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Ritambhara Singh - Publications

Affiliations: 
Department of Computer Science University of Virginia Charlottesville 
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19 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Zhang J, Singh R. Investigating the Complexity of Gene Co-expression Estimation for Single-cell Data. Biorxiv : the Preprint Server For Biology. PMID 36747724 DOI: 10.1101/2023.01.24.525447  0.339
2022 Berger B, Tian D, Li WV, El-Kebir M, Tomescu AI, Singh R, Beerenwinkel N, Li Y, Boucher C, Bar-Joseph Z. What are the keys to succeeding as a computational biologist in today's research climate? Cell Systems. 13: 781-785. PMID 36265464 DOI: 10.1016/j.cels.2022.09.005  0.474
2022 Demetci P, Santorella R, Chakravarthy M, Sandstede B, Singh R. SCOTv2: Single-Cell Multiomic Alignment with Disproportionate Cell-Type Representation. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 36251763 DOI: 10.1089/cmb.2022.0270  0.765
2022 Bigness J, Loinaz X, Patel S, Larschan E, Singh R. Integrating Long-Range Regulatory Interactions to Predict Gene Expression Using Graph Convolutional Networks. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 35325548 DOI: 10.1089/cmb.2021.0316  0.62
2022 Demetci P, Santorella R, Sandstede B, Noble WS, Singh R. SCOT: Single-Cell Multi-Omics Alignment with Optimal Transport. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 29: 3-18. PMID 35050714 DOI: 10.1089/cmb.2021.0446  0.754
2022 Demetci P, Santorella R, Sandstede B, Noble WS, Singh R. Single-Cell Multiomics Integration by SCOT. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 34985990 DOI: 10.1089/cmb.2021.0477  0.751
2021 Bonora G, Ramani V, Singh R, Fang H, Jackson DL, Srivatsan S, Qiu R, Lee C, Trapnell C, Shendure J, Duan Z, Deng X, Noble WS, Disteche CM. Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation. Genome Biology. 22: 279. PMID 34579774 DOI: 10.1186/s13059-021-02432-w  0.524
2021 Conard AM, Goodman N, Hu Y, Perrimon N, Singh R, Lawrence C, Larschan E. TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data. Nucleic Acids Research. PMID 34125906 DOI: 10.1093/nar/gkab384  0.678
2020 Singh R, Demetci P, Bonora G, Ramani V, Lee C, Fang H, Duan Z, Deng X, Shendure J, Disteche C, Noble WS. Unsupervised manifold alignment for single-cell multi-omics data. Acm-Bcb ... ... : the ... Acm Conference On Bioinformatics, Computational Biology and Biomedicine. Acm Conference On Bioinformatics, Computational Biology and Biomedicine. 2020: 1-10. PMID 33954299 DOI: 10.1145/3388440.3412410  0.75
2020 Blakely D, Collins E, Singh R, Norton A, Lanchantin J, Qi Y. FastSK: fast sequence analysis with gapped string kernels. Bioinformatics (Oxford, England). 36: i857-i865. PMID 33381828 DOI: 10.1093/bioinformatics/btaa817  0.526
2020 Schreiber J, Singh R, Bilmes J, Noble WS. A pitfall for machine learning methods aiming to predict across cell types. Genome Biology. 21: 282. PMID 33213499 DOI: 10.1186/s13059-020-02177-y  0.548
2019 Liu J, Huang Y, Singh R, Vert JP, Noble WS. Jointly Embedding Multiple Single-Cell Omics Measurements. Algorithms in Bioinformatics : ... International Workshop, Wabi ..., Proceedings. Wabi (Workshop). 143. PMID 34632462 DOI: 10.4230/LIPIcs.WABI.2019.10  0.629
2018 Sekhon A, Singh R, Qi Y. DeepDiff: DEEP-learning for predicting DIFFerential gene expression from histone modifications. Bioinformatics (Oxford, England). 34: i891-i900. PMID 30423076 DOI: 10.1093/Bioinformatics/Bty612  0.577
2017 Singh R, Lanchantin J, Sekhon A, Qi Y. Attend and Predict: Understanding Gene Regulation by Selective Attention on Chromatin. Advances in Neural Information Processing Systems. 30: 6785-6795. PMID 30147283  0.6
2017 Wang B, Singh R, Qi Y. A constrained $$\ell $$1 minimization approach for estimating multiple sparse Gaussian or nonparanormal graphical models Machine Learning. 106: 1381-1417. DOI: 10.1007/S10994-017-5635-7  0.675
2016 Lanchantin J, Singh R, Wang B, Qi Y. DEEP MOTIF DASHBOARD: VISUALIZING AND UNDERSTANDING GENOMIC SEQUENCES USING DEEP NEURAL NETWORKS. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 22: 254-265. PMID 27896980  0.682
2016 Singh R, Lanchantin J, Robins G, Qi Y. Transfer String Kernel for Cross-Context DNA-Protein Binding Prediction. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. PMID 27654939 DOI: 10.1109/Tcbb.2016.2609918  0.549
2016 Singh R, Lanchantin J, Robins G, Qi Y. DeepChrome: deep-learning for predicting gene expression from histone modifications. Bioinformatics (Oxford, England). 32: i639-i648. PMID 27587684 DOI: 10.1093/Bioinformatics/Btw427  0.545
2015 Singh R, Kuscu C, Quinlan A, Qi Y, Adli M. Cas9-chromatin binding information enables more accurate CRISPR off-target prediction. Nucleic Acids Research. PMID 26032770 DOI: 10.1093/Nar/Gkv575  0.545
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