Author: Manolis Kellis

Downloads per author, site-wide

Preprints

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

• Downloaded 5,458 times
• Download rankings, all-time:
  • Site-wide: 1,760
  • In genomics: 168
• Year to date:
  • Site-wide: 20,076
• Since beginning of last month:
  • Site-wide: 21,377

Local genetic effects on gene expression across 44 human tissues

• Downloaded 4,452 times
• Download rankings, all-time:
  • Site-wide: 2,333
  • In genomics: 257
• Year to date:
  • Site-wide: 55,410
• Since beginning of last month:
  • Site-wide: 48,145

High-resolution genome-wide functional dissection of transcriptional regulatory regions in human

• Downloaded 3,911 times
• Download rankings, all-time:
  • Site-wide: 2,810
  • In genomics: 319
• Year to date:
  • Site-wide: 68,739
• Since beginning of last month:
  • Site-wide: 57,577

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

• Downloaded 3,870 times
• Download rankings, all-time:
  • Site-wide: 2,857
  • In infectious diseases: 569
• Year to date:
  • Site-wide: 427
• Since beginning of last month:
  • Site-wide: 488

Thousands of novel unannotated proteins expand the MHC I immunopeptidome in cancer

• Downloaded 3,754 times
• Download rankings, all-time:
  • Site-wide: 2,990
  • In cancer biology: 43
• Year to date:
  • Site-wide: 2,009
• Since beginning of last month:
  • Site-wide: 1,764

Phylogenetic Identification and Functional Characterization of Orthologs and Paralogs across Human, Mouse, Fly, and Worm

• Downloaded 3,536 times
• Download rankings, all-time:
  • Site-wide: 3,255
  • In genomics: 367
• Year to date:
  • Site-wide: 13,543
• Since beginning of last month:
  • Site-wide: 14,607

Integrative analysis of 10,000 epigenomic maps across 800 samples for regulatory genomics and disease dissection

• Downloaded 3,369 times
• Download rankings, all-time:
  • Site-wide: 3,493
  • In genomics: 392
• Year to date:
  • Site-wide: 2,284
• Since beginning of last month:
  • Site-wide: 4,528

A Bayesian approach to mediation analysis predicts 206 causal target genes in Alzheimer's disease

• Downloaded 3,361 times
• Download rankings, all-time:
  • Site-wide: 3,511
  • In genetics: 137
• Year to date:
  • Site-wide: 18,110
• Since beginning of last month:
  • Site-wide: 16,164

Distant regulatory effects of genetic variation in multiple human tissues

• Downloaded 2,768 times
• Download rankings, all-time:
  • Site-wide: 4,609
  • In genomics: 514
• Year to date:
  • Site-wide: 64,297
• Since beginning of last month:
  • Site-wide: 61,970

Single-cell dissection of schizophrenia reveals neurodevelopmental-synaptic axis and transcriptional resilience

• Downloaded 2,582 times
• Download rankings, all-time:
  • Site-wide: 5,091
  • In psychiatry and clinical psychology: 15
• Year to date:
  • Site-wide: 1,719
• Since beginning of last month:
  • Site-wide: 1,816

Simultaneous profiling of DNA methylation and chromatin architecture in mixed populations and in single cells

• Downloaded 2,438 times
• Download rankings, all-time:
  • Site-wide: 5,574
  • In genomics: 639
• Year to date:
  • Site-wide: 40,734
• Since beginning of last month:
  • Site-wide: 37,693

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

• Downloaded 2,357 times
• Download rankings, all-time:
  • Site-wide: 5,840
  • In genomics: 662
• Year to date:
  • Site-wide: 4,692
• Since beginning of last month:
  • Site-wide: 5,760

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

• Downloaded 2,245 times
• Download rankings, all-time:
  • Site-wide: 6,279
  • In bioinformatics: 730
• Year to date:
  • Site-wide: 80,558
• Since beginning of last month:
  • Site-wide: 86,036

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

• Downloaded 2,092 times
• Download rankings, all-time:
  • Site-wide: 6,949
  • In genomics: 769
• Year to date:
  • Site-wide: 126,309
• Since beginning of last month:
  • Site-wide: 110,068

