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Principal Investigator
Peter Karl Sorger
Awardee Organization

Harvard Medical School
United States

Fiscal Year
2023
Activity Code
U2C
Early Stage Investigator Grants (ESI)
Not Applicable
Project End Date

Pre-cancer atlases of cutaneous and hematologic origin (PATCH Center)

The overall aims of the Center for Pre-cancer Atlases of Cutaneous and Hematologic Origin (PATCH Center) will pivot in the supplemental year to focus on data analysis and dissemination. The Administration and Project Management team will focus on the scientific management of the Center, communicate with NCI staff and HTAN Centers, and ensure regular data deposition. They will guide the other Center members to focus on all activities related to the completion and dissemination of the Center atlas. We anticipate the biospecimen and clinical teams will focus on curating clinical and biospecimen metadata and participating in the interpretation of results for publication and other dissemination activities. Most characterization activities for the atlas and the SARDANA TNP will be completed prior to the initiation of the supplement, but additional characterization will be performed for quality assurance and follow up experimentation during the publication process. The bulk of the activities will be in data analysis, software development, and dissemination of complex image data. The Center will be working on 3D segmentation and visualization tools, improvements to the MCMICRO pipeline, and advancements to Minerva Story tools to accommodate 3D visualization as well as clinical and biospecimen metadata. Our Center will continue to work with the DCC to develop and optimize the process for sharing highly complex imaging data.

Publications

  • Rashid R, Chen YA, Hoffer J, Muhlich JL, Lin JR, Krueger R, Pfister H, Mitchell R, Santagata S, Sorger PK. Narrative online guides for the interpretation of digital-pathology images and tissue-atlas data. Nature biomedical engineering. 2022 May;6(5):515-526. Epub 2021 Nov 8. PMID: 34750536
  • Coy S, Rashid R, Stemmer-Rachamimov A, Santagata S. An update on the CNS manifestations of neurofibromatosis type 2. Acta neuropathologica. 2020 Apr;139(4):643-665. Epub 2019 Jun 4. PMID: 31161239
  • Hoffer J, Rashid R, Muhlich JL, Chen YA, Russell DPW, Ruokonen J, Krueger R, Pfister H, Santagata S, Sorger PK. Minerva: a light-weight, narrative image browser for multiplexed tissue images. Journal of open source software. 2020;5. (54). Epub 2020 Oct 15. PMID: 33768192
  • Muhlich JL, Chen YA, Yapp C, Russell D, Santagata S, Sorger PK. Stitching and registering highly multiplexed whole-slide images of tissues and tumors using ASHLAR. Bioinformatics (Oxford, England). 2022 Sep 30;38(19):4613-4621. PMID: 35972352
  • Morth E, Sidak K, Maliga Z, Moller T, Gehlenborg N, Sorger P, Pfister H, Beyer J, Kruger R. Cell2Cell: Explorative Cell Interaction Analysis in Multi-Volumetric Tissue Data. IEEE transactions on visualization and computer graphics. 2025 Jan;31(1):569-579. Epub 2024 Dec 3. PMID: 39255170
