2021 | Single-cell multiomics reveals increased plasticity, resistant populations and stem-cell-like blasts in KMT2A-rearranged leukemia. Chen C, Yu W, Alikarami F, Qiu Q, Chen CH, Flournoy J, Gao P, Uzun Y, Fang L, Davenport JW, Hu Y, Zhu Q, Wang K, Libbrecht C, Felmeister A, Rozich I, Ding YY, Hunger SP, Felix CA, Wu H, Brown PA, Guest EM, Barrett DM, Bernt KM, Tan K. Blood. 2021 Dec 5:blood.2021013442. doi: 10.1182/blood.20210134420.PMID: 34864916.

2021 | Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer. Chan JM, Quintanal-Villalonga Á, Gao VR, Xie Y, Allaj V, Chaudhary O, Masilionis I, Egger J, Chow A, Walle T, Mattar M, Yarlagadda DVK, Wang JL, Uddin F, Offin M, Ciampricotti M, Qeriqi B, Bahr A, de Stanchina E, Bhanot UK, Lai WV, Bott MJ, Jones DR, Ruiz A, Baine MK, Li Y, Rekhtman N, Poirier JT, Nawy T, Sen T, Mazutis L, Hollmann TJ, Pe'er D, Rudin CM. Cancer Cell. 39 (11): 1479-1496.e18. doi: 10.1016/j.ccell.2021.09.008. PMID: 34653364PMCID:PMC8628860

2021 | Scope2Screen: Focus+Context Techniques for Pathology Tumor Assessment in Multivariate Image Data. Jessup, J, Krueger, R, Warchol, S, Hoffer, J, Muhlich, J, Ritch, CC, Gaglia, G, Coy, S, Chen, YA, Lin, JR, Santagata, S, Sorger, PK, Pfister, H. IEEE Trans Vis Comput Graph. PP : . doi: 10.1109/TVCG.2021.3114786. PubMed PMID:34606456

2021 | Narrative online guides for the interpretation of digital-pathology images and tissue-atlas data. Rashid, R, Chen, YA, Hoffer, J, Muhlich, JL, Lin, JR, Krueger, R, Pfister, H, Mitchell, R, Santagata, S, Sorger, PK. Nat Biomed Eng. : . doi: 10.1038/s41551-021-00789-8. PubMed PMID:34750536

2021 | MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging. Schapiro, D, Sokolov, A, Yapp, C, Chen, YA, Muhlich, JL, Hess, J, Creason, AL, Nirmal, AJ, Baker, GJ, Nariya, MK, Lin, JR, Maliga, Z, Jacobson, CA, Hodgman, MW, Ruokonen, J, Farhi, SL, Abbondanza, D, McKinley, ET, Persson, D, Betts, C, Sivagnanam, S, Regev, A, Goecks, J, Coffey, RJ, Coussens, LM, Santagata, S, Sorger, PK. Nat Methods. : . doi: 10.1038/s41592-021-01308-y. PubMed PMID:34824477

2021 | Highly Multiplexed Phenotyping of Immunoregulatory Proteins in the Tumor Microenvironment by CODEX Tissue Imaging. Phillips, D, Schürch, CM, Khodadoust, MS, Kim, YH, Nolan, GP, Jiang, S. Front Immunol. 12 : 687673. doi: 10.3389/fimmu.2021.687673. PubMed PMID:34093591 PubMed Central PMC8170307

2021 | Strategies for Accurate Cell Type Identification in CODEX Multiplexed Imaging Data. Hickey, JW, Tan, Y, Nolan, GP, Goltsev, Y. Front Immunol. 12 : 727626. doi: 10.3389/fimmu.2021.727626. PubMed PMID:34484237 PubMed Central PMC8415085

2021 | Smoking Modulates Different Secretory Subpopulations Expressing SARS-CoV-2 Entry Genes in the Nasal and Bronchial Airways. Xu, K, Shi, X, Husted, C, Hong, R, Wang, Y, Ning, B, Sullivan, T, Rieger-Christ, K, Duan, F, Marques, H, Gower, A, Xiao, X, Liu, H, Liu, G, Duclos, G, Platt, M, Spira, A, Mazzilli, S, Billatos, E, Lenburg, M, Campbell, J, Beane, J. Res Sq. : . doi: 10.21203/ PubMed PMID:34729557 PubMed Central PMC8562543

2021 | scMRMA: single cell multiresolution marker-based annotation. Li, J, Sheng, Q, Shyr, Y, Liu, Q. Nucleic Acids Res. : . doi: 10.1093/nar/gkab931. PubMed PMID:34648021

2021 | Chromatin accessibility associates with protein-RNA correlation in human cancer. Sanghi, A, Gruber, JJ, Metwally, A, Jiang, L, Reynolds, W, Sunwoo, J, Orloff, L, Chang, HY, Kasowski, M, Snyder, MP. Nat Commun. 12 (1): 5732. doi: 10.1038/s41467-021-25872-1. PubMed PMID:34593797 PubMed Central PMC8484618

2021 | In-depth triacylglycerol profiling using MS3 Q-Trap mass spectrometry. Cabruja, M, Priotti, J, Domizi, P, Papsdorf, K, Kroetz, DL, Brunet, A, Contrepois, K, Snyder, MP. Anal Chim Acta. 1184 : 339023. doi: 10.1016/j.aca.2021.339023. PubMed PMID:34625255 PubMed Central PMC8502232

2021 | Multiomics analysis of serial PARP inhibitor treated metastatic TNBC inform on rational combination therapies. Labrie, M, Li, A, Creason, A, Betts, C, Keck, J, Johnson, B, Sivagnanam, S, Boniface, C, Ma, H, Blucher, A, Chang, YH, Chin, K, Vuky, J, Guimaraes, AR, Downey, M, Lim, JY, Gao, L, Siex, K, Parmar, S, Kolodzie, A, Spellman, PT, Goecks, J, Coussens, LM, Corless, CL, Bergan, R, Gray, JW, Mills, GB, Mitri, ZI. NPJ Precis Oncol. 5 (1): 92. doi: 10.1038/s41698-021-00232-w. PubMed PMID:34667258 PubMed Central PMC8526613

2021 | Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices. Alseekh, S, Aharoni, A, Brotman, Y, Contrepois, K, D’Auria, J, Ewald, J, C Ewald, J, Fraser, PD, Giavalisco, P, Hall, RD, Heinemann, M, Link, H, Luo, J, Neumann, S, Nielsen, J, Perez de Souza, L, Saito, K, Sauer, U, Schroeder, FC, Schuster, S, Siuzdak, G, Skirycz, A, Sumner, LW, Snyder, MP, Tang, H, Tohge, T, Wang, Y, Wen, W, Wu, S, Xu, G, Zamboni, N, Fernie, AR. Nat Methods. 18 (7): 747-756. doi: 10.1038/s41592-021-01197-1. PubMed PMID:34239102

2021 | Characterization of the tumor immune microenvironment of sinonasal squamous-cell carcinoma. Gu, JT, Claudio, N, Betts, C, Sivagnanam, S, Geltzeiler, M, Pucci, F. Int Forum Allergy Rhinol. : . doi: 10.1002/alr.22867. PubMed PMID:34510766

2021 | Adjacent Cell Marker Lateral Spillover Compensation and Reinforcement for Multiplexed Images. Bai, Y, Zhu, B, Rovira-Clave, X, Chen, H, Markovic, M, Chan, CN, Su, TH, McIlwain, DR, Estes, JD, Keren, L, Nolan, GP, Jiang, S. Front Immunol. 12 : 652631. doi: 10.3389/fimmu.2021.652631. PubMed PMID:34295327 PubMed Central PMC8289709

