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Author: Joseph DeRisi

Rankings

  • All-time downloads: 81,150 (rank: 2,148 )
  • Categories:
    • biochemistry: 729 (rank: 9,275 (tie) )
    • bioengineering: 613 (rank: 7,494 (tie) )
    • bioinformatics: 2,522 (rank: 6,497 (tie) )
    • biophysics: 519 (rank: 12,167 (tie) )
    • cell biology: 18,924 (rank: 56 )
    • clinical trials: 1,633 (rank: 288 (tie) )
    • genomics: 4,398 (rank: 6,157 (tie) )
    • immunology: 4,455 (rank: 2,498 )
    • infectious diseases: 25,706 (rank: 2,431 )
    • intensive care and critical care medicine: 718 (rank: 1,545 (tie) )
    • microbiology: 14,072 (rank: 1,330 )
    • molecular biology: 2,828 (rank: 1,757 )
    • pediatrics: 177 (rank: 2,366 (tie) )
    • pharmacology and toxicology: 1,242 (rank: 1,091 (tie) )
    • public and global health: 722 (rank: 5,946 (tie) )
    • scientific communication and education: 703 (rank: 1,512 (tie) )
    • systems biology: 914 (rank: 5,576 (tie) )
    • zoology: 275 (rank: 2,394 (tie) )

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Preprints

Discovering disease-causing pathogens in resource-scarce Southeast Asia using a global metagenomic pathogen monitoring system

infectious diseases more details view paper

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No Significant Difference in Viral Load Between Vaccinated and Unvaccinated, Asymptomatic and Symptomatic Groups Infected with SARS-CoV-2 Delta Variant

infectious diseases more details view paper

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Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California.

epidemiology more details view paper

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Single-cell transcriptomic characterization of 20 organs and tissues from individual mice creates a Tabula Muris

cell biology more details view paper
  • Downloaded 13,611 times
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    • Site-wide: 693
    • In cell biology: 4
  • Year to date:
    • Site-wide: 11,165
  • Since beginning of last month:
    • Site-wide: 15,049

Direct detection of SARS-CoV-2 using CRISPR-Cas13a and a mobile phone

infectious diseases more details view paper
  • Downloaded 12,074 times
  • Download rankings, all-time:
    • Site-wide: 810
    • In infectious diseases: 265
  • Year to date:
    • Site-wide: 2,576
  • Since beginning of last month:
    • Site-wide: 7,594

Zika Virus in the Human Placenta and Developing Brain: Cell Tropism and Drug Inhibition

cell biology more details view paper
  • Downloaded 5,010 times
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    • Site-wide: 2,552
    • In cell biology: 40
  • Year to date:
    • Site-wide: 70,363
  • Since beginning of last month:
    • Site-wide: 71,969

Performance characteristics of a rapid SARS-CoV-2 antigen detection assay at a public plaza testing site in San Francisco

infectious diseases more details view paper
  • Downloaded 4,514 times
  • Download rankings, all-time:
    • Site-wide: 2,922
    • In infectious diseases: 671
  • Year to date:
    • Site-wide: 1,681
  • Since beginning of last month:
    • Site-wide: 2,326

Serological and metagenomic interrogation of cerebrospinal fluid implicates enteroviruses in pediatric acute flaccid myelitis

microbiology more details view paper
  • Downloaded 3,721 times
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    • Site-wide: 3,843
    • In microbiology: 265
  • Year to date:
    • Site-wide: 52,610
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    • Site-wide: 60,624

Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia

microbiology more details view paper
  • Downloaded 3,204 times
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    • Site-wide: 4,748
    • In microbiology: 319
  • Year to date:
    • Site-wide: 19,051
  • Since beginning of last month:
    • Site-wide: 54,417

Upper airway gene expression differentiates COVID-19 from other acute respiratory illnesses and reveals suppression of innate immune responses by SARS-CoV-2

infectious diseases more details view paper
  • Downloaded 3,004 times
  • Download rankings, all-time:
    • Site-wide: 5,193
    • In infectious diseases: 972
  • Year to date:
    • Site-wide: 17,588
  • Since beginning of last month:
    • Site-wide: 34,738

