi, Haoran Sun, Ragunathan Mariappan, Xi Chen, Xinyu Chen, Mika S Jain, Mirjana Efremova, Sarah A Teichmann, Vaibhav Rajan, and Xiuwei Zhang. 2023. “scMoMaT Jointly Performs Single Cell Mosaic Integration and Multi-Modal Bio-Marker Detection.” Nature Communications 14 (1): 384.
Zhang, Ziqi, Chengkai Yang, and Xiuwei Zhang. 2022. “scDART: Integrating Unmatched scRNA-Seq and scATAC-Seq Data and Learning Cross-Modality Relationship Simultaneously.” Genome Biology 23 (1): 139.
Zhao, Ruzhang, Jiuyao Lu, Weiqiang Zhou, Ni Zhao, and Hongkai Ji. 2024. “A Systematic Evaluation of Highly Variable Gene Selection Methods for Single-Cell RNA-Sequencing.” bioRxiv, 2024–08.
Zhou, Jessica L, Karthik Guruvayurappan, Shushan Toneyan, Hsiuyi V Chen, Aaron R Chen, Peter Koo, and Graham McVicker. 2024. “Analysis of Single-Cell CRISPR Perturbations Indicates That Enhancers Predominantly Act Multiplicatively.” Cell Genomics 4 (11).
Zhou, Ran, Gaoxia Yang, Yan Zhang, and Yuan Wang. 2023. “Spatial Transcriptomics in Development and Disease.” Molecular Biomedicine 4 (1): 32.
Zhou, Yichao, Temidayo Adeluwa, Lisha Zhu, Sofia Salazar, Sarah Sumner, Hyunki Kim, Saideep Gona, et al. 2024. “scPrediXcan Integrates Advances in Deep Learning and Single-Cell Data into a Powerful Cell-Type–Specific Transcriptome-Wide Association Study Framework.” bioRxiv, 2024–11.
Zhou, Yifan, Kaixuan Luo, Lifan Liang, Mengjie Chen, and Xin He. 2023. “A New Bayesian Factor Analysis Method Improves Detection of Genes and Biological Processes Affected by Perturbations in Single-Cell CRISPR Screening.” Nature Methods 20 (11): 1693–703.
Zhou, Yi, Hongjun Song, and Guo-li Ming. 2024. “Genetics of Human Brain Development.” Nature Reviews Genetics 25 (1): 26–45.
Zhu, Bokai, Shuxiao Chen, Yunhao Bai, Han Chen, Nilanjan Mukherjee, Gustavo Vazquez, David R McIlwain, et al. 2021. “Robust Single-Cell Matching and Multi-Modal Analysis Using Shared and Distinct Features Reveals Orchestrated Immune Responses.” bioRxiv.
Zhu, Chenxu, Yanxiao Zhang, Yang Eric Li, Jacinta Lucero, M Margarita Behrens, and Bing Ren. 2021. “Joint Profiling of Histone Modifications and Transcriptome in Single Cells from Mouse Brain.” Nature Methods, 1–10.
Zhuang, Yonghua, Kristen Wade, Laura M Saba, and Katerina Kechris. 2019. “Development of a Tissue Augmented Bayesian Model for Expression Quantitative Trait Loci Analysis.” Mathematical Biosciences and Engineering: MBE 17 (1): 122.
Ziegler, Lukas M von, Amalia Floriou-Servou, Rebecca Waag, Rebecca R Das Gupta, Oliver Sturman, Katharina Gapp, Christina A Maat, et al. 2022. “Multiomic Profiling of the Acute Stress Response in the Mouse Hippocampus.” Nature Communications 13 (1): 1824.
Zou, Yuxin, Peter Carbonetto, Gao Wang, and Matthew Stephens. 2022. “Fine-Mapping from Summary Data with the ‘Sum of Single Effects’ Model.” PLoS Genetics 18 (7): e1010299.
Zverinova, Stepanka, and Victor Guryev. 2022. “Variant Calling: Considerations, Practices, and Developments.” Human Mutation 43 (8): 976–85.