Author: George McDonald Church

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Preprints

Vibrio natriegens, a new genomic powerhouse

• Downloaded 19,539 times
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  • Site-wide: 454
  • In genomics: 19
• Year to date:
  • Site-wide: 2,218
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  • Site-wide: 4,297

Reversal of ageing- and injury-induced vision loss by Tet-dependent epigenetic reprogramming

• Downloaded 18,961 times
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  • Site-wide: 465
  • In molecular biology: 5
• Year to date:
  • Site-wide: 1,637
• Since beginning of last month:
  • Site-wide: 6,071

Unified rational protein engineering with sequence-only deep representation learning

• Downloaded 12,047 times
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  • Site-wide: 820
  • In synthetic biology: 4
• Year to date:
  • Site-wide: 2,533
• Since beginning of last month:
  • Site-wide: 5,711

Inter-homologue repair in fertilized human eggs?

• Downloaded 10,432 times
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  • Site-wide: 1,003
  • In cell biology: 8
• Year to date:
  • Site-wide: 61,677
• Since beginning of last month:
  • Site-wide: 64,263

Expansion Sequencing: Spatially Precise In Situ Transcriptomics in Intact Biological Systems

• Downloaded 8,751 times
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  • Site-wide: 1,224
  • In genomics: 88
• Year to date:
  • Site-wide: 2,141
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  • Site-wide: 9,980

Highly-efficient Cas9-mediated transcriptional programming

• Downloaded 6,755 times
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  • Site-wide: 1,700
  • In synthetic biology: 13
• Year to date:
  • Site-wide: 8,087
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  • Site-wide: 9,791

Conneconomics: The Economics of Dense, Large-Scale, High-Resolution Neural Connectomics

• Downloaded 6,666 times
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  • Site-wide: 1,729
  • In neuroscience: 82
• Year to date:
  • Site-wide: 44,419
• Since beginning of last month:
  • Site-wide: 63,459

Extensive sequencing of seven human genomes to characterize benchmark reference materials

• Downloaded 6,469 times
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  • Site-wide: 1,805
  • In genomics: 145
• Year to date:
  • Site-wide: 46,087
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  • Site-wide: 75,852

Rapidly evolving homing CRISPR barcodes

• Downloaded 6,220 times
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  • Site-wide: 1,910
  • In synthetic biology: 15
• Year to date:
  • Site-wide: 70,373
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  • Site-wide: 74,955

Enabling large-scale genome editing by reducing DNA nicking

• Downloaded 6,159 times
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  • Site-wide: 1,933
  • In synthetic biology: 16
• Year to date:
  • Site-wide: 51,227
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  • Site-wide: 74,761

Highly multiplexed in situ protein imaging with signal amplification by Immuno-SABER

• Downloaded 5,877 times
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  • Site-wide: 2,055
  • In cell biology: 25
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  • Site-wide: 25,673
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  • Site-wide: 43,246

The predictive power of the microbiome exceeds that of genome-wide association studies in the discrimination of complex human disease

• Downloaded 5,717 times
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  • Site-wide: 2,138
  • In bioinformatics: 151
• Year to date:
  • Site-wide: 6,400
• Since beginning of last month:
  • Site-wide: 8,040

Barcoded oligonucleotides ligated on RNA amplified for multiplex and parallel in-situ analyses

• Downloaded 5,691 times
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  • Site-wide: 2,152
  • In cell biology: 30
• Year to date:
  • Site-wide: 12,322
• Since beginning of last month:
  • Site-wide: 43,122

Daisy-chain gene drives for the alteration of local populations

• Downloaded 5,444 times
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  • Site-wide: 2,274
  • In synthetic biology: 18
• Year to date:
  • Site-wide: 65,159
• Since beginning of last month:
  • Site-wide: 102,720

CasFinder: Flexible algorithm for identifying specific Cas9 targets in genomes

• Downloaded 5,414 times
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  • Site-wide: 2,290
  • In genomics: 199
• Year to date:
  • Site-wide: 18,268
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  • Site-wide: 15,790

Enzymatic DNA synthesis for digital information storage

• Downloaded 5,330 times
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  • Site-wide: 2,337
  • In synthetic biology: 19
• Year to date:
  • Site-wide: 20,139
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  • Site-wide: 14,493

Accurate chromosome-scale haplotype-resolved assembly of human genomes

• Downloaded 4,351 times
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  • Site-wide: 3,107
  • In bioinformatics: 252
• Year to date:
  • Site-wide: 6,516
• Since beginning of last month:
  • Site-wide: 11,736