2021 | MITI Minimum Information guidelines for highly multiplexed tissue images. Denis Schapiro, Clarence Yapp, Artem Sokolov, Sheila M. Reynolds, Yu-An Chen, Damir Sudar, Yubin Xie, Jeremy Muhlich, Raquel Arias-Camison, Milen Nikolov, Madison Tyler, Jia-Ren Lin, Erik A. Burlingame, Sarah Arena, Human Tumor Atlas Network, Young H. Chang, Samouil L Farhi, Vésteinn Thorsson, Nithya Venkatamohan, Julia L. Drewes, Dana Pe’er, David A. Gutman, Markus D. Herrmann, Nils Gehlenborg, Peter Bankhead, Joseph T. Roland, John M. Herndon, Michael P. Snyder, Michael Angelo, Garry Nolan, Jason Swedlow, Nikolaus Schultz, Daniel T. Merrick, Sarah A. Mazzilli, Ethan Cerami, Scott J. Rodig, Sandro Santagata, Peter K. Sorger. arXiv:2108.09499

2021 | Co-clinical FDG-PET radiomic signature in predicting response to neoadjuvant chemotherapy in triple-negative breast cancer. Roy, S, Whitehead, TD, Li, S, Ademuyiwa, FO, Wahl, RL, Dehdashti, F, Shoghi, KI. Eur J Nucl Med Mol Imaging. : . doi: 10.1007/s00259-021-05489-8. PubMed PMID:34328530

2021 | Deep Learning Segmentation of Triple-Negative Breast Cancer (TNBC) Patient Derived Tumor Xenograft (PDX) and Sensitivity of Radiomic Pipeline to Tumor Probability Boundary. Dutta, K, Roy, S, Whitehead, TD, Luo, J, Jha, AK, Li, S, Quirk, JD, Shoghi, KI. Cancers (Basel). 13 (15): . doi: 10.3390/cancers13153795. PubMed PMID:34359696 PubMed Central PMC8345151

2021 | A domain damage index to prioritizing the pathogenicity of missense variants. Chen, HC, Wang, J, Liu, Q, Shyr, Y. Hum Mutat. : . doi: 10.1002/humu.24269. PubMed PMID:34350656

2021 | DCIS genomic signatures define biology and correlate with clinical outcome: a Human Tumor Atlas Network (HTAN) analysis of TBCRC 038 and RAHBT cohorts.  Siri H Strand, Belén Rivero-Gutiérrez, Kathleen E Houlahan, Jose A Seoane, Lorraine King, Tyler Risom, Lunden A Simpson, Sujay Vennam, Aziz Khan, Luis Cisneros, Timothy Hardman, Bryan Harmon, Fergus Couch, Kristalyn Gallagher, Mark Kilgore, Shi Wei, Angela DeMichele, Tari King, Priscilla F McAuliffe, Julie Nangia, Joanna Lee, Jennifer Tseng, Anna Maria Storniolo, Alastair Thompson, Gaorav Gupta, Robyn Burns, Deborah J Veis, Katherine DeSchryver, Chunfang Zhu, Magdalena Matusiak, Jason Wang, Shirley X Zhu, Jen Tappenden, Daisy Yi Ding, Dadong Zhang, Jingqin Luo, Shu Jiang, Sushama Varma, Lauren Anderson, Cody Straub, Sucheta Srivastava, Christina Curtis, Rob Tibshirani, Robert Michael Angelo, Allison Hall, Kouros Owzar, Kornelia Polyak, Carlo Maley, Jeffrey R Marks, Graham A Colditz, E Shelley Hwang, Robert B West. bioRxiv 2021.06.16.448585; doi:

2021 | Immu-Mela: An open resource for exploring immunotherapy-related multidimensional genomic profiles in melanoma. Yang, J, Zhao, S, Wang, J, Sheng, Q, Liu, Q, Shyr, Y. J Genet Genomics. : . doi: 10.1016/j.jgg.2021.03.016. PubMed PMID:34127402

2021 | Ex Vivo Analysis of Primary Tumor Specimens for Evaluation of Cancer Therapeutics. Tognon, CE, Sears, RC, Mills, GB, Gray, JW, Tyner, JW. Annu Rev Cancer Biol. 5 : 39-57. doi: 10.1146/annurev-cancerbio-043020-125955. PubMed PMID:34222745 PubMed Central PMC8248658

2021 | A new method to accurately identify single nucleotide variants using small FFPE breast samples. Fortunato, A, Mallo, D, Rupp, SM, King, LM, Hardman, T, Lo, JY, Hall, A, Marks, JR, Hwang, ES, Maley, CC. Brief Bioinform. : . doi: 10.1093/bib/bbab221. PubMed PMID:34117742

2021 | Resolving the spatial and cellular architecture of lung adenocarcinoma by multiregion single-cell sequencing. Sinjab, A, Han, G, Treekitkarnmongkol, W, Hara, K, Brennan, PM, Dang, M, Hao, D, Wang, R, Dai, E, Dejima, H, Zhang, J, Bogatenkova, E, Sanchez-Espiridion, B, Chang, K, Little, DR, Bazzi, S, Tran, LM, Krysan, K, Behrens, C, Duose, DY, Parra, ER, Raso, MG, Solis, LM, Fukuoka, J, Zhang, J, Sepesi, B, Cascone, T, Byers, LA, Gibbons, DL, Chen, J, Moghaddam, SJ, Ostrin, EJ, Rosen, D, Heymach, JV, Scheet, P, Dubinett, SM, Fujimoto, J, Wistuba, II, Stevenson, CS, Spira, A, Wang, L, Kadara, H. Cancer Discov. : . doi: 10.1158/2159-8290.CD-20-1285. PubMed PMID:33972311

2021 | CODEX multiplexed tissue imaging with DNA-conjugated antibodies. Black, S, Phillips, D, Hickey, JW, Kennedy-Darling, J, Venkataraaman, VG, Samusik, N, Goltsev, Y, Schürch, CM, Nolan, GP. Nat Protoc. : . doi: 10.1038/s41596-021-00556-8. PubMed PMID:34215862

2021 | The Human Tumor Atlas Network (HTAN) Breast PreCancer Atlas: A multi-omic integrative analysis of ductal carcinoma in situ with clinical outcomes. Siri H Strand, Belen Rivero-Gutierrez, Kathleen E Houlahan, Jose A Seoane, Lorraine King, Tyler Risom, Lunden A Simpson, Sujay Vennam, Aziz Khan, Luis Cisneros, Timothy Hardman, Bryan Harmon, Fergus Couch, Kristalyn Gallagher, Mark Kilgore, Gabrielle B Rocque, Angela DeMichele, Tari King, Priscilla McAuliffe, Julie Nangia, Joanna Lee, Jennifer Tseng, Ana Maria Storniolo, Alastair Thompson, Gaorav Gupta, Robyn Burns, Deborah J Veis, Katherine DeSchryver, Chunfang Zhu, Magdalena Matusiak, Jason Wang, Shirley X Zhu, Jen Tappenden, Daisy Yi Ding, Dadong Zhang, Jingqin Luo, Shu Jiang, Sushama Varma, Lauren Anderson, Cody Straub, Sucheta Srivastava, Christina Curtis, Rob Tibshirani, Robert Michael Angelo, Allison Hall, Kouros Owzar, Kornelia Polyak, Carlo Maley, Jeffrey R Marks, Graham A Colditz, E Shelley Hwang, Robert B West
bioRxiv 2021.06.16.448585; doi:

