Publications

Papers and preprints

91 publications by Blake Wiedenheft and colleagues. New work also appears on Google Scholar.

Publications per year2001–2026, from PubMed (2026 so far)
051020012006201192016202152026

Wiedenheft B in bold. Lab members and alumni underlined.

20265

  1. A prophage-encoded sRNA limits phage infection of adherent-invasive E. coli

    Pershing NL, Brzozowski RS, Schmidt AK, Faith DR, Joyce AC, de Ora LO, …, Henriques WS, …, Wiedenheft B, …, Round JL, Secor PR

    PLOS Pathogens 22(1):e1013836PubMedFree full textPreprint (bioRxiv 2025)

  2. A census of anti-CRISPR proteins reveals AcrIE9 and AcrIE13 as inhibitors of the Escherichia coli K12 type IE CRISPR-Cas system

    Taranenko D, Kotovskaya O, Kuznedelov K, Yanovskaya D, Demkina A, Fardeeva S, …, Vierra K, Burman N, …, Wiedenheft B, …, Semenova E, Isaev A

    PNAS 123(24):e2529903123PubMedFree full textPreprint (bioRxiv 2025)

  3. Integrating mass spectrometry with Nanopore direct RNA sequencing for de novo modification profiling of bacteriophage MS2

    Jones JD, Ghohabi Esfahani N, Goemann CL, Wiegand T, Nemudryi A, Ruan M, Li X, Tardu M, Kennedy RT, Wiedenheft B, Jain M, Koutmou KS

    PreprintbioRxivPubMedFree full text

  4. Identification and structure determination of a type III-Bv CRISPR complex that post-translationally modifies an associated toxin

    Pandey S, Burman N, Henriques WS, Wiegand T, Zahl T, Nyquist H, Spreeuw T, Buyukyoruk M, Wiedenheft B

    Structure 34(8):1109-1122.e7PubMedFree full text

  5. Stress-Induced Metabolic Reprogramming in the Green Microalga Chlorella sp. SLA-04

    Goemann CLC, Bui H, Rincon Miranda S, Arnold AD, Carlson RP, Viamajala S, Gerlach R, Wiedenheft B

    Microorganisms 14(9)PubMedFree full text

20256

  1. Principles for introducing new genes and species for conservation

    Schwartz MK, Dunn SL, Gendron WAC, Helm JE, Kamau WS, Mark-Shadbolt M, …, Wiedenheft B, Emmel AS, Brodie JF

    ReviewTrends in Ecology & Evolution 40(3):296-307PubMed

  2. The retrotransposon-derived capsid genes PNMA1 and PNMA4 maintain reproductive capacity

    Wood TWP, Henriques WS, Cullen HB, Romero M, Blengini CS, Sarathy S, …, Wiedenheft B, Berchowitz LE

    Nature Aging 5(5):765-779PubMedFree full textPreprint (bioRxiv 2024)

  3. Protein-primed homopolymer synthesis by an antiviral reverse transcriptase

    Tang S, Žedaveinytė R, Burman N, Pandey S, Ramirez JL, Kulber LM, Wiegand T, Wilkinson RA, …, Wiedenheft B, Sternberg SH

    Nature 643(8074):1352-1362PubMedFree full textPreprint (bioRxiv 2025)

  4. Structural basis of antiphage defence by an ATPase-associated reverse transcriptase

    George JT, Burman N, Wilkinson RA, de Silva S, McKelvey-Pham Q, Buyukyoruk M, Dale A, Landman H, Graham AB, DeLuca SZ, Wiedenheft B

    Nature Communications 16(1):8459PubMedFree full textPreprint (bioRxiv 2025)

  5. Structures reveal how the Cas1-2/3 integrase captures, delivers, and integrates foreign DNA into CRISPR loci

    Henriques WS, Bowman J, Hall LN, Gauvin CC, Wei H, Kuang H, Zimanyi CM, Eng ET, Santiago-Frangos A, Wiedenheft B

    Structure 33(12):2058-2070.e6PubMedFree full textPreprint (bioRxiv 2025)

20245

  1. CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes

    Adler BA, Trinidad MI, Bellieny-Rabelo D, Zhang E, Karp HM, Skopintsev P, …, Wiedenheft B, …, Savage DF, Doudna JA