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

• Downloaded 2,037 times
• Download rankings, all-time:
  • Site-wide: 7,217
  • In bioinformatics: 858
• Year to date:
  • Site-wide: 94,488
• Since beginning of last month:
  • Site-wide: 128,933

mRNA structure dynamics identifies the embryonic RNA regulome

• Downloaded 1,927 times
• Download rankings, all-time:
  • Site-wide: 7,860
  • In molecular biology: 196
• Year to date:
  • Site-wide: 69,968
• Since beginning of last month:
  • Site-wide: 56,768

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

• Downloaded 1,877 times
• Download rankings, all-time:
  • Site-wide: 8,193
  • In bioinformatics: 993
• Year to date:
  • Site-wide: 27,715
• Since beginning of last month:
  • Site-wide: 19,162

A multiresolution framework to characterize single-cell state landscapes

• Downloaded 1,872 times
• Download rankings, all-time:
  • Site-wide: 8,217
  • In genomics: 899
• Year to date:
  • Site-wide: 34,181
• Since beginning of last month:
  • Site-wide: 44,873

Modeling prediction error improves power of transcriptome-wide association studies

• Downloaded 1,856 times
• Download rankings, all-time:
  • Site-wide: 8,323
  • In genetics: 391
• Year to date:
  • Site-wide: 52,390
• Since beginning of last month:
  • Site-wide: 61,725

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

• Downloaded 1,807 times
• Download rankings, all-time:
  • Site-wide: 8,674
  • In systems biology: 157
• Year to date:
  • Site-wide: 47,054
• Since beginning of last month:
  • Site-wide: 37,735

Multi-tissue polygenic models for transcriptome-wide association studies

• Downloaded 1,800 times
• Download rankings, all-time:
  • Site-wide: 8,712
  • In genetics: 410
• Year to date:
  • Site-wide: 86,187
• Since beginning of last month:
  • Site-wide: 91,045

Convergence of dispersed regulatory mutations predicts driver genes in prostate cancer

• Downloaded 1,798 times
• Download rankings, all-time:
  • Site-wide: 8,719
  • In genomics: 951
• Year to date:
  • Site-wide: 24,683
• Since beginning of last month:
  • Site-wide: 26,216

Conserved epigenetic regulatory logic infers genes governing cell identity

• Downloaded 1,796 times
• Download rankings, all-time:
  • Site-wide: 8,738
  • In cell biology: 214
• Year to date:
  • Site-wide: 34,221
• Since beginning of last month:
  • Site-wide: 48,412

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

• Downloaded 1,750 times
• Download rankings, all-time:
  • Site-wide: 9,104
  • In genomics: 998
• Year to date:
  • Site-wide: 25,059
• Since beginning of last month:
  • Site-wide: 42,915

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

• Downloaded 1,634 times
• Download rankings, all-time:
  • Site-wide: 10,072
  • In synthetic biology: 107
• Year to date:
  • Site-wide: 9,836
• Since beginning of last month:
  • Site-wide: 6,739

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

• Downloaded 1,633 times
• Download rankings, all-time:
  • Site-wide: 10,076
  • In bioinformatics: 1,221
• Year to date:
  • Site-wide: 57,083
• Since beginning of last month:
  • Site-wide: 42,452

Single-cell deconvolution of 3,000 post-mortem brain samples for eQTL and GWAS dissection in mental disorders

• Downloaded 1,563 times
• Download rankings, all-time:
  • Site-wide: 10,735
  • In genomics: 1,169
• Year to date:
  • Site-wide: 606
• Since beginning of last month:
  • Site-wide: 1,773

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

• Downloaded 1,260 times
• Download rankings, all-time:
  • Site-wide: 14,848
  • In genetics: 735
• Year to date:
  • Site-wide: 99,391
• Since beginning of last month:
  • Site-wide: 91,415

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

• Downloaded 1,094 times
• Download rankings, all-time:
  • Site-wide: 18,311
  • In developmental biology: 314
• Year to date:
  • Site-wide: 27,844
• Since beginning of last month:
  • Site-wide: 26,093

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

• Downloaded 935 times
• Download rankings, all-time:
  • Site-wide: 23,006
  • In bioinformatics: 2,718
• Year to date:
  • Site-wide: 71,858
• Since beginning of last month:
  • Site-wide: 74,820

