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Understanding TCR affinity, antigen specificity, and cross-reactivity to improve TCR gene-modified T cells for cancer immunotherapy.

Spear TT, Evavold BD, Baker BM, Nishimura MI.

Cancer Immunol Immunother. 2019 Oct 8. doi: 10.1007/s00262-019-02401-0. [Epub ahead of print] Review.


Geometrical characterization of T cell receptor binding modes reveals class-specific binding to maximize access to antigen.

Singh NK, Abualrous ET, Ayres CM, Noé F, Gowthaman R, Pierce BG, Baker BM.

Proteins. 2019 Oct 7. doi: 10.1002/prot.25829. [Epub ahead of print]


Structure Based Prediction of Neoantigen Immunogenicity.

Riley TP, Keller GLJ, Smith AR, Davancaze LM, Arbuiso AG, Devlin JR, Baker BM.

Front Immunol. 2019 Aug 28;10:2047. doi: 10.3389/fimmu.2019.02047. eCollection 2019.


LRRK2 binds to the Rab32 subfamily in a GTP-dependent manner via its armadillo domain.

McGrath E, Waschbüsch D, Baker BM, Khan AR.

Small GTPases. 2019 Sep 25:1-14. doi: 10.1080/21541248.2019.1666623. [Epub ahead of print]


Requirement for scleraxis in the recruitment of mesenchymal progenitors during embryonic tendon elongation.

Huang AH, Watson SS, Wang L, Baker BM, Akiyama H, Brigande JV, Schweitzer R.

Development. 2019 Oct 4;146(20). pii: dev182782. doi: 10.1242/dev.182782.


Mass spectrometry driven exploration reveals nuances of neoepitope-driven tumor rejection.

Ebrahimi-Nik H, Michaux J, Corwin WL, Keller GL, Shcheglova T, Pak H, Coukos G, Baker BM, Mandoiu II, Bassani-Sternberg M, Srivastava PK.

JCI Insight. 2019 Jun 20;5. pii: 129152. doi: 10.1172/jci.insight.129152.


Dynamically Driven Allostery in MHC Proteins: Peptide-Dependent Tuning of Class I MHC Global Flexibility.

Ayres CM, Abualrous ET, Bailey A, Abraham C, Hellman LM, Corcelli SA, Noé F, Elliott T, Baker BM.

Front Immunol. 2019 May 3;10:966. doi: 10.3389/fimmu.2019.00966. eCollection 2019.


Genetics of cocaine and methamphetamine consumption and preference in Drosophila melanogaster.

Highfill CA, Baker BM, Stevens SD, Anholt RRH, Mackay TFC.

PLoS Genet. 2019 May 20;15(5):e1007834. doi: 10.1371/journal.pgen.1007834. eCollection 2019 May.


Extracellular matrix alignment dictates the organization of focal adhesions and directs uniaxial cell migration.

Wang WY, Pearson AT, Kutys ML, Choi CK, Wozniak MA, Baker BM, Chen CS.

APL Bioeng. 2018 Dec 26;2(4):046107. doi: 10.1063/1.5052239. eCollection 2018 Dec.


Actomyosin contractility-dependent matrix stretch and recoil induces rapid cell migration.

Wang WY, Davidson CD, Lin D, Baker BM.

Nat Commun. 2019 Mar 12;10(1):1186. doi: 10.1038/s41467-019-09121-0.


Cell force-mediated matrix reorganization underlies multicellular network assembly.

Davidson CD, Wang WY, Zaimi I, Jayco DKP, Baker BM.

Sci Rep. 2019 Jan 9;9(1):12. doi: 10.1038/s41598-018-37044-1.


Improving T Cell Receptor On-Target Specificity via Structure-Guided Design.

Hellman LM, Foley KC, Singh NK, Alonso JA, Riley TP, Devlin JR, Ayres CM, Keller GLJ, Zhang Y, Vander Kooi CW, Nishimura MI, Baker BM.

Mol Ther. 2019 Feb 6;27(2):300-313. doi: 10.1016/j.ymthe.2018.12.010. Epub 2018 Dec 14.


The intersection of affinity and specificity in the development and optimization of T cell receptor based therapeutics.

Riley TP, Baker BM.

Semin Cell Dev Biol. 2018 Dec;84:30-41. doi: 10.1016/j.semcdb.2017.10.017. Review.


T cell receptor cross-reactivity expanded by dramatic peptide-MHC adaptability.

Riley TP, Hellman LM, Gee MH, Mendoza JL, Alonso JA, Foley KC, Nishimura MI, Vander Kooi CW, Garcia KC, Baker BM.

