PhIP-Seq: PHAGE DISPLAY IMMUNOPRECIPITATION SEQUENCING

Overview of PhIP-Seq.

Bacteriophage Immunoprecipitation Sequencing (PhIP-Seq) is a powerful new method of multiplexed analysis that combines DNA high-throughput sequencing with next-generation proteomics. PhIP-Seq allows researchers to determine what antibodies were created by an individual’s unique history of immune exposures. PhIP-Seq is the highest-coverage antigen-specific assay yet developed, able to detect antibodies versus virtually any antigen via overlapping long peptides.

PhIP-Seq was developed at Harvard University in 2011. This work created a synthetic representation of the complete human proteome as a T7 bacteriophage display library. They built upon this work in 2015 by creating a synthetic representation of the complete human virome: the universe of known infectious viruses.

Since then, teams at UCSF and the Chan Zuckerberg Biohub have built upon and expanded the universe of antigen-specific profiling available via PhiP-Seq. PhIP-Seq has been used to perform revolutionary immune profiling on people suffering from multiple sclerosis, diabetes, rheumatoid arthritis, and more.  CDI Labs was the first company to commercialize PhIP-Seq technology.

Technology overview.

PhIP-Seq: HuScan™ — Human proteome phage display.

The entire human proteome in a single antibody detection assay.

HuScan™ v2.0, an application of Bacteriophage-Display Immunoprecipitation Sequencing (PhIP-Seq), is composed of an entire normal human proteome as defined by the NCBI RefSeq database. The library contains proteins expressed as overlapping 49mer peptide tiles on the surface of bacteriophages. For an assay, an aliquot from this library is reacted with diluted patient serum or other antibody-containing fluid. Bound antibodies are immunoprecipitated with protein A/G beads, the precipitate amplified by PCR, and the sequences quantified by a next-generation sequencing and analysis pipeline that compares patient-sample IP read counts to negative controls with no antibody input (mock IPs) in the context of overall clonal frequency of individual peptides in the parent library. Output data are then created at both the peptide and whole-protein level.

PhIP-Seq: MouseScan™ — Murine proteome phage display.

The entire mouse proteome in a single antibody detection assay.

MouseScan™, an application of Bacteriophage-Display Immunoprecipitation Sequencing (PhIP-Seq), is composed of the entire normal mouse proteome (GRCm38.p5). The library contains all proteins expressed as overlapping 62mer peptide tiles on the surface of bacteriophages. For an assay, an aliquot from this library is reacted with diluted mouse serum or other antibody-containing fluid. Bound antibodies are immunoprecipitated with protein A/G beads, the precipitate amplified by PCR, and the sequences quantified by a next-generation sequencing and analysis pipeline that compares patient-sample IP read counts to negative controls with no antibody input (mock IPs) in the context of overall clonal frequency of individual peptides in the parent library. Output data are then created at both the peptide level.

Learn more about our ANTYGEN™ PhIP-Seq analysis services.

huscan human proteome phage display phip-seq button
CDI Labs Order Product Button

PhIP-Seq References: Projects by CDI Labs

[1]
A. Xagara, S. Fortis, M. Goulielmaki, F. Koinis, E. Chantzara, I. Samaras, V.N. Papadopoulos, V. Georgoulias, C.N. Baxevanis, A. Kotsakis, 21P Peripheral pre-existing T cell immunity as predictive biomarker in cancer immunotherapy for NSCLC patients, Immuno-Oncology and Technology. 16 (2022) 100126. https://doi.org/10.1016/j.iotech.2022.100126.
[2]
C. Valencia-Sanchez, A.M. Knight, M.B. Hammami, Y. Guo, J.R. Mills, T.J. Kryzer, A.L. Piquet, A. Amin, M. Heinzelmann, C.F. Lucchinetti, V.A. Lennon, A. McKeon, S.J. Pittock, D. Dubey, Characterisation of TRIM46 autoantibody-associated paraneoplastic neurological syndrome, J Neurol Neurosurg Psychiatry. 93 (2022) 196–200. https://doi.org/10.1136/jnnp-2021-326656.
[3]
M. Naigeon, M. Roulleaux Dugage, F.-X. Danlos, C. De Oliveira, L. Boselli, J.-M. Jouniaux, F. Griscelli, A. Marabelle, L. Cassard, G. Roman, T. Hulett, B. Besse, N. Chaput-Gras, 20P Human virome epitope-level antiviral antibody profiling identified the cytomegalovirus (CMV) as the main driver of senescent immune phenotype (SIP) in patients with advanced non-small cell lung cancer (aNSCLC), Immuno-Oncology and Technology. 16 (2022) 100125. https://doi.org/10.1016/j.iotech.2022.100125.
[4]
E.M. Gordon‐Lipkin, C.S. Marcum, S. Kruk, E. Thompson, S.E.M. Kelly, H. Kalish, L. Bellusci, S. Khurana, K. Sadtler, P.J. McGuire, Comprehensive profiling of the human viral exposome in households containing an at‐risk child with mitochondrial disease during the 2020–2021 COVID‐19 pandemic, Clinical & Translational Med. 12 (2022). https://doi.org/10.1002/ctm2.1100.
[5]
F.G. Dall’Olio, M. Lerousseau, G. Roman, F.-X. Danlos, M. Aldea, N. Chaput-Gras, D. Planchard, F. Barlesi, T. Hulett, A. Marabelle, B. Besse, 1070P Previous viral infections assessed by pan-virus phage immunoprecipitation sequencing (PhIP-Seq) predict response to immune checkpoint blockers (ICBs) in non-small cell lung cancer (NSCLC), Annals of Oncology. 33 (2022) S1043. https://doi.org/10.1016/j.annonc.2022.07.1196.
[6]
L. Chouchane, J.-C. Grivel, E.A.B.A. Farag, I. Pavlovski, S. Maacha, A. Sathappan, H.E. Al-Romaihi, S.W.J. Abuaqel, M.M.A. Ata, A.I. Chouchane, S. Remadi, N. Halabi, A. Rafii, M.H. Al-Thani, N. Marr, M. Subramanian, J. Shan, Dromedary camels as a natural source of neutralizing nanobodies against SARS-CoV-2, JCI Insight. 6 (2021) e145785. https://doi.org/10.1172/jci.insight.145785.