  • Prabhakaran S, Yapp C, Baker GJ, Beyer J, Chang YH, Creason AL, Krueger R, Muhlich J, Patterson NH, Sidak K, Sudar D, Taylor AJ, Ternes L, Troidl J, Xie Y, Sokolov A, Tyson DR, Cell Imaging Hackathon 2022 Participants. Addressing persistent challenges in digital image analysis of cancerous tissues. bioRxiv : the preprint server for biology. 2023 Jul 24. PMID: 37547011
  • Russell-Goldman E, Murphy GF. The Pathobiology of Skin Aging: New Insights into an Old Dilemma. The American journal of pathology. 2020 Jul;190(7):1356-1369. Epub 2020 Apr 1. PMID: 32246919
  • Maliga Z, Kim DY, Bui AN, Lin JR, Dewan AK, Jadeja S, Murphy GF, Nirmal AJ, Lian CG, Sorger PK, LeBoeuf NR. Immune Profiling of Dermatologic Adverse Events from Checkpoint Blockade Using Tissue Cyclic Immunofluorescence: A Pilot Study. The Journal of investigative dermatology. 2024 Aug;144(8):1887-1890.e5. Epub 2024 Feb 14. PMID: 38360200
  • Coy S, Lee JS, Chan SJ, Woo T, Jones J, Alexandrescu S, Wen PY, Sorger PK, Ligon KL, Santagata S. Systematic characterization of antibody-drug conjugate targets in central nervous system tumors. Neuro-oncology. 2024 Mar 4;26(3):458-472. PMID: 37870091
  • Schapiro D, Yapp C, Sokolov A, Reynolds SM, Chen YA, Sudar D, Xie Y, Muhlich J, Arias-Camison R, Arena S, Taylor AJ, Nikolov M, Tyler M, Lin JR, Burlingame EA, Human Tumor Atlas Network, Chang YH, Farhi SL, Thorsson V, Venkatamohan N, Drewes JL, Pe'er D, Gutman DA, Herrmann MD, Gehlenborg N, Bankhead P, Roland JT, Herndon JM, Snyder MP, Angelo M, Nolan G, Swedlow JR, Schultz N, Merrick DT, Mazzili SA, Cerami E, Rodig SJ, Santagata S, Sorger PK, Abravanel DL, Achilefu S, Ademuyiwa FO, Adey AC, Aft R, Ahn KJ, Alikarami F, Alon S, Ashenberg O, Baker E, Baker GJ, Bandyopadhyay S, Bayguinov P, Beane J, Becker W, Bernt K, Betts CB, Bletz J, Blosser T, Boire A, Boland GM, Boyden ES, Bucher E, Bueno R, Cai Q, Cambuli F, Campbell J, Cao S, Caravan W, Chaligné R, Chan JM, Chasnoff S, Chatterjee D, Chen AA, Chen C, Chen CH, Chen B, Chen F, Chen S, Chheda MG, Chin K, Cho H, Chun J, Cisneros L, Coffey RJ, Cohen O, Colditz GA, Cole KA, Collins N, Cotter D, Coussens LM, Coy S, Creason AL, Cui Y, Zhou DC, Curtis C, Davies SR, Bruijn I, Delorey TM, Demir E, Denardo D, Diep D, Ding L, DiPersio J, Dubinett SM, Eberlein TJ, Eddy JA, Esplin ED, Factor RE, Fatahalian K, Feiler HS, Fernandez J, Fields A, Fields RC, Fitzpatrick JAJ, Ford JM, Franklin J, Fulton B, Gaglia G, Galdieri L, Ganesh K, Gao J, Gaudio BL, Getz G, Gibbs DL, Gillanders WE, Goecks J, Goodwin D, Gray JW, Greenleaf W, Grimm LJ, Gu Q, Guerriero JL, Guha T, Guimaraes AR, Gutierrez B, Hacohen N, Hanson CR, Harris CR, Hawkins WG, Heiser CN, Hoffer J, Hollmann TJ, Hsieh JJ, Huang J, Hunger SP, Hwang ES, Iacobuzio-Donahue C, Iglesia MD, Islam M, Izar B, Jacobson CA, Janes S, Jayasinghe RG, Jeudi T, Johnson BE, Johnson BE, Ju T, Kadara H, Karnoub ER, Karpova A, Khan A, Kibbe W, Kim AH, King LM, Kozlowski E, Krishnamoorthy P, Krueger R, Kundaje A, Ladabaum U, Laquindanum R, Lau C, Lau KSK, LeBoeuf NR, Lee H, Lenburg M, Leshchiner I, Levy R, Li Y, Lian CG, Liang WW, Lim KH, Lin Y, Liu D, Liu Q, Liu R, Lo J, Lo P, Longabaugh WJ, Longacre T, Luckett K, Ma C, Maher