Nat Chem Biol. 2018 Oct;14(10):934-942. doi: 10.1038/s41589-018-0130-4. Epub 2018 Sep 17.


Molecular properties of gp100-reactive T-cell receptors drive the cytokine profile and antitumor efficacy of transgenic host T cells.

Eby JM, Smith AR, Riley TP, Cosgrove C, Ankney CM, Henning SW, Paulos CM, Garrett-Mayer E, Luiten RM, Nishimura MI, Baker BM, Le Poole IC.

Pigment Cell Melanoma Res. 2019 Jan;32(1):68-78. doi: 10.1111/pcmr.12724. Epub 2018 Aug 13.


Altered Peptide Ligands Impact the Diversity of Polyfunctional Phenotypes in T Cell Receptor Gene-Modified T Cells.

Spear TT, Wang Y, Smith TW Jr, Simms PE, Garrett-Mayer E, Hellman LM, Baker BM, Nishimura MI.

Mol Ther. 2018 Apr 4;26(4):996-1007. doi: 10.1016/j.ymthe.2018.01.015. Epub 2018 Feb 2.


Engineering Control over 3D Morphogenesis by Tissue Origami.

Sakar MS, Baker BM.

Dev Cell. 2018 Jan 22;44(2):131-132. doi: 10.1016/j.devcel.2018.01.005.


Correction to: Clinical and immunologic evaluation of three metastatic melanoma patients treated with autologous melanoma-reactive TCR-transduced T cells.

Moore T, Wagner CR, Scurti GM, Hutchens KA, Godellas C, Clark AL, Kolawole EM, Hellman LM, Singh NK, Huyke FA, Wang SY, Calabrese KM, Embree HD, Orentas R, Shirai K, Dellacecca E, Garrett-Mayer E, Li M, Eby JM, Stiff PJ, Evavold BD, Baker BM, Le Poole IC, Dropulic B, Clark JI, Nishimura MI.

Cancer Immunol Immunother. 2018 Feb;67(2):327. doi: 10.1007/s00262-017-2102-z.


Clinical and immunologic evaluation of three metastatic melanoma patients treated with autologous melanoma-reactive TCR-transduced T cells.

Moore T, Wagner CR, Scurti GM, Hutchens KA, Godellas C, Clark AL, Kolawole EM, Hellman LM, Singh NK, Huyke FA, Wang SY, Calabrese KM, Embree HD, Orentas R, Shirai K, Dellacecca E, Garrett-Mayer E, Li M, Eby JM, Stiff PJ, Evavold BD, Baker BM, Le Poole IC, Dropulic B, Clark JI, Nishimura MI.

Cancer Immunol Immunother. 2018 Feb;67(2):311-325. doi: 10.1007/s00262-017-2073-0. Epub 2017 Oct 20. Erratum in: Cancer Immunol Immunother. 2017 Dec 20;:.


Emerging Concepts in TCR Specificity: Rationalizing and (Maybe) Predicting Outcomes.

Singh NK, Riley TP, Baker SCB, Borrman T, Weng Z, Baker BM.

J Immunol. 2017 Oct 1;199(7):2203-2213. doi: 10.4049/jimmunol.1700744. Review.


Therapeutic Targeting of TAZ and YAP by Dimethyl Fumarate in Systemic Sclerosis Fibrosis.

Toyama T, Looney AP, Baker BM, Stawski L, Haines P, Simms R, Szymaniak AD, Varelas X, Trojanowska M.

J Invest Dermatol. 2018 Jan;138(1):78-88. doi: 10.1016/j.jid.2017.08.024. Epub 2017 Sep 1.


Matrix degradability controls multicellularity of 3D cell migration.

Trappmann B, Baker BM, Polacheck WJ, Choi CK, Burdick JA, Chen CS.

Nat Commun. 2017 Aug 29;8(1):371. doi: 10.1038/s41467-017-00418-6.


Peptide and Peptide-Dependent Motions in MHC Proteins: Immunological Implications and Biophysical Underpinnings.

Ayres CM, Corcelli SA, Baker BM.

Front Immunol. 2017 Aug 7;8:935. doi: 10.3389/fimmu.2017.00935. eCollection 2017. Review.


Modeling Sequence-Dependent Peptide Fluctuations in Immunologic Recognition.

Ayres CM, Riley TP, Corcelli SA, Baker BM.

J Chem Inf Model. 2017 Aug 28;57(8):1990-1998. doi: 10.1021/acs.jcim.7b00118. Epub 2017 Jul 25.