All Publications

[1]
E. Rackaityte, I. Proekt, H.S. Miller, A. Ramesh, J.F. Brooks, A.F. Kung, C. Mandel-Brehm, D. Yu, C. Zamecnik, R. Bair, S.E. Vazquez, S. Sunshine, C.L. Abram, C.A. Lowell, G. Rizzuto, M.R. Wilson, J. Zikherman, M.S. Anderson, J.L. DeRisi, Validation of a murine proteome-wide phage display library for the identification of autoantibody specificities, (2023) 2023.04.07.535899. https://doi.org/10.1101/2023.04.07.535899.
[2]
M.L. Paull, Development of Bioinformatic Tools to Identify and Characterize Linear Protein Epitopes, Ph.D., University of California, Santa Barbara, 2022. https://www.proquest.com/docview/2116567051/abstract/85F692BD8D3C4D63PQ/1 (accessed May 23, 2022).
[3]
T. Kula, High-Throughput Approaches to Profiling Antibody and T Cell Targets, Ph.D., Harvard University, 2022. https://www.proquest.com/docview/2465806854/abstract/20D32AA7A91442E0PQ/1 (accessed May 23, 2022).
[4]
T. Venkataraman, H. Swaminathan, C.A. Arze, S.M. Jacobo, A. Bhattacharyya, T. David, D.M. Nawandar, S. Delagrave, V. Mani, N.L. Yozwiak, H.B. Larman, Comprehensive profiling of antibody responses to the human anellome using programmable phage display, (2022) 2022.03.28.486145. https://doi.org/10.1101/2022.03.28.486145.
[5]
S.E. Vazquez, S.A. Mann, A. Bodansky, A.F. Kung, Z. Quandt, E.M.N. Ferré, N. Landegren, D. Eriksson, P. Bastard, S.-Y. Zhang, J. Liu, A. Mitchell, C. Mandel-Brehm, B. Miao, G. Sowa, K. Zorn, A.Y. Chan, C. Shimizu, A. Tremoulet, K. Lynch, M.R. Wilson, O. Kampe, K. Dobbs, O.M. Delmonte, L.D. Notarangelo, J.C. Burns, J.-L. Casanova, M.S. Lionakis, T.R. Torgerson, M.S. Anderson, J.L. DeRisi, Autoantibody discovery across monogenic, acquired, and COVID19-associated autoimmunity with scalable PhIP-Seq, Immunology, 2022. https://doi.org/10.1101/2022.03.23.485509.
[6]
P. Taeschler, C. Cervia, Y. Zurbuchen, S. Hasler, C. Pou, Z. Tan, S. Adamo, M.E. Raeber, E. Bächli, A. Rudiger, M. Stüssi-Helbling, L.C. Huber, P. Brodin, J. Nilsson, E. Probst-Müller, O. Boyman, Autoantibodies in COVID-19 correlate with anti-viral humoral responses and distinct immune signatures, (2022) 2022.01.08.22268901. https://doi.org/10.1101/2022.01.08.22268901.
[7]
Y. Hosono, B. Sie, I. Pinal-Fernandez, K. Pak, C.A. Mecoli, M. Casal-Dominguez, B.M. Warner, M.J. Kaplan, J. Albayda, S.K. Danoff, T.E. Lloyd, J. Paik, E. Tiniakou, J.C. Milisenda, J.M. Grau-Junyent, A. Selva-O’Callaghan, L. Christopher-Stine, H.B. Larman, A.L. Mammen, Coexisting autoantibodies against transcription factor Sp4 are associated with decreased cancer risk in dermatomyositis patients with anti-TIF1γ autoantibodies, (2022) 2022.02.28.22271555. https://doi.org/10.1101/2022.02.28.22271555.
[8]
A. Chen, K. Kammers, H.B. Larman, R.B. Scharpf, I. Ruczinski, Detecting Antibody Reactivities in Phage ImmunoPrecipitation Sequencing Data, (2022) 2022.01.19.476926. https://doi.org/10.1101/2022.01.19.476926.
[9]
H. Yue, Y. Li, M. Yang, C. Mao, T7 Phage as an Emerging Nanobiomaterial with Genetically Tunable Target Specificity, Advanced Science. 9 (2022) 2103645. https://doi.org/10.1002/advs.202103645.
[10]
T. Venkataraman, C. Valencia, M. Mangino, W. Morgenlander, S.J. Clipman, T. Liechti, A. Valencia, P. Christofidou, T. Spector, M. Roederer, P. Duggal, H.B. Larman, Analysis of antibody binding specificities in twin and SNP-genotyped cohorts reveals that antiviral antibody epitope selection is a heritable trait, Immunity. 55 (2022) 174-184.e5. https://doi.org/10.1016/j.immuni.2021.12.004.
[11]
C. Valencia-Sanchez, A.M. Knight, M.B. Hammami, Y. Guo, J.R. Mills, T.J. Kryzer, A.L. Piquet, A. Amin, M. Heinzelmann, C.F. Lucchinetti, V.A. Lennon, A. McKeon, S.J. Pittock, D. Dubey, Characterisation of TRIM46 autoantibody-associated paraneoplastic neurological syndrome, J Neurol Neurosurg Psychiatry. 93 (2022) 196–200. https://doi.org/10.1136/jnnp-2021-326656.
[12]
C.K. Tiu, F. Zhu, L.-F. Wang, R. de Alwis, Phage ImmunoPrecipitation Sequencing (PhIP-Seq): The Promise of High Throughput Serology, Pathogens. 11 (2022) 568. https://doi.org/10.3390/pathogens11050568.
[13]
C. Mandel-Brehm, L.A. Benson, B. Tran, A.F. Kung, S.A. Mann, S.E. Vazquez, H. Retallack, H.A. Sample, K.C. Zorn, L.M. Khan, L.M. Kerr, P.L. McAlpine, L. Zhang, F. McCarthy, J.E. Elias, U. Katwa, C.M. Astley, S. Tomko, J. Dalmau, W.W. Seeley, S.J. Pleasure, M.R. Wilson, M.P. Gorman, J.L. DeRisi, ZSCAN1 autoantibodies are associated with pediatric paraneoplastic ROHHAD, Annals of Neurology. n/a (2022). https://doi.org/10.1002/ana.26380.
[14]
L. Ma, H. Ouyang, A. Su, Y. Zhang, D. Pang, T. Zhang, R. Sun, W. Wang, Z. Xie, D. Lv, AbSE Workflow: Rapid Identification of the Coding Sequence and Linear Epitope of the Monoclonal Antibody at the Single-cell Level, ACS Synth. Biol. 11 (2022) 1856–1864. https://doi.org/10.1021/acssynbio.2c00018.
[15]
J. Liu, K.A. Knopp, E. Rackaityte, C.Y. Wang, M.T. Laurie, S. Sunshine, A.S. Puschnik, J.L. DeRisi, Genome-Wide Knockout Screen Identifies Human Sialomucin CD164 as an Essential Entry Factor for Lymphocytic Choriomeningitis Virus, MBio. (2022) e00205-22. https://doi.org/10.1128/mbio.00205-22.
[16]
T.V. Lanz, R.C. Brewer, P.P. Ho, J.-S. Moon, K.M. Jude, D. Fernandez, R.A. Fernandes, A.M. Gomez, G.-S. Nadj, C.M. Bartley, R.D. Schubert, I.A. Hawes, S.E. Vazquez, M. Iyer, J.B. Zuchero, B. Teegen, J.E. Dunn, C.B. Lock, L.B. Kipp, V.C. Cotham, B.M. Ueberheide, B.T. Aftab, M.S. Anderson, J.L. DeRisi, M.R. Wilson, R.J.M. Bashford-Rogers, M. Platten, K.C. Garcia, L. Steinman, W.H. Robinson, Clonally Expanded B Cells in Multiple Sclerosis Bind EBV EBNA1 and GlialCAM, Nature. (2022) 1–12. https://doi.org/10.1038/s41586-022-04432-7.
[17]
