Faculty Appointments
Professor of Cell & Developmental Biology
Professor of Surgery
Education
Ph.D., Proteomics and Bioinformatics , University of Toronto, Toronto, CanadaB.Sc., Molecular Genetics, University of Toronto, Toronto, Canada
Office Address
2215 Garland Ave, MRB IV 10405A
Nashville, TN 37232
Nashville, TN 37232
Research Description
The central goal of the Lau Lab is to understand how microenvironmental factors, including stromal/immune cells and microbiota, affect epithelial cell behaviors in the context of an inflammatory environment in the gut. Epithelial cells can differentiate, exhibit plasticity (reversion to stemness – dedifferentiation or transition to non-native states – metaplasia), undergo cell death, and alter their turnover when exposed to different environmental cues. Changes to these behaviors in diseases lead to aberrant tissue structure and function. Our laboratory utilizes high content, single-cell and spatial experimental techniques in conjunction with computational tools to interrogate organoids, mouse models, and human specimens. We vertically integrate technological development, algorithm development, and derivation of biological insights from large datasets in order to make translatable advances to Inflammatory Bowel Disease and colorectal cancer.
Research Keywords
single-cell biology, computational biology, inflammation, colorectal cancer, stem cell biology, epithelial biology, developmental biology, genomics, cancer biology, imaging, microbiology and immunology, quantitative biology, systems biology
Publications
Short SP, Brown RE, Chen Z, Pilat JM, McElligott BA, Meenderink LM, Bickart AC, Blunt KM, Jacobse J, Wang J, Simmons AJ, Xu Y, Yang Y, Parang B, Choksi YA, Goettel JA, Lau KS, Hiebert SW, Williams CS. MTGR1 is required to maintain small intestinal stem cell populations. Cell Death Differ [print-electronic]. 2024 Jul 7/25/2024; PMID: 39048708, PII: 10.1038/s41418-024-01346-x, DOI: 10.1038/s41418-024-01346-x, ISSN: 1476-5403.
Xiong J, Kaur H, Heiser CN, McKinley ET, Roland JT, Coffey RJ, Shrubsole MJ, Wrobel J, Ma S, Lau KS, Vandekar S. GammaGateR: semi-automated marker gating for single-cell multiplexed imaging. Bioinformatics. 2024 Jun 6/3/2024; 40(6): PMID: 38833684, PMCID: PMC11193056, PII: 7687782, DOI: 10.1093/bioinformatics/btae356, ISSN: 1367-4811.
Contreras-Panta EW, Lee SH, Won Y, Norlander AE, Simmons AJ, Peebles RS, Lau KS, Choi E, Goldenring JR. Interleukin 13 Promotes Maturation and Proliferation in Metaplastic Gastroids. Cell Mol Gastroenterol Hepatol [print-electronic]. 2024 May 5/29/2024; 18(3): 101366. PMID: 38815928, PII: S2352-345X(24)00120-6, DOI: 10.1016/j.jcmgh.2024.101366, ISSN: 2352-345X.
Deng R, Cui C, Remedios LW, Bao S, Womick RM, Chiron S, Li J, Roland JT, Lau KS, Liu Q, Wilson KT, Wang Y, Coburn LA, Landman BA, Huo Y. Cross-scale multi-instance learning for pathological image diagnosis. Med Image Anal [print-electronic]. 2024 May; 94: 103124. PMID: 38428271, PMCID: PMC11016375, PII: S1361-8415(24)00049-5, DOI: 10.1016/j.media.2024.103124, ISSN: 1361-8423.
Chen Z, Guo X, Tao R, Huyghe JR, Law PJ, Fernandez-Rozadilla C, Ping J, Jia G, Long J, Li C, Shen Q, Xie Y, Timofeeva MN, Thomas M, Schmit SL, Díez-Obrero V, Devall M, Moratalla-Navarro F, Fernandez-Tajes J, Palles C, Sherwood K, Briggs SEW, Svinti V, Donnelly K, Farrington SM, Blackmur J, Vaughan-Shaw PG, Shu XO, Lu Y, Broderick P, Studd J, Harrison TA, Conti DV, Schumacher FR, Melas M, Rennert G, Obón-Santacana M, Martín-Sánchez V, Oh JH, Kim J, Jee SH, Jung KJ, Kweon SS, Shin MH, Shin A, Ahn YO, Kim DH, Oze I, Wen W, Matsuo K, Matsuda K, Tanikawa C, Ren Z, Gao YT, Jia WH, Hopper JL, Jenkins MA, Win AK, Pai RK, Figueiredo JC, Haile RW, Gallinger S, Woods MO, Newcomb PA, Duggan D, Cheadle JP, Kaplan R, Kerr R, Kerr D, Kirac I, Böhm J, Mecklin JP, Jousilahti P, Knekt P, Aaltonen LA, Rissanen H, Pukkala E, Eriksson JG, Cajuso T, Hänninen U, Kondelin J, Palin K, Tanskanen T, Renkonen-Sinisalo L, Männistö S, Albanes D, Weinstein SJ, Ruiz-Narvaez E, Palmer JR, Buchanan DD, Platz EA, Visvanathan K, Ulrich CM, Siegel E, Brezina S, Gsur A, Campbell PT, Chang-Claude J, Hoffmeister M, Brenner H, Slattery ML, Potter JD, Tsilidis KK, Schulze MB, Gunter MJ, Murphy N, Castells A, Castellví-Bel S, Moreira L, Arndt V, Shcherbina A, Bishop DT, Giles GG, Southey MC, Idos GE, McDonnell KJ, Abu-Ful Z, Greenson JK, Shulman K, Lejbkowicz F, Offit K, Su YR, Steinfelder R, Keku TO, van Guelpen B, Hudson TJ, Hampel H, Pearlman R, Berndt SI, Hayes RB, Martinez ME, Thomas SS, Pharoah PDP, Larsson SC, Yen Y, Lenz HJ, White E, Li L, Doheny KF, Pugh E, Shelford T, Chan AT, Cruz-Correa M, Lindblom A, Hunter DJ, Joshi AD, Schafmayer C, Scacheri PC, Kundaje A, Schoen RE, Hampe J, Stadler ZK, Vodicka P, Vodickova L, Vymetalkova V, Edlund CK, Gauderman WJ, Shibata D, Toland A, Markowitz S, Kim A, Chanock SJ, van Duijnhoven F, Feskens EJM, Sakoda LC, Gago-Dominguez M, Wolk A, Pardini B, FitzGerald LM, Lee SC, Ogino S, Bien SA, Kooperberg C, Li CI, Lin Y, Prentice R, Qu C, Bézieau S, Yamaji T, Sawada N, Iwasaki M, Le Marchand L, Wu AH, Qu C, McNeil CE, Coetzee G, Hayward C, Deary IJ, Harris SE, Theodoratou E, Reid S, Walker M, Ooi LY, Lau KS, Zhao H, Hsu L, Cai Q, Dunlop MG, Gruber SB, Houlston RS, Moreno V, Casey G, Peters U, Tomlinson I, Zheng W. Fine-mapping analysis including over 254,000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes. Nat Commun. 2024 Apr 4/26/2024; 15(1): 3557. PMID: 38670944, PMCID: PMC11053150, PII: 10.1038/s41467-024-47399-x, DOI: 10.1038/s41467-024-47399-x, ISSN: 2041-1723.
Stangis MM, Chen Z, Min J, Glass SE, Jackson JO, Radyk MD, Hoi XP, Brennen WN, Yu M, Dinh HQ, Coffey RJ, Shrubsole MJ, Chan KS, Grady WM, Yegnasubramanian S, Lyssiotis CA, Maitra A, Halberg RB, Dey N, Lau KS. The Hallmarks of Precancer. Cancer Discov. 2024 Apr 4/4/2024; 14(4): 683-9. PMID: 38571435, PMCID: PMC11170686, PII: 741985, DOI: 10.1158/2159-8290.CD-23-1550, ISSN: 2159-8290.
Silverman JB, Vega PN, Tyska MJ, Lau KS. Intestinal Tuft Cells: Morphology, Function, and Implications for Human Health. Annu Rev Physiol [print-electronic]. 2024 Feb 2/12/2024; 86: 479-504. PMID: 37863104, PMCID: PMC11193883, DOI: 10.1146/annurev-physiol-042022-030310, ISSN: 1545-1585.
Grabski IN, Heymach JV, Kehl KL, Kopetz S, Lau KS, Riely GJ, Schrag D, Yaeger R, Irizarry RA, Haigis KM. Effects of KRAS Genetic Interactions on Outcomes in Cancers of the Lung, Pancreas, and Colorectum. Cancer Epidemiol Biomarkers Prev. 2024 Jan 1/9/2024; 33(1): 158-69. PMID: 37943166, PMCID: PMC10841605, PII: 730073, DOI: 10.1158/1055-9965.EPI-23-0262, ISSN: 1538-7755.
Bao S, Lee HH, Yang Q, Remedios LW, Deng R, Cui C, Cai LY, Xu K, Yu X, Chiron S, Li Y, Patterson NH, Wang Y, Li J, Liu Q, Lau KS, Roland JT, Coburn LA, Wilson KT, Landman BA, Huo Y. Alleviating tiling effect by random walk sliding window in high-resolution histological whole slide image synthesis. Proc Mach Learn Res. 2024; 227: 1406-22. PMID: 38993526, PMCID: PMC11238901, ISSN: 2640-3498.
Heiser CN, Simmons AJ, Revetta F, McKinley ET, Ramirez-Solano MA, Wang J, Kaur H, Shao J, Ayers GD, Wang Y, Glass SE, Tasneem N, Chen Z, Qin Y, Kim W, Rolong A, Chen B, Vega PN, Drewes JL, Markham NO, Saleh N, Nikolos F, Vandekar S, Jones AL, Washington MK, Roland JT, Chan KS, Schürpf T, Sears CL, Liu Q, Shrubsole MJ, Coffey RJ, Lau KS. Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors. Cell. 2023 Dec 12/7/2023; 186(25): 5620-5637.e16-5637.e16. PMID: 38065082, PMCID: PMC10756562, PII: S0092-8674(23)01222-9, DOI: 10.1016/j.cell.2023.11.006, ISSN: 1097-4172.
Cui C, Wang Y, Bao S, Tang Y, Deng R, Remedios LW, Asad Z, Roland JT, Lau KS, Liu Q, Coburn LA, Wilson KT, Landman BA, Huo Y. Feasibility of Universal Anomaly Detection without Knowing the Abnormality in Medical Images. Med Image Learn Ltd Noisy Data (2023) [print-electronic]. 2023 Oct; 14307: 82-92. PMID: 38523773, PMCID: PMC10959499, DOI: 10.1007/978-3-031-44917-8_8.
Chen Z, Lau KS. Advances in Mapping Tumor Progression from Precancer Atlases. Cancer Prev Res (Phila). 2023 Aug 8/1/2023; 16(8): 439-47. PMID: 37167978, PII: 726356, DOI: 10.1158/1940-6207.CAPR-22-0473, ISSN: 1940-6215.
Jain S, Pei L, Spraggins JM, Angelo M, Carson JP, Gehlenborg N, Ginty F, Gonçalves JP, Hagood JS, Hickey JW, Kelleher NL, Laurent LC, Lin S, Lin Y, Liu H, Naba A, Nakayasu ES, Qian WJ, Radtke A, Robson P, Stockwell BR, Van de Plas R, Vlachos IS, Zhou M, , Börner K, Snyder MP. Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP). Nat Cell Biol [print-electronic]. 2023 Aug; 25(8): 1089-100. PMID: 37468756, PMCID: PMC10681365, PII: 10.1038/s41556-023-01194-w, DOI: 10.1038/s41556-023-01194-w, ISSN: 1476-4679.