Extensive Mammalian Germline Genome Engineering

• Downloaded 4,212 times
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  • Site-wide: 3,242
  • In synthetic biology: 32
• Year to date:
  • Site-wide: 5,409
• Since beginning of last month:
  • Site-wide: 5,930

Current CRISPR gene drive systems are likely to be highly invasive in wild populations

• Downloaded 4,176 times
• Download rankings, all-time:
  • Site-wide: 3,288
  • In synthetic biology: 33
• Year to date:
  • Site-wide: 55,181
• Since beginning of last month:
  • Site-wide: 74,936

A homing CRISPR mouse resource for barcoding and lineage tracing

• Downloaded 3,345 times
• Download rankings, all-time:
  • Site-wide: 4,476
  • In synthetic biology: 41
• Year to date:
  • Site-wide: 101,979
• Since beginning of last month:
  • Site-wide: 86,543

Single-sequence protein structure prediction using language models from deep learning

• Downloaded 3,327 times
• Download rankings, all-time:
  • Site-wide: 4,508
  • In bioinformatics: 419
• Year to date:
  • Site-wide: 868
• Since beginning of last month:
  • Site-wide: 158

Multiplexed in situ protein imaging using DNA-barcoded antibodies with extended hybridization chain reactions

• Downloaded 3,289 times
• Download rankings, all-time:
  • Site-wide: 4,590
  • In cell biology: 82
• Year to date:
  • Site-wide: 5,737
• Since beginning of last month:
  • Site-wide: 10,217

Rapid Sequential In Situ Multiplexing With DNA-Exchange-Imaging

• Downloaded 3,253 times
• Download rankings, all-time:
  • Site-wide: 4,654
  • In bioengineering: 46
• Year to date:
  • Site-wide: 104,813
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  • Site-wide: 104,999

Recombineering in Vibrio natriegens

• Downloaded 3,030 times
• Download rankings, all-time:
  • Site-wide: 5,149
  • In synthetic biology: 45
• Year to date:
  • Site-wide: 17,258
• Since beginning of last month:
  • Site-wide: 10,415

New intranasal and injectable gene therapy for healthy life extension

• Downloaded 3,024 times
• Download rankings, all-time:
  • Site-wide: 5,162
  • In cell biology: 98
• Year to date:
  • Site-wide: 990
• Since beginning of last month:
  • Site-wide: 2,115

Evolutionary dynamics of CRISPR gene drives

• Downloaded 2,823 times
• Download rankings, all-time:
  • Site-wide: 5,711
  • In synthetic biology: 52
• Year to date:
  • Site-wide: 72,488
• Since beginning of last month:
  • Site-wide: 75,465

Assembly of Radically Recoded E. coli Genome Segments

• Downloaded 2,741 times
• Download rankings, all-time:
  • Site-wide: 5,945
  • In synthetic biology: 59
• Year to date:
  • Site-wide: 84,527
• Since beginning of last month:
  • Site-wide: 64,011

Rapid and scalable in vitro production of single-stranded DNA

• Downloaded 2,639 times
• Download rankings, all-time:
  • Site-wide: 6,291
  • In molecular biology: 141
• Year to date:
  • Site-wide: 47,440
• Since beginning of last month:
  • Site-wide: 68,806

Precise Cas9 targeting enables genomic mutation prevention

• Downloaded 2,637 times
• Download rankings, all-time:
  • Site-wide: 6,297
  • In synthetic biology: 63
• Year to date:
  • Site-wide: 116,269
• Since beginning of last month:
  • Site-wide: 104,821

An orthogonal differentiation platform for genomically programming stem cells, organoids, and bioprinted tissues

• Downloaded 2,397 times
• Download rankings, all-time:
  • Site-wide: 7,254
  • In bioengineering: 111
• Year to date:
  • Site-wide: 6,570
• Since beginning of last month:
  • Site-wide: 7,056

The experimental design and data interpretation in ‘Unexpected mutations after CRISPR Cas9 editing in vivo’ by Schaefer et al. are insufficient to support the conclusions drawn by the authors

• Downloaded 2,340 times
• Download rankings, all-time:
  • Site-wide: 7,509
  • In genetics: 322
• Year to date:
  • Site-wide: 60,401
• Since beginning of last month:
  • Site-wide: 59,452

Efficient in situ barcode sequencing using padlock probe-based BaristaSeq

• Downloaded 2,215 times
• Download rankings, all-time:
  • Site-wide: 8,126
  • In molecular biology: 195
• Year to date:
  • Site-wide: 26,737
• Since beginning of last month:
  • Site-wide: 24,764

