Author: Manolis Kellis

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Preprints

Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes

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  • Site-wide: 1,580
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Local genetic effects on gene expression across 44 human tissues

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  • Site-wide: 2,069
  • In genomics: 240
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High-resolution genome-wide functional dissection of transcriptional regulatory regions in human

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  • Site-wide: 2,485
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Phylogenetic Identification and Functional Characterization of Orthologs and Paralogs across Human, Mouse, Fly, and Worm

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  • Site-wide: 3,028
  • In genomics: 365
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A Bayesian approach to mediation analysis predicts 206 causal target genes in Alzheimer's disease

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  • Site-wide: 3,232
  • In genetics: 138
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  • Site-wide: 9,365
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Thousands of novel unannotated proteins expand the MHC I immunopeptidome in cancer

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  • Site-wide: 3,336
  • In cancer biology: 52
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Integrative analysis of 10,000 epigenomic maps across 800 samples for regulatory genomics and disease dissection

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  • Site-wide: 3,891
  • In genomics: 463
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Distant regulatory effects of genetic variation in multiple human tissues

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  • Site-wide: 4,107
  • In genomics: 489
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Simultaneous profiling of DNA methylation and chromatin architecture in mixed populations and in single cells

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DECODE-ing sparsity patterns in single-cell RNA-seq

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  • In bioinformatics: 680
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  • Site-wide: 70,380

Deep-coverage whole genome sequences and blood lipids among 16,324 individuals

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  • Site-wide: 6,159
  • In genomics: 724
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  • Site-wide: 99,017
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  • Site-wide: 117,644

SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes

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  • Site-wide: 6,318
  • In genomics: 742
• Year to date:
  • Site-wide: 5,670
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  • Site-wide: 4,981

A probabilistic framework to dissect functional cell-type-specific regulatory elements and risk loci underlying the genetics of complex traits

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  • Site-wide: 6,442
  • In bioinformatics: 793
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  • Site-wide: 48,473
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  • Site-wide: 49,769

Mathematical analysis of Cordoba calcifediol trial suggests strong role for Vitamin D in reducing ICU admissions of hospitalized COVID-19 patients

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  • Site-wide: 6,605
  • In infectious diseases: 872
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Single-cell dissection of schizophrenia reveals neurodevelopmental-synaptic axis and transcriptional resilience

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  • Site-wide: 6,741
  • In psychiatry and clinical psychology: 18
• Year to date:
  • Site-wide: 1,930
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  • Site-wide: 537

mRNA structure dynamics identifies the embryonic RNA regulome

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  • Site-wide: 7,050
  • In molecular biology: 170
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  • Site-wide: 56,112

Modeling prediction error improves power of transcriptome-wide association studies

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  • Site-wide: 7,488
  • In genetics: 372
• Year to date:
  • Site-wide: 25,719
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  • Site-wide: 33,551

A multiresolution framework to characterize single-cell state landscapes

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  • Site-wide: 7,533
  • In genomics: 857
• Year to date:
  • Site-wide: 18,568
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  • Site-wide: 30,165

Best practices for genome-wide RNA structure analysis: combination of mutational profiles and drop-off information

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  • Site-wide: 7,616
  • In bioinformatics: 967
• Year to date:
  • Site-wide: 21,872
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  • Site-wide: 13,189

Multi-tissue polygenic models for transcriptome-wide association studies

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  • Site-wide: 7,770
  • In genetics: 385
• Year to date:
  • Site-wide: 91,609
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  • Site-wide: 68,262

Single-cell interactomes of the human brain reveal cell-type specific convergence of brain disorders

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  • Site-wide: 7,902
  • In systems biology: 146
• Year to date:
  • Site-wide: 74,915
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  • Site-wide: 26,195

Conserved epigenetic regulatory logic infers genes governing cell identity

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  • Site-wide: 8,099
  • In cell biology: 199
• Year to date:
  • Site-wide: 36,761
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  • Site-wide: 16,175

Convergence of dispersed regulatory mutations predicts driver genes in prostate cancer

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  • Site-wide: 8,198
  • In genomics: 946
• Year to date:
  • Site-wide: 13,938
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  • Site-wide: 57,526

Nearly all new protein-coding predictions in the CHESS database are not protein-coding

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  • Site-wide: 8,680
  • In genomics: 1,007
• Year to date:
  • Site-wide: 40,315
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  • Site-wide: 29,141

Genome-wide regulatory model from MPRA data predicts functional regions, eQTLs, and GWAS hits

• Downloaded 1,598 times
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  • Site-wide: 9,182
  • In bioinformatics: 1,153
• Year to date:
  • Site-wide: 48,715
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  • Site-wide: 93,265

High-Throughput 5′ UTR Engineering for Enhanced Protein Production in Non-Viral Gene Therapies

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  • Site-wide: 10,736
  • In synthetic biology: 116
• Year to date:
  • Site-wide: 29,962
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  • Site-wide: 7,422

Functional enrichments of disease variants across thousands of independent loci in eight diseases

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  • Site-wide: 13,335
  • In genetics: 689
• Year to date:
  • Site-wide: 55,228
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  • Site-wide: 96,288

A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs.