Arceneaux D, Chen Z, Simmons AJ, Heiser CN, Southard-Smith AN, Brenan MJ, Yang Y, Chen B, Xu Y, Choi E, Campbell JD, Liu Q, Lau KS. A contamination focused approach for optimizing the single-cell RNA-seq experiment. IScience. 2023 Jul 7/21/2023; 26(7): 107242. PMID: 37496679, PMCID: PMC10366499, PII: S2589-0042(23)01319-6, DOI: 10.1016/j.isci.2023.107242, ISSN: 2589-0042.
Shui B, Beyett TS, Chen Z, Li X, La Rocca G, Gazlay WM, Eck MJ, Lau KS, Ventura A, Haigis KM. Oncogenic K-Ras suppresses global miRNA function. Mol Cell [print-electronic]. 2023 Jul 7/20/2023; 83(14): 2509-2523.e13-2523.e13. PMID: 37402366, PII: S1097-2765(23)00429-X, DOI: 10.1016/j.molcel.2023.06.008, ISSN: 1097-4164.
Pilat JM, Brown RE, Chen Z, Berle NJ, Othon AP, Washington MK, Anant SA, Kurokawa S, Ng VH, Thompson JJ, Jacobse J, Goettel JA, Lee E, Choksi YA, Lau KS, Short SP, Williams CS. SELENOP modifies sporadic colorectal carcinogenesis and WNT signaling activity through LRP5/6 interactions. J Clin Invest. 2023 Jul 7/3/2023; 133(13): PMID: 37166989, PMCID: PMC10313376, PII: 165988, DOI: 10.1172/JCI165988, ISSN: 1558-8238.
Taufalele PV, Wang W, Simmons AJ, Southard-Smith AN, Chen B, Greenlee JD, King MR, Lau KS, Hassane DC, Bordeleau F, Reinhart-King CA. Matrix stiffness enhances cancer-macrophage interactions and M2-like macrophage accumulation in the breast tumor microenvironment. Acta Biomater [print-electronic]. 2023 Jun; 163: 365-77. PMID: 35483629, PMCID: PMC9592676, PII: S1742-7061(22)00240-9, DOI: 10.1016/j.actbio.2022.04.031, ISSN: 1878-7568.
Zilbauer M, James KR, Kaur M, Pott S, Li Z, Burger A, Thiagarajah JR, Burclaff J, Jahnsen FL, Perrone F, Ross AD, Matteoli G, Stakenborg N, Sujino T, Moor A, Bartolome-Casado R, Bækkevold ES, Zhou R, Xie B, Lau KS, Din S, Magness ST, Yao Q, Beyaz S, Arends M, Denadai-Souza A, Coburn LA, Gaublomme JT, Baldock R, Papatheodorou I, Ordovas-Montanes J, Boeckxstaens G, Hupalowska A, Teichmann SA, Regev A, Xavier RJ, Simmons A, Snyder MP, Wilson KT, , . A Roadmap for the Human Gut Cell Atlas. Nat Rev Gastroenterol Hepatol [print-electronic]. 2023 May 5/31/2023; PMID: 37258747, PII: 10.1038/s41575-023-00784-1, DOI: 10.1038/s41575-023-00784-1, ISSN: 1759-5053.
Jacobse J, Brown RE, Li J, Pilat JM, Pham L, Short SP, Peek CT, Rolong A, Washington MK, Martinez-Barricarte R, Byndloss MX, Shelton C, Markle JG, Latour YL, Allaman MM, Cassat JE, Wilson KT, Choksi YA, Williams CS, Lau KS, Flynn CR, Casanova JL, Rings EHHM, Samsom JN, Goettel JA. Interleukin-23 receptor signaling impairs the stability and function of colonic regulatory T cells. Cell Rep [print-electronic]. 2023 Feb 2/17/2023; 42(2): 112128. PMID: 36807140, PII: S2211-1247(23)00139-0, DOI: 10.1016/j.celrep.2023.112128, ISSN: 2211-1247.
Remedios LW, Bao S, Kerley CI, Cai LY, Rheault F, Deng R, Cui C, Chiron S, Lau KS, Roland JT, Washington MK, Coburn LA, Wilson KT, Huo Y, Landman BA. Predicting Crohn's disease severity in the colon using mixed cell nucleus density from pseudo labels. Proc SPIE Int Soc Opt Eng [print-electronic]. 2023 Feb; 12471: PMID: 37465840, PMCID: PMC10353830, PII: 1247116, DOI: 10.1117/12.2653918, ISSN: 0277-786X.
Cui C, Bao S, Li J, Deng R, Remedios LW, Asad Z, Chiron S, Lau KS, Wang Y, Coburn LA, Wilson KT, Roland JT, Landman BA, Liu Q, Huo Y. Influence of Cell-type Ratio on Spatially Resolved Single-cell Transcriptomes using the Tangram Algorithm: Based on Implementation on Single-Cell and MxIF Data. Proc SPIE Int Soc Opt Eng [print-electronic]. 2023 Feb; 12471: PMID: 37324550, PMCID: PMC10270698, PII: 124710A, ISSN: 0277-786X.
Bao S, Cui C, Li J, Tang Y, Lee HH, Deng R, Remedios LW, Yu X, Yang Q, Chiron S, Patterson NH, Lau KS, Liu Q, Roland JT, Coburn LA, Wilson KT, Landman BA, Huo Y. Topological-Preserving Membrane Skeleton Segmentation in Multiplex Immunofluorescence Imaging. Proc SPIE Int Soc Opt Eng [print-electronic]. 2023 Feb; 12471: PMID: 37786583, PMCID: PMC10545297, PII: 124710B, DOI: 10.1117/12.2654087, ISSN: 0277-786X.
Lin JR, Wang S, Coy S, Chen YA, Yapp C, Tyler M, Nariya MK, Heiser CN, Lau KS, Santagata S, Sorger PK. Multiplexed 3D atlas of state transitions and immune interaction in colorectal cancer. Cell. 2023 Jan 1/19/2023; 186(2): 363-381.e19-381.e19. PMID: 36669472, PMCID: PMC10019067, PII: S0092-8674(22)01571-9, DOI: 10.1016/j.cell.2022.12.028, ISSN: 1097-4172.
Min J, Zhang C, Bliton RJ, Caldwell B, Caplan L, Presentation KS, Park DJ, Kong SH, Lee HS, Washington MK, Kim WH, Lau KS, Magness ST, Lee HJ, Yang HK, Goldenring JR, Choi E. Dysplastic Stem Cell Plasticity Functions as a Driving Force for Neoplastic Transformation of Precancerous Gastric Mucosa. Gastroenterology [print-electronic]. 2022 Oct; 163(4): 875-90. PMID: 35700772, PMCID: PMC9509466, PII: S0016-5085(22)00626-6, DOI: 10.1053/j.gastro.2022.06.021, ISSN: 1528-0012.
Groves SM, Ildefonso GV, McAtee CO, Ozawa PMM, Ireland AS, Stauffer PE, Wasdin PT, Huang X, Qiao Y, Lim JS, Bader J, Liu Q, Simmons AJ, Lau KS, Iams WT, Hardin DP, Saff EB, Holmes WR, Tyson DR, Lovly CM, Rathmell JC, Marth G, Sage J, Oliver TG, Weaver AM, Quaranta V. Archetype tasks link intratumoral heterogeneity to plasticity and cancer hallmarks in small cell lung cancer. Cell Syst [print-electronic]. 2022 Sep 9/21/2022; 13(9): 690-710.e17-710.e17. PMID: 35981544, PMCID: PMC9615940, PII: S2405-4712(22)00313-1, DOI: 10.1016/j.cels.2022.07.006, ISSN: 2405-4720.
Simmons AJ, Lau KS. Dissociation and inDrops microfluidic encapsulation of human gut tissues for single-cell atlasing studies. STAR Protoc. 2022 Sep 9/16/2022; 3(3): 101570. PMID: 35880121, PMCID: PMC9307676, PII: S2666-1667(22)00450-6, DOI: 10.1016/j.xpro.2022.101570, ISSN: 2666-1667.
Deng R, Cui C, Remedios LW, Bao S, Womick RM, Chiron S, Li J, Roland JT, Lau KS, Liu Q, Wilson KT, Wang Y, Coburn LA, Landman BA, Huo Y. Cross-scale Attention Guided Multi-instance Learning for Crohn's Disease Diagnosis with Pathological Images. Multiscale Multimodal Med Imaging (2022) [print-electronic]. 2022 Sep; 13594: 24-33. PMID: 36331283, PMCID: PMC9628695, DOI: 10.1007/978-3-031-18814-5_3.
Cui Zhou D, Jayasinghe RG, Chen S, Herndon JM, Iglesia MD, Navale P, Wendl MC, Caravan W, Sato K, Storrs E, Mo CK, Liu J, Southard-Smith AN, Wu Y, Naser Al Deen N, Baer JM, Fulton RS, Wyczalkowski MA, Liu R, Fronick CC, Fulton LA, Shinkle A, Thammavong L, Zhu H, Sun H, Wang LB, Li Y, Zuo C, McMichael JF, Davies SR, Appelbaum EL, Robbins KJ, Chasnoff SE, Yang X, Reeb AN, Oh C, Serasanambati M, Lal P, Varghese R, Mashl JR, Ponce J, Terekhanova NV, Yao L, Wang F, Chen L, Schnaubelt M, Lu RJ, Schwarz JK, Puram SV, Kim AH, Song SK, Shoghi KI, Lau KS, Ju T, Chen K, Chatterjee D, Hawkins WG, Zhang H, Achilefu S, Chheda MG, Oh ST, Gillanders WE, Chen F, DeNardo DG, Fields RC, Ding L. Spatially restricted drivers and transitional cell populations cooperate with the microenvironment in untreated and chemo-resistant pancreatic cancer. Nat Genet [print-electronic]. 2022 Sep; 54(9): 1390-405. PMID: 35995947, PMCID: PMC9470535, PII: 10.1038/s41588-022-01157-1, DOI: 10.1038/s41588-022-01157-1, ISSN: 1546-1718.
Drewes JL, Chen J, Markham NO, Knippel RJ, Domingue JC, Tam AJ, Chan JL, Kim L, McMann M, Stevens C, Dejea CM, Tomkovich S, Michel J, White JR, Mohammad F, Campodónico VL, Heiser CN, Wu X, Wu S, Ding H, Simner P, Carroll K, Shrubsole MJ, Anders RA, Walk ST, Jobin C, Wan F, Coffey RJ, Housseau F, Lau KS, Sears CL. Human Colon Cancer-Derived Clostridioides difficile Strains Drive Colonic Tumorigenesis in Mice. Cancer Discov. 2022 Aug 8/5/2022; 12(8): 1873-85. PMID: 35678528, PMCID: PMC9357196, PII: 700781, DOI: 10.1158/2159-8290.CD-21-1273, ISSN: 2159-8290.