Evidence of a recombination rate valley in human regulatory domains

• Downloaded 921 times
• Download rankings, all-time:
  • Site-wide: 23,528
  • In genomics: 2,276
• Year to date:
  • Site-wide: 84,860
• Since beginning of last month:
  • Site-wide: 109,747

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

• Downloaded 919 times
• Download rankings, all-time:
  • Site-wide: 23,622
  • In bioinformatics: 2,794
• Year to date:
  • Site-wide: 41,731
• Since beginning of last month:
  • Site-wide: 57,224

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

• Downloaded 800 times
• Download rankings, all-time:
  • Site-wide: 28,702
  • In genomics: 2,641
• Year to date:
  • Site-wide: 27,081
• Since beginning of last month:
  • Site-wide: 28,703

Structural variant selection for high-altitude adaptation using single-molecule long-read sequencing

• Downloaded 795 times
• Download rankings, all-time:
  • Site-wide: 28,944
  • In genomics: 2,652
• Year to date:
  • Site-wide: 1,455
• Since beginning of last month:
  • Site-wide: 401

Evolutionary dynamics of abundant stop codon readthrough in Anopheles and Drosophila

• Downloaded 750 times
• Download rankings, all-time:
  • Site-wide: 31,426
  • In molecular biology: 886
• Year to date:
  • Site-wide: 75,157
• Since beginning of last month:
  • Site-wide: 49,451

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

• Downloaded 740 times
• Download rankings, all-time:
  • Site-wide: 32,014
  • In genomics: 2,845
• Year to date:
  • Site-wide: 113,953
• Since beginning of last month:
  • Site-wide: 129,579

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

• Downloaded 706 times
• Download rankings, all-time:
  • Site-wide: 34,107
  • In bioinformatics: 3,813
• Year to date:
  • Site-wide: 123,307
• Since beginning of last month:
  • Site-wide: 105,255

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

• Downloaded 633 times
• Download rankings, all-time:
  • Site-wide: 39,500
  • In cancer biology: 1,068
• Year to date:
  • Site-wide: 32,649
• Since beginning of last month:
  • Site-wide: 26,603

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

• Downloaded 618 times
• Download rankings, all-time:
  • Site-wide: 40,592
  • In epidemiology: 1,935
• Year to date:
  • Site-wide: 127,661
• Since beginning of last month:
  • Site-wide: 124,775

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

• Downloaded 615 times
• Download rankings, all-time:
  • Site-wide: 40,847
  • In genetics: 1,944
• Year to date:
  • Site-wide: 112,976
• Since beginning of last month:
  • Site-wide: 81,748

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

• Downloaded 592 times
• Download rankings, all-time:
  • Site-wide: 42,918
  • In genetics: 2,020
• Year to date:
  • Site-wide: 67,156
• Since beginning of last month:
  • Site-wide: 52,061

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

• Downloaded 570 times
• Download rankings, all-time:
  • Site-wide: 45,004
  • In bioinformatics: 4,762
• Year to date:
  • Site-wide: 79,351
• Since beginning of last month:
  • Site-wide: 79,543

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

• Downloaded 535 times
• Download rankings, all-time:
  • Site-wide: 48,559
  • In cancer biology: 1,361
• Year to date:
  • Site-wide: 133,131
• Since beginning of last month:
  • Site-wide: 128,439

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

• Downloaded 504 times
• Download rankings, all-time:
  • Site-wide: 52,130
  • In genetics: 2,433
• Year to date:
  • Site-wide: 131,181
• Since beginning of last month:
  • Site-wide: 126,431

Elucidation of Codon Usage Signatures across the Domains of Life

• Downloaded 501 times
• Download rankings, all-time:
  • Site-wide: 52,435
  • In evolutionary biology: 2,855
• Year to date:
  • Site-wide: 88,627
• Since beginning of last month:
  • Site-wide: 85,269

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

• Downloaded 497 times
• Download rankings, all-time:
  • Site-wide: 52,907
  • In neuroscience: 7,826
• Year to date:
  • Site-wide: 59,552
• Since beginning of last month:
  • Site-wide: 59,206

Counterfactual inference for single-cell gene expression analysis

• Downloaded 397 times
• Download rankings, all-time:
  • Site-wide: 66,930
  • In genetic and genomic medicine: 218
• Year to date:
  • Site-wide: 3,859
• Since beginning of last month:
  • Site-wide: 10,385