T. Khan, M. Rahman, F.A. Ali, S.S.Y. Huang, M. Ata, Q. Zhang, P. Bastard, Z. Liu, E. Jouanguy, V. Béziat, A. Cobat, G.K. Nasrallah, H.M. Yassine, M.K. Smatti, A. Saeed, I. Vandernoot, J.-C. Goffard, G. Smits, I. Migeotte, F. Haerynck, I. Meyts, L. Abel, J.-L. Casanova, M.R. Hasan, N. Marr, Distinct antibody repertoires against endemic human coronaviruses in children and adults, JCI Insight. 6 (2022) e144499. https://doi.org/10.1172/jci.insight.144499.
[18]
M.E. Garrett, J.G. Galloway, C. Wolf, J.K. Logue, N. Franko, H.Y. Chu, F.A. Matsen IV, J.M. Overbaugh, Comprehensive characterization of the antibody responses to SARS-CoV-2 Spike protein finds additional vaccine-induced epitopes beyond those for mild infection, ELife. 11 (2022) e73490. https://doi.org/10.7554/eLife.73490.
[19]
L. Chouchane, J.-C. Grivel, E.A.B.A. Farag, I. Pavlovski, S. Maacha, A. Sathappan, H.E. Al-Romaihi, S.W.J. Abuaqel, M.M.A. Ata, A.I. Chouchane, S. Remadi, N. Halabi, A. Rafii, M.H. Al-Thani, N. Marr, M. Subramanian, J. Shan, Dromedary camels as a natural source of neutralizing nanobodies against SARS-CoV-2, JCI Insight. 6 (2022) e145785. https://doi.org/10.1172/jci.insight.145785.
[20]
X. Castro Dopico, G.B. Karlsson Hedestam, A family matter: Anti-viral antibody responses, Immunity. 55 (2022) 8–10. https://doi.org/10.1016/j.immuni.2021.12.008.
[21]
A.R. Bourgonje, S. Andreu-Sánchez, T. Vogl, S. Hu, A. Vich Vila, S. Leviatan, A. Kurilshikov, S. Klompus, I.N. Kalka, H.M. van Dullemen, A. Weinberger, M.C. Visschedijk, E.A.M. Festen, K.N. Faber, C. Wijmenga, G. Dijkstra, E. Segal, J. Fu, A. Zhernakova, R.K. Weersma, DOP53 In-depth characterisation of the serum antibody epitope repertoire in Inflammatory Bowel Disease by high-throughput phage-displayed immunoprecipitation sequencing, Journal of Crohn’s and Colitis. 16 (2022) i100–i102. https://doi.org/10.1093/ecco-jcc/jjab232.092.
[22]
H. Abolhassani, N. Landegren, P. Bastard, M. Materna, M. Modaresi, L. Du, M. Aranda-Guillén, F. Sardh, F. Zuo, P. Zhang, H. Marcotte, N. Marr, T. Khan, M. Ata, F. Al-Ali, R. Pescarmona, A. Belot, V. Béziat, Q. Zhang, J.-L. Casanova, O. Kämpe, S.-Y. Zhang, L. Hammarström, Q. Pan-Hammarström, Inherited IFNAR1 Deficiency in a Child with Both Critical COVID-19 Pneumonia and Multisystem Inflammatory Syndrome, J Clin Immunol. 42 (2022) 471–483. https://doi.org/10.1007/s10875-022-01215-7.
[23]
C. Valencia, CHARACTERIZATION OF THE GENETIC ARCHITECTURE OF THE HUMAN ANTIVIRAL RESPONSE AT THE EPITOPE LEVEL, Thesis, Johns Hopkins University, 2021. https://jscholarship.library.jhu.edu/handle/1774.2/66693 (accessed May 23, 2022).
[24]
N. Ghosh, this link will open in a new window Link to external site, Autoantibodies as Biomarkers of Immune-Related Adverse Events from Immune Checkpoint Inhibition, Ph.D., Weill Medical College of Cornell University, 2021. https://www.proquest.com/docview/2572580109/abstract/EBBB4710575A4CC7PQ/1 (accessed May 23, 2022).
[25]
T. Venkataraman, C. Valencia, M. Mangino, W. Morgenlander, S.J. Clipman, T. Liechti, A. Valencia, P. Christofidou, T. Spector, M. Roederer, P. Duggal, H.B. Larman, Antiviral Antibody Epitope Selection is a Heritable Trait, 2021. https://doi.org/10.1101/2021.03.25.436790.
[26]
C. Mandel-Brehm, S.E. Vazquez, C. Liverman, M. Cheng, Z. Quandt, A.F. Kung, B. Miao, E. Disse, C. Cugnet-Anceau, S. Dalle, E. Orlova, E. Frolova, B.E. Oftedal, M.S. Lionakis, E.S. Husebye, J.L. DeRisi, M.S. Anderson, Perilipin-1 autoantibodies linked to idiopathic lipodystrophy in the setting of two distinct breaks in immune tolerance, Allergy and Immunology, 2021. https://doi.org/10.1101/2021.09.24.21263657.
[27]
C. Mandel-Brehm, L.A. Benson, B. Tran, A.F. Kung, S.A. Mann, S.E. Vazquez, H. Retallack, H.A. Sample, K.C. Zorn, L.M. Khan, L.M. Kerr, P.L. McAlpine, L. Zhang, F. McCarthy, J.E. Elias, U. Katwa, C.M. Astley, S. Tomko, J. Dalmau, W.W. Seeley, S.J. Pleasure, M.R. Wilson, M.P. Gorman, J.L. DeRisi, Autoimmune profiling suggests paraneoplastic etiology in pediatric ROHHAD, (2021) 2021.06.04.21257478. https://doi.org/10.1101/2021.06.04.21257478.
[28]
T. Khan, M. Rahman, I. Ahmed, F.A. Ali, P. Jithesh, N. Marr, Human leukocyte antigen class II gene diversity tunes antibody repertoires to common pathogens, Genetics, 2021. https://doi.org/10.1101/2021.01.11.426296.
[29]
A.D. Fakhroo, G.K. Nasarallah, T. Khan, F.S. Cyprian, F.A. Ali, M.M.A. Ata, S. Taleb, A.A. Hssain, A.H. Eid, L.J. Abu-Raddad, A. Al-Khal, A.A.A. Thani, N. Marr, H.M. Yassine, Detection of autoimmune antibodies in severe but not in moderate or asymptomatic COVID-19 patients, (2021) 2021.03.02.21252438. https://doi.org/10.1101/2021.03.02.21252438.
[30]
A.D. Fakhroo, G.K. Nasarallah, T. Khan, F.S. Cyprian, F.A. Ali, M.M.A. Ata, S. Taleb, A.A. Hssain, A.H. Eid, L.J. Abu-Raddad, A. Al-Khal, A.A.A. Thani, N. Marr, H.M. Yassine, Detection of antinuclear antibodies targeting intracellular signal transduction, metabolism, apoptotic processes and cell death in critical COVID-19 patients, In Review, 2021. https://doi.org/10.21203/rs.3.rs-456551/v1.
[31]
A.R. Bourgonje, S. Andreu-Sánchez, T. Vogl, S. Hu, A.V. Vila, R. Gacesa, S. Leviatan, A. Kurilshikov, S. Klompus, I.N. Kalka, H.M. van Dullemen, A. Weinberger, M.C. Visschedijk, E.A.M. Festen, K.N. Faber, C. Wijmenga, G. Dijkstra, E. Segal, J. Fu, A. Zhernakova, R.K. Weersma, In-depth characterization of the serum antibody epitope repertoire in inflammatory bowel disease using phage-displayed immunoprecipitation sequencing, (2021) 2021.12.07.471581. https://doi.org/10.1101/2021.12.07.471581.
[32]
J.W. Angkeow, D.R. Monaco, A. Chen, T. Venkataraman, S. Jayaraman, C. Valencia, B.M. Sie, T. Liechti, P.N. Farhadi, G. Funez-dePagnier, C.A. Sherman-Baust, M.Q. Wong, C.L. Sears, P.J. Simner, J.L. Round, P. Duggal, U. Laserson, T.S. Steiner, R. Sen, T.E. Lloyd, M. Roederer, A.L. Mammen, R.S. Longman, L.G. Rider, H.B. Larman, Prevalence, persistence, and genetics of antibody responses to protein toxins and virulence factors, (2021) 2021.10.01.462481. https://doi.org/10.1101/2021.10.01.462481.