2021 | Systematic interrogation of mutation groupings reveals divergent downstream expression programs within key cancer genes. Grzadkowski, MR, Holly, HD, Somers, J, Demir, E. BMC Bioinformatics. 22 (1): 233. doi: 10.1186/s12859-021-04147-y. PubMed PMID:33957863 PubMed Central PMC8101181

2021 | Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine. Gu, Q, Kumar, A, Bray, S, Creason, A, Khanteymoori, A, Jalili, V, Grüning, B, Goecks, J. PLoS Comput Biol. 17 (6): e1009014. doi: 10.1371/journal.pcbi.1009014. PubMed PMID:34061826 PubMed Central PMC8213174

2021 | Neoadjuvant selicrelumab, an agonist CD40 antibody, induces changes in the tumor microenvironment in patients with resectable pancreatic cancer. Byrne, KT, Betts, CB, Mick, R, Sivagnanam, S, Bajor, DL, Laheru, DA, Chiorean, EG, O’Hara, MH, Liudahl, SM, Newcomb, CW, Alanio, C, Ferreira, AP, Park, BS, Ohtani, T, Huffman, AP, Väyrynen, SA, Dias Costa, A, Kaiser, JC, Lacroix, AM, Redlinger, C, Stern, M, Nowak, JA, Wherry, EJ, Cheever, MA, Wolpin, BM, Furth, EE, Jaffee, EM, Coussens, LM, Vonderheide, RH. Clin Cancer Res. : . doi: 10.1158/1078-0432.CCR-21-1047. PubMed PMID:34112709

2021 | The breast pre-cancer atlas illustrates the molecular and micro-environmental diversity of ductal carcinoma in situ. Daniela Nachmanson, Adam Officer, Hidetoshi Mori, Jonathan Gordon, Mark F. Evans, Joseph Steward, Huazhen Yao, Thomas O’Keefe, Farnaz Hasteh, Gary S. Stein, Kristen Jepsen, Donald L. Weaver, Gillian L. Hirst, Brian L. Sprague, Laura J. Esserman, Alexander D. Borowsky, Janet L. Stein, Olivier Harismendy
bioRxiv 2021.05.11.443641; doi:

2021 | The Spatial Landscape of Progression and Immunoediting in Primary Melanoma at Single-Cell Resolution. Nirmal AJ, Maliga Z, Vallius T, Quattrochi B, Chen AA, Jacobson CA, Pelletier RJ, Yapp C, Arias-Camison R, Chen YA, Lian CG, Murphy GF, Santagata S, Sorger PK.
bioRxiv 2021.05.23.445310; doi: Cancer Discov. 2022 Jun 2;12(6):1518-1541. doi: 10.1158/2159-8290.CD-21-1357. PMID: 35404441. PMCID: PMC9167783.

2021 | Stitching and registering highly multiplexed whole slide images of tissues and tumors using ASHLAR software. Jeremy Muhlich, Yu-An Chen, Douglas Russell, Peter K Sorger
bioRxiv 2021.04.20.440625; doi:

2021 | UnMICST: Deep learning with real augmentation for robust segmentation of highly multiplexed images of human tissues. Clarence Yapp, Edward Novikov, Won-Dong Jang, Yu-An Chen, Marcelo Cicconet, Zoltan Maliga, Connor A. Jacobson, Donglai Wei, Sandro Santagata, Hanspeter Pfister, Peter K. Sorger
bioRxiv 2021.04.02.438285; doi:

2021 | Co-evolution of tumor and immune cells during progression of multiple myeloma. Liu, R, Gao, Q, Foltz, SM, Fowles, JS, Yao, L, Wang, JT, Cao, S, Sun, H, Wendl, MC, Sethuraman, S, Weerasinghe, A, Rettig, MP, Storrs, EP, Yoon, CJ, Wyczalkowski, MA, McMichael, JF, Kohnen, DR, King, J, Goldsmith, SR, O’Neal, J, Fulton, RS, Fronick, CC, Ley, TJ, Jayasinghe, RG, Fiala, MA, Oh, ST, DiPersio, JF, Vij, R, Ding, L. Nat Commun. 12 (1): 2559. doi: 10.1038/s41467-021-22804-x. PubMed PMID:33963182 PubMed Central PMC8105337

2021 | Targeting Treg cells with GITR activation alleviates resistance to immunotherapy in murine glioblastomas. Amoozgar, Z, Kloepper, J, Ren, J, Tay, RE, Kazer, SW, Kiner, E, Krishnan, S, Posada, JM, Ghosh, M, Mamessier, E, Wong, C, Ferraro, GB, Batista, A, Wang, N, Badeaux, M, Roberge, S, Xu, L, Huang, P, Shalek, AK, Fukumura, D, Kim, HJ, Jain, RK. Nat Commun. 12 (1): 2582. doi: 10.1038/s41467-021-22885-8. PubMed PMID:33976133 PubMed Central PMC8113440

2021 | Tumor and immune reprogramming during immunotherapy in advanced renal cell carcinoma. Bi, K, He, MX, Bakouny, Z, Kanodia, A, Napolitano, S, Wu, J, Grimaldi, G, Braun, DA, Cuoco, MS, Mayorga, A, DelloStritto, L, Bouchard, G, Steinharter, J, Tewari, AK, Vokes, NI, Shannon, E, Sun, M, Park, J, Chang, SL, McGregor, BA, Haq, R, Denize, T, Signoretti, S, Guerriero, JL, Vigneau, S, Rozenblatt-Rosen, O, Rotem, A, Regev, A, Choueiri, TK, Van Allen, EM. Cancer Cell. 39 (5): 649-661.e5. doi: 10.1016/j.ccell.2021.02.015. PubMed PMID:33711272 PubMed Central PMC8115394

2021 | Integrative single-cell analysis of allele-specific copy number alterations and chromatin accessibility in cancer. Wu, CY, Lau, BT, Kim, HS, Sathe, A, Grimes, SM, Ji, HP, Zhang, NR. Nat Biotechnol. : . doi: 10.1038/s41587-021-00911-w. PubMed PMID:34017141

2021 | Multiplexed 3D atlas of state transitions and immune interactions in colorectal cancer. Jia-Ren Lin, Shu Wang, Shannon Coy, Madison Tyler, Clarence Yapp, Yu-An Chen, Cody N. Heiser, Ken S. Lau, Sandro Santagata, Peter K. Sorger.
bioRxiv 2021.03.31.437984; doi:

2021 | Single-cell analyses reveal a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer. Winston R. Becker, Stephanie A. Nevins, Derek C. Chen, Roxanne Chiu, Aaron Horning, Rozelle Laquindanum, Meredith Mills, Hassan Chaib, Uri Ladabaum, Teri Longacre, Jeanne Shen, Edward D. Esplin, Anshul Kundaje, James M. Ford, Christina Curtis, Michael P. Snyder, William J. Greenleaf.
bioRxiv 2021.03.24.436532; doi:

2021 | Automated quality control and cell identification of droplet-based single-cell data using dropkick. Heiser, CN, Wang, VM, Chen, B, Hughey, JJ, Lau, KS. Genome Res. : . doi: 10.1101/gr.271908.120. PubMed PMID:33837131

2021 | Beyond Programmed Death-Ligand 1: B7-H6 Emerges as a Potential Immunotherapy Target in SCLC. Thomas, PL, Groves, SM, Zhang, YK, Li, J, Gonzalez-Ericsson, P, Sivagnanam, S, Betts, CB, Chen, HC, Liu, Q, Lowe, C, Chen, H, Boyd, KL, Kopparapu, PR, Yan, Y, Coussens, LM, Quaranta, V, Tyson, DR, Iams, W, Lovly, CM. J Thorac Oncol. : . doi: 10.1016/j.jtho.2021.03.011. PubMed PMID:33839362