Genetic design automation for autonomous formation of multicellular shapes from a single cell progenitor

• Downloaded 2,097 times
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  • Site-wide: 8,806
  • In synthetic biology: 91
• Year to date:
  • Site-wide: 17,618
• Since beginning of last month:
  • Site-wide: 26,208

A DNA nanoscope that identifies and precisely localizes over a hundred unique molecular features with nanometer accuracy

• Downloaded 1,987 times
• Download rankings, all-time:
  • Site-wide: 9,503
  • In biochemistry: 181
• Year to date:
  • Site-wide: 9,686
• Since beginning of last month:
  • Site-wide: 22,613

Induced Pluripotent Stem Cell-derived CAR-Macrophage Cells with Antigen-dependent Anti-Cancer Cell Functions for Liquid and Solid Tumors

• Downloaded 1,845 times
• Download rankings, all-time:
  • Site-wide: 10,641
  • In cell biology: 254
• Year to date:
  • Site-wide: 9,099
• Since beginning of last month:
  • Site-wide: 14,581

High-throughput creation and functional profiling of eukaryotic DNA sequence variant libraries using CRISPR/Cas9

• Downloaded 1,828 times
• Download rankings, all-time:
  • Site-wide: 10,780
  • In bioengineering: 170
• Year to date:
  • Site-wide: 109,180
• Since beginning of last month:
  • Site-wide: 89,527

The whale shark genome reveals how genomic and physiological properties scale with body size

• Downloaded 1,767 times
• Download rankings, all-time:
  • Site-wide: 11,346
  • In genomics: 1,132
• Year to date:
  • Site-wide: 109,498
• Since beginning of last month:
  • Site-wide: 113,045

A systematic comparison of error correction enzymes by next-generation sequencing

• Downloaded 1,755 times
• Download rankings, all-time:
  • Site-wide: 11,465
  • In synthetic biology: 124
• Year to date:
  • Site-wide: 63,043
• Since beginning of last month:
  • Site-wide: 38,268

Photon-directed Multiplexed Enzymatic DNA Synthesis for Molecular Digital Data Storage

• Downloaded 1,721 times
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  • Site-wide: 11,784
  • In synthetic biology: 127
• Year to date:
  • Site-wide: 45,879
• Since beginning of last month:
  • Site-wide: 128,143

Multi-pronged human protein mimicry by SARS-CoV-2 reveals bifurcating potential for MHC detection and immune evasion

• Downloaded 1,699 times
• Download rankings, all-time:
  • Site-wide: 12,016
  • In evolutionary biology: 358
• Year to date:
  • Site-wide: 12,961
• Since beginning of last month:
  • Site-wide: 36,921

Reconstructing transcriptional histories by CRISPR acquisition of retron-based genetic barcodes

• Downloaded 1,668 times
• Download rankings, all-time:
  • Site-wide: 12,338
  • In synthetic biology: 135
• Year to date:
  • Site-wide: 2,121
• Since beginning of last month:
  • Site-wide: 1,425

CRISPR-mediated biocontainment

• Downloaded 1,643 times
• Download rankings, all-time:
  • Site-wide: 12,599
  • In synthetic biology: 141
• Year to date:
  • Site-wide: 26,121
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  • Site-wide: 24,134

Reprogramming protein kinase substrate specificity through synthetic mutations

• Downloaded 1,524 times
• Download rankings, all-time:
  • Site-wide: 14,070
  • In biochemistry: 281
• Year to date:
  • Site-wide: 77,841
• Since beginning of last month:
  • Site-wide: 48,896

Improved bacterial recombineering by parallelized protein discovery

• Downloaded 1,522 times
• Download rankings, all-time:
  • Site-wide: 14,102
  • In microbiology: 819
• Year to date:
  • Site-wide: 71,405
• Since beginning of last month:
  • Site-wide: 70,425

Fluorescent in situ sequencing of DNA barcoded antibodies

• Downloaded 1,505 times
• Download rankings, all-time:
  • Site-wide: 14,363
  • In neuroscience: 1,562
• Year to date:
  • Site-wide: 11,300
• Since beginning of last month:
  • Site-wide: 15,873

Citizen-Centered, Auditable, and Privacy-Preserving Population Genomics

• Downloaded 1,455 times
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  • Site-wide: 15,153
  • In genomics: 1,504
• Year to date:
  • Site-wide: 10,916
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  • Site-wide: 14,644

Concerning RNA-Guided Gene Drives for the Alteration of Wild Populations

• Downloaded 1,455 times
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  • Site-wide: 15,165
  • In synthetic biology: 171
• Year to date:
  • Site-wide: 126,827
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  • Site-wide: 132,420

Enhanced bacterial immunity and mammalian genome editing via RNA polymerase-mediated dislodging of Cas9 from double strand DNA breaks.