Brown RE, Jacobse J, Anant SA, Blunt KM, Chen B, Vega PN, Jones CT, Pilat JM, Revetta F, Gorby AH, Stengel KR, Choksi YA, Palin K, Piazuelo MB, Washington MK, Lau KS, Goettel JA, Hiebert SW, Short SP, Williams CS. MTG16 regulates colonic epithelial differentiation, colitis, and tumorigenesis by repressing E protein transcription factors. JCI Insight. 2022 May 5/23/2022; 7(10): PMID: 35503250, PMCID: PMC9220854, PII: 153045, DOI: 10.1172/jci.insight.153045, ISSN: 2379-3708.
Ma Z, Lytle NK, Chen B, Jyotsana N, Novak SW, Cho CJ, Caplan L, Ben-Levy O, Neininger AC, Burnette DT, Trinh VQ, Tan MCB, Patterson EA, Arrojo E Drigo R, Giraddi RR, Ramos C, Means AL, Matsumoto I, Manor U, Mills JC, Goldenring JR, Lau KS, Wahl GM, DelGiorno KE. Single-Cell Transcriptomics Reveals a Conserved Metaplasia Program in Pancreatic Injury. Gastroenterology [print-electronic]. 2022 Feb; 162(2): 604-620.e20. PMID: 34695382, PMCID: PMC8792222, PII: S0016-5085(21)03665-9, DOI: 10.1053/j.gastro.2021.10.027, ISSN: 1528-0012.
McKinley ET, Shao J, Ellis ST, Heiser CN, Roland JT, Macedonia MC, Vega PN, Shin S, Coffey RJ, Lau KS. MIRIAM: A machine and deep learning single-cell segmentation and quantification pipeline for multi-dimensional tissue images. Cytometry A [print-electronic]. 2022 Jan 1/27/2022; PMID: 35084791, DOI: 10.1002/cyto.a.24541, ISSN: 1552-4930.
Harris CR, McKinley ET, Roland JT, Liu Q, Shrubsole MJ, Lau KS, Coffey RJ, Wrobel J, Vandekar SN. Quantifying and correcting slide-to-slide variation in multiplexed immunofluorescence images. Bioinformatics [print-electronic]. 2022 Jan 1/4/2022; PMID: 34983062, PII: 6496920, DOI: 10.1093/bioinformatics/btab877, ISSN: 1367-4811.
Vega PN, Nilsson A, Kumar MP, Niitsu H, Simmons AJ, Ro J, Wang J, Chen Z, Joughin BA, Li W, McKinley ET, Liu Q, Roland JT, Washington MK, Coffey RJ, Lauffenburger DA, Lau KS. Cancer-Associated Fibroblasts and Squamous Epithelial Cells Constitute a Unique Microenvironment in a Mouse Model of Inflammation-Induced Colon Cancer. Front Oncol. 2022; 12: 878920. PMID: 35600339, PMCID: PMC9114773, DOI: 10.3389/fonc.2022.878920, ISSN: 2234-943X.
Chen B, Scurrah CR, McKinley ET, Simmons AJ, Ramirez-Solano MA, Zhu X, Markham NO, Heiser CN, Vega PN, Rolong A, Kim H, Sheng Q, Drewes JL, Zhou Y, Southard-Smith AN, Xu Y, Ro J, Jones AL, Revetta F, Berry LD, Niitsu H, Islam M, Pelka K, Hofree M, Chen JH, Sarkizova S, Ng K, Giannakis M, Boland GM, Aguirre AJ, Anderson AC, Rozenblatt-Rosen O, Regev A, Hacohen N, Kawasaki K, Sato T, Goettel JA, Grady WM, Zheng W, Washington MK, Cai Q, Sears CL, Goldenring JR, Franklin JL, Su T, Huh WJ, Vandekar S, Roland JT, Liu Q, Coffey RJ, Shrubsole MJ, Lau KS. Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps. Cell [print-electronic]. 2021 Dec 12/22/2021; 184(26): 6262-6280.e26. PMID: 34910928, PII: S0092-8674(21)01381-7, DOI: 10.1016/j.cell.2021.11.031, ISSN: 1097-4172.
Rolong A, Chen B, Lau KS. Deciphering the cancer microenvironment from bulk data with EcoTyper. Cell. 2021 Oct 10/14/2021; 184(21): 5306-8. PMID: 34653367, PMCID: PMC8655686, PII: S0092-8674(21)01111-9, DOI: 10.1016/j.cell.2021.09.028, ISSN: 1097-4172.
Heiser CN, Wang VM, Chen B, Hughey JJ, Lau KS. Automated quality control and cell identification of droplet-based single-cell data using dropkick. Genome Res [print-electronic]. 2021 Oct; 31(10): 1742-52. PMID: 33837131, PMCID: PMC8494217, PII: gr.271908.120, DOI: 10.1101/gr.271908.120, ISSN: 1549-5469.
Chen B, Ramirez-Solano MA, Heiser CN, Liu Q, Lau KS. Processing single-cell RNA-seq data for dimension reduction-based analyses using open-source tools. STAR Protoc. 2021 Jun 6/18/2021; 2(2): 100450. PMID: 33982010, PMCID: PMC8082116, PII: S2666-1667(21)00157-X, DOI: 10.1016/j.xpro.2021.100450, ISSN: 2666-1667.
May-Zhang AA, Tycksen E, Southard-Smith AN, Deal KK, Benthal JT, Buehler DP, Adam M, Simmons AJ, Monaghan JR, Matlock BK, Flaherty DK, Potter SS, Lau KS, Southard-Smith EM. Combinatorial Transcriptional Profiling of Mouse and Human Enteric Neurons Identifies Shared and Disparate Subtypes In Situ. Gastroenterology [print-electronic]. 2021 Feb; 160(3): 755-770.e26. PMID: 33010250, PMCID: PMC7878294, PII: S0016-5085(20)35213-6, DOI: 10.1053/j.gastro.2020.09.032, ISSN: 1528-0012.
Bao S, Chiron S, Tang Y, Heiser CN, Southard-Smith AN, Lee HH, Ramirez MA, Huo Y, Washington MK, Scoville EA, Roland JT, Liu Q, Lau KS, Wilson KT, Coburn LA, Landman BA. A cross-platform informatics system for the Gut Cell Atlas: integrating clinical, anatomical and histological data. Proc SPIE Int Soc Opt Eng [print-electronic]. 2021; 11601: PMID: 34539029, PMCID: PMC8445503, DOI: 10.1117/12.2581074, ISSN: 0277-786X.
Banerjee A, Herring CA, Chen B, Kim H, Simmons AJ, Southard-Smith AN, Allaman MM, White JR, Macedonia MC, Mckinley ET, Ramirez-Solano MA, Scoville EA, Liu Q, Wilson KT, Coffey RJ, Washington MK, Goettel JA, Lau KS. Succinate Produced by Intestinal Microbes Promotes Specification of Tuft Cells to Suppress Ileal Inflammation. Gastroenterology [print-electronic]. 2020 Dec; 159(6): 2101-2115.e5. PMID: 32828819, PMCID: PMC7725941, PII: S0016-5085(20)35068-X, DOI: 10.1053/j.gastro.2020.08.029, ISSN: 1528-0012.
Chinowsky CR, Pinette JA, Meenderink LM, Lau KS, Tyska MJ. Nonmuscle myosin-2 contractility-dependent actin turnover limits the length of epithelial microvilli. Mol Biol Cell [print-electronic]. 2020 Dec 12/1/2020; 31(25): 2803-15. PMID: 33026933, PMCID: PMC7851865, DOI: 10.1091/mbc.E20-09-0582, ISSN: 1939-4586.
Vickman RE, Faget DV, Beachy P, Beebe D, Bhowmick NA, Cukierman E, Deng WM, Granneman JG, Hildesheim J, Kalluri R, Lau KS, Lengyel E, Lundeberg J, Moscat J, Nelson PS, Pietras K, Politi K, Puré E, Scherz-Shouval R, Sherman MH, Tuveson D, Weeraratna AT, White RM, Wong MH, Woodhouse EC, Zheng Y, Hayward SW, Stewart SA. Deconstructing tumor heterogeneity: the stromal perspective. Oncotarget. 2020 Oct 10/6/2020; 11(40): 3621-32. PMID: 33088423, PMCID: PMC7546755, PII: 27736, DOI: 10.18632/oncotarget.27736, ISSN: 1949-2553.
Macedonia MC, Drewes JL, Markham NO, Simmons AJ, Roland JT, Vega PN, Scurrah CR, Coffey RJ, Shrubsole MJ, Sears CL, Lau KS. Clinically adaptable polymer enables simultaneous spatial analysis of colonic tissues and biofilms. NPJ Biofilms Microbiomes. 2020 Sep 9/24/2020; 6(1): 33. PMID: 32973205, PMCID: PMC7518420, PII: 10.1038/s41522-020-00143-x, DOI: 10.1038/s41522-020-00143-x, ISSN: 2055-5008.
Brubaker DK, Kumar MP, Chiswick EL, Gregg C, Starchenko A, Vega PN, Southard-Smith AN, Simmons AJ, Scoville EA, Coburn LA, Wilson KT, Lau KS, Lauffenburger DA. An interspecies translation model implicates integrin signaling in infliximab-resistant inflammatory bowel disease. Sci Signal. 2020 Aug 8/4/2020; 13(643): PMID: 32753478, PII: 13/643/eaay3258, DOI: 10.1126/scisignal.aay3258, ISSN: 1937-9145.
Southard-Smith AN, Simmons AJ, Chen B, Jones AL, Ramirez Solano MA, Vega PN, Scurrah CR, Zhao Y, Brenan MJ, Xuan J, Shrubsole MJ, Porter EB, Chen X, Brenan CJH, Liu Q, Quigley LNM, Lau KS. Dual indexed library design enables compatibility of in-Drop single-cell RNA-sequencing with exAMP chemistry sequencing platforms. BMC Genomics. 2020 Jul 7/2/2020; 21(1): 456. PMID: 32616006, PMCID: PMC7331155, PII: 10.1186/s12864-020-06843-0, DOI: 10.1186/s12864-020-06843-0, ISSN: 1471-2164.
Yang X, Graff SM, Heiser CN, Ho KH, Chen B, Simmons AJ, Southard-Smith AN, David G, Jacobson DA, Kaverina I, Wright CVE, Lau KS, Gu G. Coregulator Sin3a Promotes Postnatal Murine ß-Cell Fitness by Regulating Genes in Ca2+ Homeostasis, Cell Survival, Vesicle Biosynthesis, Glucose Metabolism, and Stress Response. Diabetes [print-electronic]. 2020 Jun; 69(6): 1219-31. PMID: 32245798, PMCID: PMC7243292, PII: db19-0721, DOI: 10.2337/db19-0721, ISSN: 1939-327X.
Islam M, Chen B, Spraggins JM, Kelly RT, Lau KS. Use of Single-Cell -Omic Technologies to Study the Gastrointestinal Tract and Diseases, From Single Cell Identities to Patient Features. Gastroenterology [print-electronic]. 2020 May 5/14/2020; PMID: 32417404, PII: S0016-5085(20)30656-9, DOI: 10.1053/j.gastro.2020.04.073, ISSN: 1528-0012.
Heiser CN, Lau KS. A Quantitative Framework for Evaluating Single-Cell Data Structure Preservation by Dimensionality Reduction Techniques. Cell Rep. 2020 May 5/5/2020; 31(5): 107576. PMID: 32375029, PMCID: PMC7305633, PII: S2211-1247(20)30525-8, DOI: 10.1016/j.celrep.2020.107576, ISSN: 2211-1247.
