[1]

Murray CJL, Ikuta KS, Sharara F, Swetschinski L, Robles Aguilar G, et al. 2022. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. The Lancet 399:629−655

doi: 10.1016/s0140-6736(21)02724-0
[2]

Tacconelli E, Sifakis F, Harbarth S, Schrijver R, van Mourik M, et al. 2018. Surveillance for control of antimicrobial resistance. The Lancet Infectious Diseases 18(3):e99−e106

doi: 10.1016/S1473-3099(17)30485-1
[3]

Rahimi S. 2019. Urgent action on antimicrobial resistance. The Lancet Respiratory Medicine 7(3):208−209

doi: 10.1016/S2213-2600(19)30031-1
[4]

O'Neill J. 2016. Tackling drug-resistant infections globally: final report and recommendations. Review on Antimicrobial Resistance. 84 pp
[5]

Parker DR, Nugen SR. 2024. Bacteriophage-based bioanalysis. Annual Review of Analytical Chemistry 17:393−410

doi: 10.1146/annurev-anchem-071323-084224
[6]

Lemire S, Yehl KM, Lu TK. 2018. Phage-based applications in synthetic biology. Annual Review of Virology 5(1):453−476

doi: 10.1146/annurev-virology-092917-043544
[7]

Burlage RS, Tillmann J. 2017. Biosensors of bacterial cells. Journal of Microbiological Methods 138:2−11

doi: 10.1016/j.mimet.2016.12.023
[8]

Hu Q, Lyu D, Shi X, Jiang Y, Lin Y, et al. 2014. A modified molecular beacons–based multiplex real-time PCR assay for simultaneous detection of eight foodborne pathogens in a single reaction and its application. Foodborne Pathogens and Disease 11(3):207−214

doi: 10.1089/fpd.2013.1607
[9]

Byrne B, Stack E, Gilmartin N, O'Kennedy R. 2009. Antibody-based sensors: principles, problems and potential for detection of pathogens and associated toxins. Sensors 9(6):4407−4445

doi: 10.3390/s90604407
[10]

Salmond GPC, Fineran PC. 2015. A century of the phage: past, present and future. Nature Reviews Microbiology 13(12):777−786

doi: 10.1038/nrmicro3564
[11]

O'Connell L, Marcoux PR, Roupioz Y. 2021. Strategies for surface immobilization of whole bacteriophages: a review. ACS Biomaterials Science & Engineering 7(6):1987−2014

doi: 10.1021/acsbiomaterials.1c00013
[12]

Hosseinidoust Z, Olsson ALJ, Tufenkji N. 2014. Going viral: designing bioactive surfaces with bacteriophage. Colloids and Surfaces B: Biointerfaces 124:2−16

doi: 10.1016/j.colsurfb.2014.05.036
[13]

Hermanson GT. 2013. Bioconjugate techniques, third edition. US: Academic Press. doi: 10.1016/C2009-0-64240-9
[14]

Wang J, Kanach A, Han R, Applegate B. 2021. Application of bacteriophage in rapid detection of Escherichia coli in foods. Current Opinion in Food Science 39:43−50

doi: 10.1016/j.cofs.2020.12.015
[15]

Shabani A, Marquette CA, Mandeville R, Lawrence MF. 2015. Modern probe-assisted methods for the specific detection of bacteria. Journal of Biomedical Science and Engineering 8(2):104−121

doi: 10.4236/jbise.2015.82011
[16]

Cademartiri R, Anany H, Gross I, Bhayani R, Griffiths M, et al. 2010. Immobilization of bacteriophages on modified silica particles. Biomaterials 31(7):1904−1910

doi: 10.1016/j.biomaterials.2009.11.029
[17]

Zhou Y, Marar A, Kner P, Ramasamy RP. 2017. Charge-directed immobilization of bacteriophage on nanostructured electrode for whole-cell electrochemical biosensors. Analytical Chemistry 89(11):5734−5741

doi: 10.1021/acs.analchem.6b03751
[18]

Richter Ł, Bielec K, Leśniewski A, Łoś M, Paczesny J, et al. 2017. Dense layer of bacteriophages ordered in alternating electric field and immobilized by surface chemical modification as sensing element for bacteria detection. ACS Applied Materials & Interfaces 9(23):19622−19629

doi: 10.1021/acsami.7b03497
[19]

