Computational Challenges in Very Large-Scale 'Omics'
2022-07-18..2022-07-21
Berkeley, United States
who it's for
single-cell genomics researchers, computational biologists, genomics data scientists, bioinformatics engineers, sequencing technology developers, evolutionary genomics researchers, clinical genomics researchers
topics
single-cell isoform sequencing; spatial transcriptomics integration; multimodal variational autoencoders; zero-inflated negative binomial models; long-read transcriptome analysis; petabase-scale sequence alignment; phylogenomics and tree of life; pooled iPSC single-cell eQTL mapping; nanopore basecalling methods; whole-genome methylation imputation; synthetic single-cell data simulation; single-cell Hi-C analysis
| title | author | length |
|---|---|---|
| Single Cell Brain Isoforms in Space and Time | Hagen Tilgner | 42m |
Develops long-read single-cell and single-nucleus methods (ScISOr-Seq, SnISOr-Seq) plus spatial Slide-isoform sequencing to map full-length isoforms to cell… | ||
| Benchmarking, Inference, and in Silico Controls in Single-Cell and Spatial Omics Data Science | Jingyi Jessica Li | 32m |
scDesign3 is a unified probabilistic simulator that generates single-cell and spatial omics from discrete cell types and continuous trajectories using marginal… | ||
| Learning Gene Association Networks Using Single-Cell RNA-Seq Data: A Graphical Model Approach | Davide Risso | 34m |
Framework learns gene association graphs by fitting node-conditional regressions with a zero-inflated negative binomial (covering NB and Poisson limits)… | ||
| Harnessing Multimodal Single-Cell Sequencing Data for Integrative Analysis | Elizabeth Purdom | 29m |
Presents Cobolt, a method that uses a Multimodal Variational Autoencoder with an LDA-style generative layer to learn shared latent cell states from mixed… | ||
| Learning From Large-Scale (Single-Cell) ‘Omics’ | Lior Pachter | 34m |
Argues that mechanistic bursty transcription explains the negative binomial counts and that common pipelines like depth normalization plus log or SCTransform… | ||
| Panel Discussion | Sandrine Dudoit, Ana Conesa | 01h 24m |
Surveyed panelists synthesize concrete gaps and wins: reproducibility and benchmarking lag despite production of massive single cell and long read datasets… | ||
| Mapping Gene Regulatory Dependencies with Single-Cell Resolution | Oliver Stegle | 27m |
Population-scale pooled iPSC single-cell RNA-seq generates ~1M cells from 215 donors, 10 pools of ~20 lines, sampled at days 11/30/52, and maps… | ||
| Exploratory and Model-Based Analysis of ScHi-C Data | Sunduz Keles | 35m |
Simple per-band scaling that adds back an average band decay (BandNorm) runs in ~15 minutes and often matches more complex methods on cell-type separation, but… | ||
| Multiple Sequence Alignment for Predicting Antigen-Antibody Interactions | Kazutaka Katoh | 33m |
MAFFT gains a codon-based alignment option and a multi-step workflow that preserves novel insertions so millions of SARS-CoV-2 genomes can be aligned… | ||
| The Earth Biogenome Project: Progress and the Challenges Ahead | Harris Lewin | 36m |
Global effort aims to sequence 1.8 million eukaryotic species in 10 years, with Phase I targeting ~9,600 taxonomic families in about three years; current… | ||
| Evolution of Germline Mutation Spectrum in Humans | Priya Moorjani | 33m |
Reconstructs whole-genome genealogies from 1000 Genomes (an ARG reconstruction placing ~10 million mutations on dated branches) and compares mutation-type… | ||
| Sequence Bioinformatics at Large Scale: Petabase-Scale Sequence Alignment Catalyses Viral Discovery | Rayan Chikhi | 29m |
Cloud pipeline Serratus aligns 5.7 million RNA‑seq runs (≈10 PB) without full downloads by using spot cloud instances (up to ~20,000 vCPUs) and streaming… | ||
| Long-Read Transcriptome Complexity and Cell-Type Regulatory Signatures in ENCODE4 | Ali Mortazavi | 32m |
