All Publications

Since the BIDC's inception, we have contributed to over 180 peer-reviewed publications. If you have utilized BIDC resources (microscopes, analysis, expertise), please submit the publication to [email protected] to be included in our list.

  1. Bai Y, Wang Y, Kang M, Gabe CM, Srirangapatanam S, Edwards A, Stoller M, Green SJ, Aloni S, Tamura N, et al. Organic Matrix Derived from Host–Microbe Interplay Contributes to Pathological Renal Biomineralization. ACS Nanoscience Au. 2023;3(4):335–346. [http://doi:10.1021/acsnanoscienceau.2c00060]
  2. Caruso JA, Wang X, Murrow LM, Rodriguez CI, Chen-Tanyolac C, Vu L, Chen Y-Y, Gascard P, Gartner ZJ, Kerlikowske K, et al. Loss of PPARγ activity characterizes early protumorigenic stromal reprogramming and dictates the therapeutic window of opportunity. Proceedings of the National Academy of Sciences. 2023;120(42):e2303774120. doi:10.1073/pnas.2303774120
  3. Krishna S, Choudhury A, Keough MB, Seo K, Ni L, Kakaizada S, Lee A, Aabedi A, Popova G, Lipkin B, et al. Glioblastoma remodelling of human neural circuits decreases survival. Nature. 2023;617(7961):599–607. [doi:10.1038/s41586-023-06036-1]
  4. Patel RK, Jaszczak RG, Im K, Carey ND, Courau T, Bunis DG, Samad B, Avanesyan L, Chew NW, Stenske S, et al. Cyclone: an accessible pipeline to analyze, evaluate, and optimize multiparametric cytometry data. Frontiers in Immunology. 2023;14. [https://www.frontiersin.org/articles/10.3389/fimmu.2023.1167241]
  5. Stashko C, Hayward M-K, Northey JJ, Pearson N, Ironside AJ, Lakins JN, Oria R, Goyette M-A, Mayo L, Russnes HG, et al. A convolutional neural network STIFMap reveals associations between stromal stiffness and EMT in breast cancer. Nature Communications. 2023;14(1):3561. [http://doi:10.1038/s41467-023-39085-1]
  6. Tharp Kevin M., Park Sangwoo, Timblin Greg A., Richards Alicia L., Berg Jordan A., Twells Nicholas M., Riley Nicholas M., Peltan Egan L., Shon D. Judy, Stevenson Erica, Tsui Kimberly, Palomba Francesco, Lefebvre Austin E. Y. T., Soens Ross W., Ayad Nadia M.E., ten Hoeve-Scott Johanna, Healy Kevin, Digman Michelle, Dillin Andrew, Bertozzi Carolyn R., Swaney Danielle L., Mahal Lara K., Cantor Jason R., Paszek Matthew J., Weaver Valerie M. The microenvironment dictates glycocalyx construction and immune surveillance. eLife. 2023 [https://doi.org/10.7554/eLife.91281.1]
  7. Zagorulya M, Yim L, Morgan DM, Edwards A, Torres-Mejia E, Momin N, McCreery CV, Zamora IL, Horton BL, Fox JG, et al. Tissue-specific abundance of interferon-gamma drives regulatory T cells to restrain DC1-mediated priming of cytotoxic T cells against lung cancer. Immunity. 2023;56(2):386-405.e10. [doi:10.1016/j.immuni.2023.01.010]
  8. Beppler C, Eichorst J, Marchuk K, Cai E, Castellanos CA, Sriram V, Roybal KT, Krummel MF. Hyperstabilization of T cell microvilli contacts by chimeric antigen receptors. Journal of Cell Biology. 2022;222(3):e202205118. [doi:10.1083/jcb.202205118]
  9. Combes AJ, Samad B, Tsui J, Chew NW, Yan P, Reeder GC, Kushnoor D, Shen A, Davidson B, Barczak AJ, et al. Discovering dominant tumor immune archetypes in a pan-cancer census. Cell. 2022;185(1):184-203.e19. [doi:10.1016/j.cell.2021.12.004]
  10. Rusu I, Mennillo E, Bain JL, Li Z, Sun X, Ly KM, Rosli YY, Naser M, Wang Z, Advincula R, et al. Microbial signals, MyD88, and lymphotoxin drive TNF-independent intestinal epithelial tissue damage. The Journal of Clinical Investigation. 2022;132(5).[doi:10.1172/JCI154993]
  11. You R, Artichoker J, Ray A, Gonzalez Velozo H, Rock DA, Conner KP, Krummel MF. Visualizing Spatial and Stoichiometric Barriers to Bispecific T-Cell Engager Efficacy. Cancer Immunology Research. 2022;10(6):698–712. [doi:10.1158/2326-6066.CIR-21-0594]
  12. Bhattacharyya A, Boostanpour K, Bouzidi M, Magee L, Chen TY, Wolters R, Torre P, Pillai SK, Bhattacharya M. IL10 trains macrophage profibrotic function after lung injury. American Journal of Physiology-Lung Cellular and Molecular Physiology. 2022;322(3):L495–L502. [doi:10.1152/ajplung.00458.2021]
  13. Cai E, Beppler C, Eichorst J, Marchuk K, Eastman SW, Krummel MF. T cells use distinct topographical and membrane receptor scanning strategies that individually coalesce during receptor recognition. Proceedings of the National Academy of Sciences. 2022;119(32):e2203247119. [doi:10.1073/pnas.2203247119]
  14. Cautivo KM, Matatia PR, Lizama CO, Mroz NM, Dahlgren MW, Yu X, Sbierski-Kind J, Taruselli MT, Brooks JF, Wade-Vallance A, et al. Interferon gamma constrains type 2 lymphocyte niche boundaries during mixed inflammation. Immunity. 2022;55(2):254-271.e7. doi:10.1016/j.immuni.2021.12.014
  15. Conrad C, Yildiz D, Cleary SJ, Margraf A, Cook L, Schlomann U, Panaretou B, Bowser JL, Karmouty-Quintana H, Li J, et al. ADAM8 signaling drives neutrophil migration and ARDS severity. JCI Insight. 2022;7(3). [doi:10.1172/jci.insight.149870]
  16. Crouch EE, Bhaduri A, Andrews MG, Cebrian-Silla A, Diafos LN, Birrueta JO, Wedderburn-Pugh K, Valenzuela EJ, Bennett NK, Eze UC, et al. Ensembles of endothelial and mural cells promote angiogenesis in prenatal human brain. Cell. 2022;185(20):3753-3769.e18. [http://doi:10.1016/j.cell.2022.09.004]
  17. Kersten K, Hu KH, Combes AJ, Samad B, Harwin T, Ray A, Rao AA, Cai E, Marchuk K, Artichoker J, et al. Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells in cancer. Cancer Cell. 2022;40(6):624-638.e9. doi:10.1016/j.ccell.2022.05.004
  18. Kotas ME, Moore CM, Gurrola JG, Pletcher SD, Goldberg AN, Alvarez R, Yamato S, Bratcher PE, Shaughnessy CA, Zeitlin PL, et al. IL-13–programmed airway tuft cells produce PGE2, which promotes CFTR-dependent mucociliary function. JCI Insight. 7(13):e159832. [http://doi:10.1172/jci.insight.159832]
  19. Rao P, Han DD, Tan K, Mohammadi L, Derakhshandeh R, Navabzadeh M, Goyal N, Springer ML. Comparable Impairment of Vascular Endothelial Function by a Wide Range of Electronic Nicotine Delivery Devices. Nicotine & Tobacco Research. 2022;24(7):1055–1062. [http://doi:10.1093/ntr/ntac019]
  20. Reyes NS, Krasilnikov M, Allen NC, Lee JY, Hyams B, Zhou M, Ravishankar S, Cassandras M, Wang C, Khan I, et al. Sentinel p16INK4a+ cells in the basement membrane form a reparative niche in the lung. Science. 2022;378(6616):192–201. [doi:10.1126/science.abf3326]
  21. Shariati K, Zhang Y, Giubbolini S, Parra R, Liang S, Edwards A, Hejtmancik JF, Ratto GM, Arosio D, Ku G. A Superfolder Green Fluorescent Protein-Based Biosensor Allows Monitoring of Chloride in the Endoplasmic Reticulum. ACS Sensors. 2022;7(8):2218–2224. [http://doi:10.1021/acssensors.2c00626]
  22. Smith SS, Chu D, Qu T, Aggleton JA, Schneider RA. Species-specific sensitivity to TGFβ signaling and changes to the Mmp13 promoter underlie avian jaw development and evolution. Bronner ME, Cheah KSE, editors. eLife. 2022;11:e66005. [http://doi:10.7554/eLife.66005]
  23. Valet C, Magnen M, Qiu L, Cleary SJ, Wang KM, Ranucci S, Grockowiak E, Boudra R, Conrad C, Seo Y, et al. Sepsis promotes splenic production of a protective platelet pool with high CD40 ligand expression. The Journal of Clinical Investigation. 2022 [doi:10.1172/JCI153920]
  24. You R, Artichoker J, Fries A, Edwards AW, Combes AJ, Reeder GC, Samad B, Krummel MF. Active surveillance characterizes human intratumoral T cell exhaustion. The Journal of Clinical Investigation. 2021;131(18). [doi:10.1172/JCI144353].