Rozenblatt-Rosen O, Regev A, Oberdoerffer P, Nawy T, Hupalowska A, Rood JE, Ashenberg O, Cerami E, Coffey RJ, Demir E, Ding L, Esplin ED, Ford JM, Goecks J, Ghosh S, Gray JW, Guinney J, Hanlon SE, Hughes SK, Hwang ES, Iacobuzio-Donahue CA, Jané-Valbuena J, Johnson BE, Lau KS, Lively T, Mazzilli SA, Pe'er D, Santagata S, Shalek AK, Schapiro D, Snyder MP, Sorger PK, Spira AE, Srivastava S, Tan K, West RB, Williams EH, . The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution. Cell. 2020 Apr 4/16/2020; 181(2): 236-49. PMID: 32302568, PMCID: PMC7376497, PII: S0092-8674(20)30346-9, DOI: 10.1016/j.cell.2020.03.053, ISSN: 1097-4172.
Liu Q, Sheng Q, Ping J, Ramirez MA, Lau KS, Coffey RJ, Shyr Y. ScRNABatchQC: multi-samples quality control for single cell RNA-seq data. Bioinformatics. 2019 Dec 12/15/2019; 35(24): 5306-8. PMID: 31373345, PMCID: PMC6954654, PII: 5542946, DOI: 10.1093/bioinformatics/btz601, ISSN: 1367-4811.
Min J, Vega PN, Engevik AC, Williams JA, Yang Q, Patterson LM, Simmons AJ, Bliton RJ, Betts JW, Lau KS, Magness ST, Goldenring JR, Choi E. Heterogeneity and dynamics of active Kras-induced dysplastic lineages from mouse corpus stomach. Nat Commun. 2019 Dec 12/5/2019; 10(1): 5549. PMID: 31804471, PMCID: PMC6895174, PII: 10.1038/s41467-019-13479-6, DOI: 10.1038/s41467-019-13479-6, ISSN: 2041-1723.
Vasaikar S, Huang C, Wang X, Petyuk VA, Savage SR, Wen B, Dou Y, Zhang Y, Shi Z, Arshad OA, Gritsenko MA, Zimmerman LJ, McDermott JE, Clauss TR, Moore RJ, Zhao R, Monroe ME, Wang YT, Chambers MC, Slebos RJC, Lau KS, Mo Q, Ding L, Ellis M, Thiagarajan M, Kinsinger CR, Rodriguez H, Smith RD, Rodland KD, Liebler DC, Liu T, Zhang B, . Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities. Cell [print-electronic]. 2019 May 5/2/2019; 177(4): 1035-1049.e19. PMID: 31031003, PII: S0092-8674(19)30292-2, DOI: 10.1016/j.cell.2019.03.030, ISSN: 1097-4172.
Howard AM, LaFever KS, Fenix AM, Scurrah CR, Lau KS, Burnette DT, Bhave G, Ferrell N, Page-McCaw A. DSS-induced damage to basement membranes is repaired by matrix replacement and crosslinking. J. Cell. Sci [print-electronic]. 2019 Mar 3/5/2019; PMID: 30837285, PII: jcs.226860, DOI: 10.1242/jcs.226860, ISSN: 1477-9137.
Manolopoulou M, Matlock BK, Nlandu Khodo S, Simmons AJ, Lau KS, Phillips-Mignemi M, Ivanova A, Alford CE, Flaherty DK, Gewin LS. Novel kidney dissociation protocol and image-based flow cytometry facilitate improved analysis of injured proximal tubules. Am. J. Physiol. Renal Physiol [print-electronic]. 2019 Feb 2/13/2019; PMID: 30759021, DOI: 10.1152/ajprenal.00354.2018, ISSN: 1522-1466.
Foegeding NJ, Raghunathan K, Campbell AM, Kim SW, Lau KS, Kenworthy AK, Cover TL, Ohi MD. Intracellular degradation of Helicobacter pylori VacA toxin as a determinant of gastric epithelial cell viability. Infect. Immun [print-electronic]. 2019 Jan 1/28/2019; PMID: 30692181, PII: IAI.00783-18, DOI: 10.1128/IAI.00783-18, ISSN: 1098-5522.
Vega PN, Lau KS, Goldenring JR. Not All Insults Are Created Equal for Awakening Dormant Stem Cell Abilities [editorial]. Cell Mol Gastroenterol Hepatol [print-electronic]. 2019 Jan 1/7/2019; PMID: 30629924, PII: S2352-345X(18)30178-4, DOI: 10.1016/j.jcmgh.2018.12.003, ISSN: 2352-345X.
Liu J, Banerjee A, Herring CA, Attalla J, Hu R, Xu Y, Shao Q, Simmons AJ, Dadi PK, Wang S, Jacobson DA, Liu B, Hodges E, Lau KS, Gu G. Neurog3-Independent Methylation Is the Earliest Detectable Mark Distinguishing Pancreatic Progenitor Identity. Dev. Cell. 2019 Jan 1/7/2019; 48(1): 49-63.e7. PMID: 30620902, PMCID: PMC6327977, PII: S1534-5807(18)31032-3, DOI: 10.1016/j.devcel.2018.11.048, ISSN: 1878-1551.
Scurrah CR, Simmons AJ, Lau KS. Single-Cell Mass Cytometry of Archived Human Epithelial Tissue for Decoding Cancer Signaling Pathways. Methods Mol. Biol. 2019; 1884: 215-29. PMID: 30465206, DOI: 10.1007/978-1-4939-8885-3_15, ISSN: 1940-6029.
Chen B, Herring CA, Lau KS. PyNVR: Investigating factors affecting feature selection from scRNA-seq data for lineage reconstruction. Bioinformatics [print-electronic]. 2018 Nov 11/16/2018; PMID: 30445607, PII: 5184958, DOI: 10.1093/bioinformatics/bty950, ISSN: 1367-4811.
Liu Q, Herring CA, Sheng Q, Ping J, Simmons AJ, Chen B, Banerjee A, Li W, Gu G, Coffey RJ, Shyr Y, Lau KS. Quantitative assessment of cell population diversity in single-cell landscapes. PLoS Biol. 2018 Oct; 16(10): e2006687. PMID: 30346945, PMCID: PMC6211764, PII: pbio.2006687, DOI: 10.1371/journal.pbio.2006687, ISSN: 1545-7885.
Banerjee A, McKinley ET, von Moltke J, Coffey RJ, Lau KS. Interpreting heterogeneity in intestinal tuft cell structure and function. J. Clin. Invest [print-electronic]. 2018 May 5/1/2018; 128(5): 1711-9. PMID: 29714721, PMCID: PMC5919882, PII: 120330, DOI: 10.1172/JCI120330, ISSN: 1558-8238.
Herring CA, Banerjee A, McKinley ET, Simmons AJ, Ping J, Roland JT, Franklin JL, Liu Q, Gerdes MJ, Coffey RJ, Lau KS. Unsupervised Trajectory Analysis of Single-Cell RNA-Seq and Imaging Data Reveals Alternative Tuft Cell Origins in the Gut. Cell Syst [print-electronic]. 2018 Jan 1/24/2018; 6(1): 37-51.e9. PMID: 29153838, PMCID: PMC5799016, PII: S2405-4712(17)30449-0, DOI: 10.1016/j.cels.2017.10.012, ISSN: 2405-4712.
Herring CA, Chen B, McKinley ET, Lau KS. Single-Cell Computational Strategies for Lineage Reconstruction in Tissue Systems. Cell Mol Gastroenterol Hepatol. 2018; 5(4): 539-48. PMID: 29713661, PMCID: PMC5924749, PII: S2352-345X(18)30031-6, DOI: 10.1016/j.jcmgh.2018.01.023, ISSN: 2352-345X.
Maseda D, Banerjee A, Johnson EM, Washington MK, Kim H, Lau KS, Crofford LJ. MPGES-1-Mediated Production of PGE2 and EP4 Receptor Sensing Regulate T Cell Colonic Inflammation. Front Immunol. 2018; 9: 2954. PMID: 30619314, PMCID: PMC6302013, DOI: 10.3389/fimmu.2018.02954, ISSN: 1664-3224.
Kim SW, Ehrman J, Ahn MR, Kondo J, Lopez AAM, Oh YS, Kim XH, Crawley SW, Goldenring JR, Tyska MJ, Rericha EC, Lau KS. Shear stress induces noncanonical autophagy in intestinal epithelial monolayers. Mol. Biol. Cell [print-electronic]. 2017 Nov 11/1/2017; 28(22): 3043-56. PMID: 28855375, PMCID: PMC5662261, PII: mbc.E17-01-0021, DOI: 10.1091/mbc.E17-01-0021, ISSN: 1939-4586.
McKinley ET, Sui Y, Al-Kofahi Y, Millis BA, Tyska MJ, Roland JT, Santamaria-Pang A, Ohland CL, Jobin C, Franklin JL, Lau KS, Gerdes MJ, Coffey RJ. Optimized multiplex immunofluorescence single-cell analysis reveals tuft cell heterogeneity. JCI Insight [print-electronic]. 2017 Jun 6/2/2017; 2(11): PMID: 28570279, PMCID: PMC5453701, PII: 93487, DOI: 10.1172/jci.insight.93487, ISSN: 2379-3708.
Almohazey D, Lo YH, Vossler CV, Simmons AJ, Hsieh JJ, Bucar EB, Schumacher MA, Hamilton KE, Lau KS, Shroyer NF, Frey MR. The ErbB3 receptor tyrosine kinase negatively regulates Paneth cells by PI3K-dependent suppression of Atoh1. Cell Death Differ [print-electronic]. 2017 May; 24(5): 855-65. PMID: 28304405, PMCID: PMC5423110, PII: cdd201727, DOI: 10.1038/cdd.2017.27, ISSN: 1476-5403.
Simmons AJ, Lau KS. Deciphering tumor heterogeneity from FFPE tissues: Its promise and challenges. Mol Cell Oncol. 2017; 4(1): e1260191. PMID: 28197533, PMCID: PMC5286981, PII: 1260191, DOI: 10.1080/23723556.2016.1260191, ISSN: 2372-3556.
Simmons AJ, Scurrah CR, McKinley ET, Herring CA, Irish JM, Washington MK, Coffey RJ, Lau KS. Impaired coordination between signaling pathways is revealed in human colorectal cancer using single-cell mass cytometry of archival tissue blocks. Sci Signal. 2016 Oct 10/11/2016; 9(449): rs11. PMID: 27729552, PII: 9/449/rs11, DOI: 10.1126/scisignal.aah4413, ISSN: 1937-9145.
Gierut JJ, Wood LB, Lau KS, Lin YJ, Genetti C, Samatar AA, Lauffenburger DA, Haigis KM. Network-level effects of kinase inhibitors modulate TNF-a-induced apoptosis in the intestinal epithelium. Sci Signal. 2015 Dec 12/15/2015; 8(407): ra129. PMID: 26671150, PMCID: PMC4812576, PII: 8/407/ra129, DOI: 10.1126/scisignal.aac7235, ISSN: 1937-9145.
Simmons AJ, Banerjee A, McKinley ET, Scurrah CR, Herring CA, Gewin LS, Masuzaki R, Karp SJ, Franklin JL, Gerdes MJ, Irish JM, Coffey RJ, Lau KS. Cytometry-based single-cell analysis of intact epithelial signaling reveals MAPK activation divergent from TNF-a-induced apoptosis in vivo. Mol. Syst. Biol. 2015 Oct; 11(10): 835. PMID: 26519361, PMCID: PMC4631206, ISSN: 1744-4292.