    Nucleic Acids Research 52(D1):D590-D596PubMedFree full text

  2. The Diverse Evolutionary Histories of Domesticated Metaviral Capsid Genes in Mammals

    Henriques WS, Young JM, Nemudryi A, Nemudraia A, Wiedenheft B, Malik HS

    Molecular Biology and Evolution 41(4)PubMedFree full textPreprint (bioRxiv 2023)

  3. Adenosine modifications impede SARS-CoV-2 RNA-dependent RNA transcription

    Snyder LR, Kilde I, Nemudryi A, Wiedenheft B, Koutmos M, Koutmou KS

    RNA 30(9):1141-1150PubMedFree full text

  4. A virally encoded tRNA neutralizes the PARIS antiviral defence system

    Burman N, Belukhina S, Depardieu F, Wilkinson RA, Skutel M, Santiago-Frangos A, Graham AB, …, Zahl T, Henriques WS, Buyukyoruk M, …, Wiedenheft B, Isaev A

    Nature 634(8033):424-431PubMedFree full textPreprint (bioRxiv 2024)

20235

  1. Polyamines and linear DNA mediate bacterial threat assessment of bacteriophage infection

    de Mattos CD, Faith DR, Nemudryi AA, Schmidt AK, Bublitz DC, Hammond L, …, Wiedenheft B, Secor PR

    PNAS 120(9):e2216430120PubMedFree full text

  2. Functional and Phylogenetic Diversity of Cas10 Proteins

    Wiegand T, Wilkinson R, Santiago-Frangos A, Lynes M, Hatzenpichler R, Wiedenheft B

    The CRISPR Journal 6(2):152-162PubMedFree full text

  3. CRISPR-based engineering of RNA viruses

    Nemudryi A, Nemudraia A, Nichols JE, Scherffius AM, Zahl T, Wiedenheft B

    Science Advances 9(37):eadj8277PubMedFree full textPreprint (bioRxiv 2023)

  4. Structure reveals why genome folding is necessary for site-specific integration of foreign DNA into CRISPR arrays

    Santiago-Frangos A, Henriques WS, Wiegand T, Gauvin CC, Buyukyoruk M, Graham AB, Wilkinson RA, Triem L, Neselu K, Eng ET, Lander GC, Wiedenheft B

    Nature Structural & Molecular Biology 30(11):1675-1685PubMedFree full text

20226

  1. CRISPR-Cas, Argonaute proteins and the emerging landscape of amplification-free diagnostics

    Santiago-Frangos A, Nemudryi A, Nemudraia A, Wiegand T, Nichols JE, Krishna P, Scherffius AM, Zahl TR, Wilkinson RA, Wiedenheft B

    Methods 205:1-10PubMedFree full text

  2. The Rise and Fall of SARS-CoV-2 Variants and Ongoing Diversification of Omicron

    Wiegand T, Nemudryi A, Nemudraia A, McVey A, Little A, Taylor DN, Walk ST, Wiedenheft B

    ReviewViruses 14(9)PubMedFree full text

  3. Anti-CRISPR proteins function through thermodynamic tuning and allosteric regulation of CRISPR RNA-guided surveillance complex

    Patterson A, White A, Waymire E, Fleck S, Golden S, Wilkinson RA, Wiedenheft B, Bothner B

    Nucleic Acids Research 50(19):11243-11254PubMedFree full text

  4. A viral "codebreaker" intercepts a host alarm

    Nemudryi A, Nemudraia A, Wiegand T, Sternberg SH, Wiedenheft B

    Cell Host & Microbe 30(12):1647-1648PubMed

  5. Sequence-specific capture and concentration of viral RNA by type III CRISPR system enhances diagnostic

    Nemudraia A, Nemudryi A, Buyukyoruk M, Scherffius AM, Zahl T, Wiegand T, Pandey S, …, Wilkinson RA, …, Santiago-Frangos A, Wiedenheft B

    Nature Communications 13(1):7762PubMedFree full textPreprint (Research Square 2022)

20214

  1. Metatranscriptome Analysis of Sympatric Bee Species Identifies Bee Virus Variants and a New Virus, Andrena-Associated Bee Virus-1