• Downloaded 1,403 times
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  • Site-wide: 16,045
  • In molecular biology: 435
• Year to date:
  • Site-wide: 129,804
• Since beginning of last month:
  • Site-wide: 119,023

Generative AAV capsid diversification by latent interpolation

• Downloaded 1,367 times
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  • Site-wide: 16,668
  • In synthetic biology: 194
• Year to date:
  • Site-wide: 2,813
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  • Site-wide: 6,750

Engineering post-translational proofreading to discriminate non-standard amino acids

• Downloaded 1,333 times
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  • Site-wide: 17,324
  • In synthetic biology: 205
• Year to date:
  • Site-wide: 113,954
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  • Site-wide: 94,977

Systemic post-translational control of bacterial metabolism regulates adaptation in dynamic environments

• Downloaded 1,317 times
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  • Site-wide: 17,604
  • In systems biology: 326
• Year to date:
  • Site-wide: 76,862
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  • Site-wide: 137,204

L1CAM is not Associated with Extracellular Vesicles in Human Cerebrospinal Fluid or Plasma

• Downloaded 1,314 times
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  • Site-wide: 17,670
  • In neuroscience: 2,077
• Year to date:
  • Site-wide: 6,140
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  • Site-wide: 30,910

Optimizing complex phenotypes through model-guided multiplex genome engineering

• Downloaded 1,234 times
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  • Site-wide: 19,393
  • In synthetic biology: 233
• Year to date:
  • Site-wide: 139,642
• Since beginning of last month:
  • Site-wide: 131,706

Characterizing the portability of RecT-mediated oligonucleotide recombination

• Downloaded 1,216 times
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  • Site-wide: 19,813
  • In synthetic biology: 240
• Year to date:
  • Site-wide: 29,975
• Since beginning of last month:
  • Site-wide: 30,652

Massively parallel quantification of CRISPR editing in cells by TRAP-seq enables better design of Cas9, ABE, CBE gRNAs of high efficiency and accuracy

• Downloaded 1,212 times
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  • Site-wide: 19,934
  • In systems biology: 373
• Year to date:
  • Site-wide: 36,207
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  • Site-wide: 43,687

Significant abundance of cis configurations of mutations in diploid human genomes

• Downloaded 1,137 times
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  • Site-wide: 21,900
  • In genomics: 2,056
• Year to date:
  • Site-wide: 56,390
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  • Site-wide: 51,817

Biosensor libraries harness large classes of binding domains for allosteric transcription regulators

• Downloaded 1,125 times
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  • Site-wide: 22,252
  • In synthetic biology: 281
• Year to date:
  • Site-wide: 146,101
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  • Site-wide: 154,663

Towards Practical and Robust DNA-based Data Archiving Using "Yin-Yang Codec" System

• Downloaded 1,106 times
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  • Site-wide: 22,820
  • In synthetic biology: 292
• Year to date:
  • Site-wide: 18,342
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  • Site-wide: 18,971

Attribution of genetic engineering: a practical and accurate machine learning toolkit for biosecurity

• Downloaded 1,102 times
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  • Site-wide: 22,907
  • In synthetic biology: 296
• Year to date:
  • Site-wide: 45,045
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  • Site-wide: 53,353

Dissecting limiting factors of the Protein synthesis Using Recombinant Elements (PURE) system

• Downloaded 1,019 times
• Download rankings, all-time:
  • Site-wide: 25,788
  • In bioengineering: 451
• Year to date:
  • Site-wide: 115,223
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  • Site-wide: 88,496

Ethnically relevant consensus Korean reference genome towards personal reference genomes

• Downloaded 910 times
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  • Site-wide: 30,366
  • In genomics: 2,644
• Year to date:
  • Site-wide: 112,385
• Since beginning of last month:
  • Site-wide: 138,814

Long-term adaptive evolution of genomically recoded Escherichia coli

• Downloaded 909 times
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  • Site-wide: 30,409
  • In evolutionary biology: 1,297
• Year to date:
  • Site-wide: 142,025
• Since beginning of last month:
  • Site-wide: 123,193