FLASH: A next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences

microbiology more details view paper
  • Downloaded 2,404 times
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    • Site-wide: 7,188
    • In microbiology: 432
  • Year to date:
    • Site-wide: 75,524
  • Since beginning of last month:
    • Site-wide: 85,202

Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: a comparison of patients with and without COVID-19

infectious diseases more details view paper
  • Downloaded 2,289 times
  • Download rankings, all-time:
    • Site-wide: 7,734
    • In infectious diseases: 1,234
  • Year to date:
    • Site-wide: 14,232
  • Since beginning of last month:
    • Site-wide: 24,501

Etiology of fever in Ugandan children: identification of microbial pathogens using metagenomic next-generation sequencing and IDseq, a platform for unbiased metagenomic analysis

genomics more details view paper
  • Downloaded 1,954 times
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    • Site-wide: 9,696
    • In genomics: 970
  • Year to date:
    • Site-wide: 45,918
  • Since beginning of last month:
    • Site-wide: 28,770

Topical Silver Diamine Fluoride For Dental Caries Arrest In Preschool Children: A Randomized Controlled Trial

clinical trials more details view paper
  • Downloaded 1,633 times
  • Download rankings, all-time:
    • Site-wide: 12,654
    • In clinical trials: 25
  • Year to date:
    • Site-wide: 63,162
  • Since beginning of last month:
    • Site-wide: 60,333

IDseq - An Open Source Cloud-based Pipeline and Analysis Service for Metagenomic Pathogen Detection and Monitoring

bioinformatics more details view paper
  • Downloaded 1,598 times
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    • Site-wide: 13,046
    • In bioinformatics: 1,471
  • Year to date:
    • Site-wide: 43,254
  • Since beginning of last month:
    • Site-wide: 78,316

Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19

immunology more details view paper
  • Downloaded 1,392 times
  • Download rankings, all-time:
    • Site-wide: 16,141
    • In immunology: 549
  • Year to date:
    • Site-wide: 2,703
  • Since beginning of last month:
    • Site-wide: 4,842

Identification of a polymorphism in the N gene of SARS-CoV-2 that adversely impacts detection by a widely-used RT-PCR assay

molecular biology more details view paper
  • Downloaded 1,380 times
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    • Site-wide: 16,349
    • In molecular biology: 450
  • Year to date:
    • Site-wide: 33,315
  • Since beginning of last month:
    • Site-wide: 54,221

Estimation of secondary household attack rates for emergent SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco

infectious diseases more details view paper
  • Downloaded 1,368 times
  • Download rankings, all-time:
    • Site-wide: 16,556
    • In infectious diseases: 1,826
  • Year to date:
    • Site-wide: 2,757
  • Since beginning of last month:
    • Site-wide: 6,231

Exploration of Anti-Yo and Anti-Hu paraneoplastic neurological disorders by PhIP-Seq reveals a highly restricted pattern of antibody epitopes

immunology more details view paper
  • Downloaded 1,348 times
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    • Site-wide: 16,933
    • In immunology: 581
  • Year to date:
    • Site-wide: 53,587
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    • Site-wide: 51,501

ReScan, a Multiplex Diagnostic Pipeline, Pans Human Sera for SARS-CoV-2 Antigens

infectious diseases more details view paper
  • Downloaded 1,289 times
  • Download rankings, all-time:
    • Site-wide: 18,074
    • In infectious diseases: 1,915
  • Year to date:
    • Site-wide: 52,171
  • Since beginning of last month:
    • Site-wide: 75,166

Silver microwires from treating tooth decay with silver diamine fluoride

pharmacology and toxicology more details view paper
  • Downloaded 1,242 times
  • Download rankings, all-time:
    • Site-wide: 19,105
    • In pharmacology and toxicology: 105
  • Year to date:
    • Site-wide: 57,423
  • Since beginning of last month:
    • Site-wide: 35,326