2021 | CytoTalk: De novo construction of signal transduction networks using single-cell transcriptomic data. Hu Y, Peng T, Gao L, Tan K. Sci Adv. 2021 Apr 14;7(16):eabf1356. doi: 10.1126/sciadv.abf1356. PubMed PMID: 33853780

2021 | Integrative bulk and single-cell profiling of pre-manufacture T-cell populations reveals factors mediating long-term persistence of CAR T-cell therapy. Chen, GM, Chen, C, Das, RK, Gao, P, Chen, CH, Bandyopadhyay, S, Ding, YY, Uzun, Y, Yu, W, Zhu, Q, Myers, RM, Grupp, SA, Barrett, DM, Tan, K. Cancer Discov. : . doi: 10.1158/2159-8290.CD-20-1677. PubMed PMID:33820778

2021 | ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis. Granja, JM, Corces, MR, Pierce, SE, Bagdatli, ST, Choudhry, H, Chang, HY, Greenleaf, WJ. Nat Genet. 53 (3): 403-411. doi: 10.1038/s41588-021-00790-6. PubMed PMID:33633365

2021 | Unmasking the immune microecology of ductal carcinoma in situ with deep learning. Narayanan, PL, Raza, SEA, Hall, AH, Marks, JR, King, L, West, RB, Hernandez, L, Guppy, N, Dowsett, M, Gusterson, B, Maley, C, Hwang, ES, Yuan, Y. NPJ Breast Cancer. 7 (1): 19. doi: 10.1038/s41523-020-00205-5. PubMed PMID:33649333 PubMed Central PMC7921670

2021 | Processing single-cell RNA-seq data for dimension reduction-based analyses using open-source tools. Chen, B, Ramirez-Solano, MA, Heiser, CN, Liu, Q, Lau, KS. STAR Protoc. 2 (2): 100450. doi: 10.1016/j.xpro.2021.100450. PubMed PMID:33982010 PubMed Central PMC8082116

2021 | Highly multiplexed tissue imaging using repeated oligonucleotide exchange reaction. Kennedy-Darling, J, Bhate, SS, Hickey, JW, Black, S, Barlow, GL, Vazquez, G, Venkataraaman, VG, Samusik, N, Goltsev, Y, Schürch, CM, Nolan, GP. Eur J Immunol. : . doi: 10.1002/eji.202048891. PubMed PMID:33548142

2021 | Comprehensive generation, visualization, and reporting of quality control metrics for single-cell RNA sequencing data. Hong, R., Koga, Y., Bandyadka, S., Leshchyk, A., Wang, Z., Alabdullatif, S., Wang, Y., Akavoor, V., Cao, X., Sarfraz, I., Jansen, F., Johnson, W. E., Yajima, M., Campbell, J. D.bioRxiv 2020.11.16.385328; doi:

2021 | Spatial drivers and pre-cancer populations collaborate with the microenvironment in untreated and chemo-resistant pancreatic cancer. Daniel Cui Zhou, Reyka G. Jayasinghe, John M. Herndon, Erik Storrs, Chia-Kuei Mo, Yige Wu, Robert S. Fulton, Matthew A. Wyczalkowski, Catrina C. Fronick, Lucinda A. Fulton, Lisa Thammavong, Kazuhito Sato, Houxiang Zhu, Hua Sun, Liang-Bo Wang, Yize Li, Chong Zuo, Joshua F. McMichael, Sherri R. Davies, Elizabeth L. Appelbaum, Keenan J. Robbins, Sara E. Chasnoff, Xiaolu Yang, Ruiyang Liu, Ashley N. Reeb, Michael C. Wendl, Clara Oh, Mamatha Serasanambati, Preet Lal, Rajees Varghese, R. Jay Mashl, Jennifer Ponce, Nadezhda V. Terekhanova, Nataly Naser Al Deen, Lijun Yao, Fang Wang, Lijun Chen, Michael Schnaubelt, Sidharth V. Puram, Albert H. Kim, Sheng-Kwei Song, Kooresh I. Shoghi, Tao Ju, William G. Hawkins, Ken Chen, Deyali Chatterjee, Hui Zhang, Milan G. Chheda, Samuel Achilefu, David G. DeNardo, Stephen T. Oh, Feng Chen, William E. Gillanders, Ryan C. Fields, Li Ding.bioRxiv 2021.01.13.426413; doi:

2021 | Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma. Risom T, Glass DR, Averbukh I, Liu CC, Baranski A, Kagel A, McCaffrey EF, Greenwald NF, Rivero-Gutiérrez B, Strand SH, Varma S, Kong A, Keren L, Srivastava S, Zhu C, Khair Z, Veis DJ, Deschryver K, Vennam S, Maley C, Hwang ES, Marks JR, Bendall SC, Colditz GA, West RB, Angelo M. bioRxiv 2021.01.05.425362; doi: Cell. 2022 Jan 20;185(2):299-310.e18. doi: 10.1016/j.cell.2021.12.023. PMID: 35063072. PMCID: PMC8792442

2021 | Spatially organized multicellular immune hubs in human colorectal cancer. Pelka K, Hofree M, Chen JH, Sarkizova S, Pirl JD, Jorgji V, Bejnood A, Dionne D, Ge WH, Xu KH, Chao SX, Zollinger DR, Lieb DJ, Reeves JW, Fuhrman CA, Hoang ML, Delorey T, Nguyen LT, Waldman J, Klapholz M, Wakiro I, Cohen O, Albers J, Smillie CS, Cuoco MS, Wu J, Su MJ, Yeung J, Vijaykumar B, Magnuson AM, Asinovski N, Moll T, Goder-Reiser MN, Applebaum AS, Brais LK, DelloStritto LK, Denning SL, Phillips ST, Hill EK, Meehan JK, Frederick DT, Sharova T, Kanodia A, Todres EZ, Jané-Valbuena J, Biton M, Izar B, Lambden CD, Clancy TE, Bleday R, Melnitchouk N, Irani J, Kunitake H, Berger DL, Srivastava A, Hornick JL, Ogino S, Rotem A, Vigneau S, Johnson BE, Corcoran RB, Sharpe AH, Kuchroo VK, Ng K, Giannakis M, Nieman LT, Boland GM, Aguirre AJ, Anderson AC, Rozenblatt-Rosen O, Regev A, Hacohen N.  Cell. 2021 Sep 2;184(18):4734-4752.e20. doi: 10.1016/j.cell.2021.08.003 Epub 2021 Aug 26. PMID:34450029. PMCID:PMC8772395

2021 | Expansion Sequencing: Spatially Precise In Situ Transcriptomics in Intact Biological Systems. Alon S, Goodwin DR, Sinha A, Wassie AT, Chen F, Daugharthy ER, Bando Y, Kajita A, Xue AG, Marrett K, Prior R, Cui Y, Payne AC, Yao CC, Suk HJ, Wang R, Yu CJ, Tillberg P, Reginato P, Pak N, Liu S, Punthambaker S, Iyer EPR, Kohman RE, Miller JA, Lein ES, Lako A, Cullen N, Rodig S, Helvie K, Abravanel DL, Wagle N, Johnson BE, Klughammer J, Slyper M, Waldman J, Jané-Valbuena J, Rozenblatt-Rosen O, Regev A; IMAXT Consortium, Church GM, Marblestone AH, Boyden ES. Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems. Science. 2021 Jan 29;371(6528):eaax2656. doi: 10.1126/science.aax2656. PubMed PMID: 33509999; PubMed Central PMC7900882

2021 | GLUER: integrative analysis of single-cell omics and imaging data by deep neural network. Peng, T, Chen, GM, Tan, K. bioRxiv 2021.01.25.427845; doi:

2021 | Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps. 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. Cell. 2021 Dec 22;184(26):6262-6280.e26. doi: PMID:34910928. PMCID:PMC8941949.