[33]
S. Andreu-Sánchez, A.R. Bourgonje, T. Vogl, A. Kurilshikov, S. Leviatan, A.J.R. Moreno, S. Hu, T. Sinha, A.V. Vila, S. Klompus, I.N. Kalka, K. de Leeuw, S. Arends, I. Jonkers, S. Withoff, L. cohort Study, E. Brouwer, A. Weinberger, C. Wijmenga, E. Segal, R.K. Weersma, J. Fu, A. Zhernakova, Genetic, environmental and intrinsic determinants of the human antibody epitope repertoire, (2021) 2021.12.07.471553. https://doi.org/10.1101/2021.12.07.471553.
[34]
T.L. Voyer, S. Sakata, M. Tsumura, T. Khan, A. Esteve-Sole, B.K. Al-Saud, H.E. Gungor, P. Taur, V. Jeanne-Julien, M. Christiansen, L.-M. Köhler, G.E. ElGhazali, J. Rosain, S. Nishimura, F. Sakura, M. Bouaziz, C. Oleaga-Quintas, A. Nieto-Patlán, À. Deyà-Martinez, Y.A. Torun, A.-L. Neehus, M. Roynard, S.E. Bozdemir, N.A. Kaabi, M.A. Hassani, I. Mersiyanova, F. Rozenberg, C. Speckmann, I. Hainmann, F. Hauck, M.H. Alzahrani, S.H. Alhajjar, S. Al-Muhsen, T. Cole, R. Fuleihan, P.D. Arkwright, R. Badolato, L. Alsina, L. Abel, M. Desai, H. Al-Mousa, A. Shcherbina, N. Marr, S. Boisson-Dupuis, J.-L. Casanova, S. Okada, J. Bustamante, Genetic, Immunological, and Clinical Features of 32 Patients with Autosomal Recessive STAT1 Deficiency, The Journal of Immunology. 207 (2021) 133–152. https://doi.org/10.4049/jimmunol.2001451.
[35]
T. Vogl, S. Klompus, S. Leviatan, I.N. Kalka, A. Weinberger, C. Wijmenga, J. Fu, A. Zhernakova, R.K. Weersma, E. Segal, Population-wide diversity and stability of serum antibody epitope repertoires against human microbiota, Nat Med. 27 (2021) 1442–1450. https://doi.org/10.1038/s41591-021-01409-3.
[36]
C.I. Stoddard, J. Galloway, H.Y. Chu, M.M. Shipley, K. Sung, H.L. Itell, C.R. Wolf, J.K. Logue, A. Magedson, M.E. Garrett, K.H.D. Crawford, U. Laserson, F.A. Matsen, J. Overbaugh, Epitope profiling reveals binding signatures of SARS-CoV-2 immune response in natural infection and cross-reactivity with endemic human CoVs, Cell Reports. 35 (2021) 109164. https://doi.org/10.1016/j.celrep.2021.109164.
[37]
E. Song, C.M. Bartley, R.D. Chow, T.T. Ngo, R. Jiang, C.R. Zamecnik, R. Dandekar, R.P. Loudermilk, Y. Dai, F. Liu, S. Sunshine, J. Liu, W. Wu, I.A. Hawes, B.D. Alvarenga, T. Huynh, L. McAlpine, N.-T. Rahman, B. Geng, J. Chiarella, B. Goldman-Israelow, C.B.F. Vogels, N.D. Grubaugh, A. Casanovas-Massana, B.S. Phinney, M. Salemi, J.R. Alexander, J.A. Gallego, T. Lencz, H. Walsh, A.E. Wapniarski, S. Mohanty, C. Lucas, J. Klein, T. Mao, J. Oh, A. Ring, S. Spudich, A.I. Ko, S.H. Kleinstein, J. Pak, J.L. DeRisi, A. Iwasaki, S.J. Pleasure, M.R. Wilson, S.F. Farhadian, Divergent and self-reactive immune responses in the CNS of COVID-19 patients with neurological symptoms, Cell Reports Medicine. 2 (2021) 100288. https://doi.org/10.1016/j.xcrm.2021.100288.
[38]
C. Simonich, M.M. Shipley, L. Doepker, T. Gobillot, M. Garrett, E.M. Cale, B. Hennessy, H. Itell, V. Chohan, N. Doria-Rose, R. Nduati, J. Overbaugh, A diverse collection of B cells responded to HIV infection in infant BG505, Cell Reports Medicine. 2 (2021) 100314. https://doi.org/10.1016/j.xcrm.2021.100314.
[39]
S. Sawai, M. Mori, S. Kuwabara, Methodology for identification of new target molecules in neuroimmunological disorders, Clinical and Experimental Neuroimmunology. 12 (2021) 202–207. https://doi.org/10.1111/cen3.12645.
[40]
G.D. Román-Meléndez, D.R. Monaco, J.M. Montagne, R.S. Quizon, M.F. Konig, M. Astatke, E. Darrah, H.B. Larman, Citrullination of a phage-displayed human peptidome library reveals the fine specificities of rheumatoid arthritis-associated autoantibodies, EBioMedicine. 71 (2021). https://doi.org/10.1016/j.ebiom.2021.103506.
[41]
J.V. Rajan, M. McCracken, C. Mandel-Brehm, G. Gromowski, S. Pollett, R. Jarman, J.L. DeRisi, Phage display demonstrates durable differences in serological profile by route of inoculation in primary infections of non-human primates with Dengue Virus 1, Sci Rep. 11 (2021) 10823. https://doi.org/10.1038/s41598-021-90318-z.
[42]
H. Qi, M. Ma, D. Lai, S. Tao, Phage display: an ideal platform for coupling protein to nucleic acid, Acta Biochimica et Biophysica Sinica. 53 (2021) 389–399. https://doi.org/10.1093/abbs/gmab006.
[43]
H. Qi, M. Ma, C. Hu, Z. Xu, F. Wu, N. Wang, D. Lai, Y. Li, H. Zhang, H. Jiang, Q. Meng, S. Guo, Y. Kang, X. Zhao, H. Li, S. Tao, Antibody Binding Epitope Mapping (AbMap) of Hundred Antibodies in a Single Run, Molecular & Cellular Proteomics. 20 (2021). https://doi.org/10.1074/mcp.RA120.002314.
[44]
M. Prahl, Y. Golan, A.G. Cassidy, Y. Matsui, L. Li, B. Alvarenga, H. Chen, U. Jigmeddagva, C.Y. Lin, V.J. Gonzalez, M.A. Chidboy, L. Warrier, S. Buarpung, A.P. Murtha, V.J. Flaherman, W.C. Greene, A.H.B. Wu, K.L. Lynch, J. Rajan, S.L. Gaw, Evaluation of transplacental transfer of mRNA vaccine products and functional antibodies during pregnancy and early infancy, Res Sq. (2021) rs.3.rs-1150427. https://doi.org/10.21203/rs.3.rs-1150427/v1.
[45]
M. Ogishi, R. Yang, C. Aytekin, D. Langlais, M. Bourgey, T. Khan, F.A. Ali, M. Rahman, O.M. Delmonte, M. Chrabieh, P. Zhang, C. Gruber, S.J. Pelham, A.N. Spaan, J. Rosain, W.-T. Lei, S. Drutman, M.D. Hellmann, M.K. Callahan, M. Adamow, P. Wong, J.D. Wolchok, G. Rao, C.S. Ma, Y. Nakajima, T. Yaguchi, K. Chamoto, S.C. Williams, J.-F. Emile, F. Rozenberg, M.S. Glickman, F. Rapaport, G. Kerner, G. Allington, I. Tezcan, D. Cagdas, F.O. Hosnut, F. Dogu, A. Ikinciogullari, V.K. Rao, L. Kainulainen, V. Béziat, J. Bustamante, S. Vilarinho, R.P. Lifton, B. Boisson, L. Abel, D. Bogunovic, N. Marr, L.D. Notarangelo, S.G. Tangye, T. Honjo, P. Gros, S. Boisson-Dupuis, J.-L. Casanova, Inherited PD-1 deficiency underlies tuberculosis and autoimmunity in a child, Nat Med. 27 (2021) 1646–1654. https://doi.org/10.1038/s41591-021-01388-5.