Wang C, Sauvageau D, Elias A. 2016. Immobilization of active bacteriophages on polyhydroxyalkanoate surfaces. ACS Applied Materials & Interfaces 8(2):1128−1138

doi: 10.1021/acsami.5b08664
[20]

Love JC, Estroff LA, Kriebel JK, Nuzzo RG, Whitesides GM. 2005. Self-assembled monolayers of thiolates on metals as a form of nanotechnology. Chemical Reviews 105(4):1103−1170

doi: 10.1021/cr0300789
[21]

Gervais L, Gel M, Allain B, Tolba M, Brovko L, et al. 2007. Immobilization of biotinylated bacteriophages on biosensor surfaces. Sensors and Actuators B: Chemical 125(2):615−621

doi: 10.1016/j.snb.2007.03.007
[22]

Tolba M, Minikh O, Brovko LY, Evoy S, Griffiths MW. 2010. Oriented immobilization of bacteriophages for biosensor applications. Applied and Environmental Microbiology 76(2):528−535

doi: 10.1128/aem.02294-09
[23]

Carmody CM, Nugen SR. 2023. Monomeric streptavidin phage display allows efficient immobilization of bacteriophages on magnetic particles for the capture, separation, and detection of bacteria. Scientific Reports 13:16207

doi: 10.1038/s41598-023-42626-9
[24]

Zurier HS, Duong MM, Goddard JM, Nugen SR. 2020. Engineering biorthogonal phage-based nanobots for ultrasensitive, in situ bacteria detection. ACS Applied Bio Materials 3(9):5824−5831

doi: 10.1021/acsabm.0c00546
[25]

Calendar R, Abedon ST. 2005. The bacteriophages, second edition. Oxford: Oxford University Press. doi: 10.1093/oso/9780195148503.001.0001
[26]

Cox CR, Jensen KR, Mondesire RR, Voorhees KJ. 2015. Rapid detection of Bacillus anthracis by γ phage amplification and lateral flow immunochromatography. Journal of Microbiological Methods 118:51−56

doi: 10.1016/j.mimet.2015.08.011
[27]

Kim S, Kim M, Ryu S. 2014. Development of an engineered bioluminescent reporter phage for the sensitive detection of viable Salmonella typhimurium. Analytical Chemistry 86(12):5858−5864

doi: 10.1021/ac500645c
[28]

Born Y, Fieseler L, Thöny V, Leimer N, Duffy B, et al. 2017. Engineering of bacteriophages Y2:: dpoL1-Cand Y2:: luxABfor efficient control and rapid detection of the fire blight pathogen, Erwinia amylovora. Applied and Environmental Microbiology 83(12):e00341-17

doi: 10.1128/aem.00341-17
[29]

Oda M, Morita M, Unno H, Tanji Y. 2004. Rapid detection ofEscherichia coli O157: H7 by using green fluorescent protein-labeled PP01 bacteriophage. Applied and Environmental Microbiology 70(1):527−534

doi: 10.1128/aem.70.1.527-534.2004
[30]

Pires DP, Monteiro R, Mil-Homens D, Fialho A, Lu TK, et al. 2021. Designing P. aeruginosa synthetic phages with reduced genomes. Scientific Reports 11:2164

doi: 10.1038/s41598-021-81580-2
[31]

Zhang D, Coronel-Aguilera CP, Romero PL, Perry L, Minocha U, et al. 2016. The use of a novel NanoLuc-based reporter phage for the detection of Escherichia coli O157: H7. Scientific Reports 6:33235

doi: 10.1038/srep33235
[32]

El-Moghazy AY, Wisuthiphaet N, Yang X, Sun G, Nitin N. 2022. Electrochemical biosensor based on genetically engineered bacteriophage T7 for rapid detection of Escherichia coli on fresh produce. Food Control 135:108811

doi: 10.1016/j.foodcont.2022.108811
[33]

Smith GP, Petrenko VA. 1997. Phage display. Chemical Reviews 97(2):391−410

doi: 10.1021/cr960065d
[34]