2021 | Dynamic transcriptional and epigenetic changes drive cellular plasticity in the liver. Merrell, AJ, Peng, T, Li, J, Sun, K, Li, B, Katsuda, T, Grompe, M, Tan, K, Stanger, BZ. Hepatology. : . doi: 10.1002/hep.31704. PubMed PMID:33423324

2021 | Predictive modeling of single-cell DNA methylome data enhances integration with transcriptome data. Uzun, Y, Wu, H, Tan, K. Genome Res. 2021 Jan; 31 (1): 101-109. doi: 10.1101/gr.267047.120. PubMed PMID: 33219054 

2020 | Single-cell characterization of subsolid and solid lesions in the lung adenocarcinoma spectrum. Yanagawa, J., Tran, L. M., Fung, E., Wallace, W. D., Prosper, A. E., Fishbein, G. A., Shea, C., Hong, R., Liu, B., Salehi-Rad, R., Deng, J. Z., Gower, A., Campbell, J. D., Mazzilli, S. A., Beane, J., Kadara, H., Lenburg, M. E., Spira, A., Aberle, D. R., Krysan, K., Dubinett, S. M. 

2020 | An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer. Johnson BE, Creason AL, Stommel JM, Keck JM, Parmar S, Betts CB, Blucher A, Boniface C, Bucher E, Burlingame E, Camp T, Chin K, Eng J, Estabrook J, Feiler HS, Heskett MB, Hu Z, Kolodzie A, Kong BL, Labrie M, Lee J, Leyshock P, Mitri S, Patterson J, Riesterer JL, Sivagnanam S, Somers J, Sudar D, Thibault G, Weeder BR, Zheng C, Nan X, Thompson RF, Heiser LM, Spellman PT, Thomas G, Demir E, Chang YH, Coussens LM, Guimaraes AR, Corless C, Goecks J, Bergan R, Mitri Z, Mills GB, Gray JW.  Cell Rep Med. 2022 Feb 15;3(2):100525. doi: 10.1016/j.xcrm.2022.100525. PMID: 35243422. PMCID: PMC8861971Explore Publication in Portal.

2020 | Single-cell multi-omics reveals elevated plasticity and stem-cell-like blasts relevant to the poor prognosis of KMT2A-rearranged leukemia. Chen, C., Yu, W., Alikarami, F., Qiu, Q., Chen, C.-h., Flournoy, J., Gao, P., Uzun, Y., Fang, L., Yu, Y., Zhu, Q., Wang, K., Libbrecht, C., Felmeister, A., Rozich, I., Ding, Y.-y., Hunger, S. P., Wu, H., Brown, P. A., Guest, E. M., Barrett, D. M., Bernt, K. M., Tan, K. 

2020 | Succinate Produced by Intestinal Microbes Promotes Specification of Tuft Cells to Suppress Ileal Inflammation. 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. Gastroenterology. 2020 Dec;159(6):2101-2115.e5. doi: 10.1053/j.gastro.2020.08.029. PubMed PMID: 32828819; PubMed Central PMC7725941.

2020 | Diverse noncoding mutations contribute to deregulation of cis-regulatory landscape in pediatric cancers. He, B, Gao, P, Ding, Y.-y, Chen, C.-h, Chen, G, Chen, C, Kim, H, Tasian, SK, Hunger, SP, Tan, K. Sci Adv. 2020 Jul 24;6(30):eaba3064. doi: 10.1126/sciadv.aba3064. PubMed PMID:32832663; PubMed Central PMC7439310.

2020 | SHIFT: speedy histological-to-immunofluorescent translation of a tumor signature enabled by deep learning. Burlingame, EA, McDonnell, M, Schau, GF, Thibault, G, Lanciault, C, Morgan, T, Johnson, BE, Corless, C, Gray, JW, Chang, YH. Sci Rep. 10 (1): 17507. doi: 10.1038/s41598-020-74500-3. PubMed PMID:33060677 PubMed Central PMC7566625

2020 | VISTA: VIsual Semantic Tissue Analysis for pancreatic disease quantification in murine cohorts. Ternes, L, Huang, G, Lanciault, C, Thibault, G, Riggers, R, Gray, JW, Muschler, J, Chang, YH. Sci Rep. 10 (1): 20904. doi: 10.1038/s41598-020-78061-3. PubMed PMID:33262400 PubMed Central PMC7708430

2020 | Lifetime cancer prevalence and life history traits in mammals. Boddy, AM, Abegglen, LM, Pessier, AP, Aktipis, A, Schiffman, JD, Maley, CC, Witte, C. Evol Med Public Health. 2020 (1): 187-195. doi: 10.1093/emph/eoaa015. PubMed PMID:33209304 PubMed Central PMC7652303

2020 | Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front. Schürch, CM, Bhate, SS, Barlow, GL, Phillips, DJ, Noti, L, Zlobec, I, Chu, P, Black, S, Demeter, J, McIlwain, DR, Kinoshita, S, Samusik, N, Goltsev, Y, Nolan, GP. Cell. 182 (5): 1341-1359.e19. doi: 10.1016/j.cell.2020.07.005. PubMed PMID:32763154 PubMed Central PMC7479520

2020 | Landscape of coordinated immune responses to H1N1 challenge in humans. Rahil, Z, Leylek, R, Schürch, CM, Chen, H, Bjornson-Hooper, Z, Christensen, SR, Gherardini, PF, Bhate, SS, Spitzer, MH, Fragiadakis, GK, Mukherjee, N, Kim, N, Jiang, S, Yo, J, Gaudilliere, B, Affrime, M, Bock, B, Hensley, SE, Idoyaga, J, Aghaeepour, N, Kim, K, Nolan, GP, McIlwain, DR. J Clin Invest. 130 (11): 5800-5816. doi: 10.1172/JCI137265. PubMed PMID:33044226 PubMed Central PMC7598057

2020 | Biomarkers for Lung Cancer Screening and Detection. Ostrin, EJ, Sidransky, D, Spira, A, Hanash, SM. Cancer Epidemiol Biomarkers Prev. 29 (12): 2411-2415. doi: 10.1158/1055-9965.EPI-20-0865. PubMed PMID:33093160 PubMed Central PMC7710615

2020 | Massively parallel and time-resolved RNA sequencing in single cells with scNT-seq. Qiu, Q, Hu, P, Qiu, X, Govek, KW, Cámara, PG, Wu, H. Nat Methods. 17 (10): 991-1001. doi: 10.1038/s41592-020-0935-4. PubMed PMID:32868927

2020 | The Evolution of Human Cancer Gene Duplications across Mammals. Tollis, M, Schneider-Utaka, AK, Maley, CC. Mol Biol Evol. 37 (10): 2875-2886. doi: 10.1093/molbev/msaa125. PubMed PMID:32421773 PubMed Central PMC7530603

2020 | The Pathobiology of Skin Aging: New Insights into an Old Dilemma. Russell-Goldman, E, Murphy, GF. Am J Pathol. 190 (7): 1356-1369. doi: 10.1016/j.ajpath.2020.03.007. PubMed PMID:32246919 PubMed Central PMC7481755