Critical biological parameters modulate affinity as a determinant of function in T-cell receptor gene-modified T-cells.

Spear TT, Wang Y, Foley KC, Murray DC, Scurti GM, Simms PE, Garrett-Mayer E, Hellman LM, Baker BM, Nishimura MI.

Cancer Immunol Immunother. 2017 Nov;66(11):1411-1424. doi: 10.1007/s00262-017-2032-9. Epub 2017 Jun 20.


How an alloreactive T-cell receptor achieves peptide and MHC specificity.

Wang Y, Singh NK, Spear TT, Hellman LM, Piepenbrink KH, McMahan RH, Rosen HR, Vander Kooi CW, Nishimura MI, Baker BM.

Proc Natl Acad Sci U S A. 2017 Jun 13;114(24):E4792-E4801. doi: 10.1073/pnas.1700459114. Epub 2017 Jun 1.


Multiscale model predicts increasing focal adhesion size with decreasing stiffness in fibrous matrices.

Cao X, Ban E, Baker BM, Lin Y, Burdick JA, Chen CS, Shenoy VB.

Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):E4549-E4555. doi: 10.1073/pnas.1620486114. Epub 2017 May 3.


Using Global Analysis to Extend the Accuracy and Precision of Binding Measurements with T cell Receptors and Their Peptide/MHC Ligands.

Blevins SJ, Baker BM.

Front Mol Biosci. 2017 Jan 31;4:2. doi: 10.3389/fmolb.2017.00002. eCollection 2017.


ATLAS: A database linking binding affinities with structures for wild-type and mutant TCR-pMHC complexes.

Borrman T, Cimons J, Cosiano M, Purcaro M, Pierce BG, Baker BM, Weng Z.

Proteins. 2017 May;85(5):908-916. doi: 10.1002/prot.25260. Epub 2017 Feb 16.


MHC Bias by T Cell Receptors: Genetic Evidence for MHC and TCR Coevolution.

Baker BM, Evavold BD.

Trends Immunol. 2017 Jan;38(1):2-4. doi: 10.1016/ Epub 2016 Dec 9.


Differentiation alters stem cell nuclear architecture, mechanics, and mechano-sensitivity.

Heo SJ, Driscoll TP, Thorpe SD, Nerurkar NL, Baker BM, Yang MT, Chen CS, Lee DA, Mauck RL.

Elife. 2016 Nov 30;5. pii: e18207. doi: 10.7554/eLife.18207.


Ligand-Driven T Cell Receptor Selection in Celiac Disease.

Singh NK, Baker BM.

Structure. 2016 Oct 4;24(10):1623-1624. doi: 10.1016/j.str.2016.09.004.


Deep Mutational Scans as a Guide to Engineering High Affinity T Cell Receptor Interactions with Peptide-bound Major Histocompatibility Complex.

Harris DT, Wang N, Riley TP, Anderson SD, Singh NK, Procko E, Baker BM, Kranz DM.

J Biol Chem. 2016 Nov 18;291(47):24566-24578. Epub 2016 Sep 28.


A generalized framework for computational design and mutational scanning of T-cell receptor binding interfaces.

Riley TP, Ayres CM, Hellman LM, Singh NK, Cosiano M, Cimons JM, Anderson MJ, Piepenbrink KH, Pierce BG, Weng Z, Baker BM.

Protein Eng Des Sel. 2016 Dec;29(12):595-606. Epub 2016 Sep 13.


An Engineered Switch in T Cell Receptor Specificity Leads to an Unusual but Functional Binding Geometry.

Harris DT, Singh NK, Cai Q, Smith SN, Vander Kooi C, Procko E, Kranz DM, Baker BM.

Structure. 2016 Jul 6;24(7):1142-1154. doi: 10.1016/j.str.2016.04.011. Epub 2016 May 26.


Differential utilization of binding loop flexibility in T cell receptor ligand selection and cross-reactivity.

Ayres CM, Scott DR, Corcelli SA, Baker BM.

Sci Rep. 2016 Apr 27;6:25070. doi: 10.1038/srep25070.


Computational Modeling of T Cell Receptor Complexes.

Riley TP, Singh NK, Pierce BG, Weng Z, Baker BM.

Methods Mol Biol. 2016;1414:319-40. doi: 10.1007/978-1-4939-3569-7_19.


Computational Reprogramming of T Cell Antigen Receptor Binding Properties.

Riley TP, Singh NK, Pierce BG, Baker BM, Weng Z.

Methods Mol Biol. 2016;1414:305-18. doi: 10.1007/978-1-4939-3569-7_18.