C, Maier A, Makowski D, Maley C, Maliga Z, Manoj P, Maris JM, Markham N, Marks JR, Martinez D, Mashl J, Masilionis I, Massague J, Mazurowski MA, McKinley ET, McMichael J, Meyerson M, Mills GB, Mitri ZI, Moorman A, Mudd J, Murphy GF, Deen NNA, Navin NE, Nawy T, Ness RM, Nevins S, Nirmal AJ, Novikov E, Oh ST, Oldridge DA, Owzar K, Pant SM, Park W, Patti GJ, Paul K, Pelletier R, Persson D, Petty C, Pfister H, Polyak K, Puram SV, Qiu Q, Villalonga ÁQ, Ramirez MA, Rashid R, Reeb AN, Reid ME, Remsik J, Riesterer JL, Risom T, Ritch CC, Rolong A, Rudin CM, Ryser MD, Sato K, Sears CL, Semenov YR, Shen J, Shoghi KI, Shrubsole MJ, Shyr Y, Sibley AB, Simmons AJ, Sinha A, Sivagnanam S, Song SK, Southar-Smith A, Spira AE, Cyr JS, Stefankiewicz S, Storrs EP, Stover EH, Strand SH, Straub C, Street C, Su T, Surrey LF, Suver C, Tan K, Terekhanova NV, Ternes L, Thadi A, Thomas G, Tibshirani R, Umeda S, Uzun Y, Vallius T, Van Allen ER, Vandekar S, Vega PN, Veis DJ, Vennam S, Verma A, Vigneau S, Wagle N, Wahl R, Walle T, Wang LB, Warchol S, Washington MK, Watson C, Weimer AK, Wendl MC, West RB, White S, Windon AL, Wu H, Wu CY, Wu Y, Wyczalkowski MA, Xu J, Yao L, Yu W, Zhang K, Zhu X. MITI minimum information guidelines for highly multiplexed tissue images. Nature methods. 2022 Mar;19(3):262-267. PMID: 35277708
  • Baker GJ, Novikov E, Zhao Z, Vallius T, Davis JA, Lin JR, Muhlich JL, Mittendorf EA, Santagata S, Guerriero JL, Sorger PK. Quality Control for Single Cell Analysis of High-plex Tissue Profiles using CyLinter. bioRxiv : the preprint server for biology. 2024 Mar 22. PMID: 37961235
  • Smith NP, Yan Y, Pan Y, Williams JB, Manakongtreecheep K, Pant S, Zhao J, Tian T, Pan T, Stingley C, Wu K, Zhang J, Kley AL, Sorger PK, Villani AC, Kupper TS. Resident memory T cell development is associated with AP-1 transcription factor upregulation across anatomical niches. bioRxiv : the preprint server for biology. 2023 Oct 2. PMID: 37873428
  • Herzberger L, Hadwiger M, Kruger R, Sorger P, Pfister H, Groller E, Beyer J. Residency Octree: A Hybrid Approach for Scalable Web-Based Multi-Volume Rendering. IEEE transactions on visualization and computer graphics. 2024 Jan;30(1):1380-1390. Epub 2023 Dec 25. PMID: 37889813
  • Irvine EB, O'Neil A, Darrah PA, Shin S, Choudhary A, Li W, Honnen W, Mehra S, Kaushal D, Gideon HP, Flynn JL, Roederer M, Seder RA, Pinter A, Fortune S, Alter G. Robust IgM responses following intravenous vaccination with Bacille Calmette-Guérin associate with prevention of Mycobacterium tuberculosis infection in macaques. Nature immunology. 2021 Dec;22(12):1515-1523. Epub 2021 Nov 22. PMID: 34811542
  • Ternes L, Lin JR, Chen YA, Gray JW, Chang YH. Computational multiplex panel reduction to maximize information retention in breast cancer tissue microarrays. PLoS computational biology. 2022 Sep 30;18(9):e1010505. doi: 10.1371/journal.pcbi.1010505. eCollection 2022 Sep. PMID: 36178966
  • Smith NP, Yan Y, Pan Y, Williams JB, Manakongtreecheep K, Pant SM, Zhao J, Tian T, Pan T, Stingley C, Wu K, Zhang J, Kley AL, Sorger PK, Villani AC, Kupper TS. Resident memory T cell development is gradual and shows AP-1 gene expression in mature cells. JCI insight. 2025 Jun 23;10. (12). doi: 10.1172/jci.insight.187381. eCollection 2025 Jun 23. PMID: 40548376