[46]
W.R. Morgenlander, S.N. Henson, D.R. Monaco, A. Chen, K. Littlefield, E.M. Bloch, E. Fujimura, I. Ruczinski, A.R. Crowley, H. Natarajan, S.E. Butler, J.A. Weiner, M.Z. Li, T.S. Bonny, S.E. Benner, A. Balagopal, D. Sullivan, S. Shoham, T.C. Quinn, S.H. Eshleman, A. Casadevall, A.D. Redd, O. Laeyendecker, M.E. Ackerman, A. Pekosz, S.J. Elledge, M. Robinson, A.A.R. Tobian, H.B. Larman, Antibody responses to endemic coronaviruses modulate COVID-19 convalescent plasma functionality, Journal of Clinical Investigation. 131 (2021) e146927. https://doi.org/10.1172/JCI146927.
[47]
D.R. Monaco, B.M. Sie, T.R. Nirschl, A.C. Knight, H.A. Sampson, A. Nowak-Wegrzyn, R.A. Wood, R.G. Hamilton, P.A. Frischmeyer-Guerrerio, H.B. Larman, Profiling serum antibodies with a pan allergen phage library identifies key wheat allergy epitopes, Nat Commun. 12 (2021) 379. https://doi.org/10.1038/s41467-020-20622-1.
[48]
C. Markosian, D.I. Staquicini, P. Dogra, E. Dodero-Rojas, F.H.F. Tang, T.L. Smith, V.G. Contessoto, S.K. Libutti, Z. Wang, V. Cristini, P.C. Whitford, S.K. Burley, J.N. Onuchic, R. Pasqualini, W. Arap, Apropos of Universal Epitope Discovery for COVID-19 Vaccines: A Framework for Targeted Phage Display-Based Delivery and Integration of New Evaluation Tools, BioRxiv. (2021) 2021.08.30.458222. https://doi.org/10.1101/2021.08.30.458222.
[49]
M. Ma, H. Qi, C. Hu, Z. Xu, F. Wu, N. Wang, D. Lai, Y. Li, H. Zhang, H. Jiang, Q. Meng, S. Guo, Y. Kang, X. Zhao, H. Li, S. Tao, The binding epitope of sintilimab on PD-1 revealed by AbMap, Acta Biochimica et Biophysica Sinica. 53 (2021) 628–635. https://doi.org/10.1093/abbs/gmab020.
[50]
Z.A. Lopez-Bujanda, A. Obradovic, T.R. Nirschl, L. Crowley, R. Macedo, A. Papachristodoulou, T. O’Donnell, U. Laserson, J.C. Zarif, R. Reshef, T. Yuan, M.K. Soni, E.S. Antonarakis, M.C. Haffner, H.B. Larman, M.M. Shen, P. Muranski, C.G. Drake, TGM4: an immunogenic prostate-restricted antigen, J Immunother Cancer. 9 (2021) e001649. https://doi.org/10.1136/jitc-2020-001649.
[51]
T. Le Voyer, A.-L. Neehus, R. Yang, M. Ogishi, J. Rosain, F. Alroqi, M. Alshalan, S. Blumental, F. Al Ali, T. Khan, M. Ata, L. Rozen, A. Demulder, P. Bastard, C. Gruber, M. Roynard, Y. Seeleuthener, F. Rapaport, B. Bigio, M. Chrabieh, D. Sng, L. Berteloot, N. Boddaert, F. Rozenberg, S. Al-Muhsen, A. Bertoli-Avella, L. Abel, D. Bogunovic, N. Marr, D. Mansouri, F. Al Mutairi, V. Béziat, D. Weil, S.A. Mahdaviani, A. Ferster, S.-Y. Zhang, B. Reversade, S. Boisson-Dupuis, J.-L. Casanova, J. Bustamante, Inherited deficiency of stress granule ZNFX1 in patients with monocytosis and mycobacterial disease, Proceedings of the National Academy of Sciences. 118 (2021) e2102804118. https://doi.org/10.1073/pnas.2102804118.
[52]
S. Klompus, S. Leviatan, T. Vogl, R.D. Mazor, I.N. Kalka, L. Stoler-Barak, N. Nathan, A. Peres, L. Moss, A. Godneva, S.K.B. Tikva, E. Shinar, H. Cohen-Dvashi, R. Gabizon, N. London, R. Diskin, G. Yaari, A. Weinberger, Z. Shulman, E. Segal, Cross-reactive antibodies against human coronaviruses and the animal coronavirome suggest diagnostics for future zoonotic spillovers, Science Immunology. 6 (2021) eabe9950. https://doi.org/10.1126/sciimmunol.abe9950.
[53]
K. Kammers, A. Chen, D.R. Monaco, S.E. Hudelson, W. Grant-McAuley, R.D. Moore, G. Alter, S.G. Deeks, C.S. Morrison, L.A. Eller, J.N. Blankson, O. Laeyendecker, I. Ruczinski, S.H. Eshleman, H.B. Larman, HIV Antibody Profiles in HIV Controllers and Persons With Treatment-Induced Viral Suppression, Frontiers in Immunology. 12 (2021) 3459. https://doi.org/10.3389/fimmu.2021.740395.
[54]
H. Ishikawa, C. Mandel-Brehm, A. Shindo, M.A. Cady, S.A. Mann, A. Niwa, K. Miyashita, Y. Ii, K.C. Zorn, A. Taniguchi, M. Maeda, M.R. Wilson, J.L. DeRisi, H. Tomimoto, Long-term MRI changes in a patient with Kelch-like protein 11-associated paraneoplastic neurological syndrome, European Journal of Neurology. n/a (2021). https://doi.org/10.1111/ene.15120.
[55]
M.R. Hasan, M. Rahman, T. Khan, A. Saeed, S. Sundararaju, A. Flores, P. Hawken, A. Rawat, N. Elkum, K. Hussain, R. Tan, P. Tang, N. Marr, Virome-wide serological profiling reveals association of herpesviruses with obesity, Sci Rep. 11 (2021) 2562. https://doi.org/10.1038/s41598-021-82213-4.
[56]
A. Guennoun, S. Bougarn, T. Khan, R. Mackeh, M. Rahman, F. Al-Ali, M. Ata, W. Aamer, D. Prosser, T. Habib, E. Chin-Smith, K. Al-Darwish, Q. Zhang, A. Al-Shakaki, A. Robay, R.G. Crystal, K. Fakhro, A. Al-Naimi, E. Al Maslamani, A. Tuffaha, I. Janahi, M. Janahi, D.R. Love, M.Y. Karim, B. Lo, A. Hassan, M. Adeli, N. Marr, A Novel STK4 Mutation Impairs T Cell Immunity Through Dysregulation of Cytokine-Induced Adhesion and Chemotaxis Genes, J Clin Immunol. 41 (2021) 1839–1852. https://doi.org/10.1007/s10875-021-01115-2.
[57]
C. Grönwall, V. Malmström, New technologies laying a foundation for next generation clinical serology, EBioMedicine. 72 (2021). https://doi.org/10.1016/j.ebiom.2021.103585.
[58]
J. Goudsmit, A.H.J. van den Biggelaar, W. Koudstaal, A. Hofman, W.C. Koff, T. Schenkelberg, G. Alter, M.J. Mina, J.W. Wu, Immune age and biological age as determinants of vaccine responsiveness among elderly populations: the Human Immunomics Initiative research program, Eur J Epidemiol. 36 (2021) 753–762. https://doi.org/10.1007/s10654-021-00767-z.
[59]
G. Chen, E.L. Shrock, M.Z. Li, J.M. Spergel, K.C. Nadeau, J.A. Pongracic, D.T. Umetsu, R. Rachid, A.J. MacGinnitie, W. Phipatanakul, L. Schneider, H.C. Oettgen, S.J. Elledge, High-resolution epitope mapping by AllerScan reveals relationships between IgE and IgG repertoires during peanut oral immunotherapy, Cell Reports Medicine. 2 (2021) 100410. https://doi.org/10.1016/j.xcrm.2021.100410.
[60]