    Daughenbaugh KF, Kahnonitch I, Carey CC, McMenamin AJ, Wiegand T, Erez T, …, Wiedenheft B, …, Mandelik Y, Flenniken ML

    Viruses 13(2)PubMedFree full text

  2. SARS-CoV-2 genomic surveillance identifies naturally occurring truncation of ORF7a that limits immune suppression

    Nemudryi A, Nemudraia A, Wiegand T, Nichols J, Snyder DT, Hedges JF, Cicha C, Lee H, Vanderwood KK, Bimczok D, Jutila MA, Wiedenheft B

    Cell Reports 35(9):109197PubMedFree full textPreprint (medRxiv 2021)

  3. Intrinsic signal amplification by type III CRISPR-Cas systems provides a sequence-specific SARS-CoV-2 diagnostic

    Santiago-Frangos A, Hall LN, Nemudraia A, Nemudryi A, Krishna P, Wiegand T, Wilkinson RA, …, Graham A, …, Taylor MP, Wiedenheft B

    Cell Reports Medicine 2(6):100319PubMedFree full text

  4. Distribution and phasing of sequence motifs that facilitate CRISPR adaptation

    Santiago-Frangos A, Buyukyoruk M, Wiegand T, Krishna P, Wiedenheft B

    Current Biology 31(16):3515-3524.e6PubMedFree full text

20206

  1. CRISPR Surveillance Turns Transposon Taxi

    Wiegand T, Wiedenheft B

    The CRISPR Journal 3(1):10-12PubMedFree full text

  2. Complete Genome Sequence of Brucella abortus Phage EF4, Determined Using Long-Read Sequencing

    Cicha C, Hedges J, Novak I, Snyder D, Jutila M, Wiedenheft B

    Microbiology Resource Announcements 9(18)PubMedFree full text

  3. AcrIF9 tethers non-sequence specific dsDNA to the CRISPR RNA-guided surveillance complex

    Hirschi M, Lu WT, Santiago-Frangos A, Wilkinson R, Golden SM, Davidson AR, Lander GC, Wiedenheft B

    Nature Communications 11(1):2730PubMedFree full text

  4. Structures and Strategies of Anti-CRISPR-Mediated Immune Suppression

    Wiegand T, Karambelkar S, Bondy-Denomy J, Wiedenheft B

    ReviewAnnual Review of Microbiology 74:21-37PubMedFree full text

  5. Temporal Detection and Phylogenetic Assessment of SARS-CoV-2 in Municipal Wastewater

    Nemudryi A, Nemudraia A, Wiegand T, Surya K, Buyukyoruk M, Cicha C, Vanderwood KK, Wilkinson R, Wiedenheft B

    Cell Reports Medicine 1(6):100098PubMedFree full textPreprint (medRxiv 2020)

  6. Reproducible Antigen Recognition by the Type I-F CRISPR-Cas System

    Wiegand T, Semenova E, Shiriaeva A, Fedorov I, Datsenko K, Severinov K, Wiedenheft B

    The CRISPR Journal 3(5):378-387PubMedFree full text

20194

  1. CRISPR RNA-guided autonomous delivery of Cas9

    Wilkinson RA, Martin C, Nemudryi AA, Wiedenheft B

    ReviewNature Structural & Molecular Biology 26(1):14-24PubMedFree full text

  2. Cas9 slide-and-seek for phage defense and genome engineering

    Santiago-Frangos A, Wiegand T, Wiedenheft B

    CommentaryThe EMBO Journal 38(4)PubMedFree full text

  3. Structure Reveals a Mechanism of CRISPR-RNA-Guided Nuclease Recruitment and Anti-CRISPR Viral Mimicry

    Rollins MF, Chowdhury S, Carter J, Golden SM, Miettinen HM, Santiago-Frangos A, Faith D, Lawrence CM, Lander GC, Wiedenheft B

    Molecular Cell 74(1):132-142.e5PubMedFree full text

20185

  1. Conformational Dynamics of DNA Binding and Cas3 Recruitment by the CRISPR RNA-Guided Cascade Complex

    van Erp PBG, Patterson A, Kant R, Berry L, Golden SM, Forsman BL, Carter J, Jackson RN, Bothner B, Wiedenheft B