  25. Pipathsouk A, Brunetti RM, Town JP, Graziano BR, Breuer A, Pellett PA, Marchuk K, Tran N-HT, Krummel MF, Stamou D, et al. The WAVE complex associates with sites of saddle membrane curvature. Journal of Cell Biology. 2021;220(8):e202003086. [doi:10.1083/jcb.202003086]
  26. Boothby IC, Kinet MJ, Boda DP, Kwan EY, Clancy S, Cohen JN, Habrylo I, Lowe MM, Pauli M, Yates AE, et al. Early-life inflammation primes a T helper 2 cell–fibroblast niche in skin. Nature. 2021;599(7886):667–672. doi:10.1038/s41586-021-04044-7
  27. Drain AP, Zahir N, Northey JJ, Zhang H, Huang P-J, Maller O, Lakins JN, Yu X, Leight JL, Alston-Mills BP, et al. Matrix compliance permits NF-κB activation to drive therapy resistance in breast cancer. Journal of Experimental Medicine. 2021;218(5):e20191360. [doi:10.1084/jem.20191360]
  28. Frumm SM, Yu SK, Chang J, Artichoker JA, Scaria SM, Lee KP, Byrnes LE, Sneddon JB, Tward AD. A Hierarchy of Proliferative and Migratory Keratinocytes Maintains the Tympanic Membrane. Cell Stem Cell. 2021;28(2):315-330.e5. [doi:10.1016/j.stem.2020.10.006]
  29. Lopez-Ichikawa M, Vu NK, Nijagal A, Rubinsky B, Chang TT. Neutrophils are important for the development of pro-reparative macrophages after irreversible electroporation of the liver in mice. Scientific Reports. 2021;11(1):14986. [doi:10.1038/s41598-021-94016-8]
  30. Mehta P, Gouirand V, Boda DP, Zhang J, Gearty SV, Zirak B, Lowe MM, Clancy S, Boothby I, Mahuron KM, et al. Layilin Anchors Regulatory T Cells in Skin. The Journal of Immunology. 2021;207(7):1763–1775. [doi:10.4049/jimmunol.2000970]
  31. Somebang K, Rudolph J, Imhof I, Li L, Niemi EC, Shigenaga J, Tran H, Gill TM, Lo I, Zabel BA, et al. CCR2 deficiency alters activation of microglia subsets in traumatic brain injury. Cell Reports. 2021;36(12):109727. [doi:10.1016/j.celrep.2021.109727]
  32. Soygur B, Jaszczak RG, Fries A, Nguyen DH, Malki S, Hu G, Demir N, Arora R, Laird DJ. Intercellular bridges coordinate the transition from pluripotency to meiosis in mouse fetal oocytes. Science Advances. 2021;7(15):eabc6747. [doi:10.1126/sciadv.abc6747]
  33. Walter ND, Born SEM, Robertson GT, Reichlen M, Dide-Agossou C, Ektnitphong VA, Rossmassler K, Ramey ME, Bauman AA, Ozols V, et al. Mycobacterium tuberculosis precursor rRNA as a measure of treatment-shortening activity of drugs and regimens. Nature Communications. 2021;12(1):2899. [doi:10.1038/s41467-021-22833-6]
  34. Wang Y, Bernard A, Comblain F, Yue X, Paillart C, Zhang S, Reiter JF, Vaisse C. Melanocortin 4 receptor signals at the neuronal primary cilium to control food intake and body weight. The Journal of Clinical Investigation. 2021;131(9). [doi:10.1172/JCI142064]
  35. Hu KH, Eichorst JP, McGinnis CS, Patterson DM, Chow ED, Kersten K, Jameson SC, Gartner ZJ, Rao AA, Krummel MF. ZipSeq: barcoding for real-time mapping of single cell transcriptomes. Nature Methods. 2020;17(8):833–843. [doi:10.1038/s41592-020-0880-2]
  36. Boissonnas A, Louboutin F, Laviron M, Loyher P-L, Reboussin E, Barthelemy S, Réaux-Le Goazigo A, Lobsiger CS, Combadière B, Mélik Parsadaniantz S, et al. Imaging resident and recruited macrophage contribution to Wallerian degeneration. Journal of Experimental Medicine. 2020;217(11):e20200471. [doi:10.1084/jem.20200471]
  37. Cassandras M, Wang C, Kathiriya J, Tsukui T, Matatia P, Matthay M, Wolters P, Molofsky A, Sheppard D, Chapman H, et al. Gli1+ mesenchymal stromal cells form a pathological niche to promote airway progenitor metaplasia in the fibrotic lung. Nature Cell Biology. 2020;22(11):1295–1306. [doi:10.1038/s41556-020-00591-9]
  38. Chu D, Nguyen A, Smith SS, Vavrušová Z, Schneider RA. Stable integration of an optimized inducible promoter system enables spatiotemporal control of gene expression throughout avian development. Biology Open. 2020;9(10):bio055343. [doi:10.1242/bio.055343]
  39. Cleary SJ, Kwaan N, Tian JJ, Calabrese DR, Mallavia B, Magnen M, Greenland JR, Urisman A, Singer JP, Hays SR, et al. Complement activation on endothelium initiates antibody-mediated acute lung injury. The Journal of Clinical Investigation. 2020;130(11):5909–5923. [doi:10.1172/JCI138136]
  40. Mallavia B, Liu F, Lefrançais E, Cleary SJ, Kwaan N, Tian JJ, Magnen M, Sayah DM, Soong A, Chen J, et al. Mitochondrial DNA Stimulates TLR9-Dependent Neutrophil Extracellular Trap Formation in Primary Graft Dysfunction. American Journal of Respiratory Cell and Molecular Biology. 2020;62(3):364–372. [doi:10.1165/rcmb.2019-0140OC]
  41. Northey JJ, Barrett AS, Acerbi I, Hayward M-K, Talamantes S, Dean IS, Mouw JK, Ponik SM, Lakins JN, Huang P-J, et al. Stiff stroma increases breast cancer risk by inducing the oncogene ZNF217. The Journal of Clinical Investigation. 2020;130(11):5721–5737. [doi:10.1172/JCI129249]
  42. Looney MR, Headley MB. Live imaging of the pulmonary immune environment. Cell Immunol. 2020;350:103862. [doi:10.1016/j.cellimm.2018.09.007].
  43. Cleary SJ, Hobbs C, Amison RT, Arnold S, O’Shaughnessy BG, Lefrançais E, Mallavia B, Looney MR, Page CP, Pitchford SC. LPS-induced Lung Platelet Recruitment Occurs Independently from Neutrophils, PSGL-1, and P-Selectin. American Journal of Respiratory Cell and Molecular Biology. 2019;61(2):232–243. [doi:10.1165/rcmb.2018-0182OC].
  44. Dahlgren MW, Jones SW, Cautivo KM, et al. "Adventitial Stromal Cells Define Group 2 Innate Lymphoid Cell Tissue Niches." Immunity. 2019;50(3):707‐722.e6. [doi:10.1016/j.immuni.2019.02.002].
  45. Hagerling, C., H. Gonzalez, K. Salari, C.-Y. Wang, C. Lin, I. Robles, M. van Gogh, A. Dejmek, K. Jirström & Z. Werb (2019). Immune effector monocyte - neutrophil cooperation induced by the primary tumor prevents metastatic progression of breast cancer.  Proc. Natl. Acad. Sci. USA. 116(43):21704-21714. [Epub ahead of print 10/7/19]. PMID:31591235; PMCID:[PMC6815161].
  46. Jason Wong, Sara L. Sampson, Hildegarde Bell-Briones, Ann Ouyang, Ann A. Lazar, Jeffrey C. Lotz, Aaron J. Fields. “Nutrient supply and nucleus pulposus cell function: effects of the transport properties of the cartilage endplate and potential implications for intradiscal biologic therapy” Osteoarthritis Cartilage. 2019 Jun; 27(6): 956–964. Published online 2019 Feb 2. [doi: 10.1016/j.joca.2019.01.013].
  47. Jones KB, Furukawa S, Marangoni P, et al. Quantitative Clonal Analysis and Single-Cell Transcriptomics Reveal Division Kinetics, Hierarchy, and Fate of Oral Epithelial Progenitor Cells. Cell Stem Cell. 2019;24(1):183‐192.e8. [doi:10.1016/j.stem.2018.10.015].