Lyons J, Herring CA, Banerjee A, Simmons AJ, Lau KS. Multiscale analysis of the murine intestine for modeling human diseases. Integr Biol (Camb). 2015 Jul; 7(7): 740-57. PMID: 26040649, PMCID: PMC4569017, DOI: 10.1039/c5ib00030k, ISSN: 1757-9708.
Lau KS, Schrier SB, Gierut J, Lyons J, Lauffenburger DA, Haigis KM. Network analysis of differential Ras isoform mutation effects on intestinal epithelial responses to TNF-a. Integr Biol (Camb) [print-electronic]. 2013 Nov; 5(11): 1355-65. PMID: 24084984, PMCID: PMC3966991, DOI: 10.1039/c3ib40062j, ISSN: 1757-9708.
Miraldi ER, Sharfi H, Friedline RH, Johnson H, Zhang T, Lau KS, Ko HJ, Curran TG, Haigis KM, Yaffe MB, Bonneau R, Lauffenburger DA, Kahn BB, Kim JK, Neel BG, Saghatelian A, White FM. Molecular network analysis of phosphotyrosine and lipid metabolism in hepatic PTP1b deletion mice. Integr Biol (Camb) [print-electronic]. 2013 Jul 7/24/2013; 5(7): 940-63. PMID: 23685806, PMCID: PMC3759823, DOI: 10.1039/c3ib40013a, ISSN: 1757-9708.
Lau KS, Cortez-Retamozo V, Philips SR, Pittet MJ, Lauffenburger DA, Haigis KM. Multi-scale in vivo systems analysis reveals the influence of immune cells on TNF-a-induced apoptosis in the intestinal epithelium. PLoS Biol [print-electronic]. 2012; 10(9): e1001393. PMID: 23055830, PMCID: PMC3463506, PII: PBIOLOGY-D-12-01984, DOI: 10.1371/journal.pbio.1001393, ISSN: 1545-7885.
Lau KS, Zhang T, Kendall KR, Lauffenburger D, Gray NS, Haigis KM. BAY61-3606 affects the viability of colon cancer cells in a genotype-directed manner. PLoS ONE [print-electronic]. 2012; 7(7): e41343. PMID: 22815993, PMCID: PMC3399817, PII: PONE-D-12-03440, DOI: 10.1371/journal.pone.0041343, ISSN: 1932-6203.
Lau KS, Juchheim AM, Cavaliere KR, Philips SR, Lauffenburger DA, Haigis KM. In vivo systems analysis identifies spatial and temporal aspects of the modulation of TNF-a-induced apoptosis and proliferation by MAPKs. Sci Signal. 2011; 4(165): ra16. PMID: 21427409, PMCID: PMC3963028, PII: 4/165/ra16, DOI: 10.1126/scisignal.2001338, ISSN: 1937-9145.
Mkhikian H, Grigorian A, Li CF, Chen HL, Newton B, Zhou RW, Beeton C, Torossian S, Tatarian GG, Lee SU, Lau K, Walker E, Siminovitch KA, Chandy KG, Yu Z, Dennis JW, Demetriou M. Genetics and the environment converge to dysregulate N-glycosylation in multiple sclerosis. Nat Commun. 2011; 2: 334. PMID: 21629267, PMCID: PMC3133923, PII: ncomms1333, DOI: 10.1038/ncomms1333, ISSN: 2041-1723.
Dennis JW, Lau KS, Demetriou M, Nabi IR. Adaptive regulation at the cell surface by N-glycosylation. Traffic [print-electronic]. 2009 Nov; 10(11): 1569-78. PMID: 19761541, PII: TRA981, DOI: 10.1111/j.1600-0854.2009.00981.x, ISSN: 1600-0854.
Lau KS, Haigis KM. Non-redundancy within the RAS oncogene family: insights into mutational disparities in cancer. Mol. Cells [print-electronic]. 2009 Oct 10/31/2009; 28(4): 315-20. PMID: 19812895, PMCID: PMC3976423, DOI: 10.1007/s10059-009-0143-7, ISSN: 0219-1032.
Lau KS, Dennis JW. N-Glycans in cancer progression. Glycobiology [print-electronic]. 2008 Oct; 18(10): 750-60. PMID: 18701722, PII: cwn071, DOI: 10.1093/glycob/cwn071, ISSN: 1460-2423.
Beheshti Zavareh R, Lau KS, Hurren R, Datti A, Ashline DJ, Gronda M, Cheung P, Simpson CD, Liu W, Wasylishen AR, Boutros PC, Shi H, Vengopal A, Jurisica I, Penn LZ, Reinhold VN, Ezzat S, Wrana J, Rose DR, Schachter H, Dennis JW, Schimmer AD. Inhibition of the sodium/potassium ATPase impairs N-glycan expression and function. Cancer Res. 2008 Aug 8/15/2008; 68(16): 6688-97. PMID: 18701493, PII: 68/16/6688, DOI: 10.1158/0008-5472.CAN-07-6833, ISSN: 1538-7445.
Lau KS, Khan S, Dennis JW. Genome-scale identification of UDP-GlcNAc-dependent pathways. Proteomics. 2008 Aug; 8(16): 3294-302. PMID: 18646010, DOI: 10.1002/pmic.200800208, ISSN: 1615-9861.
Katz D, Ito E, Lau KS, Mocanu JD, Bastianutto C, Schimmer AD, Liu FF. Increased efficiency for performing colony formation assays in 96-well plates: novel applications to combination therapies and high-throughput screening. BioTechniques. 2008 Feb; 44(2): ix-xiv. PMID: 18422490, PII: 000112757, DOI: 10.2144/000112757, ISSN: 0736-6205.
Mendelsohn R, Cheung P, Berger L, Partridge E, Lau K, Datti A, Pawling J, Dennis JW. Complex N-glycan and metabolic control in tumor cells. Cancer Res. 2007 Oct 10/15/2007; 67(20): 9771-80. PMID: 17942907, PII: 67/20/9771, DOI: 10.1158/0008-5472.CAN-06-4580, ISSN: 0008-5472.
Lau KS, Partridge EA, Grigorian A, Silvescu CI, Reinhold VN, Demetriou M, Dennis JW. Complex N-glycan number and degree of branching cooperate to regulate cell proliferation and differentiation. Cell. 2007 Apr 4/6/2007; 129(1): 123-34. PMID: 17418791, PII: S0092-8674(07)00315-7, DOI: 10.1016/j.cell.2007.01.049, ISSN: 0092-8674.
Cheung J, Estivill X, Khaja R, MacDonald JR, Lau K, Tsui LC, Scherer SW. Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence. Genome Biol [print-electronic]. 2003; 4(4): R25. PMID: 12702206, PMCID: PMC154576, ISSN: 1474-760X.
Lau, KS, Mantas, M, Chass, GA, Ferretti, FH, Estrada M, Zamarbide G, Csizmadia, IG.. Ab initio and DFT conformational analysis of selected flavones: 5,7-dihydroxyflavone (chrysin) and 7,8-dihydroxyflavone. 2002.
Xiong J, Kaur H, Heiser CN, McKinley ET, Roland JT, Coffey RJ, Shrubsole MJ, Wrobel J, Ma S, Lau KS, Vandekar S. GammaGateR: semi-automated marker gating for single-cell multiplexed imaging. Bioinformatics. 2024 Jun 6/3/2024; 40(6): PMID: 38833684, PMCID: PMC11193056, PII: 7687782, DOI: 10.1093/bioinformatics/btae356, ISSN: 1367-4811.
Contreras-Panta EW, Lee SH, Won Y, Norlander AE, Simmons AJ, Peebles RS, Lau KS, Choi E, Goldenring JR. Interleukin 13 Promotes Maturation and Proliferation in Metaplastic Gastroids. Cell Mol Gastroenterol Hepatol [print-electronic]. 2024 May 5/29/2024; 18(3): 101366. PMID: 38815928, PII: S2352-345X(24)00120-6, DOI: 10.1016/j.jcmgh.2024.101366, ISSN: 2352-345X.
Deng R, Cui C, Remedios LW, Bao S, Womick RM, Chiron S, Li J, Roland JT, Lau KS, Liu Q, Wilson KT, Wang Y, Coburn LA, Landman BA, Huo Y. Cross-scale multi-instance learning for pathological image diagnosis. Med Image Anal [print-electronic]. 2024 May; 94: 103124. PMID: 38428271, PMCID: PMC11016375, PII: S1361-8415(24)00049-5, DOI: 10.1016/j.media.2024.103124, ISSN: 1361-8423.
Chen Z, Guo X, Tao R, Huyghe JR, Law PJ, Fernandez-Rozadilla C, Ping J, Jia G, Long J, Li C, Shen Q, Xie Y, Timofeeva MN, Thomas M, Schmit SL, Díez-Obrero V, Devall M, Moratalla-Navarro F, Fernandez-Tajes J, Palles C, Sherwood K, Briggs SEW, Svinti V, Donnelly K, Farrington SM, Blackmur J, Vaughan-Shaw PG, Shu XO, Lu Y, Broderick P, Studd J, Harrison TA, Conti DV, Schumacher FR, Melas M, Rennert G, Obón-Santacana M, Martín-Sánchez V, Oh JH, Kim J, Jee SH, Jung KJ, Kweon SS, Shin MH, Shin A, Ahn YO, Kim DH, Oze I, Wen W, Matsuo K, Matsuda K, Tanikawa C, Ren Z, Gao YT, Jia WH, Hopper JL, Jenkins MA, Win AK, Pai RK, Figueiredo JC, Haile RW, Gallinger S, Woods MO, Newcomb PA, Duggan D, Cheadle JP, Kaplan R, Kerr R, Kerr D, Kirac I, Böhm J, Mecklin JP, Jousilahti P, Knekt P, Aaltonen LA, Rissanen H, Pukkala E, Eriksson JG, Cajuso T, Hänninen U, Kondelin J, Palin K, Tanskanen T, Renkonen-Sinisalo L, Männistö S, Albanes D, Weinstein SJ, Ruiz-Narvaez E, Palmer JR, Buchanan DD, Platz EA, Visvanathan K, Ulrich CM, Siegel E, Brezina S, Gsur A, Campbell PT, Chang-Claude J, Hoffmeister M, Brenner H, Slattery ML, Potter JD, Tsilidis KK, Schulze MB, Gunter MJ, Murphy N, Castells A, Castellví-Bel S, Moreira L, Arndt V, Shcherbina A, Bishop DT, Giles GG, Southey MC, Idos GE, McDonnell KJ, Abu-Ful Z, Greenson JK, Shulman K, Lejbkowicz F, Offit K, Su YR, Steinfelder R, Keku TO, van Guelpen B, Hudson TJ, Hampel H, Pearlman R, Berndt SI, Hayes RB, Martinez ME, Thomas SS, Pharoah PDP, Larsson SC, Yen Y, Lenz HJ, White E, Li L, Doheny KF, Pugh E, Shelford T, Chan AT, Cruz-Correa M, Lindblom A, Hunter DJ, Joshi AD, Schafmayer C, Scacheri PC, Kundaje A, Schoen RE, Hampe J, Stadler ZK, Vodicka P, Vodickova L, Vymetalkova V, Edlund CK, Gauderman WJ, Shibata D, Toland A, Markowitz S, Kim A, Chanock SJ, van Duijnhoven F, Feskens EJM, Sakoda LC, Gago-Dominguez M, Wolk A, Pardini B, FitzGerald LM, Lee SC, Ogino S, Bien SA, Kooperberg C, Li CI, Lin Y, Prentice R, Qu C, Bézieau S, Yamaji T, Sawada N, Iwasaki M, Le Marchand L, Wu AH, Qu C, McNeil CE, Coetzee G, Hayward C, Deary IJ, Harris SE, Theodoratou E, Reid S, Walker M, Ooi LY, Lau KS, Zhao H, Hsu L, Cai Q, Dunlop MG, Gruber SB, Houlston RS, Moreno V, Casey G, Peters U, Tomlinson I, Zheng W. Fine-mapping analysis including over 254,000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes. Nat Commun. 2024 Apr 4/26/2024; 15(1): 3557. PMID: 38670944, PMCID: PMC11053150, PII: 10.1038/s41467-024-47399-x, DOI: 10.1038/s41467-024-47399-x, ISSN: 2041-1723.