Deng X, Wang L, You X, Dai P, Zeng Y. 2018. Advances in the T7 phage display system (Review). Molecular Medicine Reports 17(1):714−720

doi: 10.3892/mmr.2017.7994
[35]

Huo J, Zhang G, Wang L, Sun W, Jia L, et al. 2021. Combining the advantages of prokaryotic expression and T7 phage display systems to obtain antigens for antibody preparation. Protein Expression and Purification 184:105808

doi: 10.1016/j.pep.2020.105808
[36]

Xie J, Schultz PG. 2005. Adding amino acids to the genetic repertoire. Current Opinion in Chemical Biology 9(6):548−554

doi: 10.1016/j.cbpa.2005.10.011
[37]

Kolb HC, Finn MG, Sharpless KB. 2001. Click chemistry: diverse chemical function from a few good reactions. Angewandte Chemie International Edition 40(11):2004−2021

doi: 10.1002/1521-3773(20010601)40:11<2004::AID-ANIE2004>3.0.CO;2-5
[38]

Witte MD, Wu T, Guimaraes CP, Theile CS, Blom AEM, et al. 2015. Site-specific protein modification using immobilized sortase in batch and continuous-flow systems. Nature Protocols 10(3):508−516

doi: 10.1038/nprot.2015.026
[39]

Hufziger KA, Farquharson EL, Werner BG, Chen Q, Goddard JM, et al. 2022. In vivo capsid engineering of bacteriophages for oriented surface conjugation. ACS Applied Bio Materials 5(11):5104−5112

doi: 10.1021/acsabm.2c00428
[40]

Taniguchi K, Nomura K, Hata Y, Nishimura T, Asami Y, et al. 2007. The Si-tag for immobilizing proteins on a silica surface. Biotechnology and Bioengineering 96(6):1023−1029

doi: 10.1002/bit.21208
[41]

Ikeda T, Kuroda A. 2011. Why does the silica-binding protein "Si-tag" bind strongly to silica surfaces? Implications of conformational adaptation of the intrinsically disordered polypeptide to solid surfaces. Colloids and Surfaces B: Biointerfaces 86(2):359−363

doi: 10.1016/j.colsurfb.2011.04.020
[42]

Chen X, Zaro JL, Shen WC. 2013. Fusion protein linkers: property, design and functionality. Advanced Drug Delivery Reviews 65(10):1357−1369

doi: 10.1016/j.addr.2012.09.039
[43]

Abdelhamied N, Abdelrahman F, El-Shibiny A, Hassan RYA. 2023. Bacteriophage-based nano-biosensors for the fast impedimetric determination of pathogens in food samples. Scientific Reports 13:3498

doi: 10.1038/s41598-023-30520-3
[44]

Xiang X, Ye Q, Shang Y, Li F, Zhou B, et al. 2021. Quantitative detection of aflatoxin B1 using quantum dots-based immunoassay in a recyclable gravity-driven microfluidic chip. Biosensors and Bioelectronics 190:113394

doi: 10.1016/j.bios.2021.113394
[45]

Arya SK, Singh A, Naidoo R, Wu P, McDermott MT, et al. 2011. Chemically immobilized T4-bacteriophage for specific Escherichia coli detection using surface plasmon resonance. The Analyst 136(3):486−492

doi: 10.1039/c0an00697a
[46]

Guntupalli R, Sorokulova I, Olsen E, Globa L, Pustovyy O, et al. 2012. Detection and identification of methicillin resistant and sensitive strains of Staphylococcus aureus using tandem measurements. Journal of Microbiological Methods 90(3):182−191

doi: 10.1016/j.mimet.2012.05.003
[47]

Singh A, Poshtiban S, Evoy S. 2013. Recent advances in bacteriophage based biosensors for food-borne pathogen detection. Sensors 13(2):1763−1786

doi: 10.3390/s130201763
[48]

Hinkley TC, Singh S, Garing S, Le Ny AM, Nichols KP, et al. 2018. A phage-based assay for the rapid, quantitative, and single CFU visualization of E. coli (ECOR #13) in drinking water. Scientific Reports 8:14630

doi: 10.1038/s41598-018-33097-4
[49]

