PUBLICATIONS

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 | 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 | 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.