Stangis MM, Chen Z, Min J, Glass SE, Jackson JO, Radyk MD, Hoi XP, Brennen WN, Yu M, Dinh HQ, Coffey RJ, Shrubsole MJ, Chan KS, Grady WM, Yegnasubramanian S, Lyssiotis CA, Maitra A, Halberg RB, Dey N, Lau KS. The Hallmarks of Precancer. Cancer Discov. 2024 Apr 4/4/2024; 14(4): 683-9. PMID: 38571435, PMCID: PMC11170686, PII: 741985, DOI: 10.1158/2159-8290.CD-23-1550, ISSN: 2159-8290.
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Grabski IN, Heymach JV, Kehl KL, Kopetz S, Lau KS, Riely GJ, Schrag D, Yaeger R, Irizarry RA, Haigis KM. Effects of KRAS Genetic Interactions on Outcomes in Cancers of the Lung, Pancreas, and Colorectum. Cancer Epidemiol Biomarkers Prev. 2024 Jan 1/9/2024; 33(1): 158-69. PMID: 37943166, PMCID: PMC10841605, PII: 730073, DOI: 10.1158/1055-9965.EPI-23-0262, ISSN: 1538-7755.
Bao S, Lee HH, Yang Q, Remedios LW, Deng R, Cui C, Cai LY, Xu K, Yu X, Chiron S, Li Y, Patterson NH, Wang Y, Li J, Liu Q, Lau KS, Roland JT, Coburn LA, Wilson KT, Landman BA, Huo Y. Alleviating tiling effect by random walk sliding window in high-resolution histological whole slide image synthesis. Proc Mach Learn Res. 2024; 227: 1406-22. PMID: 38993526, PMCID: PMC11238901, ISSN: 2640-3498.
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Cui C, Wang Y, Bao S, Tang Y, Deng R, Remedios LW, Asad Z, Roland JT, Lau KS, Liu Q, Coburn LA, Wilson KT, Landman BA, Huo Y. Feasibility of Universal Anomaly Detection without Knowing the Abnormality in Medical Images. Med Image Learn Ltd Noisy Data (2023) [print-electronic]. 2023 Oct; 14307: 82-92. PMID: 38523773, PMCID: PMC10959499, DOI: 10.1007/978-3-031-44917-8_8.
Chen Z, Lau KS. Advances in Mapping Tumor Progression from Precancer Atlases. Cancer Prev Res (Phila). 2023 Aug 8/1/2023; 16(8): 439-47. PMID: 37167978, PII: 726356, DOI: 10.1158/1940-6207.CAPR-22-0473, ISSN: 1940-6215.
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Arceneaux D, Chen Z, Simmons AJ, Heiser CN, Southard-Smith AN, Brenan MJ, Yang Y, Chen B, Xu Y, Choi E, Campbell JD, Liu Q, Lau KS. A contamination focused approach for optimizing the single-cell RNA-seq experiment. IScience. 2023 Jul 7/21/2023; 26(7): 107242. PMID: 37496679, PMCID: PMC10366499, PII: S2589-0042(23)01319-6, DOI: 10.1016/j.isci.2023.107242, ISSN: 2589-0042.
Shui B, Beyett TS, Chen Z, Li X, La Rocca G, Gazlay WM, Eck MJ, Lau KS, Ventura A, Haigis KM. Oncogenic K-Ras suppresses global miRNA function. Mol Cell [print-electronic]. 2023 Jul 7/20/2023; 83(14): 2509-2523.e13-2523.e13. PMID: 37402366, PII: S1097-2765(23)00429-X, DOI: 10.1016/j.molcel.2023.06.008, ISSN: 1097-4164.
Pilat JM, Brown RE, Chen Z, Berle NJ, Othon AP, Washington MK, Anant SA, Kurokawa S, Ng VH, Thompson JJ, Jacobse J, Goettel JA, Lee E, Choksi YA, Lau KS, Short SP, Williams CS. SELENOP modifies sporadic colorectal carcinogenesis and WNT signaling activity through LRP5/6 interactions. J Clin Invest. 2023 Jul 7/3/2023; 133(13): PMID: 37166989, PMCID: PMC10313376, PII: 165988, DOI: 10.1172/JCI165988, ISSN: 1558-8238.
Taufalele PV, Wang W, Simmons AJ, Southard-Smith AN, Chen B, Greenlee JD, King MR, Lau KS, Hassane DC, Bordeleau F, Reinhart-King CA. Matrix stiffness enhances cancer-macrophage interactions and M2-like macrophage accumulation in the breast tumor microenvironment. Acta Biomater [print-electronic]. 2023 Jun; 163: 365-77. PMID: 35483629, PMCID: PMC9592676, PII: S1742-7061(22)00240-9, DOI: 10.1016/j.actbio.2022.04.031, ISSN: 1878-7568.
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Remedios LW, Bao S, Kerley CI, Cai LY, Rheault F, Deng R, Cui C, Chiron S, Lau KS, Roland JT, Washington MK, Coburn LA, Wilson KT, Huo Y, Landman BA. Predicting Crohn's disease severity in the colon using mixed cell nucleus density from pseudo labels. Proc SPIE Int Soc Opt Eng [print-electronic]. 2023 Feb; 12471: PMID: 37465840, PMCID: PMC10353830, PII: 1247116, DOI: 10.1117/12.2653918, ISSN: 0277-786X.
Cui C, Bao S, Li J, Deng R, Remedios LW, Asad Z, Chiron S, Lau KS, Wang Y, Coburn LA, Wilson KT, Roland JT, Landman BA, Liu Q, Huo Y. Influence of Cell-type Ratio on Spatially Resolved Single-cell Transcriptomes using the Tangram Algorithm: Based on Implementation on Single-Cell and MxIF Data. Proc SPIE Int Soc Opt Eng [print-electronic]. 2023 Feb; 12471: PMID: 37324550, PMCID: PMC10270698, PII: 124710A, ISSN: 0277-786X.
Bao S, Cui C, Li J, Tang Y, Lee HH, Deng R, Remedios LW, Yu X, Yang Q, Chiron S, Patterson NH, Lau KS, Liu Q, Roland JT, Coburn LA, Wilson KT, Landman BA, Huo Y. Topological-Preserving Membrane Skeleton Segmentation in Multiplex Immunofluorescence Imaging. Proc SPIE Int Soc Opt Eng [print-electronic]. 2023 Feb; 12471: PMID: 37786583, PMCID: PMC10545297, PII: 124710B, DOI: 10.1117/12.2654087, ISSN: 0277-786X.
Lin JR, Wang S, Coy S, Chen YA, Yapp C, Tyler M, Nariya MK, Heiser CN, Lau KS, Santagata S, Sorger PK. Multiplexed 3D atlas of state transitions and immune interaction in colorectal cancer. Cell. 2023 Jan 1/19/2023; 186(2): 363-381.e19-381.e19. PMID: 36669472, PMCID: PMC10019067, PII: S0092-8674(22)01571-9, DOI: 10.1016/j.cell.2022.12.028, ISSN: 1097-4172.
Min J, Zhang C, Bliton RJ, Caldwell B, Caplan L, Presentation KS, Park DJ, Kong SH, Lee HS, Washington MK, Kim WH, Lau KS, Magness ST, Lee HJ, Yang HK, Goldenring JR, Choi E. Dysplastic Stem Cell Plasticity Functions as a Driving Force for Neoplastic Transformation of Precancerous Gastric Mucosa. Gastroenterology [print-electronic]. 2022 Oct; 163(4): 875-90. PMID: 35700772, PMCID: PMC9509466, PII: S0016-5085(22)00626-6, DOI: 10.1053/j.gastro.2022.06.021, ISSN: 1528-0012.
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Simmons AJ, Lau KS. Dissociation and inDrops microfluidic encapsulation of human gut tissues for single-cell atlasing studies. STAR Protoc. 2022 Sep 9/16/2022; 3(3): 101570. PMID: 35880121, PMCID: PMC9307676, PII: S2666-1667(22)00450-6, DOI: 10.1016/j.xpro.2022.101570, ISSN: 2666-1667.
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Drewes JL, Chen J, Markham NO, Knippel RJ, Domingue JC, Tam AJ, Chan JL, Kim L, McMann M, Stevens C, Dejea CM, Tomkovich S, Michel J, White JR, Mohammad F, Campodónico VL, Heiser CN, Wu X, Wu S, Ding H, Simner P, Carroll K, Shrubsole MJ, Anders RA, Walk ST, Jobin C, Wan F, Coffey RJ, Housseau F, Lau KS, Sears CL. Human Colon Cancer-Derived Clostridioides difficile Strains Drive Colonic Tumorigenesis in Mice. Cancer Discov. 2022 Aug 8/5/2022; 12(8): 1873-85. PMID: 35678528, PMCID: PMC9357196, PII: 700781, DOI: 10.1158/2159-8290.CD-21-1273, ISSN: 2159-8290.
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McKinley ET, Shao J, Ellis ST, Heiser CN, Roland JT, Macedonia MC, Vega PN, Shin S, Coffey RJ, Lau KS. MIRIAM: A machine and deep learning single-cell segmentation and quantification pipeline for multi-dimensional tissue images. Cytometry A [print-electronic]. 2022 Jan 1/27/2022; PMID: 35084791, DOI: 10.1002/cyto.a.24541, ISSN: 1552-4930.
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Vega PN, Nilsson A, Kumar MP, Niitsu H, Simmons AJ, Ro J, Wang J, Chen Z, Joughin BA, Li W, McKinley ET, Liu Q, Roland JT, Washington MK, Coffey RJ, Lauffenburger DA, Lau KS. Cancer-Associated Fibroblasts and Squamous Epithelial Cells Constitute a Unique Microenvironment in a Mouse Model of Inflammation-Induced Colon Cancer. Front Oncol. 2022; 12: 878920. PMID: 35600339, PMCID: PMC9114773, DOI: 10.3389/fonc.2022.878920, ISSN: 2234-943X.
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Rolong A, Chen B, Lau KS. Deciphering the cancer microenvironment from bulk data with EcoTyper. Cell. 2021 Oct 10/14/2021; 184(21): 5306-8. PMID: 34653367, PMCID: PMC8655686, PII: S0092-8674(21)01111-9, DOI: 10.1016/j.cell.2021.09.028, ISSN: 1097-4172.
