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scDOT: optimal transport for mapping senescent cells in spatial transcriptomics.
- Published in:
- Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03426-0
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- Publication type:
- Article
Carbon catabolite repression correlates with the maintenance of near invariant molecular crowding in proliferating E. coli cells.
- Published in:
- BMC Systems Biology, 2013, v. 7, n. 1, p. 2, doi. 10.1186/1752-0509-7-138
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- Publication type:
- Article
DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data.
- Published in:
- BMC Systems Biology, 2012, v. 6, n. 1, p. 104, doi. 10.1186/1752-0509-6-104
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- Publication type:
- Article
Impact of the solvent capacity constraint on E. coli metabolism.
- Published in:
- BMC Systems Biology, 2008, v. 2, p. 1, doi. 10.1186/1752-0509-2-7
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- Publication type:
- Article
MassExodus: modeling evolving networks in harsh environments.
- Published in:
- Data Mining & Knowledge Discovery, 2015, v. 29, n. 5, p. 1211, doi. 10.1007/s10618-014-0399-1
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- Publication type:
- Article
Selecting the most appropriate time points to profile in high-throughput studies.
- Published in:
- eLife, 2017, p. 1, doi. 10.7554/eLife.18541
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- Publication type:
- Article
Hercules: a profile HMM-based hybrid error correction algorithm for long reads.
- Published in:
- Nucleic Acids Research, 2018, v. 46, n. 21, p. e125, doi. 10.1093/nar/gky724
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- Publication type:
- Article
Using neural networks for reducing the dimensions of single-cell RNA-Seq data.
- Published in:
- Nucleic Acids Research, 2017, v. 45, n. 17, p. 1, doi. 10.1093/nar/gkx681
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- Publication type:
- Article
ModuleBlast: identifying activated sub-networks within and across species.
- Published in:
- Nucleic Acids Research, 2015, v. 43, n. 3, p. e20, doi. 10.1093/nar/gku1224
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- Publication type:
- Article
Probabilistic error correction for RNA sequencing.
- Published in:
- Nucleic Acids Research, 2013, v. 41, n. 10, p. e109, doi. 10.1093/nar/gkt215
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- Publication type:
- Article
Discovering pathways by orienting edges in protein interaction networks.
- Published in:
- Nucleic Acids Research, 2011, v. 39, n. 4, p. e22, doi. 10.1093/nar/gkq1207
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- Publication type:
- Article
A probabilistic generative model for GO enrichment analysis.
- Published in:
- Nucleic Acids Research, 2008, v. 36, n. 17, p. e109, doi. 10.1093/nar/gkn434
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- Publication type:
- Article
Interactive single-cell data analysis using Cellar.
- Published in:
- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-29744-0
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- Publication type:
- Article
Membrane marker selection for segmenting single cell spatial proteomics data.
- Published in:
- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-29667-w
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- Publication type:
- Article
Combined static and dynamic analysis for determining the quality of time-series expression profiles.
- Published in:
- Nature Biotechnology, 2005, v. 23, n. 12, p. 1503, doi. 10.1038/nbt1164
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- Publication type:
- Article
ExpressionBlast: mining large, unstructured expression databases.
- Published in:
- Nature Methods, 2013, v. 10, n. 10, p. 925, doi. 10.1038/nmeth.2630
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- Publication type:
- Article
Construction of integrated microRNA and mRNA immune cell signatures to predict survival of patients with breast and ovarian cancer.
- Published in:
- Genes, Chromosomes & Cancer, 2019, v. 58, n. 1, p. 34, doi. 10.1002/gcc.22688
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- Publication type:
- Article
SpatialOne: end-to-end analysis of visium data at scale.
- Published in:
- Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae509
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- Publication type:
- Article
Integrating patients in time series clinical transcriptomics data.
- Published in:
- Bioinformatics, 2024, v. 40, p. i151, doi. 10.1093/bioinformatics/btae241
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- Publication type:
- Article
Representations of lipid nanoparticles using large language models for transfection efficiency prediction.
- Published in:
- Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae342
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- Publication type:
- Article
Deriving spatial features from in situ proteomics imaging to enhance cancer survival analysis.
- Published in:
- Bioinformatics, 2023, v. 39, p. i140, doi. 10.1093/bioinformatics/btad245
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- Publication type:
- Article
Clustering spatial transcriptomics data.
- Published in:
- Bioinformatics, 2022, v. 38, n. 4, p. 997, doi. 10.1093/bioinformatics/btab704
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- Publication type:
- Article
Dhaka: variational autoencoder for unmasking tumor heterogeneity from single cell genomic data.
- Published in:
- Bioinformatics, 2021, v. 37, n. 11, p. 1535, doi. 10.1093/bioinformatics/btz095
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- Publication type:
- Article
Identifying signaling genes in spatial single-cell expression data.
- Published in:
- Bioinformatics, 2021, v. 37, n. 7, p. 968, doi. 10.1093/bioinformatics/btaa769
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- Publication type:
- Article
scSTEM: clustering pseudotime ordered single-cell data.
- Published in:
- Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02716-9
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- Publication type:
- Article
TraSig: inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data.
- Published in:
- Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02629-7
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- Publication type:
- Article
GCNG: graph convolutional networks for inferring gene interaction from spatial transcriptomics data.