  • Du Z, Lin JR, Rashid R, Maliga Z, Wang S, Aster JC, Izar B, Sorger PK, Santagata S. Qualifying antibodies for image-based immune profiling and multiplexed tissue imaging. Nature protocols. 2019 Oct;14(10):2900-2930. Epub 2019 Sep 18. PMID: 31534232
  • 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. The Spatial Landscape of Progression and Immunoediting in Primary Melanoma at Single-Cell Resolution. Cancer discovery. 2022 Jun 2;12(6):1518-1541. PMID: 35404441
  • Lecky E, Mukherji A, German R, Antonellis G, Lin JR, Yorsz M, McQueeney KE, Ryan J, Ng K, Sicinska E, Sorger PK, Letai A, Bhola PD. Sequential apoptotic and multiplexed proteomic evaluation of single cancer cells. Science advances. 2023 Jun 23;9(25):eadg4128. Epub 2023 Jun 23. PMID: 37352344
  • 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. MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging. Nature methods. 2022 Mar;19(3):311-315. Epub 2021 Nov 25. PMID: 34824477
  • Fang R, Vallius T, Zhang A, Van Cura D, Alicandri F, Fischer G, Draper E, Xu S, Pelletier R, Katsyv I, Sorger PK, Murphy GF, Lian CG. PRAME expression in melanoma is negatively regulated by TET2-mediated DNA hydroxymethylation. bioRxiv : the preprint server for biology. 2024 Jul 26. PMID: 39091741
  • Baker GJ, Novikov E, Zhao Z, Vallius T, Davis JA, Lin JR, Muhlich JL, Mittendorf EA, Santagata S, Guerriero JL, Sorger PK. Quality control for single-cell analysis of high-plex tissue profiles using CyLinter. Nature methods. 2024 Dec;21(12):2248-2259. Epub 2024 Oct 30. PMID: 39478175
  • 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 19;186(2):363-381.e19. PMID: 36669472
  • Gaglia G, Burger ML, Ritch CC, Rammos D, Dai Y, Crossland GE, Tavana SZ, Warchol S, Jaeger AM, Naranjo S, Coy S, Nirmal AJ, Krueger R, Lin JR, Pfister H, Sorger PK, Jacks T, Santagata S. Lymphocyte networks are dynamic cellular communities in the immunoregulatory landscape of lung adenocarcinoma. Cancer cell. 2023 May 8;41(5):871-886.e10. Epub 2023 Apr 13. PMID: 37059105
  • Nirmal AJ, Yapp C, Santagata S, Sorger PK. Cell Spotter (CSPOT): A machine-learning approach to automated cell spotting and quantification of highly multiplexed tissue images. bioRxiv : the preprint server for biology. 2023 Nov 17. PMID: 38014110
  • Rashid R, Gaglia G, Chen YA, Lin JR, Du Z, Maliga Z, Schapiro D, Yapp C, Muhlich J, Sokolov A, Sorger P, Santagata S. Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer. Scientific data. 2019 Dec 17;6(1):323. PMID: 31848351
  • Mollaoglu G, Tepper A, Falcomatà C, Potak HT, Pia L, Amabile A, Mateus-Tique J, Rabinovich N, Park MD, LaMarche NM, Brody R, Browning L, Lin JR, Zamarin D, Sorger PK, Santagata S, Merad M, Baccarini A, Brown BD. Ovarian cancer-derived IL-4 promotes immunotherapy resistance. Cell. 2024 Dec 26;187(26):7492-7510.e22. Epub 2024 Oct 30. PMID: 39481380