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May-Zhang AA, Tycksen E, Southard-Smith AN, Deal KK, Benthal JT, Buehler DP, Adam M, Simmons AJ, Monaghan JR, Matlock BK, Flaherty DK, Potter SS, Lau KS, Southard-Smith EM. Combinatorial Transcriptional Profiling of Mouse and Human Enteric Neurons Identifies Shared and Disparate Subtypes In Situ. Gastroenterology [print-electronic]. 2021 Feb; 160(3): 755-770.e26. PMID: 33010250, PMCID: PMC7878294, PII: S0016-5085(20)35213-6, DOI: 10.1053/j.gastro.2020.09.032, ISSN: 1528-0012.
Bao S, Chiron S, Tang Y, Heiser CN, Southard-Smith AN, Lee HH, Ramirez MA, Huo Y, Washington MK, Scoville EA, Roland JT, Liu Q, Lau KS, Wilson KT, Coburn LA, Landman BA. A cross-platform informatics system for the Gut Cell Atlas: integrating clinical, anatomical and histological data. Proc SPIE Int Soc Opt Eng [print-electronic]. 2021; 11601: PMID: 34539029, PMCID: PMC8445503, DOI: 10.1117/12.2581074, ISSN: 0277-786X.
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Macedonia MC, Drewes JL, Markham NO, Simmons AJ, Roland JT, Vega PN, Scurrah CR, Coffey RJ, Shrubsole MJ, Sears CL, Lau KS. Clinically adaptable polymer enables simultaneous spatial analysis of colonic tissues and biofilms. NPJ Biofilms Microbiomes. 2020 Sep 9/24/2020; 6(1): 33. PMID: 32973205, PMCID: PMC7518420, PII: 10.1038/s41522-020-00143-x, DOI: 10.1038/s41522-020-00143-x, ISSN: 2055-5008.
Brubaker DK, Kumar MP, Chiswick EL, Gregg C, Starchenko A, Vega PN, Southard-Smith AN, Simmons AJ, Scoville EA, Coburn LA, Wilson KT, Lau KS, Lauffenburger DA. An interspecies translation model implicates integrin signaling in infliximab-resistant inflammatory bowel disease. Sci Signal. 2020 Aug 8/4/2020; 13(643): PMID: 32753478, PII: 13/643/eaay3258, DOI: 10.1126/scisignal.aay3258, ISSN: 1937-9145.
Southard-Smith AN, Simmons AJ, Chen B, Jones AL, Ramirez Solano MA, Vega PN, Scurrah CR, Zhao Y, Brenan MJ, Xuan J, Shrubsole MJ, Porter EB, Chen X, Brenan CJH, Liu Q, Quigley LNM, Lau KS. Dual indexed library design enables compatibility of in-Drop single-cell RNA-sequencing with exAMP chemistry sequencing platforms. BMC Genomics. 2020 Jul 7/2/2020; 21(1): 456. PMID: 32616006, PMCID: PMC7331155, PII: 10.1186/s12864-020-06843-0, DOI: 10.1186/s12864-020-06843-0, ISSN: 1471-2164.
Yang X, Graff SM, Heiser CN, Ho KH, Chen B, Simmons AJ, Southard-Smith AN, David G, Jacobson DA, Kaverina I, Wright CVE, Lau KS, Gu G. Coregulator Sin3a Promotes Postnatal Murine ß-Cell Fitness by Regulating Genes in Ca2+ Homeostasis, Cell Survival, Vesicle Biosynthesis, Glucose Metabolism, and Stress Response. Diabetes [print-electronic]. 2020 Jun; 69(6): 1219-31. PMID: 32245798, PMCID: PMC7243292, PII: db19-0721, DOI: 10.2337/db19-0721, ISSN: 1939-327X.
Islam M, Chen B, Spraggins JM, Kelly RT, Lau KS. Use of Single-Cell -Omic Technologies to Study the Gastrointestinal Tract and Diseases, From Single Cell Identities to Patient Features. Gastroenterology [print-electronic]. 2020 May 5/14/2020; PMID: 32417404, PII: S0016-5085(20)30656-9, DOI: 10.1053/j.gastro.2020.04.073, ISSN: 1528-0012.
Heiser CN, Lau KS. A Quantitative Framework for Evaluating Single-Cell Data Structure Preservation by Dimensionality Reduction Techniques. Cell Rep. 2020 May 5/5/2020; 31(5): 107576. PMID: 32375029, PMCID: PMC7305633, PII: S2211-1247(20)30525-8, DOI: 10.1016/j.celrep.2020.107576, ISSN: 2211-1247.
Rozenblatt-Rosen O, Regev A, Oberdoerffer P, Nawy T, Hupalowska A, Rood JE, Ashenberg O, Cerami E, Coffey RJ, Demir E, Ding L, Esplin ED, Ford JM, Goecks J, Ghosh S, Gray JW, Guinney J, Hanlon SE, Hughes SK, Hwang ES, Iacobuzio-Donahue CA, Jané-Valbuena J, Johnson BE, Lau KS, Lively T, Mazzilli SA, Pe'er D, Santagata S, Shalek AK, Schapiro D, Snyder MP, Sorger PK, Spira AE, Srivastava S, Tan K, West RB, Williams EH, . The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution. Cell. 2020 Apr 4/16/2020; 181(2): 236-49. PMID: 32302568, PMCID: PMC7376497, PII: S0092-8674(20)30346-9, DOI: 10.1016/j.cell.2020.03.053, ISSN: 1097-4172.
Liu Q, Sheng Q, Ping J, Ramirez MA, Lau KS, Coffey RJ, Shyr Y. ScRNABatchQC: multi-samples quality control for single cell RNA-seq data. Bioinformatics. 2019 Dec 12/15/2019; 35(24): 5306-8. PMID: 31373345, PMCID: PMC6954654, PII: 5542946, DOI: 10.1093/bioinformatics/btz601, ISSN: 1367-4811.
Min J, Vega PN, Engevik AC, Williams JA, Yang Q, Patterson LM, Simmons AJ, Bliton RJ, Betts JW, Lau KS, Magness ST, Goldenring JR, Choi E. Heterogeneity and dynamics of active Kras-induced dysplastic lineages from mouse corpus stomach. Nat Commun. 2019 Dec 12/5/2019; 10(1): 5549. PMID: 31804471, PMCID: PMC6895174, PII: 10.1038/s41467-019-13479-6, DOI: 10.1038/s41467-019-13479-6, ISSN: 2041-1723.
Vasaikar S, Huang C, Wang X, Petyuk VA, Savage SR, Wen B, Dou Y, Zhang Y, Shi Z, Arshad OA, Gritsenko MA, Zimmerman LJ, McDermott JE, Clauss TR, Moore RJ, Zhao R, Monroe ME, Wang YT, Chambers MC, Slebos RJC, Lau KS, Mo Q, Ding L, Ellis M, Thiagarajan M, Kinsinger CR, Rodriguez H, Smith RD, Rodland KD, Liebler DC, Liu T, Zhang B, . Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities. Cell [print-electronic]. 2019 May 5/2/2019; 177(4): 1035-1049.e19. PMID: 31031003, PII: S0092-8674(19)30292-2, DOI: 10.1016/j.cell.2019.03.030, ISSN: 1097-4172.
Howard AM, LaFever KS, Fenix AM, Scurrah CR, Lau KS, Burnette DT, Bhave G, Ferrell N, Page-McCaw A. DSS-induced damage to basement membranes is repaired by matrix replacement and crosslinking. J. Cell. Sci [print-electronic]. 2019 Mar 3/5/2019; PMID: 30837285, PII: jcs.226860, DOI: 10.1242/jcs.226860, ISSN: 1477-9137.
Manolopoulou M, Matlock BK, Nlandu Khodo S, Simmons AJ, Lau KS, Phillips-Mignemi M, Ivanova A, Alford CE, Flaherty DK, Gewin LS. Novel kidney dissociation protocol and image-based flow cytometry facilitate improved analysis of injured proximal tubules. Am. J. Physiol. Renal Physiol [print-electronic]. 2019 Feb 2/13/2019; PMID: 30759021, DOI: 10.1152/ajprenal.00354.2018, ISSN: 1522-1466.
Foegeding NJ, Raghunathan K, Campbell AM, Kim SW, Lau KS, Kenworthy AK, Cover TL, Ohi MD. Intracellular degradation of Helicobacter pylori VacA toxin as a determinant of gastric epithelial cell viability. Infect. Immun [print-electronic]. 2019 Jan 1/28/2019; PMID: 30692181, PII: IAI.00783-18, DOI: 10.1128/IAI.00783-18, ISSN: 1098-5522.
Vega PN, Lau KS, Goldenring JR. Not All Insults Are Created Equal for Awakening Dormant Stem Cell Abilities [editorial]. Cell Mol Gastroenterol Hepatol [print-electronic]. 2019 Jan 1/7/2019; PMID: 30629924, PII: S2352-345X(18)30178-4, DOI: 10.1016/j.jcmgh.2018.12.003, ISSN: 2352-345X.
Liu J, Banerjee A, Herring CA, Attalla J, Hu R, Xu Y, Shao Q, Simmons AJ, Dadi PK, Wang S, Jacobson DA, Liu B, Hodges E, Lau KS, Gu G. Neurog3-Independent Methylation Is the Earliest Detectable Mark Distinguishing Pancreatic Progenitor Identity. Dev. Cell. 2019 Jan 1/7/2019; 48(1): 49-63.e7. PMID: 30620902, PMCID: PMC6327977, PII: S1534-5807(18)31032-3, DOI: 10.1016/j.devcel.2018.11.048, ISSN: 1878-1551.
Scurrah CR, Simmons AJ, Lau KS. Single-Cell Mass Cytometry of Archived Human Epithelial Tissue for Decoding Cancer Signaling Pathways. Methods Mol. Biol. 2019; 1884: 215-29. PMID: 30465206, DOI: 10.1007/978-1-4939-8885-3_15, ISSN: 1940-6029.
Chen B, Herring CA, Lau KS. PyNVR: Investigating factors affecting feature selection from scRNA-seq data for lineage reconstruction. Bioinformatics [print-electronic]. 2018 Nov 11/16/2018; PMID: 30445607, PII: 5184958, DOI: 10.1093/bioinformatics/bty950, ISSN: 1367-4811.
Liu Q, Herring CA, Sheng Q, Ping J, Simmons AJ, Chen B, Banerjee A, Li W, Gu G, Coffey RJ, Shyr Y, Lau KS. Quantitative assessment of cell population diversity in single-cell landscapes. PLoS Biol. 2018 Oct; 16(10): e2006687. PMID: 30346945, PMCID: PMC6211764, PII: pbio.2006687, DOI: 10.1371/journal.pbio.2006687, ISSN: 1545-7885.
Banerjee A, McKinley ET, von Moltke J, Coffey RJ, Lau KS. Interpreting heterogeneity in intestinal tuft cell structure and function. J. Clin. Invest [print-electronic]. 2018 May 5/1/2018; 128(5): 1711-9. PMID: 29714721, PMCID: PMC5919882, PII: 120330, DOI: 10.1172/JCI120330, ISSN: 1558-8238.
Herring CA, Banerjee A, McKinley ET, Simmons AJ, Ping J, Roland JT, Franklin JL, Liu Q, Gerdes MJ, Coffey RJ, Lau KS. Unsupervised Trajectory Analysis of Single-Cell RNA-Seq and Imaging Data Reveals Alternative Tuft Cell Origins in the Gut. Cell Syst [print-electronic]. 2018 Jan 1/24/2018; 6(1): 37-51.e9. PMID: 29153838, PMCID: PMC5799016, PII: S2405-4712(17)30449-0, DOI: 10.1016/j.cels.2017.10.012, ISSN: 2405-4712.