Smith HO, Hutchison CA III, Pfannkoch C, Venter JC. 2003. Generating a synthetic genome by whole genome assembly: φX174 bacteriophage from synthetic oligonucleotides. Proceedings of the National Academy of Sciences of the United States of America 100(26):15440−15445

doi: 10.1073/pnas.2237126100
[50]

Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H, et al. 2008. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319(5867):1215−1220

doi: 10.1126/science.1151721
[51]

Jaschke PR, Lieberman EK, Rodriguez J, Sierra A, Endy D. 2012. A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast. Virology 434(2):278−284

doi: 10.1016/j.virol.2012.09.020
[52]

Ando H, Lemire S, Pires DP, Lu TK. 2015. Engineering modular viral scaffolds for targeted bacterial population editing. Cell Systems 1(3):187−196

doi: 10.1016/j.cels.2015.08.013
[53]

Cuervo A, Pulido-Cid M, Chagoyen M, Arranz R, González-García VA, et al. 2013. Structural characterization of the bacteriophage T7 tail machinery. Journal of Biological Chemistry 288(36):26290−26299

doi: 10.1074/jbc.M113.491209
[54]

Kilcher S, Studer P, Muessner C, Klumpp J, Loessner MJ. 2018. Cross-genus rebooting of custom-made, synthetic bacteriophage genomes in L-form bacteria. Proceedings of the National Academy of Sciences of the United States of America 115(3):567−572

doi: 10.1073/pnas.1714658115
[55]

Pardee K, Green AA, Takahashi MK, Braff D, Lambert G, et al. 2016. Rapid, low-cost detection of zika virus using programmable biomolecular components. Cell 165(5):1255−1266

doi: 10.1016/j.cell.2016.04.059
[56]

Martel B, Moineau S. 2014. CRISPR-Cas: an efficient tool for genome engineering of virulent bacteriophages. Nucleic Acids Research 42(14):9504−9513

doi: 10.1093/nar/gku628
[57]

Kiro R, Shitrit D, Qimron U. 2014. Efficient engineering of a bacteriophage genome using the type I-E CRISPR-Cas system. RNA Biology 11(1):42−44

doi: 10.4161/rna.27766
[58]

Tao P, Wu X, Tang WC, Zhu J, Rao V. 2017. Engineering of bacteriophage T4 genome using CRISPR-Cas9. ACS Synthetic Biology 6(10):1952−1961

doi: 10.1021/acssynbio.7b00179
[59]

Smith GP. 1985. Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 228(4705):1315−1317

doi: 10.1126/science.4001944
[60]

Esvelt KM, Carlson JC, Liu DR. 2011. A system for the continuous directed evolution of biomolecules. Nature 472(7344):499−503

doi: 10.1038/nature09929
[61]

Badran AH, Guzov VM, Huai Q, Kemp MM, Vishwanath P, et al. 2016. Continuous evolution of Bacillus thuringiensis toxins overcomes insect resistance. Nature 533(7601):58−63

doi: 10.1038/nature17938
[62]

Temme K, Hill R, Segall-Shapiro TH, Moser F, Voigt CA. 2012. Modular control of multiple pathways using engineered orthogonal T7 polymerases. Nucleic Acids Research 40(17):8773−8781

doi: 10.1093/nar/gks597
[63]

Segall‐Shapiro TH, Meyer AJ, Ellington AD, Sontag ED, Voigt CA. 2014. A 'resource allocator' for transcription based on a highly fragmented T7 RNA polymerase. Molecular Systems Biology 10(7):MSB145299

doi: 10.15252/msb.20145299
[64]

Fogg PCM, Colloms S, Rosser S, Stark M, Smith MCM. 2014. New applications for phage integrases. Journal of Molecular Biology 426(15):2703−2716

doi: 10.1016/j.jmb.2014.05.014
[65]

Siuti P, Yazbek J, Lu TK. 2013. Synthetic circuits integrating logic and memory in living cells. Nature Biotechnology 31(5):448−452

doi: 10.1038/nbt.2510
[66]

Roquet N, Soleimany AP, Ferris AC, Aaronson S, Lu TK. 2016. Synthetic recombinase-based state machines in living cells. Science 353(6297):aad8559

doi: 10.1126/science.aad8559
[67]