  • Haddox CL, Nathenson MJ, Mazzola E, Lin JR, Baginska J, Nau A, Weirather JL, Choy E, Marino-Enriquez A, Morgan JA, Cote GM, Merriam P, Wagner AJ, Sorger PK, Santagata S, George S. Phase II Study of Eribulin plus Pembrolizumab in Metastatic Soft-tissue Sarcomas: Clinical Outcomes and Biological Correlates. Clinical cancer research : an official journal of the American Association for Cancer Research. 2024 Apr 1;30(7):1281-1292. PMID: 38236580
  • Yapp C, Novikov E, Jang WD, Vallius T, Chen YA, Cicconet M, Maliga Z, Jacobson CA, Wei D, Santagata S, Pfister H, Sorger PK. UnMICST: Deep learning with real augmentation for robust segmentation of highly multiplexed images of human tissues. Communications biology. 2022 Nov 18;5(1):1263. PMID: 36400937
  • Irvine EB, Nikolov A, Khan MZ, Peters JM, Lu R, Sixsmith J, Wallace A, van Woudenbergh E, Shin S, Karpinski W, Hsiao JC, Casadevall A, Bryson BD, Cavacini L, Grace PS, Alter G, Fortune SM. Fc-engineered antibodies promote neutrophil-dependent control of Mycobacterium tuberculosis. Nature microbiology. 2024 Sep;9(9):2369-2382. Epub 2024 Aug 22. PMID: 39174703
  • de Bruijn I, Nikolov M, Lau C, Clayton A, Gibbs DL, Mitraka E, Pozhidayeva D, Lash A, Sumer SO, Altreuter J, Anton K, DeFelice M, Li X, Lisman A, Longabaugh WJR, Muhlich J, Santagata S, Nandakumar S, Sorger PK, Suver C, Doan X, Guinney J, Schultz N, Taylor AJ, Thorsson V, Cerami E, Eddy JA. Sharing data from the Human Tumor Atlas Network through standards, infrastructure and community engagement. Nature methods. 2025 Apr;22(4):664-671. Epub 2025 Mar 31. PMID: 40164800
  • Inde Z, Yapp C, Joshi GN, Spetz J, Fraser C, Deskin B, Ghelfi E, Sodhi C, Hackam DJ, Kobzik L, Croker BA, Brownfield D, Jia H, Sarosiek KA. Age-dependent regulation of SARS-CoV-2 cell entry genes and cell death programs correlates with COVID-19 disease severity. bioRxiv : the preprint server for biology. 2020 Sep 13. PMID: 32935109
  • Kader T, Lin JR, Hug CB, Coy S, Chen YA, de Bruijn I, Shih N, Jung E, Pelletier RJ, Lopez Leon M, Mingo G, Omran DK, Lee JS, Yapp C, Satravada BA, Kundra R, Xu Y, Chan S, Tefft JB, Muhlich JL, Kim SH, Gysler SM, Agudo J, Heath JR, Schultz N, Drescher CW, Sorger PK, Drapkin R, Santagata S. Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma. Cancer discovery. 2025 Jun 3;15(6):1180-1202. PMID: 39704522
  • Jain Y, Jepson J, Chen R, Maier E, Herr BW 2nd, Puig-Barbe A, Quardokus EM, Qaurooni D, Yapp C, Ewing SL, Enninful A, Farzad N, Bueckle A, Easter QT, Matuck B, Zhu C, Monte EM, Purkerson JM, Jehrio M, Misra RS, Fan R, Ginty F, Karunamurthy A, Fan J, Campbell-Thompson M, Pryhuber GS, Byrd KM, Hickey JW, Börner K. Exploring endothelial cell environments across organs in spatially resolved omics data. bioRxiv : the preprint server for biology. 2025 Sep 25. PMID: 41040203
  • Baker GJ, Novikov E, Coy S, Chen YA, Hug CB, Ahmed Z, Cajas Ordóñez SA, Huang S, Yapp C, Sokolov A, Pfister H, Santagata S, Sorger PK. Morphology-Aware Profiling of Highly Multiplexed Tissue Images using Variational Autoencoders. bioRxiv : the preprint server for biology. 2025 Jun 27. PMID: 40667089
  • Vallius T, Shi Y, Novikov E, Pant SM, Pelletier R, Chen YA, Tefft JB, Johnson AN, Maliga Z, Wan G, Murphy G, Santagata S, Semenov YR, Liu D, Lian CG, Sorger PK. Spatial determinants of tumor cell dedifferentiation and plasticity in primary cutaneous melanoma. bioRxiv : the preprint server for biology. 2025 Jun 24. PMID: 40667360
