2024
Islam M, Yang Y, Simmons AJ, Shah V, Pavan Musale K, Xu Y, Tasneem N, Chen Z, Trinh LT, Molina P, Ramirez-Solano MA, Sadien I, Dou J, Rolong A, Chen K, Magnuson MA, Rathmell JC, Macara IG, Winton DJ, Liu Q, Zafar H, Kalhor R, Church GM, Shrubsole MJ, Coffey RJ*, Lau KS*. Temporal recording of mammalian development and precancer. Nature, 634 (8036): 1187–1195, 2024. * Corresponding Authors
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 X, Lyssiotis CA, Maitra A, Halberg RB, Dey N*, Lau KS*. The Hallmarks of Precancer. Cancer Discovery, 14(4):683-689, 2024. * Corresponding Authors
Kaur H, Heiser CN, McKinley ET, Ventura-Antunes L, Harris CR, Roland JT, Farrow MA, Selden HJ, Pingry EL, Moore JF, Ehrlich LIR, Shrubsole MJ, Spraggins JM, Coffey RJ, Lau KS*, Vandekar SN*. Consensus tissue domain detection in spatial omics data using multiplex image labeling with regional morphology (MILWRM). Communications Biology, 7 (1): 1295, 2024. * Corresponding Authors
Silverman JB, Vega PN, Tyska MJ*, Lau KS*. Intestinal Tuft Cells: Morphology, Function, and Implications for Human Health. Annual Reviews of Physiology, 86:479-504, 2024. * Corresponding Authors
Li J, Simmons AJ, Chiron S, Ramirez-Solano MA, Tasneem N, Kaur H, Xu Y, Revetta F, Vega PN, Bao S, Cui C, Tyree RN, Raber LW, Conner AN, Beaulieu DB, Dalal RL, Horst SN, Pabla BS, Huo Y, Landman BA, Roland JT, Scoville EA, Schwartz DA, Washington MK, Shyr Y, Wilson KT*, Coburn LA*, Lau KS*, Liu Q*. A Specialized Epithelial Cell Type Regulating Mucosal Immunity and Driving Human Crohn’s Disease. Nature Communications, 15(1):7204, 2024. * Corresponding Authors
Kjar A, Haschert MR, Zepeda JC, Simmons AJ, Yates A, Chavarria D, Fernandez M, Robertson G, Abdulrahman AM, Kim H, Marguerite NT, Moen RK, Drake LE, Curry CW, O’Grady BJ, Gama V, Lau KS, Grueter B, Brunger JM, Lippmann ES. Biofunctionalized gelatin hydrogels support development and maturation of iPSC-derived cortical organoids. Cell Reports , 43(11):114874, 2024.
Silverman JB, Krystofiak EE, Caplan LR, Lau KS, Tyska MJ. Organization of a cytoskeletal superstructure in the apical domain of intestinal tuft cells. Journal of Cell Biology, 223(12):e202404070,2024.
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, Epidemiology Biomarkers and Prevention, 33(1):158-169, 2024.
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 and Differentiation, 31(9):1170-1183, 2024.
Contreras-Panta EW, Lee SH, Won Y, Norlander AE, Simmons AJ, Peebles RS Jr, Lau KS, Choi E, Goldenring JR. Interleukin 13 promotes maturation and proliferation in metaplastic gastroids. Cellular and Molecular Gastroenterology and Hepatology, 18(3):101366, 2024.
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. Medical Image Analysis, 94:103124, 2024.
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. Nature Communications, 5(1):3557, 2024.
Bao S, Zhu S, Kolachala VL, Remedios LW, Hwang Y, Sun Y, Deng R, Cui C, Zhang R, Li Y, Li J, Roland JT, Liu Q, Lau KS, Kugathasan S, Qiu P, Wilson KT, Coburn LA, Landman BA, Huo Y. Cell Spatial Analysis in Crohn’s Disease: Unveiling Local Cell Arrangement Pattern with Graph-based Signatures. Proceedings of Society of Photo-Optical Instrumentation Engineers, 12933:1293314, 2024.
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, 40(6): btae356, 2024.
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. Proceedings of Machine Learning Research, 227:1406-1422, 2024.
Remedios LW, Bao S, Remedios SW, Lee HH, Cai LY, Li T, Deng R, Cui C, Li J, Liu Q, Lau KS , Roland JT, Washington MK, Coburn LA, Wilson KT, Huo Y, Landman BA. Nucleus subtype classification using inter-modality learning. Proceedings of Society of Photo-Optical Instrumentation Engineers , 12933:129330F, 2024.
2023
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 SN, Jones AL, Washington MK, Roland JT, Chan KS, Schuerpf T, Sears CL, Liu Q, Shrubsole MJ, Coffey RJ*, Lau KS*. Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors. Cell, 186(25): 5620-5637, 2023. * Corresponding Authors
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. Proceedings of Society of Photo-Optical Instrumentation Engineers, 12471:124710B, 2023.