  48. Lyu C, Lopez-Ichikawa M, Rubinsky B, Chang TT. Normal and fibrotic liver parenchyma respond differently to irreversible electroporation. HPB. 2019;21(10):1344–1353. doi:10.1016/j.hpb.2019.01.019
  49. Owyong, M., J. Chou, R. J. E. van den Bijgaart, N. Kong, G. Efe, C. Maynard, D. Talmi-Frank, I. Solomonov, C. Koopman, E. Hadler-Olsen, M. Headley, C. Lin, C.-Y. Wang, I. Sagi, Z. Werb* & V. Plaks* (2019). MMP9 modulates the metastatic cascade and immune landscape for breast cancer anti-metastatic therapy. Life Sci Alliance. 2(6):  pii: e201800226; [doi.org/10.26508/lsa.201800226]. PMID:31727800; PMCID:PMC6856766.
  50. Sharir, A., Marangoni, P., Zilionis, R. et al. A large pool of actively cycling progenitors orchestrates self-renewal and injury repair of an ectodermal appendage. Nat Cell Biol 21, 1102–1112 (2019). [https://doi.org/10.1038/s41556-019-0378-2].
  51. Alex J. Hughes, Hikaru Miyazaki, Maxwell C. Coyle, et al. “Engineered Tissue Folding by Mechanical Compaction of the Mesenchyme.” Developmental Cell 44, 1–14, January 22, 2018. [doi:10.1016/j.devcel.2017.12.004].
  52. Krummel MF, Mahale JN, Uhl LFK, Hardison EA, Mujal AM, Mazet JM, Weber RJ, Gartner ZJ, Gérard A. Paracrine costimulation of IFN-γ signaling by integrins modulates CD8 T cell differentiation. Proceedings of the National Academy of Sciences. 2018;115(45):11585–11590. doi:10.1073/pnas.1804556115
  53. Lachowicz-Scroggins, M.E., Gordon, E.D., Wesolowska-Andersen, A. et al. Cadherin-26 (CDH26) regulates airway epithelial cell cytoskeletal structure and polarity. Cell Discov 4, 7 (2018). [https://doi.org/10.1038/s41421-017-0006-x].
  54. Lefrançais E, Mallavia B, Zhuo H, Calfee CS, Looney MR. Maladaptive role of neutrophil extracellular traps in pathogen-induced lung injury. JCI Insight. 2018;3(3):e98178. Published 2018 Feb 8. [doi:10.1172/jci.insight.98178].
  55. Miller CN, Proekt I, von Moltke J, Wells KL, Rajpurkar AR, Wang H, Rattay K, Khan IS, Metzger TC, Pollack JL, et al. Thymic tuft cells promote an IL-4-enriched medulla and shape thymocyte development. Nature. 2018;559(7715):627–631. doi:10.1038/s41586-018-0345-2
  56. Roth TL, Puig-Saus C, Yu R, Shifrut E, Carnevale J, Li PJ, Hiatt J, Saco J, Krystofinski P, Li H, et al. Reprogramming human T cell function and specificity with non-viral genome targeting. Nature. 2018;559(7714):405–409. doi:10.1038/s41586-018-0326-5
  57. Schneider C, O'Leary CE, von Moltke J, et al. A Metabolite-Triggered Tuft Cell-ILC2 Circuit Drives Small Intestinal Remodeling. Cell. 2018;174(2):271‐284.e14. [doi:10.1016/j.cell.2018.05.014].
  58. Woronowicz KC, Gline SE, Herfat ST, Fields AJ, Schneider RA. FGF and TGFβ signaling link form and function during jaw development and evolution. Developmental Biology. 2018;444:S219–S236. (The Neural Crest: 150 years after His’ discovery). [doi:10.1016/j.ydbio.2018.05.002]
  59. Cai E, Marchuk K, Beemiller P, Beppler C, Rubashkin MG, Weaver VM, Gérard A, Liu T-L, Chen B-C, Betzig E, et al. Visualizing dynamic microvillar search and stabilization during ligand detection by T cells. Science. 2017;356(6338):eaal3118. [doi:10.1126/science.aal3118].
  60. Ali N, Zirak B, Rodriguez RS, Pauli ML, Truong H-A, Lai K, Ahn R, Corbin K, Lowe MM, Scharschmidt TC, et al. Regulatory T Cells in Skin Facilitate Epithelial Stem Cell Differentiation. Cell. 2017;169(6):1119-1129.e11. [doi:10.1016/j.cell.2017.05.002]
  61. Lefrançais E, Ortiz-Muñoz G, Caudrillier A, Mallavia B, Liu F, Sayah DM, Thornton EE, Headley MB, David T, Coughlin SR, et al. The lung is a site of platelet biogenesis and a reservoir for haematopoietic progenitors. Nature. 2017;544(7648):105–109. [doi:10.1038/nature21706].
  62. Myers DR, Lau T, Markegard E, et al. Tonic LAT-HDAC7 Signals Sustain Nur77 and Irf4 Expression to Tune Naive CD4 T Cells. Cell Rep. 2017;19(8):1558‐1571. [doi:10.1016/j.celrep.2017.04.076].
  63. Roy S, Leidal AM, Ye J, Ronen SM, Debnath J. Autophagy-Dependent Shuttling of TBC1D5 Controls Plasma Membrane Translocation of GLUT1 and Glucose Uptake. Molecular Cell. 2017;67(1):84-95.e5. [doi:10.1016/j.molcel.2017.05.020]
  64. Smith AJ, Yao X, Dix JA, Jin BJ, Verkman AS. “Test of the 'glymphatic' hypothesis demonstrates diffusive and aquaporin-4-independent solute transport in rodent brain parenchyma.” Elife. 2017 Aug 21;6. [doi:10.7554/eLife.27679].
  65. Vercoulen Y, Kondo Y, Iwig JS, et al. A Histidine pH sensor regulates activation of the Ras-specific guanine nucleotide exchange factor RasGRP1. Elife. 2017;6:e29002. Published 2017 Sep 27. [doi:10.7554/eLife.29002].
  66. Wong PT, Roberts EW1, Tang S, Mukherjee J, Cannon J, Nip AJ, Corbin K, Krummel MF, Choi SK. “Control of an Unusual Photo-Claisen Rearrangement in Coumarin Caged Tamoxifen through an Extended Spacer.” ACS Chem Biol. 2017 Apr 21;12(4):1001-1010. [doi:10.1021/acschembio.6b00999].
  67. Xi Y, Kim T, Brumwell AN, Driver IH, Wei Y, Tan V, Jackson JR, Xu J, Lee D-K, Gotts JE, et al. Local lung hypoxia determines epithelial fate decisions during alveolar regeneration. Nature Cell Biology. 2017;19(8):904–914. [doi:10.1038/ncb3580]
  68. Arora R, Fries A, Oelerich K, Marchuk K, Sabeur K, Giudice LC, Laird DJ. Insights from imaging the implanting embryo and the uterine environment in three-dimensions. Development. 2016 Jan 1:dev.144386. [doi:10.1242/dev.144386].
  69. Gordon ED, Simpson LJ, Rios CL, Ringel L, Lachowicz-Scroggins ME, Peters MC, Wesolowska-Andersen A, Gonzalez JR, MacLeod HJ, Christian LS, Yuan S, Barry L, Woodruff PG, Ansel KM, Nocka K, Seibold MA, Fahy JV. “Alternative splicing ofinterleukin-33 and type 2 inflammation in asthma.” Proc Natl Acad Sci U S A. 2016  Aug 2;113(31):8765-70. [doi:10.1073/pnas.1601914113].
  70. Johnston, Michael J., Shaked Bar-Cohen, Ze ’ev Paroush, and Todd G. Nystul. 2016. “Phosphorylated Groucho Delays Differentiation in the Follicle Stem Cell Lineage by Providing a Molecular Memory of EGFR Signaling in the Niche.” Development 143 (24):4631–42. [doi: 10.1242/dev.143263].
  71. Kenific CM, Stehbens SJ, Goldsmith J, Leidal AM, Faure N, Ye J, Wittmann T, Debnath J. NBR1 enables autophagy-dependent focal adhesion turnover. Journal of Cell Biology. 2016;212(5):577–590. [doi:10.1083/jcb.201503075]
  72. Lefrançais, Emma, Beñat Mallavia, and Mark R. Looney. 2016. “Lung Imaging in Animal Models.” In Acute Lung Injury and Repair, edited by Lynn M. Schnapp and Carol Feghali-Bostwick, 107–32. Respiratory Medicine. Springer International Publishing. [doi:10.1007/978-3-319-46527-2_8].
  73. Mujal, Adriana M., Julia K. Gilden, Audrey Gérard, Makoto Kinoshita, and Matthew F. Krummel. 2016. “A Septin Requirement Differentiates Autonomous- and Contact-Facilitated T Cell Proliferation.” Nature Immunology 17 (3): 315–22. [doi:10.1038/ni.3330].