ENCODE4 sequences 216 long‑read RNA libraries (about 1 billion CCS reads) across 60 human and mouse samples and reports >100,000 full‑length transcripts with… | ||
| Leveraging Long Reads Sequencing for Developing a Functional Iso-Transcriptomics Analysis Framework | Ana Conesa | 36m |
A functional iso‑transcriptomics pipeline (FIT) combines SQANTI curation of long‑read (PacBio/Nanopore) transcripts, IsoAnnot annotation of RNA/protein… | ||
| Multi-Omic Integration for Understanding Disease | Ron Shamir | 32m |
Benchmarks on 10 TCGA cancers using three omics (mRNA, miRNA, methylation) produce a kernel neighbor–based integrator called NEMO that averages per-omic… | ||
| The Epigenetic Logic of Gene Activation | Roderic Guigó | 36m |
Dense RNA-seq and ChIP-seq are collected across 12 time points during B‑cell to macrophage transdifferentiation and show that steady‑state correlations… | ||
| Profiling of Antibody Repertoires and Immunoglobulin Loci Enables Large-Scale Analysis of... | Yana Safonova | 30m |
Uses Rep-seq and WGS data to link specific germline variation and recombination mechanics to real repertoire outcomes. QTLs show a ~5 kb locus controlling… | ||
| Leveraging Molecular Data for Drug Discovery | Haiyan Huang | 30m |
Proposes a rank-based count statistic with derived asymptotic properties to detect drug–disease expression reversals and a gene-level score to flag potential… | ||
| The Rewards and Challenges of Constructing Patient Registries in Mexico | Alejandra Medina-Rivera | 28m |
Three nationwide registries (TwinsMX, LupusRGMX, MEX‑PD) collect online REDCap surveys, biobanked DNA and genotypes to fill a Latino gap in genomics: ~3,000… | ||
| Whole Genome Methylation Patterns as a Biomarkers for EHR Imputation | Eran Halperin | 31m |
Whole‑genome blood methylation yields measurable imputation gains over genetics and simple baselines using only ~800 biobank samples, with the biggest wins on… | ||
| Biological Discovery and Consumer Genomics Databases Activate Latent Privacy Risk in... | Steven Brenner | 28m |
Claims that summary omics (gene expression, methylation) can be linked to unique genomes by inferring genotype from QTL signals and then matched to GEDmatch or… | ||
| How Do We Deliver Precision Health at Scale for All? | Carlos Bustamante | 32m |
Built a CLIA CAP lab in Miami and a Biobank of the Americas that already stores 80,000 samples (62,000 recontactable), sequences ~10,000 this year with a goal… | ||
| Longitudinal Phenotypes and Disease Trajectories at Population Scale | Søren Brunak | 34m |
Population-wide Danish healthcare data is condensed into recurrent longitudinal phenotypes by testing directional co-occurrence and building linear… | ||
| Towards Making Identification of Noncoding Causes of Human Disease Routine | Timothy Reddy | 31m |
Workflows move from GWAS hit to mechanism: a gestational‑hyperglycemia locus leads to cloning and enzymatic assay showing HKDC1 has low but real hexokinase… | ||
| Nanopore Basecalling for Directed Evolution | Ian Holmes | 28m |
Derives a systematic approximation that turns an infinitesimal indel generator into a time-dependent pair HMM with nine transition probabilities reduced to… | ||
| Breaking the Winner's Curse in Mendelian Randomization: Rerandomized Inverse Variance... | Jingshen Wang | 29m |
Proposes a rerandomized inverse-variance weighted (RIVW) estimator that adds Gaussian noise to selection statistics, then constructs unbiased association… | ||
| Computational Challenges in a Densely Sequenced Tree of Life | Katie Pollard | 44m |
Genome alignment to huge reference collections breaks: simulations show up to 50% of reads cross-map to a close neighbor, degrading SNV recall especially for… | ||
| New Approaches for Phylogenetic Species Tree Estimation | Tandy Warnow | 32m |
Three concrete claims: quartet theory gives statistically consistent species-tree inference under ILS/GDL/HGT and is implemented in ASTRAL/ASTRAL‑Pro which… | ||
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