2020 | Accelerated single cell seeding in relapsed multiple myeloma. Landau, HJ, Yellapantula, V, Diamond, BT, Rustad, EH, Maclachlan, KH, Gundem, G, Medina-Martinez, J, Ossa, JA, Levine, MF, Zhou, Y, Kappagantula, R, Baez, P, Attiye, M, Makohon-Moore, A, Zhang, L, Boyle, EM, Ashby, C, Blaney, P, Patel, M, Zhang, Y, Dogan, A, Chung, DJ, Giralt, S, Lahoud, OB, Peled, JU, Scordo, M, Shah, G, Hassoun, H, Korde, NS, Lesokhin, AM, Lu, S, Mailankody, S, Shah, U, Smith, E, Hultcrantz, ML, Ulaner, GA, van Rhee, F, Morgan, GJ, Landgren, O, Papaemmanuil, E, Iacobuzio-Donahue, C, Maura, F. Nat Commun. 11 (1): 3617. doi: 10.1038/s41467-020-17459-z. PubMed PMID:32680998 PubMed Central PMC7368016

2020 | Age-dependent regulation of SARS-CoV-2 cell entry genes and cell death programs correlates with COVID-19 disease severity. Inde, Z, Yapp, C, Joshi, GN, Spetz, J, Fraser, C, Deskin, B, Ghelfi, E, Sodhi, C, Hackam, D, Kobzik, L, Croker, B, Brownfield, D, Jia, H, Sarosiek, KA. bioRxiv. : . doi: 10.1101/2020.09.13.276923. PubMed PMID:32935109 PubMed Central PMC7491524

2020 | Clinically adaptable polymer enables simultaneous spatial analysis of colonic tissues and biofilms. Macedonia, MC, Drewes, JL, Markham, NO, Simmons, AJ, Roland, JT, Vega, PN, Scurrah, CR, Coffey, RJ, Shrubsole, MJ, Sears, CL, Lau, KS. NPJ Biofilms Microbiomes. 6 (1): 33. doi: 10.1038/s41522-020-00143-x. PubMed PMID:32973205 PubMed Central PMC7518420

2020 | Use of Single-Cell -Omic Technologies to Study the Gastrointestinal Tract and Diseases, From Single Cell Identities to Patient Features. Islam, M, Chen, B, Spraggins, JM, Kelly, RT, Lau, KS. Gastroenterology. 159 (2): 453-466.e1. doi: 10.1053/j.gastro.2020.04.073. PubMed PMID:32417404 PubMed Central PMC7484006

2020 | A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors. Slyper, M, Porter, CBM, Ashenberg, O, Waldman, J, Drokhlyansky, E, Wakiro, I, Smillie, C, Smith-Rosario, G, Wu, J, Dionne, D, Vigneau, S, Jané-Valbuena, J, Tickle, TL, Napolitano, S, Su, MJ, Patel, AG, Karlstrom, A, Gritsch, S, Nomura, M, Waghray, A, Gohil, SH, Tsankov, AM, Jerby-Arnon, L, Cohen, O, Klughammer, J, Rosen, Y, Gould, J, Nguyen, L, Hofree, M, Tramontozzi, PJ, Li, B, Wu, CJ, Izar, B, Haq, R, Hodi, FS, Yoon, CH, Hata, AN, Baker, SJ, Suvà, ML, Bueno, R, Stover, EH, Clay, MR, Dyer, MA, Collins, NB, Matulonis, UA, Wagle, N, Johnson, BE, Rotem, A, Rozenblatt-Rosen, O, Regev, A. Nat. Med.. 26 (5): 792-802. doi: 10.1038/s41591-020-0844-1. PubMed PMID:32405060 PubMed Central PMC7220853

2020 | Systematic comparison of single-cell and single-nucleus RNA-sequencing methods. Ding, J, Adiconis, X, Simmons, SK, Kowalczyk, MS, Hession, CC, Marjanovic, ND, Hughes, TK, Wadsworth, MH, Burks, T, Nguyen, LT, Kwon, JYH, Barak, B, Ge, W, Kedaigle, AJ, Carroll, S, Li, S, Hacohen, N, Rozenblatt-Rosen, O, Shalek, AK, Villani, AC, Regev, A, Levin, JZ. Nat. Biotechnol.. 38 (6): 737-746. doi: 10.1038/s41587-020-0465-8. PubMed PMID:32341560 PubMed Central PMC7289686

2020 | Minimal barriers to invasion during human colorectal tumor growth. Ryser, MD, Mallo, D, Hall, A, Hardman, T, King, LM, Tatishchev, S, Sorribes, IC, Maley, CC, Marks, JR, Hwang, ES, Shibata, D. Nat Commun. 11 (1): 1280. doi: 10.1038/s41467-020-14908-7. PubMed PMID:32152322 PubMed Central PMC7062901

2020 | Cancer cells deploy lipocalin-2 to collect limiting iron in leptomeningeal metastasis. Chi, Y, Remsik, J, Kiseliovas, V, Derderian, C, Sener, U, Alghader, M, Saadeh, F, Nikishina, K, Bale, T, Iacobuzio-Donahue, C, Thomas, T, Pe’er, D, Mazutis, L, Boire, A. Science. 369 (6501): 276-282. doi: 10.1126/science.aaz2193. PubMed PMID:32675368

2020 | A workflow for visualizing human cancer biopsies using large-format electron microscopy. Riesterer, JL, López, CS, Stempinski, ES, Williams, M, Loftis, K, Stoltz, K, Thibault, G, Lanicault, C, Williams, T, Gray, JW. Methods Cell Biol.. 158 : 163-181. doi: 10.1016/bs.mcb.2020.01.005. PubMed PMID:32423648

2020 | RESTORE: Robust intEnSiTy nORmalization mEthod for multiplexed imaging. Chang, YH, Chin, K, Thibault, G, Eng, J, Burlingame, E, Gray, JW. Commun Biol. 3 (1): 111. doi: 10.1038/s42003-020-0828-1. PubMed PMID:32152447 PubMed Central PMC7062831

2020 | Dual indexed library design enables compatibility of in-Drop single-cell RNA-sequencing with exAMP chemistry sequencing platforms. 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. BMC Genomics. 21 (1): 456. doi: 10.1186/s12864-020-06843-0. PubMed PMID:32616006 PubMed Central PMC7331155

2020 | A Quantitative Framework for Evaluating Single-Cell Data Structure Preservation by Dimensionality Reduction Techniques. Heiser, CN, Lau, KS. Cell Rep. 31 (5): 107576. doi: 10.1016/j.celrep.2020.107576. PubMed PMID:32375029 PubMed Central PMC7305633

2020 | Host responses to mucosal biofilms in the lung and gut. Domingue, JC, Drewes, JL, Merlo, CA, Housseau, F, Sears, CL. Mucosal Immunol. 13 (3): 413-422. doi: 10.1038/s41385-020-0270-1. PubMed PMID:32112046

2020 | Evolution and structure of clinically relevant gene fusions in multiple myeloma. Foltz, SM, Gao, Q, Yoon, CJ, Sun, H, Yao, L, Li, Y, Jayasinghe, RG, Cao, S, King, J, Kohnen, DR, Fiala, MA, Ding, L, Vij, R. Nat Commun. 11 (1): 2666. doi: 10.1038/s41467-020-16434-y. PubMed PMID:32471990 PubMed Central PMC7260243

2020 | scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data. Yu, W, Uzun, Y, Zhu, Q, Chen, C, Tan, K. Genome Biol.. 21 (1): 94. doi: 10.1186/s13059-020-02008-0. PubMed PMID:32312293 PubMed Central PMC7169039

2020 | Dissecting the tumor-immune landscape in chimeric antigen receptor T-cell therapy: key challenges and opportunities for a systems immunology approach. Chen, GM, Azzam, A, Ding, YY, Barrett, DM, Grupp, SA, Tan, K. Clin. Cancer Res.. : . doi: 10.1158/1078-0432.CCR-19-3888. PubMed PMID:32127393