Herring CA, Chen B, McKinley ET, Lau KS. Single-Cell Computational Strategies for Lineage Reconstruction in Tissue Systems. Cell Mol Gastroenterol Hepatol. 2018; 5(4): 539-48. PMID: 29713661, PMCID: PMC5924749, PII: S2352-345X(18)30031-6, DOI: 10.1016/j.jcmgh.2018.01.023, ISSN: 2352-345X.
Maseda D, Banerjee A, Johnson EM, Washington MK, Kim H, Lau KS, Crofford LJ. MPGES-1-Mediated Production of PGE2 and EP4 Receptor Sensing Regulate T Cell Colonic Inflammation. Front Immunol. 2018; 9: 2954. PMID: 30619314, PMCID: PMC6302013, DOI: 10.3389/fimmu.2018.02954, ISSN: 1664-3224.
Kim SW, Ehrman J, Ahn MR, Kondo J, Lopez AAM, Oh YS, Kim XH, Crawley SW, Goldenring JR, Tyska MJ, Rericha EC, Lau KS. Shear stress induces noncanonical autophagy in intestinal epithelial monolayers. Mol. Biol. Cell [print-electronic]. 2017 Nov 11/1/2017; 28(22): 3043-56. PMID: 28855375, PMCID: PMC5662261, PII: mbc.E17-01-0021, DOI: 10.1091/mbc.E17-01-0021, ISSN: 1939-4586.
McKinley ET, Sui Y, Al-Kofahi Y, Millis BA, Tyska MJ, Roland JT, Santamaria-Pang A, Ohland CL, Jobin C, Franklin JL, Lau KS, Gerdes MJ, Coffey RJ. Optimized multiplex immunofluorescence single-cell analysis reveals tuft cell heterogeneity. JCI Insight [print-electronic]. 2017 Jun 6/2/2017; 2(11): PMID: 28570279, PMCID: PMC5453701, PII: 93487, DOI: 10.1172/jci.insight.93487, ISSN: 2379-3708.
Almohazey D, Lo YH, Vossler CV, Simmons AJ, Hsieh JJ, Bucar EB, Schumacher MA, Hamilton KE, Lau KS, Shroyer NF, Frey MR. The ErbB3 receptor tyrosine kinase negatively regulates Paneth cells by PI3K-dependent suppression of Atoh1. Cell Death Differ [print-electronic]. 2017 May; 24(5): 855-65. PMID: 28304405, PMCID: PMC5423110, PII: cdd201727, DOI: 10.1038/cdd.2017.27, ISSN: 1476-5403.
Simmons AJ, Lau KS. Deciphering tumor heterogeneity from FFPE tissues: Its promise and challenges. Mol Cell Oncol. 2017; 4(1): e1260191. PMID: 28197533, PMCID: PMC5286981, PII: 1260191, DOI: 10.1080/23723556.2016.1260191, ISSN: 2372-3556.
Simmons AJ, Scurrah CR, McKinley ET, Herring CA, Irish JM, Washington MK, Coffey RJ, Lau KS. Impaired coordination between signaling pathways is revealed in human colorectal cancer using single-cell mass cytometry of archival tissue blocks. Sci Signal. 2016 Oct 10/11/2016; 9(449): rs11. PMID: 27729552, PII: 9/449/rs11, DOI: 10.1126/scisignal.aah4413, ISSN: 1937-9145.
Gierut JJ, Wood LB, Lau KS, Lin YJ, Genetti C, Samatar AA, Lauffenburger DA, Haigis KM. Network-level effects of kinase inhibitors modulate TNF-a-induced apoptosis in the intestinal epithelium. Sci Signal. 2015 Dec 12/15/2015; 8(407): ra129. PMID: 26671150, PMCID: PMC4812576, PII: 8/407/ra129, DOI: 10.1126/scisignal.aac7235, ISSN: 1937-9145.
Simmons AJ, Banerjee A, McKinley ET, Scurrah CR, Herring CA, Gewin LS, Masuzaki R, Karp SJ, Franklin JL, Gerdes MJ, Irish JM, Coffey RJ, Lau KS. Cytometry-based single-cell analysis of intact epithelial signaling reveals MAPK activation divergent from TNF-a-induced apoptosis in vivo. Mol. Syst. Biol. 2015 Oct; 11(10): 835. PMID: 26519361, PMCID: PMC4631206, ISSN: 1744-4292.
Lyons J, Herring CA, Banerjee A, Simmons AJ, Lau KS. Multiscale analysis of the murine intestine for modeling human diseases. Integr Biol (Camb). 2015 Jul; 7(7): 740-57. PMID: 26040649, PMCID: PMC4569017, DOI: 10.1039/c5ib00030k, ISSN: 1757-9708.
Lau KS, Schrier SB, Gierut J, Lyons J, Lauffenburger DA, Haigis KM. Network analysis of differential Ras isoform mutation effects on intestinal epithelial responses to TNF-a. Integr Biol (Camb) [print-electronic]. 2013 Nov; 5(11): 1355-65. PMID: 24084984, PMCID: PMC3966991, DOI: 10.1039/c3ib40062j, ISSN: 1757-9708.
Miraldi ER, Sharfi H, Friedline RH, Johnson H, Zhang T, Lau KS, Ko HJ, Curran TG, Haigis KM, Yaffe MB, Bonneau R, Lauffenburger DA, Kahn BB, Kim JK, Neel BG, Saghatelian A, White FM. Molecular network analysis of phosphotyrosine and lipid metabolism in hepatic PTP1b deletion mice. Integr Biol (Camb) [print-electronic]. 2013 Jul 7/24/2013; 5(7): 940-63. PMID: 23685806, PMCID: PMC3759823, DOI: 10.1039/c3ib40013a, ISSN: 1757-9708.
Lau KS, Cortez-Retamozo V, Philips SR, Pittet MJ, Lauffenburger DA, Haigis KM. Multi-scale in vivo systems analysis reveals the influence of immune cells on TNF-a-induced apoptosis in the intestinal epithelium. PLoS Biol [print-electronic]. 2012; 10(9): e1001393. PMID: 23055830, PMCID: PMC3463506, PII: PBIOLOGY-D-12-01984, DOI: 10.1371/journal.pbio.1001393, ISSN: 1545-7885.
Lau KS, Zhang T, Kendall KR, Lauffenburger D, Gray NS, Haigis KM. BAY61-3606 affects the viability of colon cancer cells in a genotype-directed manner. PLoS ONE [print-electronic]. 2012; 7(7): e41343. PMID: 22815993, PMCID: PMC3399817, PII: PONE-D-12-03440, DOI: 10.1371/journal.pone.0041343, ISSN: 1932-6203.
Lau KS, Juchheim AM, Cavaliere KR, Philips SR, Lauffenburger DA, Haigis KM. In vivo systems analysis identifies spatial and temporal aspects of the modulation of TNF-a-induced apoptosis and proliferation by MAPKs. Sci Signal. 2011; 4(165): ra16. PMID: 21427409, PMCID: PMC3963028, PII: 4/165/ra16, DOI: 10.1126/scisignal.2001338, ISSN: 1937-9145.
Mkhikian H, Grigorian A, Li CF, Chen HL, Newton B, Zhou RW, Beeton C, Torossian S, Tatarian GG, Lee SU, Lau K, Walker E, Siminovitch KA, Chandy KG, Yu Z, Dennis JW, Demetriou M. Genetics and the environment converge to dysregulate N-glycosylation in multiple sclerosis. Nat Commun. 2011; 2: 334. PMID: 21629267, PMCID: PMC3133923, PII: ncomms1333, DOI: 10.1038/ncomms1333, ISSN: 2041-1723.
Dennis JW, Lau KS, Demetriou M, Nabi IR. Adaptive regulation at the cell surface by N-glycosylation. Traffic [print-electronic]. 2009 Nov; 10(11): 1569-78. PMID: 19761541, PII: TRA981, DOI: 10.1111/j.1600-0854.2009.00981.x, ISSN: 1600-0854.
Lau KS, Haigis KM. Non-redundancy within the RAS oncogene family: insights into mutational disparities in cancer. Mol. Cells [print-electronic]. 2009 Oct 10/31/2009; 28(4): 315-20. PMID: 19812895, PMCID: PMC3976423, DOI: 10.1007/s10059-009-0143-7, ISSN: 0219-1032.
Lau KS, Dennis JW. N-Glycans in cancer progression. Glycobiology [print-electronic]. 2008 Oct; 18(10): 750-60. PMID: 18701722, PII: cwn071, DOI: 10.1093/glycob/cwn071, ISSN: 1460-2423.
Beheshti Zavareh R, Lau KS, Hurren R, Datti A, Ashline DJ, Gronda M, Cheung P, Simpson CD, Liu W, Wasylishen AR, Boutros PC, Shi H, Vengopal A, Jurisica I, Penn LZ, Reinhold VN, Ezzat S, Wrana J, Rose DR, Schachter H, Dennis JW, Schimmer AD. Inhibition of the sodium/potassium ATPase impairs N-glycan expression and function. Cancer Res. 2008 Aug 8/15/2008; 68(16): 6688-97. PMID: 18701493, PII: 68/16/6688, DOI: 10.1158/0008-5472.CAN-07-6833, ISSN: 1538-7445.
Lau KS, Khan S, Dennis JW. Genome-scale identification of UDP-GlcNAc-dependent pathways. Proteomics. 2008 Aug; 8(16): 3294-302. PMID: 18646010, DOI: 10.1002/pmic.200800208, ISSN: 1615-9861.
Katz D, Ito E, Lau KS, Mocanu JD, Bastianutto C, Schimmer AD, Liu FF. Increased efficiency for performing colony formation assays in 96-well plates: novel applications to combination therapies and high-throughput screening. BioTechniques. 2008 Feb; 44(2): ix-xiv. PMID: 18422490, PII: 000112757, DOI: 10.2144/000112757, ISSN: 0736-6205.
Mendelsohn R, Cheung P, Berger L, Partridge E, Lau K, Datti A, Pawling J, Dennis JW. Complex N-glycan and metabolic control in tumor cells. Cancer Res. 2007 Oct 10/15/2007; 67(20): 9771-80. PMID: 17942907, PII: 67/20/9771, DOI: 10.1158/0008-5472.CAN-06-4580, ISSN: 0008-5472.
Lau KS, Partridge EA, Grigorian A, Silvescu CI, Reinhold VN, Demetriou M, Dennis JW. Complex N-glycan number and degree of branching cooperate to regulate cell proliferation and differentiation. Cell. 2007 Apr 4/6/2007; 129(1): 123-34. PMID: 17418791, PII: S0092-8674(07)00315-7, DOI: 10.1016/j.cell.2007.01.049, ISSN: 0092-8674.
Cheung J, Estivill X, Khaja R, MacDonald JR, Lau K, Tsui LC, Scherer SW. Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence. Genome Biol [print-electronic]. 2003; 4(4): R25. PMID: 12702206, PMCID: PMC154576, ISSN: 1474-760X.
Lau, KS, Mantas, M, Chass, GA, Ferretti, FH, Estrada M, Zamarbide G, Csizmadia, IG.. Ab initio and DFT conformational analysis of selected flavones: 5,7-dihydroxyflavone (chrysin) and 7,8-dihydroxyflavone. 2002.