Unbiased metagenomic sequencing for pediatric meningitis in Bangladesh reveals neuroinvasive Chikungunya virus outbreak and other unrealized pathogens

genomics more details view paper
  • Downloaded 953 times
  • Download rankings, all-time:
    • Site-wide: 28,299
    • In genomics: 2,520
  • Year to date:
    • Site-wide: 106,216
  • Since beginning of last month:
    • Site-wide: 71,351

Determination of Ubiquitin Fitness Landscapes Under Different Chemical Stresses in a Classroom Setting

systems biology more details view paper
  • Downloaded 914 times
  • Download rankings, all-time:
    • Site-wide: 30,034
    • In systems biology: 607
  • Year to date:
    • Site-wide: 138,758
  • Since beginning of last month:
    • Site-wide: 116,425

Miniaturization and optimization of 384-well compatible metagenomic sequencing library preparation

molecular biology more details view paper
  • Downloaded 814 times
  • Download rankings, all-time:
    • Site-wide: 35,353
    • In molecular biology: 990
  • Year to date:
    • Site-wide: 79,897
  • Since beginning of last month:
    • Site-wide: 105,622

Identification of novel, clinically correlated autoantigens in the monogenic autoimmune syndrome APS1 by PhIP-Seq

immunology more details view paper
  • Downloaded 797 times
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    • Site-wide: 36,482
    • In immunology: 1,165
  • Year to date:
    • Site-wide: 59,401
  • Since beginning of last month:
    • Site-wide: 90,909

Deep profiling of protease substrate specificity enabled by dual random and scanned human proteome substrate phage libraries

biochemistry more details view paper
  • Downloaded 729 times
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    • Site-wide: 41,278
    • In biochemistry: 1,030
  • Year to date:
    • Site-wide: 48,756
  • Since beginning of last month:
    • Site-wide: 64,221

A multi-component, community-based strategy to facilitate COVID-19 vaccine uptake among Latinx populations: from theory to practice

public and global health more details view paper
  • Downloaded 722 times
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    • Site-wide: 41,796
    • In public and global health: 699
  • Year to date:
    • Site-wide: 6,965
  • Since beginning of last month:
    • Site-wide: 935

COVID-19 ARDS is characterized by a dysregulated host response that differs from cytokine storm and may be modified by dexamethasone

intensive care and critical care medicine more details view paper
  • Downloaded 718 times
  • Download rankings, all-time:
    • Site-wide: 42,157
    • In intensive care and critical care medicine: 124
  • Year to date:
    • Site-wide: 7,018
  • Since beginning of last month:
    • Site-wide: 68,077

Metagenomic next-generation sequencing reveals Miamiensis avidus (Ciliophora: Scuticociliatida) in the 2017 epizootic of leopard sharks (Triakis semifasciata) in San Francisco Bay, California

microbiology more details view paper
  • Downloaded 708 times
  • Download rankings, all-time:
    • Site-wide: 42,959
    • In microbiology: 2,591
  • Year to date:
    • Site-wide: 55,152
  • Since beginning of last month:
    • Site-wide: 124,009

Illuminating Uveitis: Metagenomic Deep Sequencing Identifies Common and Rare Pathogens

scientific communication and education more details view paper
  • Downloaded 703 times
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    • Site-wide: 43,412
    • In scientific communication and education: 272
  • Year to date:
    • Site-wide: 139,895
  • Since beginning of last month:
    • Site-wide: 121,035

Metagenomic DNA sequencing for the diagnosis of intraocular infections

genomics more details view paper
  • Downloaded 683 times
  • Download rankings, all-time:
    • Site-wide: 45,157
    • In genomics: 3,560
  • Year to date:
    • Site-wide: 142,106
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    • Site-wide: 146,754

Metagenomics for chronic meningitis: clarifying interpretation and diagnosis

microbiology more details view paper
  • Downloaded 679 times
  • Download rankings, all-time:
    • Site-wide: 45,434
    • In microbiology: 2,754
  • Year to date:
    • Site-wide: 115,114
  • Since beginning of last month:
    • Site-wide: 126,750