  74. Pinkard, Henry, Kaitlin Corbin, and Matthew F. Krummel. 2016. “Spatiotemporal Rank Filtering Improves Image Quality Compared to Frame Averaging in 2-Photon Laser Scanning Microscopy.” PLOS ONE 11 (3): e0150430. [doi:10.1371/journal.pone.0150430].
  75. Pinkard, Henry, Nico Stuurman, Kaitlin Corbin, Ronald Vale, and Matthew F. Krummel. 2016. “Micro-Magellan: Open-Source, Sample-Adaptive, Acquisition Software for Optical Microscopy.” Nature Methods 13 (10): 807–9. [doi:10.1038/nmeth.3991].
  76. Sen, Debasish, Stephen M. Jones, Erin M. Oswald, Henry Pinkard, Kaitlin Corbin, and Matthew F. Krummel. 2016. “Tracking the Spatial and Functional Gradient of Monocyte-To-Macrophage Differentiation in Inflamed Lung.” PLOS ONE 11 (10): e0165064. [doi:10.1371/journal.pone.0165064].
  77. Takai, K., A. Le, V. M. Weaver & Z. Werb (2016). Targeting the cancer-associated fibroblasts as a treatment in triple-negative breast cancer. Oncotarget. 7:82889-82901 (Epub ahead of print Oct. 14). PMID: 27756881; PMCID: [PMC5341254].
  78. Ulmschneider, Bryne, Bree K. Grillo-Hill, Marimar Benitez, Dinara R. Azimova, Diane L. Barber, and Todd G. Nystul. 2016. “Increased Intracellular pH Is Necessary for Adult Epithelial and Embryonic Stem Cell Differentiation.” J Cell Biol 215 (3):345–55. [doi:10.1083/jcb.201606042].
  79. Bickler PE, Clark JP, Gabatto P, Brosnan H. Hypoxic preconditioning and cell death from oxygen/glucose deprivation co-opt a subset of the unfolded protein response in hippocampal neurons. Neuroscience. 2015;310:306–321. doi:10.1016/j.neuroscience.2015.09.021
  80. Bose, Oishee, Peter Baluk, Mark R. Looney, Laurence E. Cheng, Donald M. McDonald, George H. Caughey, and Matthew F. Krummel. 2015. “Mast Cells Present Protrusions into Blood Vessels upon Tracheal Allergen Challenge in Mice.” PLoS ONE 10 (3). [doi:10.1371/journal.pone.0118513].
  81. Cassereau, Luke, Yekaterina A. Miroshnikova, Guanqing Ou, Johnathon Lakins, and Valerie M. Weaver. 2015. “A 3D Tension Bioreactor Platform to Study the Interplay between ECM Stiffness and Tumor Phenotype.” Journal of Biotechnology 193 (January): 66–69. [doi:10.1016/j.jbiotec.2014.11.008].
  82. Chan, M. & Z. Werb (2015). Confocal imaging of myeloid cells in the corneal stroma of live mice. Bio-Protocol 5(13): e1517. http://www.bio-protocol.org/e1517. PMID: 26191537; PMCID: [PMC4505377].
  83. Cheng, Laurence E., Brandon M. Sullivan, Lizett E. Retana, Christopher D. C. Allen, Hong-Erh Liang, and Richard M. Locksley. 2015. “IgE-Activated Basophils Regulate Eosinophil Tissue Entry by Modulating Endothelial Function.” Journal of Experimental Medicine 212 (4): 513–24. [doi:10.1084/jem.20141671].
  84. Faire, Mehlika, Amanda Skillern, Ripla Arora, Daniel H. Nguyen, Jason Wang, Chester Chamberlain, Michael S. German, Jennifer C. Fung, and Diana J. Laird. 2015. “Follicle Dynamics and Global Organization in the Intact Mouse Ovary.” Developmental Biology 403 (1): 69–79. [doi:10.1016/j.ydbio.2015.04.006].
  85. Grillo-Hill, Bree K., Changhoon Choi, Maite Jimenez-Vidal, and Diane L. Barber. 2015. “Increased H+ Efflux Is Sufficient to Induce Dysplasia and Necessary for Viability with Oncogene Expression.” eLife 4 (March): e03270. [doi:10.7554/eLife.03270].
  86. Hahn, Junghyun, Xianhong Wang, and Marta Margeta. 2015. “Astrocytes Increase the Activity of Synaptic GluN2B NMDA Receptors.” Frontiers in Cellular Neuroscience 9. [doi:10.3389/fncel.2015.00117].
  87. Hashimoto, Mitsuo, Haruhiko Yanagisawa, Shunsuke Minagawa, Debasish Sen, Amanda Goodsell, Royce Ma, Catherine Moermans, et al. 2015. “A Critical Role for Dendritic Cells in the Evolution of IL-1β–Mediated Murine Airway Disease.” The Journal of Immunology 194 (8): 3962–69. [doi:10.4049/jimmunol.1403043].
  88. Hashimoto, Mitsuo, Haruhiko Yanagisawa, Shunsuke Minagawa, Debasish Sen, Royce Ma, Lynne A. Murray, Ping Tsui, et al. 2015. “TGF-β–Dependent Dendritic Cell Chemokinesis in Murine Models of Airway Disease.” The Journal of Immunology 195 (3): 1182–90. [doi:10.4049/jimmunol.1500348].
  89. Lindsay, Robin S., Kaitlin Corbin, Ashley Mahne, Bonnie E. Levitt, Matthew J. Gebert, Eric J. Wigton, Brenda J. Bradley, et al. 2015. “Antigen Recognition in the Islets Changes with Progression of Autoimmune Islet Infiltration.” The Journal of Immunology 194 (2): 522–30. [doi:10.4049/jimmunol.1400626].
  90. Matheu, Melanie P., Shivashankar Othy, Milton L. Greenberg, Tobias X. Dong, Martijn Schuijs, Kim Deswarte, Hamida Hammad, Bart N. Lambrecht, Ian Parker, and Michael D. Cahalan. 2015. “Imaging Regulatory T Cell Dynamics and CTLA4-Mediated Suppression of T Cell Priming.” Nature Communications 6 (February): 6219. [doi:10.1038/ncomms7219].
  91. Mirrashidi KM, Elwell CA, Verschueren E, Johnson JR, Frando A, Von Dollen J, Rosenberg O, Gulbahce N, Jang G, Johnson T, et al. Global Mapping of the Inc-Human Interactome Reveals that Retromer Restricts Chlamydia Infection. Cell Host & Microbe. 2015;18(1):109–121. [doi:10.1016/j.chom.2015.06.004]
  92. Molofsky, Ari B., Frédéric Van Gool, Hong-Erh Liang, Steven J. Van Dyken, Jesse C. Nussbaum, Jinwoo Lee, Jeffrey A. Bluestone, and Richard M. Locksley. 2015. “Interleukin-33 and Interferon-γ Counter-Regulate Group 2 Innate Lymphoid Cell Activation during Immune Perturbation.” Immunity 43 (1): 161–74. [doi:10.1016/j.immuni.2015.05.019].
  93. Murrow L, Malhotra R, Debnath J. ATG12–ATG3 interacts with Alix to promote basal autophagic flux and late endosome function. Nature Cell Biology. 2015;17(3):300–310. [doi:10.1038/ncb3112]
  94. Prochazka, Jan, Michaela Prochazkova, Wen Du, Frantisek Spoutil, Jolana Tureckova, Renee Hoch, Tomomi Shimogori, et al. 2015. “Migration of Founder Epithelial Cells Drives Proper Molar Tooth Positioning and Morphogenesis.” Developmental Cell 35 (6): 713–24. [doi:10.1016/j.devcel.2015.11.025].
  95. Rys, Joanna P, Christopher C DuFort, David A Monteiro, Michelle A Baird, Juan A Oses-Prieto, Shreya Chand, Alma L Burlingame, Michael W Davidson, and Tamara N Alliston. 2015. “Discrete Spatial Organization of TGFβ Receptors Couples Receptor Multimerization and Signaling to Cellular Tension.” eLife 4. Accessed January 5. [doi:10.7554/eLife.09300].
  96. Vaughan, Andrew E., Alexis N. Brumwell, Ying Xi, Jeffrey E. Gotts, Doug G. Brownfield, Barbara Treutlein, Kevin Tan, et al. 2015. “Lineage-Negative Progenitors Mobilize to Regenerate Lung Epithelium after Major Injury.” Nature 517 (7536): 621–25. [doi:10.1038/nature14112].
  97. Vlachos, Stephanie, Sharayu Jangam, Ryan Conder, Michael Chou, Todd Nystul, and Nicholas Harden. 2015. “A Pak-Regulated Cell Intercalation Event Leading to a Novel Radial Cell Polarity Is Involved in Positioning of the Follicle Stem Cell Niche in the Drosophila Ovary.” Development 142 (1): 82–91. [doi:10.1242/dev.111039].