  • Prabhakaran S, Yapp C, Baker GJ, Beyer J, Chang YH, Creason AL, Krueger R, Muhlich J, Patterson NH, Sidak K, Sudar D, Taylor AJ, Ternes L, Troidl J, Yubin X, Sokolov A, Tyson DR. Addressing persistent challenges in digital image analysis of cancer tissue: resources developed from a hackathon. Molecular oncology. 2025 Jun;19(6):1565-1581. Epub 2025 Feb 10. PMID: 39927650
  • Kader T, Lin JR, Hug C, Coy S, Chen YA, de Bruijn I, Shih N, Jung E, Pelletier RJ, Leon ML, Mingo G, Omran DK, Lee JS, Yapp C, Satravada BA, Kundra R, Xu Y, Chan S, Tefft JB, Muhlich J, Kim S, Gysler SM, Agudo J, Heath JR, Schultz N, Drescher C, Sorger PK, Drapkin R, Santagata S. Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma. bioRxiv : the preprint server for biology. 2024 Sep 27. PMID: 39386723
  • Yapp C, Nirmal AJ, Zhou F, Wong AYH, Tefft JB, Lu YD, Shang Z, Maliga Z, Llopis PM, Murphy GF, Lian CG, Danuser G, Santagata S, Sorger PK. Highly Multiplexed 3D Profiling of Cell States and Immune Niches in Human Tumours. bioRxiv : the preprint server for biology. 2025 Apr 11. PMID: 38014052
  • Guerriero JL, Lin JR, Pastorello RG, Du Z, Chen YA, Townsend MG, Shimada K, Hughes ME, Ren S, Tayob N, Zheng K, Mei S, Patterson A, Taneja KL, Metzger O, Tolaney SM, Lin NU, Dillon DA, Schnitt SJ, Sorger PK, Mittendorf EA, Santagata S. Qualification of a multiplexed tissue imaging assay and detection of novel patterns of HER2 heterogeneity in breast cancer. NPJ breast cancer. 2024 Jan 2;10(1):2. PMID: 38167908
  • 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, Aberle D, Achilefu SI, Ademuyiwa FO, Adey AC, Aft RL, Agarwal R, Aguilar RA, Alikarami F, Allaj V, Amos C, Anders RA, Angelo MR, Anton K, Ashenberg O, Aster JC, Babur O, Bahmani A, Balsubramani A, Barrett D, Beane J, Bender DE, Bernt K, Berry L, Betts CB, Bletz J, Blise K, Boire A, Boland G, Borowsky A, Bosse K, Bott M, Boyden E, Brooks J, Bueno R, Burlingame EA, Cai Q, Campbell J, Caravan W, Cerami E, Chaib H, Chan JM, Chang YH, Chatterjee D, Chaudhary O, Chen AA, Chen B, Chen C, Chen CH, Chen F, Chen YA, Chheda MG, Chin K, Chiu R, Chu SK, Chuaqui R, Chun J, Cisneros L, Coffey RJ, Colditz GA, Cole K, Collins N, Contrepois K, Coussens LM, Creason AL, Crichton D, Curtis C, Davidsen T, Davies SR, de Bruijn I, Dellostritto L, De Marzo A, Demir E, DeNardo DG, Diep D, Ding L, Diskin S, Doan X, Drewes J, Dubinett S, Dyer M, Egger J, Eng J, Engelhardt B, Erwin G, Esplin ED, Esserman L, Felmeister A, Feiler HS, Fields RC, Fisher S, Flaherty K, Flournoy J, Ford JM, Fortunato A, Frangieh A, Frye JL, Fulton RS, Galipeau D, Gan S, Gao J, Gao L, Gao P, Gao VR, Geiger T, George A, Getz G, Ghosh S, Giannakis M, Gibbs DL, Gillanders WE, Goecks J, Goedegebuure SP, Gould A, Gowers K, Gray JW, Greenleaf W, Gresham J, Guerriero JL, Guha TK, Guimaraes AR, Guinney J, Gutman D, Hacohen N, Hanlon S, Hansen CR, Harismendy O, Harris KA, Hata A, Hayashi A, Heiser C, Helvie K, Herndon JM, Hirst G, Hodi F, Hollmann T, Horning