2020 | Surface protein imputation from single cell transcriptomes by deep neural networks. Zhou, Z, Ye, C, Wang, J, Zhang, NR. Nat Commun. 11 (1): 651. doi: 10.1038/s41467-020-14391-0. PubMed PMID:32005835 PubMed Central PMC6994606

2020 | DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing. Zhou, Z, Xu, B, Minn, A, Zhang, NR. Genome Biol.. 21 (1): 10. doi: 10.1186/s13059-019-1922-x. PubMed PMID:31937348 PubMed Central PMC6961311

2020 | Pediatric high-grade glioma resources from the Children’s Brain Tumor Tissue Consortium. Ijaz, H, Koptyra, M, Gaonkar, KS, Rokita, JL, Baubet, VP, Tauhid, L, Zhu, Y, Brown, M, Lopez, G, Zhang, B, Diskin, SJ, Vaksman, Z, Children’s Brain Tumor Tissue Consortium, Mason, JL, Appert, E, Lilly, J, Lulla, R, De Raedt, T, Heath, AP, Felmeister, A, Raman, P, Nazarian, J, Santi, MR, Storm, PB, Resnick, A, Waanders, AJ, Cole, KA. Neuro-oncology. 22 (1): 163-165. doi: 10.1093/neuonc/noz192. PubMed PMID:31613963 PubMed Central PMC6954395

2020 | An update on the CNS manifestations of neurofibromatosis type 2. Coy, S, Rashid, R, Stemmer-Rachamimov, A, Santagata, S. Acta Neuropathol.. 139 (4): 643-665. doi: 10.1007/s00401-019-02029-5. PubMed PMID:31161239 PubMed Central PMC7038792

2020 | Regenerative lineages and immune-mediated pruning in lung cancer metastasis. Laughney, AM, Hu, J, Campbell, NR, Bakhoum, SF, Setty, M, Lavallée, VP, Xie, Y, Masilionis, I, Carr, AJ, Kottapalli, S, Allaj, V, Mattar, M, Rekhtman, N, Xavier, JB, Mazutis, L, Poirier, JT, Rudin, CM, Pe’er, D, Massagué, J. Nat. Med.. 26 (2): 259-269. doi: 10.1038/s41591-019-0750-6. PubMed PMID:32042191 PubMed Central PMC7021003

2020 | The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution. 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. Cell. 181 (2): 236-249. doi: 10.1016/j.cell.2020.03.053. PubMed PMID:32302568 PubMed Central PMC7376497

2020 | A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer. Wagner, AH, Walsh, B, Mayfield, G, Tamborero, D, Sonkin, D, Krysiak, K, Deu-Pons, J, Duren, RP, Gao, J, McMurry, J, Patterson, S, Del Vecchio Fitz, C, Pitel, BA, Sezerman, OU, Ellrott, K, Warner, JL, Rieke, DT, Aittokallio, T, Cerami, E, Ritter, DI, Schriml, LM, Freimuth, RR, Haendel, M, Raca, G, Madhavan, S, Baudis, M, Beckmann, JS, Dienstmann, R, Chakravarty, D, Li, XS, Mockus, S, Elemento, O, Schultz, N, Lopez-Bigas, N, Lawler, M, Goecks, J, Griffith, M, Griffith, OL, Margolin, AA, Variant Interpretation for Cancer Consortium. Nat. Genet.. 52 (4): 448-457. doi: 10.1038/s41588-020-0603-8. PubMed PMID:32246132 PubMed Central PMC7127986

2020 | Predicting primary site of secondary liver cancer with a neural estimator of metastatic origin. Schau, GF, Burlingame, EA, Thibault, G, Anekpuritanang, T, Wang, Y, Gray, JW, Corless, C, Chang, YH. J. Med. Imag. 7(1) 012706 (18 February 2020). doi: 10.1117/1.JMI.7.1.012706.

2020 | How Machine Learning Will Transform Biomedicine. Goecks, J, Jalili, V, Heiser, LM, Gray, JW. Cell. 181 (1): 92-101. doi: 10.1016/j.cell.2020.03.022. PubMed PMID:32243801 PubMed Central PMC7141410

2020 | High-dimensional multiplexed immunohistochemical characterization of immune contexture in human cancers. Banik, G, Betts, CB, Liudahl, SM, Sivagnanam, S, Kawashima, R, Cotechini, T, Larson, W, Goecks, J, Pai, SI, Clayburgh, DR, Tsujikawa, T, Coussens, LM. Meth. Enzymol.. 635 : 1-20. doi: 10.1016/bs.mie.2019.05.039. PubMed PMID:32122539

2020 | Yogurt consumption and colorectal polyps. Rifkin, SB, Giardiello, FM, Zhu, X, Hylind, LM, Ness, RM, Drewes, JL, Murff, HJ, Spence, EH, Smalley, WE, Gills, JJ, Mullin, GE, Kafonek, D, La Luna, L, Zheng, W, Sears, CL, Shrubsole, MJ, Biofilm Study Consortium. Br. J. Nutr.. : 1-12. doi: 10.1017/S0007114520000550. PubMed PMID:32077397

2020 | Cyclic Multiplexed-Immunofluorescence (cmIF), a Highly Multiplexed Method for Single-Cell Analysis. Eng, J, Thibault, G, Luoh, SW, Gray, JW, Chang, YH, Chin, K. Methods Mol. Biol.. 2055 : 521-562. doi: 10.1007/978-1-4939-9773-2_24. PubMed PMID:31502168

2020 | Comprehensive 3D phenotyping reveals continuous morphological variation across genetically diverse sorghum inflorescences. Li, M, Shao, MR, Zeng, D, Ju, T, Kellogg, EA, Topp, CN. New Phytol.. : . doi: 10.1111/nph.16533. PubMed PMID:32162345

2019 | A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution. Packer, JS, Zhu, Q, Huynh, C, Sivaramakrishnan, P, Preston, E, Dueck, H, Stefanik, D, Tan, K, Trapnell, C, Kim, J, Waterston, RH, Murray, JI. Science. 365 (6459): . doi: 10.1126/science.aax1971. PubMed PMID:31488706

2019 | Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity. van Galen, P, Hovestadt, V, Wadsworth Ii, MH, Hughes, TK, Griffin, GK, Battaglia, S, Verga, JA, Stephansky, J, Pastika, TJ, Lombardi Story, J, Pinkus, GS, Pozdnyakova, O, Galinsky, I, Stone, RM, Graubert, TA, Shalek, AK, Aster, JC, Lane, AA, Bernstein, BE. Cell. 176 (6): 1265-1281.e24. doi: 10.1016/j.cell.2019.01.031. PubMed PMID:30827681 PubMed Central PMC6515904

2019 | Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer. Rashid, R, Gaglia, G, Chen, YA, Lin, JR, Du, Z, Maliga, Z, Schapiro, D, Yapp, C, Muhlich, J, Sokolov, A, Sorger, P, Santagata, S. Sci Data. 6 (1): 323. doi: 10.1038/s41597-019-0332-y. PubMed PMID:31848351 PubMed Central PMC6917801

2019 | Qualifying antibodies for image-based immune profiling and multiplexed tissue imaging. Du, Z, Lin, JR, Rashid, R, Maliga, Z, Wang, S, Aster, JC, Izar, B, Sorger, PK, Santagata, S. Nat Protoc. 14 (10): 2900-2930. doi: 10.1038/s41596-019-0206-y. PubMed PMID:31534232 PubMed Central PMC6959005

2019 | Innate αβ T Cells Mediate Antitumor Immunity by Orchestrating Immunogenic Macrophage Programming. Hundeyin, M, Kurz, E, Mishra, A, Rossi, JAK, Liudahl, SM, Leis, KR, Mehrotra, H, Kim, M, Torres, LE, Ogunsakin, A, Link, J, Sears, RC, Sivagnanam, S, Goecks, J, Islam, KMS, Dolgalev, I, Savadkar, S, Wang, W, Aykut, B, Leinwand, J, Diskin, B, Adam, S, Israr, M, Gelas, M, Lish, J, Chin, K, Farooq, MS, Wadowski, B, Wu, J, Shah, S, Adeegbe, DO, Pushalkar, S, Vasudevaraja, V, Saxena, D, Wong, KK, Coussens, LM, Miller, G. Cancer Discov. 9 (9): 1288-1305. doi: 10.1158/2159-8290.CD-19-0161. PubMed PMID:31266770 PubMed Central PMC6726581

2019 | Cancer cell evolution through the ages. Maley, CC, Shibata, D. Science. 365 (6452): 440-441. doi: 10.1126/science.aay2859. PubMed PMID: 31371596.