  98. Bonnans, C., M. Lohela & Z. Werb (2014). Real-time imaging of myeloid cells dynamics in ApcMin/+ intestinal tumors by spinning disk confocal microscopy. J. Vis. Exp. 92: e51916, doi:10.3791/51916. PMID: 25350573; PMCID: [PMC4318091].
  99. Broz, Miranda L., Mikhail Binnewies, Bijan Boldajipour, Amanda E. Nelson, Joshua L. Pollack, David J. Erle, Andrea Barczak, et al. 2014. “Dissecting the Tumor Myeloid Compartment Reveals Rare Activating Antigen-Presenting Cells Critical for T Cell Immunity.” Cancer Cell 26 (5): 638–52. [doi:10.1016/j.ccell.2014.09.007].
  100. Castanieto, Angela, Michael J. Johnston, and Todd G. Nystul. 2014. “EGFR Signaling Promotes Self-Renewal through the Establishment of Cell Polarity in Drosophila Follicle Stem Cells.” eLife 3 (December): e04437. [doi:10.7554/eLife.04437].
  101. Corbin, Kaitlin, Henry Pinkard, Sebastian Peck, Peter Beemiller, and Matthew F. Krummel. 2014. “Assessing and Benchmarking Multiphoton Microscopes for Biologists.” In Methods in Cell Biology, edited by Jennifer C. Waters and Torsten Wittman, 123:135–51. Quantitative Imaging in Cell Biology. Academic Press. [doi:10.1016/B9780124201385000082].
  102. Feuer SK, Liu X, Donjacour A, Lin W, Simbulan RK, Giritharan G, Piane LD, Kolahi K, Ameri K, Maltepe E, et al. Use of a Mouse In Vitro Fertilization Model to Understand the Developmental Origins of Health and Disease Hypothesis. Endocrinology. 2014;155(5):1956–1969. [doi:10.1210/en.2013-2081]
  103. Galmozzi, Andrea, Si B. Sonne, Svetlana Keylin, Yutaka Hasegawa, Kosaku Shinoda, Ineke H. N. Luijten, Jae Won Chang, et al. 2014. “ThermoMouse: An in Vivo Model to Identify Modulators of UCP1 Expression in Brown Adipose Tissue.” Cell Reports 9 (5): 1584–93. [doi:10.1016/j.celrep.2014.10.066].
  104. Gérard, Audrey, Genaro Patino-Lopez, Peter Beemiller, Rajalakshmi Nambiar, Khadija Ben-Aissa, Yin Liu, Fadi J. Totah, Matthew J. Tyska, Stephen Shaw, and Matthew F. Krummel. 2014. “Detection of Rare Antigen-Presenting Cells through T Cell-Intrinsic Meandering Motility, Mediated by Myo1g.” Cell 158 (3): 492–505. [doi:10.1016/j.cell.2014.05.044].
  105. Greer AM, Wu N, Putnam AL, Woodruff PG, Wolters P, Kinet J-P, Shin J-S. Serum IgE clearance is facilitated by human FcεRI internalization. The Journal of Clinical Investigation. 2014;124(3):1187–1198. [doi:10.1172/JCI68964]
  106. Lelkes, E., M.B. Headley, E.E. Thornton, M.R. Looney, and M.F. Krummel. 2014. “The Spatiotemporal Cellular Dynamics of Lung Immunity.” Trends in Immunology 35 (8): 379–86. [doi:10.1016/j.it.2014.05.005].
  107. Lin Y, Jiang W, Ng J, Jina A, Wang RA. Endothelial Ephrin-B2 is Essential for Arterial Vasodilation in Mice. Microcirculation. 2014;21(7):578–586. [doi:10.1111/micc.12135]
  108. Lohela, M., A.-J. Casbon, A. Olowa, L. Bonham, D. Branstetter, N. Weng, J. Smith & Z. Werb (2014). Intravital imaging reveals distinct responses of depleting dynamic tumor-associated macrophage and dendritic cell subpopulations. Proc. Natl. Acad. Sci. U.S.A. 111:E5086-5095. [Nov. 10. Epub ahead of print]. PMID: 25385645; PMCID: [PMC4250128].
  109. Looney, Mark R., and Jahar Bhattacharya. 2014. “Live Imaging of the Lung.” Annual Review of Physiology 76 (1): 431–45. [doi:10.1146/annurev-physiol-021113-170331].
  110. Moon, Hyang Mi, Yong Ha Youn, Hayley Pemble, Jessica Yingling, Torsten Wittmann, and Anthony Wynshaw-Boris. 2014. “LIS1 Controls Mitosis and Mitotic Spindle Organization via the LIS1–NDEL1–dynein Complex.” Human Molecular Genetics 23 (2): 449–66. [doi:10.1093/hmg/ddt436].
  111. Nielsen CM, Cuervo H, Ding VW, Kong Y, Huang EJ, Wang RA. Deletion of Rbpj from postnatal endothelium leads to abnormal arteriovenous shunting in mice. Development. 2014;141(19):3782–3792. [doi:10.1242/dev.108951]
  112. Ortiz-Muñoz, Guadalupe, Beñat Mallavia, Adriaan Bins, Mark Headley, Matthew F. Krummel, and Mark R. Looney. 2014. “Aspirin-Triggered 15-Epi-Lipoxin A4 Regulates Neutrophil-Platelet Aggregation and Attenuates Acute Lung Injury in Mice.” Blood 124 (17): 2625–34. [doi:10.1182/blood-2014-03-562876].
  113. Paszek MJ, DuFort CC, Rossier O, Bainer R, Mouw JK, Godula K, Hudak JE, Lakins JN, Wijekoon AC, Cassereau L, et al. The cancer glycocalyx mechanically primes integrin-mediated growth and survival. Nature. 2014;511(7509):319–325. [doi:10.1038/nature13535]
  114. Patnode, Michael L., Jennifer K. Bando, Matthew F. Krummel, Richard M. Locksley, and Steven D. Rosen. 2014. “Leukotriene B4 Amplifies Eosinophil Accumulation in Response to Nematodes.” Journal of Experimental Medicine 211 (7): 1281–88. [doi:10.1084/jem.20132336].
  115. Stehbens, Samantha J., Matthew Paszek, Hayley Pemble, Andreas Ettinger, Sarah Gierke, and Torsten Wittmann. 2014. “CLASPs Link Focal-Adhesion-Associated Microtubule Capture to Localized Exocytosis and Adhesion Site Turnover.” Nature Cell Biology 16 (6): 558–70. [doi:10.1038/ncb2975].
  116. Van Dyken, Steven J., Alexander Mohapatra, Jesse C. Nussbaum, Ari B. Molofsky, Emily E. Thornton, Steven F. Ziegler, Andrew N. J. McKenzie, Matthew F. Krummel, Hong-Erh Liang, and Richard M. Locksley. 2014. “Chitin Activates Parallel Immune Modules That Direct Distinct Inflammatory Responses via Innate Lymphoid Type 2 and Γδ T Cells.” Immunity 40 (3): 414–24. [doi:10.1016/j.immuni.2014.02.003].
  117. Ameri K, Rajah AM, Nguyen V, Sanders TA, Jahangiri A, DeLay M, Donne M, Choi HJ, Tormos KV, Yeghiazarians Y, et al. Nuclear Localization of the Mitochondrial Factor HIGD1A during Metabolic Stress. PLOS ONE. 2013;8(4):e62758. [doi:10.1371/journal.pone.0062758]
  118. Brosnan H, Bickler PE. Xenon Neurotoxicity in Rat Hippocampal Slice Cultures Is Similar to Isoflurane and Sevoflurane. Anesthesiology. 2013;119(2):335–344. [doi:10.1097/ALN.0b013e31829417f0]
  119. Cheng, Laurence E., Karin Hartmann, Axel Roers, Matthew F. Krummel, and Richard M. Locksley. 2013. “Perivascular Mast Cells Dynamically Probe Cutaneous Blood Vessels to Capture Immunoglobulin E.” Immunity 38 (1): 166–75. [doi:10.1016/j.immuni.2012.09.022].
  120. Chou J, Lin JH, Brenot A, Kim J, Provot S, Werb Z. GATA3 suppresses metastasis and modulates the tumour microenvironment by regulating microRNA-29b expression. Nature Cell Biology. 2013;15(2):201–213. [doi:10.1038/ncb2672]
  121. Devi S, Wang Y, Chew WK, Lima R, A-González N, Mattar CNZ, Chong SZ, Schlitzer A, Bakocevic N, Chew S, et al. Neutrophil mobilization via plerixafor-mediated CXCR4 inhibition arises from lung demargination and blockade of neutrophil homing to the bone marrow. Journal of Experimental Medicine. 2013;210(11):2321–2336. [doi:10.1084/jem.20130056]
  122. Gérard, Audrey, Omar Khan, Peter Beemiller, Erin Oswald, Joyce Hu, Mehrdad Matloubian, and Matthew F. Krummel. 2013. “Secondary T Cell-T Cell Synaptic Interactions Drive the Differentiation of Protective CD8+ T Cells.” Nature Immunology 14 (4): 356–63. [doi:10.1038/ni.2547].