Yang L, Nielsen AAK, Fernandez-Rodriguez J, McClune CJ, Laub MT, et al. 2014. Permanent genetic memory with > 1-byte capacity. Nature Methods 11(12):1261−1266

doi: 10.1038/nmeth.3147
[68]

Jacobs WR Jr, Barletta RG, Udani R, Chan J, Kalkut G, et al. 1993. Rapid assessment of drug susceptibilities of Mycobacterium tuberculosis by means of luciferase reporter phages. Science 260(5109):819−822

doi: 10.1126/science.8484123
[69]

Schmidt A, Rabsch W, Broeker NK, Barbirz S. 2016. Bacteriophage tailspike protein based assay to monitor phase variable glucosylations in Salmonella O-antigens. BMC Microbiology 16(1):207

doi: 10.1186/s12866-016-0826-0
[70]

Han L, Shao C, Liang B, Liu A. 2016. Genetically engineered phage-templated MnO2 nanowires: synthesis and their application in electrochemical glucose biosensor operated at neutral pH condition. ACS Applied Materials & Interfaces 8(22):13768−13776

doi: 10.1021/acsami.6b03266
[71]

Sulakvelidze A, Alavidze Z, Morris JG Jr. 2001. Bacteriophage therapy. Antimicrobial Agents and Chemotherapy 45(3):649−659

doi: 10.1128/aac.45.3.649-659.2001
[72]

Lu TK, Collins JJ. 2007. Dispersing biofilms with engineered enzymatic bacteriophage. Proceedings of the National Academy of Sciences of the United States of America 104(27):11197−11202

doi: 10.1073/pnas.0704624104
[73]

Lu TK, Collins JJ, Demain AL. 2009. Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy. Proceedings of the National Academy of Sciences of the United States of America 106(12):4629−4634

doi: 10.1073/pnas.0800442106
[74]

Citorik RJ, Mimee M, Lu TK. 2014. Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases. Nature Biotechnology 32(11):1141−1145

doi: 10.1038/nbt.3011
[75]

Briers Y, Walmagh M, Van Puyenbroeck V, Cornelissen A, Cenens W, et al. 2014. Engineered endolysin-based "artilysins" to combat multidrug-resistant gram-negative pathogens. mBio 5(4):e01379-14

doi: 10.1128/mbio.01379-14
[76]

Lukacik P, Barnard TJ, Keller PW, Chaturvedi KS, Seddiki N, et al. 2012. Structural engineering of a phage lysin that targets gram-negative pathogens. Proceedings of the National Academy of Sciences of the United States of America 109(25):9857−9862

doi: 10.1073/pnas.1203472109
[77]

Kovacs EW, Hooker JM, Romanini DW, Holder PG, Berry KE, et al. 2007. Dual-surface-modified bacteriophage MS2 as an ideal scaffold for a viral capsid-based drug delivery system. Bioconjugate Chemistry 18(4):1140−1147

doi: 10.1021/bc070006e
[78]

Ashley CE, Carnes EC, Phillips GK, Durfee PN, Buley MD, et al. 2011. Cell-specific delivery of diverse cargos by bacteriophage MS2 virus-like particles. ACS Nano 5(7):5729−5745

doi: 10.1021/nn201397z
[79]

Pouillot F, Blois H, Iris F. 2010. Genetically engineered virulent phage banks in the detection and control of emergent pathogenic bacteria. Biosecurity and Bioterrorism 8(2):155−169

doi: 10.1089/bsp.2009.0057
[80]

Wang D, Hinkley T, Chen J, Talbert JN, Nugen SR. 2019. Phage based electrochemical detection of Escherichia coli in drinking water using affinity reporter probes. The Analyst 144(4):1345−1352

doi: 10.1039/c8an01850b
[81]

Hoang HA, Dien LT. 2015. Rapid and simple colorimetric detection of Escherichia coli O157: H7 in apple juice using a novel recombinant bacteriophage-based method. Biocontrol Science 20(2):99−103

doi: 10.4265/bio.20.99
[82]

Alcaine SD, Law K, Ho S, Kinchla AJ, Sela DA, et al. 2016. Bioengineering bacteriophages to enhance the sensitivity of phage amplification-based paper fluidic detection of bacteria. Biosensors and Bioelectronics 82:14−19

doi: 10.1016/j.bios.2016.03.047
[83]