A, Hsieh JJ, Hughes S, Huh WJ, Hunger S, Hwang SE, Iacobuzio-Donahue CA, Ijaz H, Izar B, Jacobson CA, Janes S, Jané-Valbuena J, Jayasinghe RG, Jiang L, Johnson BE, Johnson B, Ju T, Kadara H, Kaestner K, Kagan J, Kalinke L, Keith R, Khan A, Kibbe W, Kim AH, Kim E, Kim J, Kolodzie A, Kopytra M, Kotler E, Krueger R, Krysan K, Kundaje A, Ladabaum U, Lake BB, Lam H, Laquindanum R, Lau KS, Laughney AM, Lee H, Lenburg M, Leonard C, Leshchiner I, Levy R, Li J, Lian CG, Lim KH, Lin JR, Lin Y, Liu Q, Liu R, Lively T, Longabaugh WJR, Longacre T, Ma CX, Macedonia MC, Madison T, Maher CA, Maitra A, Makinen N, Makowski D, Maley C, Maliga Z, Mallo D, Maris J, Markham N, Marks J, Martinez D, Mashl RJ, Masilionais I, Mason J, Massagué J, Massion P, Mattar M, Mazurchuk R, Mazutis L, Mazzilli SA, McKinley ET, McMichael JF, Merrick D, Meyerson M, Miessner JR, Mills GB, Mills M, Mondal SB, Mori M, Mori Y, Moses E, Mosse Y, Muhlich JL, Murphy GF, Navin NE, Nawy T, Nederlof M, Ness R, Nevins S, Nikolov M, Nirmal AJ, Nolan G, Novikov E, Oberdoerffer P, O'Connell B, Offin M, Oh ST, Olson A, Ooms A, Ossandon M, Owzar K, Parmar S, Patel T, Patti GJ, Pe'er D, Pe'er I, Peng T, Persson D, Petty M, Pfister H, Polyak K, Pourfarhangi K, Puram SV, Qiu Q, Quintanal-Villalonga Á, Raj A, Ramirez-Solano M, Rashid R, Reeb AN, Regev A, Reid M, Resnick A, Reynolds SM, Riesterer JL, Rodig S, Roland JT, Rosenfield S, Rotem A, Roy S, Rozenblatt-Rosen O, Rudin CM, Ryser MD, Santagata S, Santi-Vicini M, Sato K, Schapiro D, Schrag D, Schultz N, Sears CL, Sears RC, Sen S, Sen T, Shalek A, Sheng J, Sheng Q, Shoghi KI, Shrubsole MJ, Shyr Y, Sibley AB, Siex K, Simmons AJ, Singer DS, Sivagnanam S, Slyper M, Snyder MP, Sokolov A, Song SK, Sorger PK, Southard-Smith A, Spira A, Srivastava S, Stein J, Storm P, Stover E, Strand SH, Su T, Sudar D, Sullivan R, Surrey L, Suvà M, Tan K, Terekhanova NV, Ternes L, Thammavong L, Thibault G, Thomas GV, Thorsson V, Todres E, Tran L, Tyler M, Uzun Y, Vachani A, Van Allen E, Vandekar S, Veis DJ, Vigneau S, Vossough A, Waanders A, Wagle N, Wang LB, Wendl MC, West R, Williams EH, Wu CY, Wu H, Wu HY, Wyczalkowski MA, Xie Y, Yang X, Yapp C, Yu W, Yuan Y, Zhang D, Zhang K, Zhang M, Zhang N, Zhang Y, Zhao Y, Zhou DC, Zhou Z, Zhu H, Zhu Q, Zhu X, Zhu Y, Zhuang X. The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution. Cell. 2020 Apr 16;181(2):236-249. PMID: 32302568
  • Fang R, Vallius T, Zhang A, Van Cura D, Alicandri F, Fischer G, Draper E, Xu S, Pelletier R, Wang J, Mandinova A, Katsyv I, Sorger PK, Murphy GF, Lian CG. PRAME Expression in Melanoma is Negatively Regulated by TET2-Mediated DNA Hydroxymethylation. Laboratory investigation; a journal of technical methods and pathology. 2025 May;105(5):104123. Epub 2025 Feb 28. PMID: 40024557
  • Coy S, Cheng B, Lee JS, Rashid R, Browning L, Xu Y, Chakrabarty SS, Yapp C, Chan S, Tefft JB, Scott E, Spektor A, Ligon KL, Baker GJ, Pellman D, Sorger PK, Santagata S. 2D and 3D multiplexed subcellular profiling of nuclear instability in human cancer. bioRxiv : the preprint server for biology. 2023 Nov 11. PMID: 37986801
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