  123. Jacobelli, Jordan, Miriam Estin Matthews, Stephanie Chen, and Matthew F. Krummel. 2013. “Activated T Cell Trans-Endothelial Migration Relies on Myosin-IIA Contractility for Squeezing the Cell Nucleus through Endothelial Cell Barriers.” PLOS ONE 8 (9): e75151. [doi:10.1371/journal.pone.0075151].
  124. Kessenbrock, K., G.J.P. Dijkgraaf, D. A. Lawson, L. E. Littlepage, P. Shahi, U. Pieper & Z. Werb (2013). A role for matrix metalloproteinases in regulating mammary stem cell function via the Wnt signaling pathway. Cell Stem Cell. 13:300-313. [Epub ahead of print July 18]. PMID: 23871604; PMCID: [PMC3769456].
  125. Metzger TC, Khan IS, Gardner JM, Mouchess ML, Johannes KP, Krawisz AK, Skrzypczynska KM, Anderson MS. Lineage Tracing and Cell Ablation Identify a Post-Aire-Expressing Thymic Epithelial Cell Population. Cell Reports. 2013;5(1):166–179. [doi:10.1016/j.celrep.2013.08.038]
  126. Nussbaum, Jesse C., Steven J. Van Dyken, Jakob von Moltke, Laurence E. Cheng, Alexander Mohapatra, Ari B. Molofsky, Emily E. Thornton, et al. 2013. “Type 2 Innate Lymphoid Cells Control Eosinophil Homeostasis.” Nature 502 (7470): 245–48. [doi:10.1038/nature12526].
  127. Plaks, V., A. Brenot, D. A. Lawson, J. Linneman, E. Van Kappel, K. Wong, F. de Sauvage, O. D. Klein & Z. Werb (2013). Lgr5 expressing cells are sufficient and necessary for postnatal mammary gland organogenesis. Cell Rep. 3 :70-78. [2013 Jan 23, Epub ahead of print]. PMID: 23352663; PMCID: [PMC3563842].
  128. Pickup MW, Laklai H, Acerbi I, Owens P, Gorska AE, Chytil A, Aakre M, Weaver VM, Moses HL. Stromally Derived Lysyl Oxidase Promotes Metastasis of Transforming Growth Factor-β–Deficient Mouse Mammary Carcinomas. Cancer Research. 2013;73(17):5336–5346. [doi:10.1158/0008-5472.CAN-13-0012]
  129. Beemiller, Peter, Jordan Jacobelli, and Matthew F. Krummel. 2012. “Integration of the Movement of Signaling Microclusters with Cellular Motility in Immunological Synapses.” Nature Immunology 13 (8): 787–95. [doi:10.1038/ni.2364].
  130. Caudrillier, Axelle, Kai Kessenbrock, Brian M. Gilliss, John X. Nguyen, Marisa B. Marques, Marc Monestier, Pearl Toy, Zena Werb, and Mark R. Looney. 2012. “Platelets Induce Neutrophil Extracellular Traps in Transfusion-Related Acute Lung Injury.” The Journal of Clinical Investigation 122 (7): 2661–71. [doi:10.1172/JCI61303].
  131. Engelhardt, John J., Bijan Boldajipour, Peter Beemiller, Priya Pandurangi, Caitlin Sorensen, Zena Werb, Mikala Egeblad, and Matthew F. Krummel. 2012. “Marginating Dendritic Cells of the Tumor Microenvironment Cross-Present Tumor Antigens and Stably Engage Tumor-Specific T Cells.” Cancer Cell 21 (3): 402–17. [doi:10.1016/j.ccr.2012.01.008].
  132. Ewald, A. J., R. Huebner, H. Palsdottir, J. K. Lee, M. Perez, D. M. Jorgens, K. J. Cheung, A. Tauscher, Z. Werb & M.  Auer (2012). Mammary collective cell migration involves transient loss of epithelial features and individual cell migration within the epithelium. J. Cell Sci. 125:2638-2654. [Epub 17 Feb] PMID: 22344263; PMCID: [PMC3403234].
  133. Gilden, Julia K., Sebastian Peck, Yi-Chun M. Chen, and Matthew F. Krummel. 2012. “The Septin Cytoskeleton Facilitates Membrane Retraction during Motility and Blebbing.” J Cell Biol 196 (1): 103–14. [doi:10.1083/jcb.201105127].
  134. Haass-Koffler CL, Naeemuddin M, Bartlett SE. An Analytical Tool that Quantifies Cellular Morphology Changes from Three-dimensional Fluorescence Images. Journal of Visualized Experiments. 2012;(66):4233. [doi:10.3791/4233]
  135. Motion JPM, Nguyen J, Szoka FC. Phosphatase-Triggered Fusogenic Liposomes for Cytoplasmic Delivery of Cell-Impermeable Compounds. Angewandte Chemie. 2012;124(36):9181–9185. [doi:10.1002/ange.201204198]
  136. Nakasone, E., H. A. Askautrud, T. Kees, V. Plaks, A. J.  Ewald, M. G. Rasch, Y. X. Tan, J. Qin, M. Fein, J. Park, P. Sinha, M. J. Bissell, E. Frengen, Z. Werb & M. Egeblad (2012). Imaging tumor-stroma interactions during chemotherapy reveals microenvironmental contributions to chemoresistance. Cancer Cell. 21:488-503. PMID: 22516258;PMCID: [PMC3332002].
  137. Paszek, Matthew J., Christopher C. DuFort, Matthew G. Rubashkin, Michael W. Davidson, Kurt S. Thorn, Jan T. Liphardt, and Valerie M. Weaver. 2012. “Scanning Angle Interference Microscopy Reveals Cell Dynamics at the Nanoscale.” Nature Methods 9 (8): 825–27. [doi:10.1038/nmeth.2077].
  138. Phillips, Joanna J., Emmanuelle Huillard, Aaron E. Robinson, Anna Ward, David H. Lum, Mei-Yin Polley, Steven D. Rosen, David H. Rowitch, and Zena Werb. 2012. “Heparan Sulfate Sulfatase SULF2 Regulates PDGFRα Signaling and Growth in Human and Mouse Malignant Glioma.” The Journal of Clinical Investigation 122 (3): 911–22. [doi:10.1172/JCI58215].
  139. Sockolosky JT, Tiffany MR, Szoka FC. Engineering neonatal Fc receptor-mediated recycling and transcytosis in recombinant proteins by short terminal peptide extensions. Proceedings of the National Academy of Sciences. 2012;109(40):16095–16100. [doi:10.1073/pnas.1208857109]
  140. Thornton, Emily E., Mark R. Looney, Oishee Bose, Debasish Sen, Dean Sheppard, Richard Locksley, Xiaozhu Huang, and Matthew F. Krummel. 2012. “Spatiotemporally Separated Antigen Uptake by Alveolar Dendritic Cells and Airway Presentation to T Cells in the Lung.” Journal of Experimental Medicine 209 (6): 1183–99. [doi:10.1084/jem.20112667].
  141. Thornton, Emily E., Matthew F. Krummel, and Mark R. Looney. 2012. “Live Imaging of the Lung.” In Current Protocols in Cytometry. John Wiley & Sons, Inc. [doi:10.1002/0471142956.cy1228s60].
  142. Widdicombe JH, Borthwell RM, Hajighasemi-Ossareh M, Lachowicz-Scroggins ME, Finkbeiner WE, Stevens JE, Modlin S. Chloride secretion by cultures of pig tracheal gland cells. American Journal of Physiology-Lung Cellular and Molecular Physiology. 2012;302(10):L1098–L1106. [doi:10.1152/ajplung.00253.2011]
  143. Zhang, Yafeng, Yi-Chun Maria Chen, Matthew F. Krummel, and Steven D. Rosen. 2012. “Autotaxin through Lysophosphatidic Acid Stimulates Polarization, Motility, and Transendothelial Migration of Naive T Cells.” The Journal of Immunology 189 (8): 3914–24. [doi:10.4049/jimmunol.1201604].
  144. Ewald, A. J., Z. Werb & M. Egeblad (2011). Dynamic, long-term in vivo imaging of tumor-stroma interactions in mouse models of breast cancer using spinning-disk confocal microscopy. Cold Spring Harb. Protoc. 2011 Feb 1; doi: 10.1101/pdb.top97. PMID: 21285277 ; PMCID: [PMC3533368].
  145. Ewald, A. J., Z. Werb & M. Egeblad (2011). Monitoring of vital signs for long-term survival of mice under anesthesia. Cold Spring Harb. Protoc. 2011 Feb 1;2011:pdb.prot5563. doi: 10.1101/pdb.prot5563. PMID: 21285263 ; PMCID: [PMC3531964].