Yang H, Gou Z, Yuan H, Yue X, Lu S, et al. 2023. Employment of the phage cocktail as a species-specific recognition agent for wide-spectrum detection of bacterial strains. Analytical Chemistry 95(26):10008−10016

doi: 10.1021/acs.analchem.3c01313
[84]

Ilhan H, Tayyarcan EK, Caglayan MG, Boyaci İH, Saglam N, et al. 2021. Replacement of antibodies with bacteriophages in lateral flow assay of Salmonella Enteritidis. Biosensors and Bioelectronics 189:113383

doi: 10.1016/j.bios.2021.113383
[85]

Wu P, Xue F, Zuo W, Yang J, Liu X, et al. 2022. A universal bacterial catcher Au–PMBA-nanocrab-based lateral flow immunoassay for rapid pathogens detection. Analytical Chemistry 94(10):4277−4285

doi: 10.1021/acs.analchem.1c04909
[86]

Nie S, Emory S. 1997. Probing single molecules and single nanoparticles by surface-enhanced Raman scattering. Science 275:1102−1106

doi: 10.1126/science.275.5303.1102
[87]

Fabris L. 2012. Bottom-up optimization of SERS hot-spots. Chemical Communications 48(75):9346−9348

doi: 10.1039/c2cc34068b
[88]

Bright FV. 1988. Bioanalytical applications of fluorescence spectroscopy. Analytical Chemistry 60(18):1031A−1039A

doi: 10.1021/ac00169a713
[89]

Cheng Q, Brajter-Toth A. 1996. Permselectivity, sensitivity, and amperometric pH sensing at thioctic acid monolayer microelectrodes. Analytical Chemistry 68(23):4180−4185

doi: 10.1021/ac960329w
[90]

Chen RJ, Bangsaruntip S, Drouvalakis KA, Wong Shi Kam N, Shim M, et al. 2003. Noncovalent functionalization of carbon nanotubes for highly specific electronic biosensors. Proceedings of the National Academy of Sciences of the United States of America 100(9):4984−4989

doi: 10.1073/pnas.0837064100
[91]

Bakker E, Pretsch E. 2007. Modern potentiometry. Angewandte Chemie International Edition 46(30):5660−5668

doi: 10.1002/anie.200605068
[92]

Chan JK, Anderson BM. 1975. A novel diazonium-sulfhydryl reaction in the inactivation of yeast alcohol dehydrogenase by diazotized 3-aminopyridine adenine dinucleotide. Journal of Biological Chemistry 250(1):67−72

doi: 10.1016/S0021-9258(19)41980-7
[93]

Olsson ALJ, Wargenau A, Tufenkji N. 2016. Optimizing bacteriophage surface densities for bacterial capture and sensing in quartz crystal microbalance with dissipation monitoring. ACS Applied Materials & Interfaces 8(22):13698−13706

doi: 10.1021/acsami.6b02227
[94]

Lakshmanan RS, Guntupalli R, Hu J, Kim DJ, Petrenko VA, et al. 2007. Phage immobilized magnetoelastic sensor for the detection of Salmonella typhimurium. Journal of Microbiological Methods 71(1):55−60

doi: 10.1016/j.mimet.2007.07.012
[95]

Seguritan V, Alves N Jr, Arnoult M, Raymond A, Lorimer D, et al. 2012. Artificial neural networks trained to detect viral and phage structural proteins. PLoS Computational Biology 8(8):e1002657

doi: 10.1371/journal.pcbi.1002657
[96]

Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos GA, Thomas AD, Huntemann M, et al. 2016. Uncovering earth's virome. Nature 536(7617):425−430

doi: 10.1038/nature19094
[97]

Ahlgren NA, Ren J, Lu YY, Fuhrman JA, Sun F. 2017. Alignment-free d*2 oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences. Nucleic Acids Research 45(1):39−53

doi: 10.1093/nar/gkw1002
[98]

Stern A, Mick E, Tirosh I, Sagy O, Sorek R. 2012. CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome. Genome Research 22(10):1985−1994

doi: 10.1101/gr.138297.112
[99]

Burstein D, Sun CL, Brown CT, Sharon I, Anantharaman K, et al. 2016. Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems. Nature Communications 7:10613

doi: 10.1038/ncomms10613
[100]