    ACS Chemical Biology 13(2):481-490PubMedFree full text

  2. Live imaging analysis of human gastric epithelial spheroids reveals spontaneous rupture, rotation and fusion events

    Sebrell TA, Sidar B, Bruns R, Wilkinson RA, Wiedenheft B, Taylor PJ, Perrino BA, Samuelson LC, Wilking JN, Bimczok D

    Cell and Tissue Research 371(2):293-307PubMedFree full text

  3. A PAX5-OCT4-PRDM1 developmental switch specifies human primordial germ cells

    Fang F, Angulo B, Xia N, Sukhwani M, Wang Z, Carey CC, …, Wilkinson R, Wiedenheft B, …, Orwig KE, Reijo Pera RA

    Nature Cell Biology 20(6):655-665PubMedFree full text

  4. Bacteriophage Cooperation Suppresses CRISPR-Cas3 and Cas9 Immunity

    Borges AL, Zhang JY, Rollins MF, Osuna BA, Wiedenheft B, Bondy-Denomy J

    Cell 174(4):917-925.e10PubMedFree full text

  5. A Unified Resource for Tracking Anti-CRISPR Names

    Bondy-Denomy J, Davidson AR, Doudna JA, Fineran PC, Maxwell KL, Moineau S, Peng X, Sontheimer EJ, Wiedenheft B

    CommentaryThe CRISPR Journal 1(5):304-305PubMedFree full text

20175

  1. CRISPR control of virulence in Pseudomonas aeruginosa

    Wiedenheft B, Bondy-Denomy J

    CommentaryCell Research 27(2):163-164PubMedFree full text

  2. The Interfaces of Genetic Conflict Are Hot Spots for Innovation

    Carter J, Hoffman C, Wiedenheft B

    CommentaryCell 168(1-2):9-11PubMedFree full text

  3. Structure Reveals Mechanisms of Viral Suppressors that Intercept a CRISPR RNA-Guided Surveillance Complex

    Chowdhury S, Carter J, Rollins MF, Golden SM, Jackson RN, Hoffmann C, …, Lander GC, Wiedenheft B

    Cell 169(1):47-57.e11PubMedFree full text

  4. Cas1 and the Csy complex are opposing regulators of Cas2/3 nuclease activity

    Rollins MF, Chowdhury S, Carter J, Golden SM, Wilkinson RA, Bondy-Denomy J, Lander GC, Wiedenheft B

    PNAS 114(26):E5113-E5121PubMedFree full text

  5. Conformational regulation of CRISPR-associated nucleases

    Jackson RN, van Erp PB, Sternberg SH, Wiedenheft B

    ReviewCurrent Opinion in Microbiology 37:110-119PubMedFree full text

20163

  1. Structural basis for promiscuous PAM recognition in type I-E Cascade from E. coli

    Hayes RP, Xiao Y, Ding F, van Erp PB, Rajashankar K, Bailey S, Wiedenheft B, Ke A

    Nature 530(7591):499-503PubMedFree full text

  2. Programmed Self-Assembly of an Active P22-Cas9 Nanocarrier System

    Qazi S, Miettinen HM, Wilkinson RA, McCoy K, Douglas T, Wiedenheft B

    Molecular Pharmaceutics 13(3):1191-6PubMedFree full text

  3. The CRISPR RNA-guided surveillance complex in Escherichia coli accommodates extended RNA spacers

    Luo ML, Jackson RN, Denny SR, Tokmina-Lukaszewska M, Maksimchuk KR, Lin W, Bothner B, Wiedenheft B, Beisel CL