A. Chen, O. Laeyendecker, S.H. Eshleman, D.R. Monaco, K. Kammers, H.B. Larman, I. Ruczinski, A top scoring pairs classifier for recent HIV infections, Statistics in Medicine. 40 (2021) 2604–2612. https://doi.org/10.1002/sim.8920.
[61]
P.V. Belousov, Analysis of the Repertoires of Circulating Autoantibodies’ Specificities as a Tool for Identification of the Tumor-Associated Antigens: Current Problems and Solutions, Biochemistry Moscow. 86 (2021) 1225–1242. https://doi.org/10.1134/S0006297921100060.
[62]
C.M. Bartley, N.N. Parikshak, T.T. Ngo, J.A. Alexander, K.C. Zorn, B.A. Alvarenga, M.K. Kang, M. Pedriali, S.J. Pleasure, M.R. Wilson, Case Report: A False Negative Case of Anti-Yo Paraneoplastic Myelopathy, Frontiers in Neurology. 12 (2021) 1826. https://doi.org/10.3389/fneur.2021.728700.
[63]
J.V. Rajan, M. McCracken, C. Mandel-Brehm, G. Gromowski, S. Pollett, R. Jarman, J.L. DeRisi, Inoculation by mosquito induces durable differences in serological profile in non-human primates infected with DENV1, Immunology, 2020. https://doi.org/10.1101/2020.09.28.315218.
[64]
S. Klompus, S. Leviatan, T. Vogl, I.N. Kalka, A. Godneva, E. Shinar, A. Weinberger, E. Segal, Cross-reactive antibody responses against SARS-CoV-2 and seasonal common cold coronaviruses, Infectious Diseases (except HIV/AIDS), 2020. https://doi.org/10.1101/2020.09.01.20182220.
[65]
J. Zhou, S. Li, K.K. Leung, B. O’Donovan, J.Y. Zou, J.L. DeRisi, J.A. Wells, Deep profiling of protease substrate specificity enabled by dual random and scanned human proteome substrate phage libraries, Proc. Natl. Acad. Sci. U.S.A. 117 (2020) 25464–25475. https://doi.org/10.1073/pnas.2009279117.
[66]
C.R. Zamecnik, J.V. Rajan, K.A. Yamauchi, S.A. Mann, R.P. Loudermilk, G.M. Sowa, K.C. Zorn, B.D. Alvarenga, C. Gaebler, M. Caskey, M. Stone, P.J. Norris, W. Gu, C.Y. Chiu, D. Ng, J.R. Byrnes, X.X. Zhou, J.A. Wells, D.F. Robbiani, M.C. Nussenzweig, J.L. DeRisi, M.R. Wilson, ReScan, a Multiplex Diagnostic Pipeline, Pans Human Sera for SARS-CoV-2 Antigens, Cell Reports Medicine. 1 (2020) 100123. https://doi.org/10.1016/j.xcrm.2020.100123.
[67]
S.E. Vazquez, E.M. Ferré, D.W. Scheel, S. Sunshine, B. Miao, C. Mandel-Brehm, Z. Quandt, A.Y. Chan, M. Cheng, M. German, M. Lionakis, J.L. DeRisi, M.S. Anderson, Identification of novel, clinically correlated autoantigens in the monogenic autoimmune syndrome APS1 by proteome-wide PhIP-Seq, ELife. 9 (2020) e55053. https://doi.org/10.7554/eLife.55053.
[68]
E. Song, C.M. Bartley, R.D. Chow, T.T. Ngo, R. Jiang, C.R. Zamecnik, R. Dandekar, R.P. Loudermilk, Y. Dai, F. Liu, I.A. Hawes, B.D. Alvarenga, T. Huynh, L. McAlpine, N.-T. Rahman, B. Geng, J. Chiarella, B. Goldman-Israelow, C.B.F. Vogels, N.D. Grubaugh, A. Casanovas-Massana, B.S. Phinney, M. Salemi, J. Alexander, J.A. Gallego, T. Lencz, H. Walsh, C. Lucas, J. Klein, T. Mao, J. Oh, A. Ring, S. Spudich, A.I. Ko, S.H. Kleinstein, J.L. DeRisi, A. Iwasaki, S.J. Pleasure, M.R. Wilson, S.F. Farhadian, Exploratory neuroimmune profiling identifies CNS-specific alterations in COVID-19 patients with neurological involvement, BioRxiv. (2020) 2020.09.11.293464. https://doi.org/10.1101/2020.09.11.293464.
[69]
E. Shrock, E. Fujimura, T. Kula, R.T. Timms, I.-H. Lee, Y. Leng, M.L. Robinson, B.M. Sie, M.Z. Li, Y. Chen, J. Logue, A. Zuiani, D. McCulloch, F.J.N. Lelis, S. Henson, D.R. Monaco, M. Travers, S. Habibi, W.A. Clarke, P. Caturegli, O. Laeyendecker, A. Piechocka-Trocha, J.Z. Li, A. Khatri, H.Y. Chu, MGH COVID-19 Collection & Processing Team, A.-C. Villani, K. Kays, M.B. Goldberg, N. Hacohen, M.R. Filbin, X.G. Yu, B.D. Walker, D.R. Wesemann, H.B. Larman, J.A. Lederer, S.J. Elledge, Viral epitope profiling of COVID-19 patients reveals cross-reactivity and correlates of severity, Science. 370 (2020) eabd4250. https://doi.org/10.1126/science.abd4250.
[70]
G.D. Román-Meléndez, T. Venkataraman, D.R. Monaco, H.B. Larman, Protease Activity Profiling via Programmable Phage Display of Comprehensive Proteome-Scale Peptide Libraries, Cels. 11 (2020) 375-381.e4. https://doi.org/10.1016/j.cels.2020.08.013.
[71]
D. Quiat, T. Kula, C. Shimizu, J.T. Kanegaye, A.H. Tremoulet, Z. Pitkowsky, M. Son, J.W. Newburger, S.J. Elledge, J.C. Burns, High-Throughput Screening of Kawasaki Disease Sera for Antiviral Antibodies, The Journal of Infectious Diseases. 222 (2020) 1853–1857. https://doi.org/10.1093/infdis/jiaa253.
[72]
B. O’Donovan, C. Mandel-Brehm, S.E. Vazquez, J. Liu, A.V. Parent, M.S. Anderson, T. Kassimatis, A. Zekeridou, S.L. Hauser, S.J. Pittock, E. Chow, M.R. Wilson, J.L. DeRisi, High-resolution epitope mapping of anti-Hu and anti-Yo autoimmunity by programmable phage display, Brain Communications. 2 (2020). https://doi.org/10.1093/braincomms/fcaa059.
[73]
J. Liu, W. Tang, A. Budhu, M. Forgues, M.O. Hernandez, J. Candia, Y. Kim, E.D. Bowman, S. Ambs, Y. Zhao, B. Tran, X. Wu, C. Koh, P. Surana, T.J. Liang, M. Guarnera, D. Mann, M. Rajaure, T.F. Greten, Z. Wang, H. Yu, X.W. Wang, A Viral Exposure Signature Defines Early Onset of Hepatocellular Carcinoma, Cell. 182 (2020) 317-328.e10. https://doi.org/10.1016/j.cell.2020.05.038.
[74]
K. Kamath, J. Reifert, T. Johnston, C. Gable, R.J. Pantazes, H.N. Rivera, I. McAuliffe, S. Handali, P.S. Daugherty, Antibody epitope repertoire analysis enables rapid antigen discovery and multiplex serology, Sci Rep. 10 (2020) 5294. https://doi.org/10.1038/s41598-020-62256-9.
[75]
A.T. Irving, P. Rozario, P.-S. Kong, K. Luko, J.J. Gorman, M.L. Hastie, W.N. Chia, S. Mani, B.P.-H. Lee, G.J.D. Smith, I.H. Mendenhall, H.B. Larman, S.J. Elledge, L.-F. Wang, Robust dengue virus infection in bat cells and limited innate immune responses coupled with positive serology from bats in IndoMalaya and Australasia, Cell. Mol. Life Sci. 77 (2020) 1607–1622. https://doi.org/10.1007/s00018-019-03242-x.
[76]