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, 26(7):107242, 2023.
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. Proceedings of Society of Photo-Optical Instrumentation Engineers, 12471:1247116, 2023.
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. Molecular Cell, 83(14):2509-2523, 2023.
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. Proceedings of Society of Photo-Optical Instrumentation Engineers, 12471:124710A, 2023.
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; Gut Cell Atlas Consortium; Human Cell Atlas Gut Biological Network Consortium. A Roadmap for the Human Gut Cell Atlas. Nature Reviews Gastroenterology and Hepatology, 20(9):597-614, 2023.
Chen Z, Lau KS . Advances in Mapping Tumor Progression from Precancer Atlases. Cancer Prevention Research, 16(8):439-447, 2023.
Pilat JM, Brown RE, Chen Z, Berle NJ, Othon AP, Washington M, 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. Journal of Clinical Investigation, 133(13):e165988, 2023.
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 Reports, 42(2):112128, 2023.
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, 186(2):363-38, 2023.
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 Biomaterialia, 163: 365-377, 2023.
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. Medical Image Learning with Limited and Noisy Data, 14307:82-92, 2023.
2022
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 Medical Imaging, 13594:24-33, 2022.
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 RJ, Ponce J, Terekhanova NV, Yao L, Wang F, Chen L, Schnaubelt M, Lu J, 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. Nature Genetics, 54(9): 1390-1405, 2022.
Simmons AJ, Lau KS. Dissociation and inDrops microfluidic encapsulation of human gut tissues for single-cell atlasing studies. STAR Protocols, 3(3):101570, 2022.
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 Systems, 13(9):690-710, 2022.
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, Campodonico 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 Discovery, 12(8):1873-1885, 2022. *Corresponding Authors
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 pre-cancerous gastric mucosa. Gastroenterology, 163(4):875-890, 2022.
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 Part A, 101(6):521-528, 2022.
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 (CBFA2T3) regulates colonic epithelial differentiation, colitis, and tumorigenesis by repressing E protein transcription factors. JCI Insight, 7(10):e153045, 2022.
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. Frontiers in Oncology, 12:878920, 2022. *Corresponding Authors
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, 162(2):604-620, 2022.
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, 38(6):1700–1707, 2022.
2021
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, 184(26):6262-6280, 2021. *Corresponding Authors
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 Research, 31(10):1742-1752, 2021.
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 Protocols, 2(2):100450, 2021.
Rolong A, Chen B, Lau KS. Deciphering the cancer microenvironment from bulk data with EcoTyper. Cell, 184(21):5306-5308, 2021.
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, 160(3):755-770, 2021.
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. Proceedings of Society of Photo-Optical Instrumentation Engineers, 11601-1160106, 2021.
2020
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, 159(6):2101-2115, 2020.
Heiser CN,Lau KS. A quantitative framework for evaluating single-cell data structure preservation by dimensionality reduction techniques. Cell Reports, 31(5):107576, 2020.
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, 6(1): 33, 2020.
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 LMN*, Lau KS*. Dual indexed library design enables compatibility of in-Drop single-cell RNA-sequencing with exAMP chemistry sequencing platforms. BMC Genomics, 21: 456, 2020. *Corresponding Authors
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, 159(2):453-466, 2020.
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 β-Cell fitness by regulating genes in Ca2+ homeostasis, cell survival, vesicle Biosynthesis, glucose metabolism, and stress response. Diabetes, 69(6):1219-1231, 2020.
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. Science Signaling, 13(643): eaay3258, 2020.
Chinowsky CR, Pinette JA, Meederink LM, Lau KS, Tyska MJ. Non-muscle myosin-2 contractility-dependent actin turnover limits the length of epithelial microvilli. Molecular Biology of the Cell, 31(25):2803-2815, 2020.
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; Human Tumor Atlas Network. The Human Tumor Atlas Network: charting tumor transitions across space and time at single-cell resolution. Cell, 181(2):236-249, 2020.
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, 11(40):3621-3632, 2020.
2019
Chen B, Herring CA, Lau KS. pyNVR: Investigating factors affecting feature selection from scRNA-seq data for lineage reconstruction. Bioinformatics, 35(13):2335-2337, 2019.
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. Developmental Cell, 48(1):49-63, 2019. *Corresponding Authors
Scurrah CR, Simmons AJ, Lau KS. Single-cell mass cytometry of archived human epithelial tissue for decoding cancer signaling pathways. Methods in Molecular Biology, 1884:215-229, 2019.
Vega PN, Lau KS*, Goldenring JR*. Not all insults are created equal for awakening dormant stem cell abilities. Cellular and Molecular Gastroenterology and Hepatology, 7(3):619-621, 2019. *Corresponding Authors
Kim SW, Banerjee A, Starchenko A, Yilmaz OH, Lau KS. Defining the intestinal stem cell niche for tissue engineering and disease modeling. Encyclopedia of Tissue Engineering and Regenerative Medicine Vol 2, ed. Rui Reis, Academic Press (Elsevier): 375-385, 2019.