Investigating Transfusion-Related Sepsis using Culture-Independent Metagenomic Sequencing

microbiology more details view paper
  • Downloaded 634 times
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    • Site-wide: 49,705
    • In microbiology: 3,066
  • Year to date:
    • Site-wide: 104,703
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    • Site-wide: 142,900

A Metagenomic Comparison of Tracheal Aspirate and Mini-Bronchial Alveolar Lavage for Assessment of Respiratory Microbiota

microbiology more details view paper
  • Downloaded 628 times
  • Download rankings, all-time:
    • Site-wide: 50,311
    • In microbiology: 3,110
  • Year to date:
    • Site-wide: 101,700
  • Since beginning of last month:
    • Site-wide: 141,451

Low-Cost Touchscreen Driven Programmable Dual Syringe Pump for Life Science Applications

bioengineering more details view paper
  • Downloaded 613 times
  • Download rankings, all-time:
    • Site-wide: 51,924
    • In bioengineering: 979
  • Year to date:
    • Site-wide: 104,378
  • Since beginning of last month:
    • Site-wide: 145,725

Extending Chemical Perturbations Of The Ubiquitin Fitness Landscape In A Classroom Setting

bioinformatics more details view paper
  • Downloaded 610 times
  • Download rankings, all-time:
    • Site-wide: 52,198
    • In bioinformatics: 5,285
  • Year to date:
    • Site-wide: 139,936
  • Since beginning of last month:
    • Site-wide: 142,950

Nasopharyngeal SARS-CoV2 viral loads in young children do not differ significantly from those in older children and adults

infectious diseases more details view paper
  • Downloaded 586 times
  • Download rankings, all-time:
    • Site-wide: 54,988
    • In infectious diseases: 3,368
  • Year to date:
    • Site-wide: 67,251
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    • Site-wide: 43,369

The Plasmodium falciparum cytoplasmic translation apparatus: a promising therapeutic target not yet exploited by clinically approved antimalarials.

molecular biology more details view paper
  • Downloaded 530 times
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    • Site-wide: 62,068
    • In molecular biology: 1,771
  • Year to date:
    • Site-wide: 110,735
  • Since beginning of last month:
    • Site-wide: 121,361

Exposures to different SARS-CoV-2 spike variants elicit neutralizing antibody responses with differential specificity towards established and emerging strains

infectious diseases more details view paper
  • Downloaded 529 times
  • Download rankings, all-time:
    • Site-wide: 62,224
    • In infectious diseases: 3,568
  • Year to date:
    • Site-wide: 11,103
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    • Site-wide: 647

Label-free imaging and classification of live P. falciparum

biophysics more details view paper
  • Downloaded 519 times
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    • Site-wide: 63,557
    • In biophysics: 2,191
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    • Site-wide: 91,392

Designing and implementing programmable depletion in sequencing libraries with DASHit

microbiology more details view paper
  • Downloaded 503 times
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    • Site-wide: 65,799
    • In microbiology: 4,249
  • Year to date:
    • Site-wide: 63,333
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    • Site-wide: 92,941

Evidence for Alternative Complement Cascade Activation in Primary CNS Vasculitis

immunology more details view paper
  • Downloaded 498 times
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    • Site-wide: 66,619
    • In immunology: 2,032
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    • Site-wide: 127,873
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    • Site-wide: 105,371

Integrating Host Response and Unbiased Microbe Detection for Lower Respiratory Tract Infection Diagnosis in Critically Ill Adults

genomics more details view paper
  • Downloaded 473 times
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    • Site-wide: 70,655
    • In genomics: 4,882
  • Year to date:
    • Site-wide: 131,172
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    • Site-wide: 106,976

Pediatric Brainstem Encephalitis Outbreak Investigation with Metagenomic Next-Generation Sequencing

microbiology more details view paper
  • Downloaded 394 times
  • Download rankings, all-time:
    • Site-wide: 84,772
    • In microbiology: 5,754
  • Year to date:
    • Site-wide: 134,023
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    • Site-wide: 121,369