  146. Ewald, A. J., Z. Werb & M. Egeblad (2011). Preparation of mice for long-term intravital imaging of the mammary gland. Cold Spring Harb. Protoc. 2011 Epub Feb 1;2011:pdb.prot5562. doi: 10.1101/pdb.prot5562. PMID: 21285262 ; PMCID: [PMC3531961].
  147. Lemieux, George A., Jason Liu, Nasima Mayer, Roland J. Bainton, Kaveh Ashrafi, and Zena Werb. 2011. “A Whole-Organism Screen Identifies New Regulators of Fat Storage.” Nature Chemical Biology 7 (4): 206–13. [doi:10.1038/nchembio.534].
  148. Looney, Mark R., Emily E. Thornton, Debasish Sen, Wayne J. Lamm, Robb W. Glenny, and Matthew F. Krummel. 2011. “Stabilized Imaging of Immune Surveillance in the Mouse Lung.” Nature Methods 8 (1): 91–96. [doi:10.1038/nmeth.1543].
  149. Pramparo, Tiziano, Ondrej Libiger, Sonia Jain, Hong Li, Yong Ha Youn, Shinji Hirotsune, Nicholas J. Schork, and Anthony Wynshaw-Boris. 2011. “Global Developmental Gene Expression and Pathway Analysis of Normal Brain Development and Mouse Models of Human Neuronal Migration Defects.” PLOS Genetics 7 (3): e1001331. [doi:10.1371/journal.pgen.1001331].
  150. Slorach, Euan M., Jonathan Chou, and Zena Werb. 2011. “Zeppo1 Is a Novel Metastasis Promoter That Represses E-Cadherin Expression and Regulates p120-Catenin Isoform Expression and Localization.” Genes & Development 25 (5): 471–84. [doi:10.1101/gad.1998111].
  151. Wang, Xiaoyin, Junya Takagawa, Viola C. Lam, Daniel J. Haddad, Diana L. Tobler, Pamela Y. Mok, Yan Zhang, et al. 2011. “Donor Myocardial Infarction Impairs the Therapeutic Potential of Bone Marrow Cells by an Interleukin-1–Mediated Inflammatory Response.” Science Translational Medicine 3 (100): 100ra90-100ra90. [doi:10.1126/scitranslmed.3002814].
  152. Beemiller, Peter, and Matthew F. Krummel. 2010. “Mediation of T-Cell Activation by Actin Meshworks.” Cold Spring Harbor Perspectives in Biology 2 (9): a002444. [doi:10.1101/cshperspect.a002444].
  153. Chen, Ying-Ting, Karina Nikulina, Stanislav Lazarev, Ahmad F. Bahrami, Lisa B. Noble, Marianne Gallup, and Nancy A. McNamara. 2010. “Interleukin-1 as a Phenotypic Immunomodulator in Keratinizing Squamous Metaplasia of the Ocular Surface in Sjögren’s Syndrome.” The American Journal of Pathology 177 (3): 1333–43. [doi:10.2353/ajpath.2010.100227].
  154. Chen, Ying-Ting, Marianne Gallup, Karina Nikulina, Stanislav Lazarev, Lorna Zlock, Walter Finkbeiner, and Nancy McNamara. 2010. “Cigarette Smoke Induces Epidermal Growth Factor Receptor-Dependent Redistribution of Apical MUC1 and Junctional β-Catenin in Polarized Human Airway Epithelial Cells.” The American Journal of Pathology 177 (3): 1255–64. [doi:10.2353/ajpath.2010.091129].
  155. Doh, Junsang, and Matthew F. Krummel. 2010. “Immunological Synapses Within Context: Patterns of Cell–Cell Communication and Their Application in T–T Interactions.” In Immunological Synapse, edited by Takashi Saito and Facundo D. Batista, 25–50. Current Topics in Microbiology and Immunology 340. Springer Berlin Heidelberg. [doi:10.1007/978-3-642-03858-7_2].
  156. Doh, Junsang, Miju Kim, and Matthew F. Krummel. 2010. “Cell-Laden Microwells for the Study of Multicellularity in Lymphocyte Fate Decisions.” Biomaterials 31 (12): 3422–28. [doi:10.1016/j.biomaterials.2010.01.018].
  157. Friedman, Rachel S., Peter Beemiller, Caitlin M. Sorensen, Jordan Jacobelli, and Matthew F. Krummel. 2010. “Real-Time Analysis of T Cell Receptors in Naive Cells in Vitro and in Vivo Reveals Flexibility in Synapse and Signaling Dynamics.” The Journal of Experimental Medicine 207 (12): 2733–49. [doi:10.1084/jem.20091201].
  158. Hashimoto, Masakazu, Kyosuke Shinohara, Jianbo Wang, Shingo Ikeuchi, Satoko Yoshiba, Chikara Meno, Shigenori Nonaka, et al. 2010. “Planar Polarization of Node Cells Determines the Rotational Axis of Node Cilia.” Nature Cell Biology 12 (2): 170–76. [doi:10.1038/ncb2020].
  159. Hippenmeyer, Simon, Yong Ha Youn, Hyang Mi Moon, Kazunari Miyamichi, Hui Zong, Anthony Wynshaw-Boris, and Liqun Luo. 2010. “Genetic Mosaic Dissection of Lis1 and Ndel1 in Neuronal Migration.” Neuron 68 (4): 695–709. [doi:10.1016/j.neuron.2010.09.027].
  160. Jacobelli, Jordan, Rachel S. Friedman, Mary Anne Conti, Ana-Maria Lennon-Dumenil, Matthieu Piel, Caitlin M. Sorensen, Robert S. Adelstein, and Matthew F. Krummel. 2010. “Confinement-Optimized 3-Dimensional T Cell Amoeboid Motility Is Modulated via Myosin IIA-Regulated Adhesions.” Nature Immunology 11 (10): 953–61. [doi:10.1038/ni.1936].
  161. Katzman, Shoshana D., William E. O’Gorman, Alejandro V. Villarino, Eugenio Gallo, Rachel S. Friedman, Matthew F. Krummel, Garry P. Nolan, and Abul K. Abbas. 2010. “Duration of Antigen Receptor Signaling Determines T-Cell Tolerance or Activation.” Proceedings of the National Academy of Sciences 107 (42): 18085–90. [doi:10.1073/pnas.1010560107].
  162. Lohela, M. & Z. Werb (2010). Intravital imaging of stromal cell dynamics in tumors. Curr. Opin. Genet. Dev. 20: 72-28. [2009 Nov 24. Epub ahead of print]. PMID: 19942428; PMCID: [PMC2821950].
  163. Pham, Trung H. M., Peter Baluk, Ying Xu, Irina Grigorova, Alex J. Bankovich, Rajita Pappu, Shaun R. Coughlin, Donald M. McDonald, Susan R. Schwab, and Jason G. Cyster. 2010. “Lymphatic Endothelial Cell Sphingosine Kinase Activity Is Required for Lymphocyte Egress and Lymphatic Patterning.” Journal of Experimental Medicine 207 (1): 17–27. [doi:10.1084/jem.20091619].
  164. Phan, Tri Giang, and Andrew Bullen. 2010. “Practical Intravital Two-Photon Microscopy for Immunological Research: Faster, Brighter, Deeper.” Immunology and Cell Biology 88 (4): 438–44. [doi:10.1038/icb.2009.116].
  165. Phee H, Dzhagalov I, Mollenauer M, Wang Y, Irvine DJ, Robey E, Weiss A. Regulation of thymocyte positive selection and motility by GIT2. Nature immunology. 2010 Jun;11(6):503-11. [https://doi.org/10.1038/ni.1868]
  166. Pramparo, Tiziano, Yong Ha Youn, Jessica Yingling, Shinji Hirotsune, and Anthony Wynshaw-Boris. 2010. “Novel Embryonic Neuronal Migration and Proliferation Defects in Dcx Mutant Mice Are Exacerbated by Lis1 Reduction.” The Journal of Neuroscience : The Official Journal of the Society for Neuroscience 30 (8): 3002–12. [doi:10.1523/JNEUROSCI.4851-09.2010].
  167. Radoshevich, Lilliana, Lyndsay Murrow, Nan Chen, Estefania Fernandez, Srirupa Roy, Christopher Fung, and Jayanta Debnath. 2010. “ATG12 Conjugation to ATG3 Regulates Mitochondrial Homeostasis and Cell Death.” Cell 142 (4): 590–600. [doi:10.1016/j.cell.2010.07.018].
  168. Bullen, Andrew, Rachel S. Friedman, and Matthew F. Krummel. 2009. “Two-Photon Imaging of the Immune System: A Custom Technology Platform for High-Speed, Multicolor Tissue Imaging of Immune Responses.” In Visualizing Immunity, edited by Michael Dustin and Dorian McGavern, 1–29. Current Topics in Microbiology and Immunology 334. Springer Berlin Heidelberg. [doi: 10.1007/978-3-540-93864-4_1].