L.E. Doepker, C.A. Simonich, D. Ralph, M.M. Shipley, M. Garrett, T. Gobillot, V. Vigdorovich, D.N. Sather, R. Nduati, F.A. Matsen, J.M. Overbaugh, Diversity and Function of Maternal HIV-1-Specific Antibodies at the Time of Vertical Transmission, J Virol. 94 (2020) e01594-19. https://doi.org/10.1128/JVI.01594-19.
[77]
C. Cantarelli, M. Jarque, A. Angeletti, J. Manrique, S. Hartzell, T. O’Donnell, E. Merritt, U. Laserson, L. Perin, C. Donadei, L. Anderson, C. Fischman, E. Chan, J. Draibe, X. Fulladosa, J. Torras, L.V. Riella, G.L. Manna, E. Fiaccadori, U. Maggiore, O. Bestard, P. Cravedi, A Comprehensive Phenotypic and Functional Immune Analysis Unravels Circulating Anti–Phospholipase A2 Receptor Antibody Secreting Cells in Membranous Nephropathy Patients, Kidney International Reports. 5 (2020) 1764–1776. https://doi.org/10.1016/j.ekir.2020.07.028.
[78]
Z. (Areli) L. Bujanda, A. Obradovic, T. Nirschl, T. O’Donnell, U. Laserson, R. Macedo-Gonzales, R. Reshef, T. Yuan, M. Soni, E. Antonarakis, B. Larman, P. Muranski, C. Drake, Z. (Areli) L. Bujanda, 168 A novel prostate-restricted tumor-associated antigen: a potential therapeutic target, J Immunother Cancer. 8 (2020). https://doi.org/10.1136/jitc-2020-SITC2020.0168.
[79]
G. Adamus, Current techniques to accurately measure anti-retinal autoantibodies, Expert Review of Ophthalmology. 15 (2020) 111–118. https://doi.org/10.1080/17469899.2020.1739522.
[80]
R.D. Schubert, I. Hawes, P.S. Ramachandran, A. Ramesh, E.D. Crawford, J.E. Pak, W. Wu, C.K. Cheung, B.D. O’Donovan, C.M. Tato, A. Lyden, M. Tan, R. Sit, G. Sowa, H.A. Sample, K.C. Zorn, D. Banerji, L.M. Khan, R. Bove, S.L. Hauser, A.A. Gelfand, B. Johnson-Kerner, K. Nash, K.S. Krishnamoorthy, T. Chitnis, J.Z. Ding, H.J. McMillan, C.Y. Chiu, B. Briggs, C.A. Glaser, C. Yen, V. Chu, D.A. Wadford, S.R. Dominguez, T.F.F. Ng, R.L. Marine, A.S. Lopez, W.A. Nix, A. Soldatos, M.P. Gorman, L. Benson, K. Messacar, J.L. Konopka-Anstadt, M.S. Oberste, J.L. DeRisi, M.R. Wilson, Serological and metagenomic interrogation of cerebrospinal fluid implicates enteroviruses in pediatric acute flaccid myelitis, (2019) 666230. https://doi.org/10.1101/666230.
[81]
F.-L. Wu, D.-Y. Lai, H.-H. Ding, Y.-J. Tang, Z.-W. Xu, M.-L. Ma, S.-J. Guo, J.-F. Wang, N. Shen, X.-D. Zhao, H. Qi, H. Li, S.-C. Tao, Identification of Serum Biomarkers for Systemic Lupus Erythematosus Using a Library of Phage Displayed Random Peptides and Deep Sequencing *[S], Molecular & Cellular Proteomics. 18 (2019) 1851–1863. https://doi.org/10.1074/mcp.RA119.001582.
[82]
J. Talan, A Novel Sequencing Technology Helps Identify an Autoimmune Paraneoplastic Disorder Associated with Testicular Cancer, Neurology Today. 19 (2019) 37. https://doi.org/10.1097/01.NT.0000579408.78760.d9.
[83]
R.D. Schubert, I.A. Hawes, P.S. Ramachandran, A. Ramesh, E.D. Crawford, J.E. Pak, W. Wu, C.K. Cheung, B.D. O’Donovan, C.M. Tato, A. Lyden, M. Tan, R. Sit, G.M. Sowa, H.A. Sample, K.C. Zorn, D. Banerji, L.M. Khan, R. Bove, S.L. Hauser, A.A. Gelfand, B.L. Johnson-Kerner, K. Nash, K.S. Krishnamoorthy, T. Chitnis, J.Z. Ding, H.J. McMillan, C.Y. Chiu, B. Briggs, C.A. Glaser, C. Yen, V. Chu, D.A. Wadford, S.R. Dominguez, T.F.F. Ng, R.L. Marine, A.S. Lopez, W.A. Nix, A. Soldatos, M.P. Gorman, L. Benson, K. Messacar, J.L. Konopka-Anstadt, M.S. Oberste, J.L. DeRisi, M.R. Wilson, Pan-viral serology implicates enteroviruses in acute flaccid myelitis, Nat Med. 25 (2019) 1748–1752. https://doi.org/10.1038/s41591-019-0613-1.
[84]
M.J. Mina, T. Kula, Y. Leng, M. Li, R.D. de Vries, M. Knip, H. Siljander, M. Rewers, D.F. Choy, M.S. Wilson, H.B. Larman, A.N. Nelson, D.E. Griffin, R.L. de Swart, S.J. Elledge, Measles virus infection diminishes preexisting antibodies that offer protection from other pathogens, Science. 366 (2019) 599–606. https://doi.org/10.1126/science.aay6485.
[85]
T.P. Johnson, H.B. Larman, M.-H. Lee, S.S. Whitehead, J. Kowalak, C. Toro, C.C. Lau, J. Kim, K.R. Johnson, L.B. Reoma, A. Faustin, C.A. Pardo, S. Kottapalli, J. Howard, D. Monaco, J. Weisfeld-Adams, C. Blackstone, S. Galetta, M. Snuderl, W.A. Gahl, I. Kister, A. Nath, Chronic Dengue Virus Panencephalitis in a Patient with Progressive Dementia with Extrapyramidal Features, Annals of Neurology. 86 (2019) 695–703. https://doi.org/10.1002/ana.25588.
[86]
S.H. Eshleman, O. Laeyendecker, K. Kammers, A. Chen, M.V. Sivay, S. Kottapalli, B.M. Sie, T. Yuan, D.R. Monaco, D. Mohan, D. Wansley, T. Kula, C. Morrison, S.J. Elledge, R. Brookmeyer, I. Ruczinski, H.B. Larman, Comprehensive Profiling of HIV Antibody Evolution, Cell Reports. 27 (2019) 1422-1433.e4. https://doi.org/10.1016/j.celrep.2019.03.097.
[87]
S. Deutscher, Phage Display to Detect and Identify Autoantibodies in Disease, New England Journal of Medicine. 381 (2019) 89–91. https://doi.org/10.1056/NEJMcibr1903249.
[88]
A.J. Brown, I. Snapkov, R. Akbar, M. Pavlović, E. Miho, G.K. Sandve, V. Greiff, Augmenting adaptive immunity: progress and challenges in the quantitative engineering and analysis of adaptive immune receptor repertoires, Mol. Syst. Des. Eng. 4 (2019) 701–736. https://doi.org/10.1039/C9ME00071B.
[89]
D. Ardeljan, X. Wang, M. Oghbaie, M.S. Taylor, D. Husband, V. Deshpande, J.P. Steranka, M. Gorbounov, W.R. Yang, B. Sie, H.B. Larman, H. Jiang, K.R. Molloy, I. Altukhov, Z. Li, W. McKerrow, D. Fenyö, K.H. Burns, J. LaCava, LINE-1 ORF2p expression is nearly imperceptible in human cancers, Mobile DNA. 11 (2019) 1. https://doi.org/10.1186/s13100-019-0191-2.
[90]
T. Yuan, D. Mohan, U. Laserson, I. Ruczinski, A.N. Baer, H.B. Larman, Improved Analysis of Phage ImmunoPrecipitation Sequencing (PhIP-Seq) Data Using a Z-score Algorithm, 2018. https://doi.org/10.1101/285916.
[91]