- Published in:
- Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-02214-w
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- Publication type:
- Article
Comparative Expression Profile of miRNA and mRNA in Primary Peripheral Blood Mononuclear Cells Infected with Human Immunodeficiency Virus (HIV-1).
- Published in:
- PLoS ONE, 2011, v. 6, n. 7, p. 1, doi. 10.1371/journal.pone.0022730
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- Publication type:
- Article
IL-3 and Oncogenic Abl Regulate the Myeloblast Transcriptome by Altering mRNA Stability.
- Published in:
- PLoS ONE, 2009, v. 4, n. 10, p. 1, doi. 10.1371/journal.pone.0007469
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- Publication type:
- Article
Evaluation of different biological data and computational classification methods for use in protein interaction prediction.
- Published in:
- Proteins, 2006, v. 63, n. 3, p. 490, doi. 10.1002/prot.20865
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- Publication type:
- Article
MicroRNA regulation and its effects on cellular transcriptome in Human Immunodeficiency Virus-1 (HIV-1) infected individuals with distinct viral load and CD4 cell counts.
- Published in:
- BMC Infectious Diseases, 2013, v. 13, n. 1, p. 1, doi. 10.1186/1471-2334-13-250
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- Publication type:
- Article
MicroRNA regulation and its effects on cellular transcriptome in human immunodeficiency virus-1 (HIV-1) infected individuals with distinct viral load and CD4 cell counts.
- Published in:
- 2013
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- Publication type:
- journal article
Systematic prediction of human membrane receptor interactions.
- Published in:
- Proteomics, 2009, v. 9, n. 23, p. 5243, doi. 10.1002/pmic.200900259
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- Publication type:
- Article
Studying and modelling dynamic biological processes using time-series gene expression data.
- Published in:
- Nature Reviews Genetics, 2012, v. 13, n. 8, p. 552, doi. 10.1038/nrg3244
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- Publication type:
- Article
Hierarchical Context-based Pixel Ordering.
- Published in:
- Computer Graphics Forum, 2003, v. 22, n. 3, p. 349, doi. 10.1111/1467-8659.00682
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- Publication type:
- Article
A web server for comparative analysis of single-cell RNA-seq data.
- Published in:
- Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-07165-2
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- Publication type:
- Article
Reconstructing cancer drug response networks using multitask learning.
- Published in:
- BMC Systems Biology, 2017, v. 11, p. 1, doi. 10.1186/s12918-017-0471-8
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- Publication type:
- Article
CINS: Cell Interaction Network inference from Single cell expression data.
- Published in:
- PLoS Computational Biology, 2022, v. 18, n. 9, p. 1, doi. 10.1371/journal.pcbi.1010468
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- Publication type:
- Article
Algorithms in nature: the convergence of systems biology and computational thinking.
- Published in:
- Molecular Systems Biology, 2011, v. 7, n. 1, p. 1, doi. 10.1038/msb.2011.78
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- Publication type:
- Article
Backup in gene regulatory networks explains differences between binding and knockout results.
- Published in:
- Molecular Systems Biology, 2009, v. 5, n. 1, p. 276, doi. 10.1038/msb.2009.33
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- Publication type:
- Article
Reconstructing dynamic regulatory maps.
- Published in:
- Molecular Systems Biology, 2007, v. 3, n. 1, p. 74, doi. 10.1038/msb4100115
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- Publication type:
- Article
Decreasing-Rate Pruning Optimizes the Construction of Efficient and Robust Distributed Networks.
- Published in:
- PLoS Computational Biology, 2015, v. 11, n. 7, p. 1, doi. 10.1371/journal.pcbi.1004347
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- Publication type:
- Article
Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu.
- Published in:
- PLoS Computational Biology, 2014, v. 10, n. 12, p. 1, doi. 10.1371/journal.pcbi.1003943
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- Publication type:
- Article
A Network-based Approach for Predicting Missing Pathway Interactions.
- Published in:
- PLoS Computational Biology, 2012, v. 8, n. 8, p. 1, doi. 10.1371/journal.pcbi.1002640
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- Publication type:
- Article
A Semi-Supervised Method for Predicting Transcription Factor--Gene Interactions in Escherichia coli.
- Published in:
- PLoS Computational Biology, 2008, v. 4, n. 3, p. 1, doi. 10.1371/journal.pcbi.1000044
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- Publication type:
- Article
De novo ChIP-seq analysis.
- Published in:
- Genome Biology, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s13059-015-0756-4
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- Publication type:
- Article
Gene Expression in Relation to Exhaled Nitric Oxide Identifies Novel Asthma Phenotypes with Unique Biomolecular Pathways.
- Published in:
- American Journal of Respiratory & Critical Care Medicine, 2014, v. 190, n. 12, p. 1363, doi. 10.1164/rccm.201406-1099OC
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- Publication type:
- Article
Future directions in idiopathic pulmonary fibrosis research. An NHLBI workshop report.
- Published in:
- 2014
- By:
- Publication type:
- journal article
Future Directions in Idiopathic Pulmonary Fibrosis Research An NHLBI Workshop Report.
- Published in:
- American Journal of Respiratory & Critical Care Medicine, 2014, v. 189, n. 2, p. 214, doi. 10.1164/rccm.201306-1141WS
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- Publication type:
- Article
Protein interaction disruption in cancer.
- Published in:
- 2019
- By:
- Publication type:
- journal article