Microbiome and Antimicrobial Resistance Gene Dynamics in International Travelers

microbiology more details view paper
  • Downloaded 364 times
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    • Site-wide: 91,043
    • In microbiology: 6,262
  • Year to date:
    • Site-wide: 158,288
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    • Site-wide: 154,713

An exploration of ambigrammatic sequences in narnaviruses

genomics more details view paper
  • Downloaded 335 times
  • Download rankings, all-time:
    • Site-wide: 97,746
    • In genomics: 5,983
  • Year to date:
    • Site-wide: 134,495
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    • Site-wide: 137,822

Poecivirus is present in individuals with beak deformities in seven species of North American birds

microbiology more details view paper
  • Downloaded 317 times
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    • Site-wide: 102,013
    • In microbiology: 7,160
  • Year to date:
    • Site-wide: 77,659
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    • Site-wide: 94,116

MinorityReport, software for generalized analysis of causal genetic variants

bioinformatics more details view paper
  • Downloaded 314 times
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    • Site-wide: 102,885
    • In bioinformatics: 8,759
  • Year to date:
    • Site-wide: 158,172
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    • Site-wide: 151,909

Zika virus alters centrosome organization to suppress the innate immune response

cell biology more details view paper
  • Downloaded 303 times
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    • Site-wide: 105,428
    • In cell biology: 4,887
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    • Site-wide: 98,577
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    • Site-wide: 109,316

A Fixed Moderate-dose Combination of Tiletamine+Zolazepam Outperforms Midazolam in Induction of Short-term Immobilization of Ball Pythons (Python regius)

zoology more details view paper
  • Downloaded 275 times
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    • Site-wide: 112,509
    • In zoology: 460
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    • Site-wide: 148,407
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    • Site-wide: 101,505

Elevated N-glycosylation of immunoglobulin G variable regions in myasthenia gravis highlights a commonality across autoantibody-associated diseases

immunology more details view paper
  • Downloaded 263 times
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    • Site-wide: 115,509
    • In immunology: 3,454
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    • Site-wide: 30,512
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    • Site-wide: 21,360

Persistence of ambigrammatic narnaviruses requires translation of the reverse open reading frame

microbiology more details view paper
  • Downloaded 260 times
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    • Site-wide: 116,249
    • In microbiology: 8,360
  • Year to date:
    • Site-wide: 56,608
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    • Site-wide: 154,008

Avian keratin disorder of Alaska black-capped chickadees is associated with Poecivirus infection

microbiology more details view paper
  • Downloaded 256 times
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    • Site-wide: 117,315
    • In microbiology: 8,470
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    • Site-wide: 150,145
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    • Site-wide: 142,663

Inoculation by mosquito induces durable differences in serological profile in non-human primates infected with DENV1

immunology more details view paper
  • Downloaded 157 times
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    • Site-wide: 142,171
    • In immunology: 4,268
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    • Site-wide: 101,191
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    • Site-wide: 89,387

Autoimmune profiling suggests paraneoplastic etiology in pediatric ROHHAD

pediatrics more details view paper
  • Downloaded 138 times
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    • Site-wide: 146,338
    • In pediatrics: 286
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    • Site-wide: 33,740

Functional characterization of 5' UTR cis-acting sequence elements that modulate translational efficiency in P. falciparum and humans

molecular biology more details view paper
  • Downloaded 104 times
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    • Site-wide: 152,492
    • In molecular biology: 4,594
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Genomic epidemiologic assessment implicates prolonged silent carriage, virulence factors and transmission between staff and patients in a NICU outbreak of MRSA.

infectious diseases more details view paper
  • Downloaded 53 times
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    • Site-wide: 157,868
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    • Site-wide: 131,087
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    • Site-wide: 136,816

Metatranscriptomic Signatures of Lung Function in Pediatric Hematopoietic Cell Transplant Candidates

pediatrics more details view paper
  • Downloaded 39 times
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