    Nucleic Acids Research 44(15):7385-94PubMedFree full text

20159

  1. Mechanism of foreign DNA recognition by a CRISPR RNA-guided surveillance complex from Pseudomonas aeruginosa

    Rollins MF, Schuman JT, Paulus K, Bukhari HS, Wiedenheft B

    Nucleic Acids Research 43(4):2216-22PubMedFree full text

  2. The history and market impact of CRISPR RNA-guided nucleases

    van Erp PB, Bloomer G, Wilkinson R, Wiedenheft B

    Current Opinion in Virology 12:85-90PubMedFree full text

  3. X-ray structure determination using low-resolution electron microscopy maps for molecular replacement

    Jackson RN, McCoy AJ, Terwilliger TC, Read RJ, Wiedenheft B

    Nature Protocols 10(9):1275-84PubMedFree full text

  4. Mechanism of CRISPR-RNA guided recognition of DNA targets in Escherichia coli

    van Erp PB, Jackson RN, Carter J, Golden SM, Bailey S, Wiedenheft B

    Nucleic Acids Research 43(17):8381-91PubMedFree full text

  5. Multiple mechanisms for CRISPR-Cas inhibition by anti-CRISPR proteins

    Bondy-Denomy J, Garcia B, Strum S, Du M, Rollins MF, Hidalgo-Reyes Y, Wiedenheft B, Maxwell KL, Davidson AR

    Nature 526(7571):136-9PubMedFree full text

  6. Surveillance and Processing of Foreign DNA by the Escherichia coli CRISPR-Cas System

    Redding S, Sternberg SH, Marshall M, Gibb B, Bhat P, Guegler CK, Wiedenheft B, Doudna JA, Greene EC

    Cell 163(4):854-65PubMedFree full text

  7. Foreign DNA acquisition by the I-F CRISPR-Cas system requires all components of the interference machinery

    Vorontsova D, Datsenko KA, Medvedeva S, Bondy-Denomy J, Savitskaya EE, Pougach K, Logacheva M, Wiedenheft B, Davidson AR, Severinov K, Semenova E

    Nucleic Acids Research 43(22):10848-60PubMedFree full text

20144

  1. Fitting CRISPR-associated Cas3 into the helicase family tree

    Jackson RN, Lavin M, Carter J, Wiedenheft B

    ReviewCurrent Opinion in Structural Biology 24:106-14PubMedFree full text

  2. A CRISPR method for genome engineering

    Wilkinson R, Wiedenheft B

    ReviewF1000Prime Reports 6:3PubMedFree full text

  3. Unravelling the structural and mechanistic basis of CRISPR-Cas systems

    van der Oost J, Westra ER, Jackson RN, Wiedenheft B

    ReviewNature Reviews Microbiology 12(7):479-92PubMedFree full text

  4. Structural biology. Crystal structure of the CRISPR RNA-guided surveillance complex from Escherichia coli

    Jackson RN, Golden SM, van Erp PB, Carter J, Westra ER, Brouns SJ, van der Oost J, Terwilliger TC, Read RJ, Wiedenheft B

    Science 345(6203):1473-9PubMedFree full text

20133

  1. CRISPR-mediated adaptive immune systems in bacteria and archaea

    Sorek R, Lawrence CM, Wiedenheft B

    ReviewAnnual Review of Biochemistry 82:237-66PubMed

  2. Type I-E CRISPR-cas systems discriminate target from non-target DNA through base pairing-independent PAM recognition

    Westra ER, Semenova E, Datsenko KA, Jackson RN, Wiedenheft B, Severinov K, Brouns SJ

    PLOS Genetics 9(9):e1003742PubMedFree full text

20123

  1. RNA-guided genetic silencing systems in bacteria and archaea

    Wiedenheft B, Sternberg SH, Doudna JA

    ReviewNature 482(7385):331-8PubMed

  2. Mechanism of foreign DNA selection in a bacterial adaptive immune system

    Sashital DG, Wiedenheft B, Doudna JA

    Molecular Cell 46(5):606-15PubMedFree full text

  3. Native tandem and ion mobility mass spectrometry highlight structural and modular similarities in clustered-regularly-interspaced shot-palindromic-repeats (CRISPR)-associated protein complexes from Escherichia coli and Pseudomonas aeruginosa

    van Duijn E, Barbu IM, Barendregt A, Jore MM, Wiedenheft B, Lundgren M, Westra ER, Brouns SJ, Doudna JA, van der Oost J, Heck AJ

    Molecular & Cellular Proteomics 11(11):1430-41PubMedFree full text

20113

  1. Structural basis for CRISPR RNA-guided DNA recognition by Cascade

    Jore MM, Lundgren M, van Duijn E, Bultema JB, Westra ER, Waghmare SP, Wiedenheft B, …, van der Oost J, Brouns SJ

    Nature Structural & Molecular Biology 18(5):529-36PubMed

  2. RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions

    Wiedenheft B, van Duijn E, Bultema JB, Waghmare SP, Zhou K, Barendregt A, Westphal W, Heck AJ, Boekema EJ, Dickman MJ, Doudna JA