Framework for Rapid Comparison of Extracellular Vesicle Isolation Methods

• Downloaded 899 times
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  • Site-wide: 30,874
  • In biochemistry: 736
• Year to date:
  • Site-wide: 7,575
• Since beginning of last month:
  • Site-wide: 3,684

Toward D-Peptide Biosynthesis: Elongation Factor P Enables Ribosomal Incorporation Of Consecutive D-Amino Acids

• Downloaded 854 times
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  • Site-wide: 33,260
  • In biochemistry: 805
• Year to date:
  • Site-wide: 102,614
• Since beginning of last month:
  • Site-wide: 113,573

Spatial Information in Large-Scale Neural Recordings

• Downloaded 784 times
• Download rankings, all-time:
  • Site-wide: 37,474
  • In neuroscience: 5,001
• Year to date:
  • Site-wide: 152,543
• Since beginning of last month:
  • Site-wide: 149,064

Discovery and validation of novel human genomic safe harbor sites for gene and cell therapies

• Downloaded 755 times
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  • Site-wide: 39,575
  • In genomics: 3,206
• Year to date:
  • Site-wide: 6,654
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  • Site-wide: 7,102

Cushing's Syndrome mutant PKAL205R exhibits altered substrate specificity

• Downloaded 755 times
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  • Site-wide: 39,597
  • In biochemistry: 976
• Year to date:
  • Site-wide: 151,610
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  • Site-wide: 146,395

Robust differentiation of human pluripotent stem cells into endothelial cells via temporal modulation of ETV2 with modified mRNA

• Downloaded 746 times
• Download rankings, all-time:
  • Site-wide: 40,211
  • In cell biology: 1,610
• Year to date:
  • Site-wide: 84,368
• Since beginning of last month:
  • Site-wide: 71,485

One-Seq: A Highly Scalable Sequencing-Based Diagnostic for SARS-CoV-2 and Other Single-Stranded Viruses

• Downloaded 700 times
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  • Site-wide: 43,915
  • In infectious diseases: 3,015
• Year to date:
  • Site-wide: 7,457
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  • Site-wide: 22,229

Recording Temporal Signals with Minutes Resolution Using Enzymatic DNA Synthesis

• Downloaded 642 times
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  • Site-wide: 49,133
  • In synthetic biology: 613
• Year to date:
  • Site-wide: 8,507
• Since beginning of last month:
  • Site-wide: 1,834

Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli

• Downloaded 628 times
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  • Site-wide: 50,611
  • In genomics: 3,859
• Year to date:
  • Site-wide: 116,869
• Since beginning of last month:
  • Site-wide: 131,013

Multiplex single-molecule kinetics of nanopore-coupled polymerases

• Downloaded 593 times
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  • Site-wide: 54,400
  • In synthetic biology: 669
• Year to date:
  • Site-wide: 69,203
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  • Site-wide: 108,840

Simulating serial-target antibacterial drug synergies using flux balance analysis

• Downloaded 543 times
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  • Site-wide: 60,659
  • In systems biology: 1,352
• Year to date:
  • Site-wide: 143,948
• Since beginning of last month:
  • Site-wide: 155,357

Physiological Assembly Of Functionally Active 30S Ribosomal Subunits From In Vitro Synthesized Parts

• Downloaded 503 times
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  • Site-wide: 66,218
  • In biochemistry: 1,766
• Year to date:
  • Site-wide: 119,419
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  • Site-wide: 130,227

Multiplex base editing to convert TAG into TAA codons in the human genome

• Downloaded 502 times
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  • Site-wide: 66,401
  • In synthetic biology: 799
• Year to date:
  • Site-wide: 12,301
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  • Site-wide: 9,920

TBDB: A database of structurally annotated T-box riboswitch-tRNA pairs

• Downloaded 497 times
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  • Site-wide: 67,104
  • In bioinformatics: 6,436
• Year to date:
  • Site-wide: 84,103
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  • Site-wide: 90,997

Designing efficient genetic code expansion in Bacillus subtilis to gain biological insights

• Downloaded 418 times
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  • Site-wide: 80,762
  • In synthetic biology: 909
• Year to date:
  • Site-wide: 16,098
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  • Site-wide: 24,570

PGP1 personal genome assembly - a hybrid assembly dataset using ONT's PromethION and PacBio's HiFi sequencing

• Downloaded 189 times
• Download rankings, all-time:
  • Site-wide: 135,132
  • In genomics: 7,174
• Year to date:
  • Site-wide: 46,690
• Since beginning of last month:
  • Site-wide: 3,575