  169. Ewald, A. J., Z. Werb & M. Egeblad (2009). Dynamic, long-term, in vivo imaging of tumor-stroma interactions in mouse models of breast cancer using spinning disk confocal microscopy. Cold Spring Harb Protoc. 2011 Feb 1;2011(2):pdb.top97. doi: 10.1101/pdb.top97. PMID: 21285277; PMCID: [PMC3533368].
  170. Fife, Brian T., Kristen E. Pauken, Todd N. Eagar, Takashi Obu, Jenny Wu, Qizhi Tang, Miyuki Azuma, Matthew F. Krummel, and Jeffrey A. Bluestone. 2009. “Interactions between PD-1 and PD-L1 Promote Tolerance by Blocking the TCR–induced Stop Signal.” Nature Immunology 10 (11): 1185–92. [doi:10.1038/ni.1790].
  171. Grigorova, Irina L., Susan R. Schwab, Tri Giang Phan, Trung H. M. Pham, Takaharu Okada, and Jason G. Cyster. 2009. “Cortical Sinus Probing, S1P1-Dependent Entry and Flow-Based Capture of Egressing T Cells.” Nature Immunology 10 (1): 58–65. [doi:10.1038/ni.1682].
  172. Melli, Kristin, Rachel S. Friedman, Ashley E. Martin, Erik B. Finger, Gang Miao, Gregory L. Szot, Matthew F. Krummel, and Qizhi Tang. 2009. “Amplification of Autoimmune Response through Induction of Dendritic Cell Maturation in Inflamed Tissues.” The Journal of Immunology 182 (5): 2590–2600. [doi:10.4049/jimmunol.0803543].
  173. Namkung W, Song Y, Mills AD, Padmawar P, Finkbeiner WE, Verkman AS. In Situ Measurement of Airway Surface Liquid [K+] Using a Ratioable K+-sensitive Fluorescent Dye. Journal of Biological Chemistry. 2009;284(23):15916–15926. [doi:10.1074/jbc.M808021200]
  174. Phan, Tri Giang, Jesse A. Green, Elizabeth E. Gray, Ying Xu, and Jason G. Cyster. 2009. “Immune Complex Relay by Subcapsular Sinus Macrophages and Noncognate B Cells Drives Antibody Affinity Maturation.” Nature Immunology 10 (7): 786–93. [doi:10.1038/ni.1745].
  175. Song Y, Namkung W, Nielson DW, Lee J-W, Finkbeiner WE, Verkman AS. Airway surface liquid depth measured in ex vivo fragments of pig and human trachea: dependence on Na + and Cl channel function. American Journal of Physiology-Lung Cellular and Molecular Physiology. 2009;297(6):L1131–L1140. [doi:10.1152/ajplung.00085.2009]
  176. Suzuki, Kazuhiro, Irina Grigorova, Tri Giang Phan, Lisa M. Kelly, and Jason G. Cyster. 2009. “Visualizing B Cell Capture of Cognate Antigen from Follicular Dendritic Cells.” Journal of Experimental Medicine 206 (7): 1485–93. [doi:10.1084/jem.20090209].
  177. Youn, Yong Ha, Tiziano Pramparo, Shinji Hirotsune, and Anthony Wynshaw-Boris. 2009. “Distinct Dose-Dependent Cortical Neuronal Migration and
  178. Allen, Christopher D C, and Jason G Cyster. 2008. “Follicular Dendritic Cell Networks of Primary Follicles and Germinal Centers: Phenotype and Function.” Seminars in Immunology 20 (1): 14–25. [doi:10.1016/j.smim.2007.12.001].
  179. Bullen A. Microscopic imaging techniques for drug discovery. Nature Reviews Drug Discovery. 2008;7(1):54–67. [doi:10.1038/nrd2446]
  180. Crane JM, Van Hoek AN, Skach WR, Verkman AS. Aquaporin-4 Dynamics in Orthogonal Arrays in Live Cells Visualized by Quantum Dot Single Particle Tracking. Molecular Biology of the Cell. 2008;19(8):3369–3378. [doi:10.1091/mbc.e08-03-0322]
  181. Egeblad, M., A. J.  Ewald, H. A. Askautrud, B. E. Welm, M. Truitt, E. Bainbridge, G.  Peeters, M. Krummell & Z.  Werb (2008). Imaging stromal cell behavior in intact tumor microenvironments. Dis. Model. Mech. 1:155-167. PMID: 19048070; PMCID: [PMC2562195].
  182. Gardner, James M., Jason J. DeVoss, Rachel S. Friedman, David J. Wong, Ying X. Tan, Xuyu Zhou, Kellsey P. Johannes, et al. 2008. “Deletional Tolerance Mediated by Extrathymic Aire-Expressing Cells.” Science 321 (5890): 843–47. [doi:10.1126/science.1159407].
  183. Haggie PM, Verkman AS. Monomeric CFTR in Plasma Membranes in Live Cells Revealed by Single Molecule Fluorescence Imaging *. Journal of Biological Chemistry. 2008;283(35):23510–23513. [doi:10.1074/jbc.C800100200]
  184. Kouros-Mehr, H., S. K. Bechis, E.M. Slorach, L. E. Littlepage, M. Egeblad, A. J. Ewald, S.-Y. Pai, I-C. Ho & Z. Werb (2008). GATA-3 links tumor differentiation and dissemination in a luminal breast cancer model. Cancer Cell. 13:141-152. PMID: 18242514; PMCID: [PMC2262951].
  185. Pham, Trung H. M., Takaharu Okada, Mehrdad Matloubian, Charles G. Lo, and Jason G. Cyster. 2008. “S1P1 Receptor Signaling Overrides Retention Mediated by Gαi-Coupled Receptors to Promote T Cell Egress.” Immunity 28 (1): 122–33. [doi:10.1016/j.immuni.2007.11.017].
  186. Sabatos, Catherine A., Junsang Doh, Sumone Chakravarti, Rachel S. Friedman, Priya G. Pandurangi, Aaron J. Tooley, and Matthew F. Krummel. 2008. “A Synaptic Basis for Paracrine Interleukin-2 Signaling during Homotypic T Cell Interaction.” Immunity 29 (2): 238–48. [doi:10.1016/j.immuni.2008.05.017].
  187. Welm, B.E, G. J. P. Dijkgraaf, A. S. Bledau, A. L. Welm & Z. Werb (2008).  Lentiviral transduction of stem cells for genetic analysis of mammary development and breast cancer. Cell Stem Cell. 2:90-102. PMID: 18371425; PMCID: [PMC2276651].
  188. Neurite Extension Defects in Lis1 and Ndel1 Mutant Mice.” Journal of Neuroscience 29 (49): 15520–30. [doi:10.1523/JNEUROSCI.4630-09.2009].
  189. Allen, Christopher D. C., Takaharu Okada, H. Lucy Tang, and Jason G. Cyster. 2007. “Imaging of Germinal Center Selection Events During Affinity Maturation.” Science 315 (5811): 528–31. [doi:10.1126/science.1136736].
  190. Woolf, Eilon, Irina Grigorova, Adi Sagiv, Valentin Grabovsky, Sara W. Feigelson, Ziv Shulman, Tanja Hartmann, Michael Sixt, Jason G. Cyster, and Ronen Alon. 2007. “Lymph Node Chemokines Promote Sustained T Lymphocyte Motility without Triggering Stable Integrin Adhesiveness in the Absence of Shear Forces.” Nature Immunology 8 (10): 1076–85. [doi:10.1038/ni1499].
  191. Tang, Qizhi, and Matthew F Krummel. 2006. “Imaging the Function of Regulatory T Cells in Vivo.” Current Opinion in Immunology, Host–pathogen interactions / Immunological techniques, 18 (4): 496–502. [doi:10.1016/j.coi.2006.05.007].
  192. Tang, Qizhi, Jason Y. Adams, Aaron J. Tooley, Mingying Bi, Brian T. Fife, Pau Serra, Pere Santamaria, Richard M. Locksley, Matthew F. Krummel, and Jeffrey A. Bluestone. 2006. “Visualizing Regulatory T Cell Control of Autoimmune Responses in Nonobese Diabetic Mice.” Nature Immunology 7 (1): 83–92. [doi:10.1038/ni1289].
  193. Friedman, Rachel S., Jordan Jacobelli, and Matthew F. Krummel. 2005. “Mechanisms of T Cell Motility and Arrest: Deciphering the Relationship between Intra- and Extracellular Determinants.” Seminars in Immunology 17 (6): 387–99. [doi:10.1016/j.smim.2005.09.006].
  194. Okada, Takaharu, Mark J Miller, Ian Parker, Matthew F Krummel, Margaret Neighbors, Suzanne B Hartley, Anne O’Garra, Michael D Cahalan, and Jason G Cyster. 2005. “Antigen-Engaged B Cells Undergo Chemotaxis toward the T Zone and Form Motile Conjugates with Helper T Cells.” PLoS Biology 3 (6). [doi:10.1371/journal.pbio.0030150].