Min J, Vega PN, Engevik AC, Williams JA, Yang Q, Patterson LM, Simmons AJ, Bilton RJ, Betts JW, Lau KS, Magness ST, Goldenring JR, Choi E. Heterogeneity and dynamics of active Kras-induced pre-neoplastic lineages from mouse stomach. Nature Communications, 10(1): 5549, 2019.
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, 35(24):5306-5308, 2019.
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; Clinical Proteomic Tumor Analysis Consortium. Proteogenomic analysis of human colon cancer reveals new therapeutic opportunities. Cell, 177(4):1035-1049, 2019.
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. Journal of Cell Sciences, 132(7): jcs226860, 2019.
Manolopoulou M, Matlock BK, Nlandu-Khodo S, Simmons AJ, Lau KS, Phillips-Mignemi M, Ivanova A, Alford CE, Flaherty DK, Gewin LS. Improved cell cycle analysis of proximal tubules after renal injury. American Journal of Physiology-Renal Physiology, 316(5):F847-F855, 2019.
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. Infection and Immunity, 87(4):e00783-18, 2019.
2018
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 Systems, 6(1): 37-51, 2018.
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 Biology, 16(10):e2006687, 2018. *Corresponding Authors
Banerjee A, McKinley ET, von Molke J, Coffey RJ, Lau KS. Interpreting heterogeneity in intestinal tuft cell structure and function. Journal of Clinical Investigation, 5(4): 539-48, 2018.
Herring CA, Chen B, McKinley ET, Lau KS. Single-cell computational strategies for lineage reconstruction in tissue systems. Cellular and Molecular Gastroenterology and Hepatology, 5(4): 539-48, 2018.
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. Frontiers in Immunology, 9:2954 ,2018.
2017
Kim SW, Ehrman J, Ahn MR, Kondo J, Mancheno Lopez AA, Oh YS, Kim HX, Crawley SW, Goldenring JR, Tyska MJ, Rericha EC, Lau KS. Shear stress induces non-canonical autophagy in intestinal epithelial monolayers. Molecular Biology of the Cell, 28(22):3034-56, 2017.
Simmons AJ, Lau KS. Deciphering tumor heterogeneity from FFPE tissues: its promise and challenges. Molecular and Cellular Oncology, 4(1):e1260191, 2017.
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, 2(11): pii: 93487, 2017.
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 and Differentiation, 24(5):855-65, 2017.
2016
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. Science Signaling, 9(449):rs11, 2016.
2015
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-α-induced apoptosis in vivo. Molecular Systems Biology, 11(10):835, 2015.
Lyons J, Herring CA, Banerjee A, Simmons AJ, Lau KS. Multiscale analysis of the murine intestine for modeling human diseases. Integrative Biology, 7(7):740-57, 2015.
Gierut JJ, Wood LB, Lau KS , Lin YJ, Genetti C, Samatar AA, Lauffenburger DA, Haigis KM. Network-level effects of kinase inhibitors modulate TNF-α-induced apoptosis in the intestinal epithelium. Science Signaling, 8(407):ra129, 2015.
2013
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-α. Integrative Biology 5(11):1355-1365, 2013.
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. Integrative Biology 5(7): 940-963, 2013.
2012
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-α-induced apoptosis in the intestinal epithelium. PLoS Biology, 10(9):e1001393, 2012.
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, 7(7):e41343, 2012.
2011
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-α-induced apoptosis and proliferation by MAPKs. Science Signaling, 4(165):ra16, 2011.
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. Nature Communications, 2: 334, 2011.
2009
Lau KS, Haigis KM. Non-redundancy within the RAS oncogene family: insights into mutational disparities in cancer. Molecule and Cells, 28(4):315-320, 2009.
Dennis JW, Lau KS, Demetriou M, Nabi IR. Adaptive regulation at the cell surface by N-glycosylation. Traffic, 10(11):1569-1578, 2009.
2008
Lau KS, Khan S, Dennis JW. Genome-scale identification of UDP-GlcNAc-dependent pathways. Proteomics, 8(16):3294-3302, 2008.
Lau KS, Dennis JW. N-Glycans in cancer progression. Glycobiology, 18(10): 750-760, 2008.
Lau KS , Nabi IR, Demetriou M, and Dennis JW. Golgi N-glycan processing and galectin functions. Animal Lectins: A Functional View, ed. Gerado R. Vasta and Hafiz Ahmed, CRC Press (Taylor and Francis): 285-302, 2008.
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, 44(2):ix-xiv, 2008.
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 Research, 68(16): 6688-6697, 2008.
2007
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, 129(1): 123-134, 2007.
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 Research, 67(20): 9771-9780, 2007.
2003
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 Biology, 4(4): R25, 2003.
2002
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. Canadian Journal of Chemistry, 80(7): 845-855, 2002.