2019 | scRNABatchQC: Multi-samples quality control for single cell RNA-seq data. Liu, Q, Sheng, Q, Ping, J, Ramirez, MA, Lau, KS, Coffey, R, Shyr, Y. Bioinformatics. 2019 Aug 2; pii: btz601. doi: 10.1093/bioinformatics/btz601. PubMed PMID: 31373345.

2019 | An update on the CNS manifestations of neurofibromatosis type 2. Coy, S, Rashid, R, Stemmer-Rachamimov, A, Santagata, S. Acta Neuropathol. 2019 Jun 4. doi: 10.1007/s00401-019-02029-5. PubMed PMID: 31161239.

2019 | The immune contexture associates with the genomic landscape in lung adenomatous premalignancy. Krysan K, Tran LM, Grimes BS, Fishbein GA, Seki A, Gardner BK, Walser TC, Salehi-Rad R, Yanagawa J, Lee JM, Sharma S, Aberle D, Spira AE, Elashoff DA, Wallace WD, Fishbein MC, Dubinett SM. Cancer Res. Epub 2019 May 29. 2019 Oct 1;79(19):5022-5033. doi: 10.1158/0008-5472.CAN-19-0153. PubMed PMID: 31142513.

2019 | SCRABBLE: single-cell RNA-seq imputation constrained by bulk RNA-seq data. Peng T, Zhu Q, Yin P, Tan K. Genome Biol. 2019 May 6; 20(1):88. doi: 10.1186/s13059-019-1681-8. PubMed PMID: 31060596. PubMed Central PMCID: PMC6501316.

2019 | Transforming Growth Factor-β Signaling in Immunity and Cancer. Batlle, E, Massagué, J. Immunity. 50 (4): 924-940. doi: 10.1016/j.immuni.2019.03.024. PubMed PMID: 30995507.

2019 | The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution. Taylor DM, Aronow BJ, Tan K, Bernt K, Salomonis N, Greene CS, Frolova A, Henrickson SE, Wells A, Pei L, Jaiswal JK, Whitsett J, Hamilton KE, MacParland SA, Kelsen J, Heuckeroth RO, Potter SS, Vella LA, Terry NA, Ghanem LR, Kennedy BC, Helbig I, Sullivan KE, Castelo-Soccio L, Kreigstein A, Herse F, Nawijn MC, Koppelman GH, Haendel M, Harris NL, Rokita JL, Zhang Y, Regev A, Rozenblatt-Rosen O, Rood JE, Tickle TL, Vento-Tormo R, Alimohamed S, Lek M, Mar JC, Loomes KM, Barrett DM, Uapinyoying P, Beggs AH, Agrawal PB, Chen YW, Muir AB, Garmire LX, Snapper SB, Nazarian J, Seeholzer SH, Fazelinia H, Singh LN, Faryabi RB, Raman P, Dawany N, Xie HM, Devkota B, Diskin SJ, Anderson SA, Rappaport EF, Peranteau W, Wikenheiser-Brokamp KA, Teichmann S, Wallace D, Peng T, Ding YY, Kim MS, Xing Y, Kong SW, Bönnemann CG, Mandl KD, White PS. Dev Cell. 2019 Apr 8; 49(1):10-29. doi: 10.1016/j.devcel.2019.03.001. PubMed PMID: 30930166. PubMed Central PMCID: PMC6616346.

2019 | Robust Cell Detection and Segmentation for Image Cytometry Reveal Th17 Cell Heterogeneity. Tsujikawa T, Thibault G, Azimi V, Sivagnanam S, Banik G, Means C, Kawashima R, Clayburgh DR, Gray JW, Coussens LM, Chang YH. Cytometry A. 2019 Apr; 95(4):389-398. doi: 10.1002/cyto.a.23726. PubMed PMID: 30714674. PubMed Central PMCID: PMC6461524.

2019 | Therapeutic Clues from an Integrated Omic Assessment of East Asian Triple Negative Breast Cancers. Heiser LM, Mills GB, Gray JW. Cancer Cell. 2019 Mar 18; 35(3):341-343. doi: 10.1016/j.ccell.2019.02.012. PubMed PMID: 30889376. PubMed Central PMCID: PMC6499473.

2018 | pyNVR: Investigating factors affecting feature selection from scRNA-seq data for lineage reconstruction. Chen B, Herring CA, Lau KS. Bioinformatics. 2018 Nov 16; pii: 5184958. doi: 10.1093/bioinformatics/bty950. PubMed PMID: 30445607. PubMed Central PMCID: PMC6596893.

2018 | A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade. Jerby-Arnon L, Shah P, Cuoco MS, Rodman C, Su MJ, Melms JC, Leeson R, Kanodia A, Mei S, Lin JR, Wang S, Rabasha B, Liu D, Zhang G, Margolais C, Ashenberg O, Ott PA, Buchbinder EI, Haq R, Hodi FS, Boland GM, Sullivan RJ, Frederick DT, Miao B, Moll T, Flaherty KT, Herlyn M, Jenkins RW, Thummalapalli R, Kowalczyk MS, Cañadas I, Schilling B, Cartwright ANR, Luoma AM, Malu S, Hwu P, Bernatchez C, Forget MA, Barbie DA, Shalek AK, Tirosh I, Sorger PK, Wucherpfennig K, Van Allen EM, Schadendorf D, Johnson BE, Rotem A, Rozenblatt-Rosen O, Garraway LA, Yoon CH, Izar B, Regev A. Cell. 2018 Nov 1; 175(4):984-997.e24. doi: 10.1016/j.cell.2018.09.006. PubMed PMID: 30388455. PubMed Central PMCID: PMC6410377.

2018 | Quantitative assessment of cell population diversity in single-cell landscapes. Liu Q, Herring CA, Sheng Q, Ping J, Simmons AJ, Chen B, Banerjee A, Li W, Gu G, Coffey RJ, Shyr Y, Lau KS. PLoS Biol. 2018 Oct 22; 16(10):e2006687. doi: 10.1371/journal.pbio.2006687. PubMed PMID: 30346945. PubMed Central PMCID: PMC6211764.

2018 | The PreCancer Atlas (PCA). Srivastava S, Ghosh S, Kagan J, Mazurchuk R. Trends Cancer. 2018 Aug; 4(8):513-514. doi: 10.1016/j.trecan.2018.06.003. PubMed PMID: 30064657.

2018 | The Making of a PreCancer Atlas: Promises, Challenges, and Opportunities. Srivastava S, Ghosh S, Kagan J, Mazurchuk R. Trends Cancer. 2018 Aug;4(8):523-536. doi: 10.1016/j.trecan.2018.06.007. PubMed PMID: 30064661.