    PNAS 108(25):10092-7PubMedFree full text

  3. Structures of the RNA-guided surveillance complex from a bacterial immune system

    Wiedenheft B, Lander GC, Zhou K, Jore MM, Brouns SJJ, van der Oost J, Doudna JA, Nogales E

    Nature 477(7365):486-489PubMedFree full text

20101

  1. Sequence- and structure-specific RNA processing by a CRISPR endonuclease

    Haurwitz RE, Jinek M, Wiedenheft B, Zhou K, Doudna JA

    Science 329(5997):1355-8PubMedFree full text

20092

  1. Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense

    Wiedenheft B, Zhou K, Jinek M, Coyle SM, Ma W, Doudna JA

    Structure 17(6):904-12PubMed

  2. Something old, something new, something borrowed; how the thermoacidophilic archaeon Sulfolobus solfataricus responds to oxidative stress

    Maaty WS, Wiedenheft B, Tarlykov P, Schaff N, Heinemann J, Robison-Cox J, …, Young MJ, Bothner B

    PLOS ONE 4(9):e6964PubMedFree full text

20072

  1. Virus movement maintains local virus population diversity

    Snyder JC, Wiedenheft B, Lavin M, Roberto FF, Spuhler J, Ortmann AC, Douglas T, Young M

    PNAS 104(48):19102-7PubMedFree full text

  2. Bioprospecting in high temperature environments; application of thermostable protein cages

    Wiedenheft B, Flenniken ML, Allen MA, Young M, Douglas T

    ReviewSoft Matter 3(9):1091-1098PubMed

20063

  1. Dps-like protein from the hyperthermophilic archaeon Pyrococcus furiosus

    Ramsay B, Wiedenheft B, Allen M, Gauss GH, Lawrence CM, Young M, Douglas T

    Journal of Inorganic Biochemistry 100(5-6):1061-8PubMed

  2. Hot crenarchaeal viruses reveal deep evolutionary connections

    Ortmann AC, Wiedenheft B, Douglas T, Young M

    ReviewNature Reviews Microbiology 4(7):520-8PubMed

20051

  1. An archaeal antioxidant: characterization of a Dps-like protein from Sulfolobus solfataricus

    Wiedenheft B, Mosolf J, Willits D, Yeager M, Dryden KA, Young M, Douglas T

    PNAS 102(30):10551-6PubMedFree full text

20044

  1. Comparative genomic analysis of hyperthermophilic archaeal Fuselloviridae viruses

    Wiedenheft B, Stedman K, Roberto F, Willits D, Gleske AK, Zoeller L, Snyder J, Douglas T, Young M

    Journal of Virology 78(4):1954-61PubMedFree full text

  2. Structure of D-63 from sulfolobus spindle-shaped virus 1: surface properties of the dimeric four-helix bundle suggest an adaptor protein function

    Kraft P, Kümmel D, Oeckinghaus A, Gauss GH, Wiedenheft B, Young M, Lawrence CM

    Journal of Virology 78(14):7438-42PubMedFree full text

  3. Crystal structure of F-93 from Sulfolobus spindle-shaped virus 1, a winged-helix DNA binding protein

    Kraft P, Oeckinghaus A, Kümmel D, Gauss GH, Gilmore J, Wiedenheft B, Young M, Lawrence CM

    Journal of Virology 78(21):11544-50PubMedFree full text

  4. Effects of culturing on the population structure of a hyperthermophilic virus

    Snyder JC, Spuhler J, Wiedenheft B, Roberto FF, Douglas T, Young MJ

    Microbial Ecology 48(4):561-6PubMed

20031

  1. Viruses of hyperthermophilic Archaea

    Snyder JC, Stedman K, Rice G, Wiedenheft B, Spuhler J, Young MJ

    ReviewResearch in Microbiology 154(7):474-82PubMed

20011

  1. Viruses from extreme thermal environments

    Rice G, Stedman K, Snyder J, Wiedenheft B, Willits D, Brumfield S, McDermott T, Young MJ

    PNAS 98(23):13341-5PubMedFree full text

Research in the Wiedenheft Lab is supported by