Hepatitis C virus-cross-reactive TCR gene-modified T cells: a model for immunotherapy against diseases with genomic instability.

Spear TT, Riley TP, Lyons GE, Callender GG, Roszkowski JJ, Wang Y, Simms PE, Scurti GM, Foley KC, Murray DC, Hellman LM, McMahan RH, Iwashima M, Garrett-Mayer E, Rosen HR, Baker BM, Nishimura MI.

J Leukoc Biol. 2016 Sep;100(3):545-57. doi: 10.1189/jlb.2A1215-561R. Epub 2016 Feb 26.


Differential scanning fluorimetry based assessments of the thermal and kinetic stability of peptide-MHC complexes.

Hellman LM, Yin L, Wang Y, Blevins SJ, Riley TP, Belden OS, Spear TT, Nishimura MI, Stern LJ, Baker BM.

J Immunol Methods. 2016 May;432:95-101. doi: 10.1016/j.jim.2016.02.016. Epub 2016 Feb 18.


How structural adaptability exists alongside HLA-A2 bias in the human αβ TCR repertoire.

Blevins SJ, Pierce BG, Singh NK, Riley TP, Wang Y, Spear TT, Nishimura MI, Weng Z, Baker BM.

Proc Natl Acad Sci U S A. 2016 Mar 1;113(9):E1276-85. doi: 10.1073/pnas.1522069113. Epub 2016 Feb 16.


FOXO3-NF-κB RelA Protein Complexes Reduce Proinflammatory Cell Signaling and Function.

Thompson MG, Larson M, Vidrine A, Barrios K, Navarro F, Meyers K, Simms P, Prajapati K, Chitsike L, Hellman LM, Baker BM, Watkins SK.

J Immunol. 2015 Dec 15;195(12):5637-47. doi: 10.4049/jimmunol.1501758. Epub 2015 Nov 11.


Structural interplay between germline interactions and adaptive recognition determines the bandwidth of TCR-peptide-MHC cross-reactivity.

Adams JJ, Narayanan S, Birnbaum ME, Sidhu SS, Blevins SJ, Gee MH, Sibener LV, Baker BM, Kranz DM, Garcia KC.

Nat Immunol. 2016 Jan;17(1):87-94. doi: 10.1038/ni.3310. Epub 2015 Nov 2.


Cell-mediated fibre recruitment drives extracellular matrix mechanosensing in engineered fibrillar microenvironments.

Baker BM, Trappmann B, Wang WY, Sakar MS, Kim IL, Shenoy VB, Burdick JA, Chen CS.

Nat Mater. 2015 Dec;14(12):1262-8. doi: 10.1038/nmat4444. Epub 2015 Oct 12.


Citizens unite for computational immunology!

Belden OS, Baker SC, Baker BM.

Trends Immunol. 2015 Jul;36(7):385-7. doi: 10.1016/


Remodeling of fibrous extracellular matrices by contractile cells: predictions from discrete fiber network simulations.

Abhilash AS, Baker BM, Trappmann B, Chen CS, Shenoy VB.

Biophys J. 2014 Oct 21;107(8):1829-1840. doi: 10.1016/j.bpj.2014.08.029.


Changing the peptide specificity of a human T-cell receptor by directed evolution.

Smith SN, Wang Y, Baylon JL, Singh NK, Baker BM, Tajkhorshid E, Kranz DM.

Nat Commun. 2014 Nov 7;5:5223. doi: 10.1038/ncomms6223.


A DNA-based molecular probe for optically reporting cellular traction forces.

Blakely BL, Dumelin CE, Trappmann B, McGregor LM, Choi CK, Anthony PC, Duesterberg VK, Baker BM, Block SM, Liu DR, Chen CS.

Nat Methods. 2014 Dec;11(12):1229-32. doi: 10.1038/nmeth.3145. Epub 2014 Oct 12.


Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity.

Duan F, Duitama J, Al Seesi S, Ayres CM, Corcelli SA, Pawashe AP, Blanchard T, McMahon D, Sidney J, Sette A, Baker BM, Mandoiu II, Srivastava PK.

J Exp Med. 2014 Oct 20;211(11):2231-48. doi: 10.1084/jem.20141308. Epub 2014 Sep 22.


Hafnium sulfate prenucleation clusters and the Hf(18) polyoxometalate red herring.

Ruther RE, Baker BM, Son JH, Casey WH, Nyman M.

Inorg Chem. 2014 Apr 21;53(8):4234-42. doi: 10.1021/ic500375v. Epub 2014 Apr 2.


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