Flores CO, Meyer JR, Valverde S, Farr L, Weitz JS. 2011. Statistical structure of host–phage interactions. Proceedings of the National Academy of Sciences of the United States of America 108(28):E288−E297

doi: 10.1073/pnas.1101595108
[101]

Galiez C, Siebert M, Enault F, Vincent J, Söding J. 2017. WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs. Bioinformatics 33(19):3113−3114

doi: 10.1093/bioinformatics/btx383
[102]

Wang W, Ren J, Tang K, Dart E, Ignacio-Espinoza JC, et al. 2020. A network-based integrated framework for predicting virus-prokaryote interactions. NAR Genomics and Bioinformatics 2(2):lqaa044

doi: 10.1093/nargab/lqaa044
[103]

Casjens SR. 2005. Comparative genomics and evolution of the tailed-bacteriophages. Current Opinion in Microbiology 8(4):451−458

doi: 10.1016/j.mib.2005.06.014
[104]

Fokine A, Rossmann MG. 2014. Molecular architecture of tailed double-stranded DNA phages. Bacteriophage 4(2):e28281

doi: 10.4161/bact.28281
[105]

Aksyuk AA, Rossmann MG. 2011. Bacteriophage assembly. Viruses 3(3):172−203

doi: 10.3390/v3030172
[106]

Nobrega FL, Vlot M, de Jonge PA, Dreesens LL, Beaumont HJE, et al. 2018. Targeting mechanisms of tailed bacteriophages. Nature Reviews Microbiology 16(12):760−773

doi: 10.1038/s41579-018-0070-8
[107]

Manavalan B, Shin TH, Lee G. 2018. PVP-SVM: sequence-based prediction of phage virion proteins using a support vector machine. Frontiers in Microbiology 9:476

doi: 10.3389/fmicb.2018.00476
[108]

Cantu VA, Salamon P, Seguritan V, Redfield J, Salamon D, et al. 2020. PhANNs, a fast and accurate tool and web server to classify phage structural proteins. PLoS Computational Biology 16(11):e1007845

doi: 10.1371/journal.pcbi.1007845
[109]

Fang Z, Feng T, Zhou H, Chen M. 2022. DeePVP: identification and classification of phage virion proteins using deep learning. GigaScience 11:giac076

doi: 10.1093/gigascience/giac076
[110]

Fang Z, Tan J, Wu S, Li M, Xu C, et al. 2019. PPR-Meta: a tool for identifying phages and plasmids from metagenomic fragments using deep learning. GigaScience 8(6):giz066

doi: 10.1093/gigascience/giz066
[111]

Consortium TU. 2019. UniProt: a worldwide hub of protein knowledge. Nucleic Acids Research 47(D1):D506−D515

doi: 10.1093/nar/gky1049
[112]

Alipanahi B, Delong A, Weirauch MT, Frey BJ. 2015. Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning. Nature Biotechnology 33(8):831−838

doi: 10.1038/nbt.3300
[113]

Madani A, Krause B, Greene ER, Subramanian S, Mohr BP, et al. 2023. Large language models generate functional protein sequences across diverse families. Nature Biotechnology 41(8):1099−1106

doi: 10.1038/s41587-022-01618-2
[114]

King SH, Driscoll CL, Li DB, Guo D, Merchant AT, et al. 2025. Generative design of novel bacteriophages with genome language models. bioRxiv:preprint

doi: 10.1101/2025.09.12.675911v1
[115]

Jaschke PR, Dotson GA, Hung KS, Liu D, Endy D. 2019. Definitive demonstration by synthesis of genome annotation completeness. Proceedings of the National Academy of Sciences of the United States of America 116(48):24206−24213

doi: 10.1101/455428
[116]

Nguyen E, Poli M, Durrant MG, Kang B, Katrekar D, et al. 2024. Sequence modeling and design from molecular to genome scale with Evo. Science 386(6723):eado9336

doi: 10.1126/science.ado9336
[117]

Brixi G, Durrant MG, Ku J, Naghipourfar M, Poli M, et al. 2026. Genome modelling and design across all domains of life with Evo 2. Nature 00:1−13

doi: 10.1038/s41586-026-10176-5