D.R. Monaco, S.V. Kottapalli, T. Yuan, F.P. Breitwieser, D.E. Anderson, L. Wijaya, K. Tan, W.N. Chia, K. Kammers, M. Caturegli, K. Waugh, M. Rewers, L.-F. Wang, H.B. Larman, Deconvoluting Virome-Wide Antiviral Antibody Profiling Data, 2018. https://doi.org/10.1101/333625.
[92]
M.L. Paull, P.S. Daugherty, Mapping serum antibody repertoires using peptide libraries, Current Opinion in Chemical Engineering. 19 (2018) 21–26. https://doi.org/10.1016/j.coche.2017.12.001.
[93]
D. Mohan, D.L. Wansley, B.M. Sie, M.S. Noon, A.N. Baer, U. Laserson, H.B. Larman, PhIP-Seq characterization of serum antibodies using oligonucleotide-encoded peptidomes, Nat Protoc. 13 (2018) 1958–1978. https://doi.org/10.1038/s41596-018-0025-6.
[94]
S. Davoudi, T. Ahmadi, E. Papavasilieou, I. Leskov, L. Sobrin, Phage Immunoprecipitation Sequencing of Autoantigens in Autoimmune Retinopathy, Ocular Immunology and Inflammation. 26 (2018) 417–424. https://doi.org/10.1080/09273948.2016.1232738.
[95]
A.A. Shah, L. Casciola-Rosen, Mechanistic and clinical insights at the scleroderma-cancer interface, Journal of Scleroderma and Related Disorders. 2 (2017) 153–159. https://doi.org/10.5301/jsrd.5000250.
[96]
D. Quiat, T. Kula, C. Shimizu, J.T. Kanegaye, A.H. Tremoulet, Z. Pitkowsky, M. Son, J. Newburger, S. Elledge, J.C. Burns, Unbiased Screening of Kawasaki Disease Sera for Viral Antigen Exposure, Open Forum Infectious Diseases. 4 (2017) S684–S685. https://doi.org/10.1093/ofid/ofx163.1831.
[97]
G.J. Xu, A.A. Shah, M.Z. Li, Q. Xu, A. Rosen, L. Casciola-Rosen, S.J. Elledge, Systematic autoantigen analysis identifies a distinct subtype of scleroderma with coincident cancer, PNAS. 113 (2016) E7526–E7534. https://doi.org/10.1073/pnas.1615990113.
[98]
V. Ganesan, D.P. Ascherman, J.S. Minden, Immunoproteomics technologies in the discovery of autoantigens in autoimmune diseases, Biomolecular Concepts. 7 (2016) 133–143. https://doi.org/10.1515/bmc-2016-0007.
[99]
G.J. Xu, T. Kula, Q. Xu, M.Z. Li, S.D. Vernon, T. Ndung’u, K. Ruxrungtham, J. Sanchez, C. Brander, R.T. Chung, K.C. O’Connor, B. Walker, H.B. Larman, S.J. Elledge, Comprehensive serological profiling of human populations using a synthetic human virome, Science. 348 (2015) aaa0698. https://doi.org/10.1126/science.aaa0698.
[100]
R.D. Schubert, M.R. Wilson, A tale of two approaches: how metagenomics and proteomics are shaping the future of encephalitis diagnostics, Curr Opin Neurol. 28 (2015) 283–287. https://doi.org/10.1097/WCO.0000000000000198.
[101]
C. DeMarshall, A. Sarkar, E.P. Nagele, E. Goldwaser, G. Godsey, N.K. Acharya, R.G. Nagele, Utility of Autoantibodies as Biomarkers for Diagnosis and Staging of Neurodegenerative Diseases, in: International Review of Neurobiology, Elsevier, 2015: pp. 1–51. https://doi.org/10.1016/bs.irn.2015.05.005.
[102]
K. Finton, Innate and humoral immune responses to HIV-1, Thesis, 2014. https://digital.lib.washington.edu:443/researchworks/handle/1773/25106 (accessed May 23, 2022).
[103]
K.A.K. Finton, D. Friend, J. Jaffe, M. Gewe, M.A. Holmes, H.B. Larman, A. Stuart, K. Larimore, P.D. Greenberg, S.J. Elledge, L. Stamatatos, R.K. Strong, Ontogeny of Recognition Specificity and Functionality for the Broadly Neutralizing Anti-HIV Antibody 4E10, PLOS Pathogens. 10 (2014) e1004403. https://doi.org/10.1371/journal.ppat.1004403.
[104]
P.D. Burbelo, T.P. O’Hanlon, New Autoantibody Detection Technologies Yield Novel Insights into Autoimmune Disease, Curr Opin Rheumatol. 26 (2014) 717–723. https://doi.org/10.1097/BOR.0000000000000107.
[105]
H.B. Larman, U. Laserson, L. Querol, K. Verhaeghen, N.L. Solimini, G.J. Xu, P.L. Klarenbeek, G.M. Church, D.A. Hafler, R.M. Plenge, P.A. Nigrovic, P.L. De Jager, I. Weets, G.A. Martens, K.C. O’Connor, S.J. Elledge, PhIP-Seq characterization of autoantibodies from patients with multiple sclerosis, type 1 diabetes and rheumatoid arthritis, Journal of Autoimmunity. 43 (2013) 1–9. https://doi.org/10.1016/j.jaut.2013.01.013.
[106]
K.A.K. Finton, K. Larimore, H.B. Larman, D. Friend, C. Correnti, P.B. Rupert, S.J. Elledge, P.D. Greenberg, R.K. Strong, Autoreactivity and Exceptional CDR Plasticity (but Not Unusual Polyspecificity) Hinder Elicitation of the Anti-HIV Antibody 4E10, PLOS Pathogens. 9 (2013) e1003639. https://doi.org/10.1371/journal.ppat.1003639.
[107]
H. Benjamin Larman, M. Salajegheh, R. Nazareno, T. Lam, J. Sauld, H. Steen, S. Won Kong, J.L. Pinkus, A.A. Amato, S.J. Elledge, S.A. Greenberg, Cytosolic 5′-nucleotidase 1A autoimmunity in sporadic inclusion body myositis, Annals of Neurology. 73 (2013) 408–418. https://doi.org/10.1002/ana.23840.
[108]
U. Laserson, High-throughput methods for characterizing the immune repertoire, Thesis, Massachusetts Institute of Technology, 2012. https://dspace.mit.edu/handle/1721.1/79246 (accessed May 23, 2022).
[109]
H.B. Larman, Molecular display of synthetic oligonucleotide libraries and their analysis with high throughput DNA sequencing, Thesis, Massachusetts Institute of Technology, 2012. https://dspace.mit.edu/handle/1721.1/72912 (accessed September 28, 2021).
[110]
W.H. Robinson, L. Steinman, Human peptidome display, Nat Biotechnol. 29 (2011) 500–502. https://doi.org/10.1038/nbt.1888.
[111]
H.B. Larman, Z. Zhao, U. Laserson, M.Z. Li, A. Ciccia, M.A.M. Gakidis, G.M. Church, S. Kesari, E.M. LeProust, N.L. Solimini, S.J. Elledge, Autoantigen discovery with a synthetic human peptidome, Nat Biotechnol. 29 (2011) 535–541. https://doi.org/10.1038/nbt.1856.
[112]
J. Williams, Development of a phage display library for discovery of antigenic Brucella peptides, (n.d.) 48.
[113]
S.I. Reeder, CAN VIRUSES CAUSE LUPUS?, (n.d.) 63.
[114]
U. Laserson, READING THE ANTIBODY REPERTOIRE AGAINST VIRUSES, MICROBES, AND THE SELF, (n.d.) 8.
[115]
T.A. Gobillot, Characterization of Zika virus prevalence in Kenya and the innate antiviral type-I interferon response against infection, (n.d.) 143.