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  • Site-wide: 18,267
  • In developmental biology: 321
• Year to date:
  • Site-wide: 47,777
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  • Site-wide: 35,165

Predicting trait regulators by identifying co-localization of DNA binding and GWAS variants in regulatory regions

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  • Site-wide: 21,312
  • In bioinformatics: 2,602
• Year to date:
  • Site-wide: 69,529
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  • Site-wide: 76,233

Evidence of a recombination rate valley in human regulatory domains

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  • Site-wide: 21,665
  • In genomics: 2,183
• Year to date:
  • Site-wide: 92,879
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  • Site-wide: 78,214

A causal inference framework for estimating genetic variance and pleiotropy from GWAS summary data

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  • Site-wide: 22,661
  • In bioinformatics: 2,760
• Year to date:
  • Site-wide: 28,845
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  • Site-wide: 61,415

Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries

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  • Site-wide: 28,970
  • In genomics: 2,676
• Year to date:
  • Site-wide: 58,621
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  • Site-wide: 115,808

Genus-wide characterization of bumblebee genomes reveals variation associated with key ecological and behavioral traits of pollinators

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  • Site-wide: 29,313
  • In genomics: 2,708
• Year to date:
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  • Site-wide: 17,554

Evolutionary dynamics of abundant stop codon readthrough in Anopheles and Drosophila

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  • Site-wide: 29,543
  • In molecular biology: 839
• Year to date:
  • Site-wide: 116,926
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  • Site-wide: 36,931

RiVIERA-beta: Joint Bayesian inference of risk variants and tissue-specific epigenomic enrichments across multiple complex human diseases

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  • Site-wide: 30,979
  • In bioinformatics: 3,573
• Year to date:
  • Site-wide: 112,995
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  • Site-wide: 110,859

Integrative construction of regulatory region networks in 127 human reference epigenomes by matrix factorization

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  • Site-wide: 36,887
  • In epidemiology: 1,726
• Year to date:
  • Site-wide: 111,409
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  • Site-wide: 121,386

Analysis of Genetically Regulated Gene Expression identifies a trauma type specific PTSD gene, SNRNP35

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  • Site-wide: 37,327
  • In genetics: 1,856
• Year to date:
  • Site-wide: 93,766
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  • Site-wide: 101,691

Evidence for secondary-variant genetic burden and non-random distribution across biological modules in a recessive ciliopathy

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  • Site-wide: 40,623
  • In genetics: 1,982
• Year to date:
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  • Site-wide: 77,096

Plasma-derived exosomal analysis and deconvolution enables prediction and tracking of melanoma checkpoint blockade response

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  • Site-wide: 40,744
  • In cancer biology: 1,135
• Year to date:
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  • Site-wide: 47,531

Correlating predicted epigenetic marks with expression data to find interactions between SNPs and genes

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  • Site-wide: 42,458
  • In bioinformatics: 4,604
• Year to date:
  • Site-wide: 87,444
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  • Site-wide: 53,858

Pan-cancer screen for mutations in non-coding elements with conservation and cancer specificity reveals correlations with expression and survival

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  • Site-wide: 43,938
  • In cancer biology: 1,228
• Year to date:
  • Site-wide: 118,855
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  • Site-wide: 119,787

Various localized epigenetic marks predict expression across 54 samples and reveal underlying chromatin state enrichments

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  • Site-wide: 47,456
  • In genetics: 2,310
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  • Site-wide: None
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  • Site-wide: 113,267

Elucidation of Codon Usage Signatures across the Domains of Life

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  • Site-wide: 49,421
  • In evolutionary biology: 2,800
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  • Site-wide: 100,850
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  • Site-wide: 121,200

Exome-wide age-of-onset analysis reveals exonic variants in ERN1, TACR3 and SPPL2C associated with Alzheimer's disease

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  • Site-wide: 51,645
  • In neuroscience: 7,821
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  • Site-wide: 76,665