Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482 · see citing works

Fitting Linear Mixed-Effects Models Using <b>lme4</b>

Bates, D., Mächler, M., Bolker, B., & Walker, S. (2015) · Journal of Statistical Software · doi:10.18637/jss.v067.i01 · Cited by 86,835 · see citing works

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625 · see citing works

<b>lmerTest</b> Package: Tests in Linear Mixed Effects Models

Kuznetsova, A., Brockhoff, P. B., & Christensen, R. H. B. (2017) · Journal of Statistical Software · doi:10.18637/jss.v082.i13 · Cited by 24,346 · see citing works

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

Li, B., & Dewey, C. N. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-323 · Cited by 22,179 · see citing works

GSVA: gene set variation analysis for microarray and RNA-Seq data

Hänzelmann, S., Castelo, R., & Guinney, J. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-7 · Cited by 15,440 · see citing works

The Molecular Signatures Database Hallmark Gene Set Collection

Liberzon, A., Birger, C., Thorvaldsdóttir, H., Ghandi, M., Mesirov, J. P., & Tamayo, P. (2015) · Cell Systems · doi:10.1016/j.cels.2015.12.004 · Cited by 13,807 · see citing works

Fast, sensitive and accurate integration of single-cell data with Harmony

Korsunsky, I., Millard, N., Fan, J., Slowikowski, K., Zhang, F., Wei, K., Baglaenko, Y., Brenner, M., Loh, P.-R., & Raychaudhuri, S. (2019) · Nature Methods · doi:10.1038/s41592-019-0619-0 · Cited by 10,488 · see citing works

UMAP: Uniform Manifold Approximation and Projection

McInnes, L., Healy, J., Saul, N., & Großberger, L. (2018) · Journal of Open Source Software · doi:10.21105/joss.00861 · Cited by 9,826 · see citing works

SCANPY: large-scale single-cell gene expression data analysis

Wolf, F. A., Angerer, P., & Theis, F. J. (2018) · Genome Biology · doi:10.1186/s13059-017-1382-0 · Cited by 8,881 · see citing works

From Louvain to Leiden: guaranteeing well-connected communities

Traag, V. A., Waltman, L., & van Eck, N. J. (2019) · Scientific Reports · doi:10.1038/s41598-019-41695-z · Cited by 5,635 · see citing works

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

Patel, A. P., Tirosh, I., Trombetta, J. J., Shalek, A. K., Gillespie, S. M., Wakimoto, H., Cahill, D. P., Nahed, B. V., Curry, W. T., Martuza, R. L., et al. (2014) · Science · doi:10.1126/science.1254257 · Cited by 5,063 · see citing works

Genomic analyses identify molecular subtypes of pancreatic cancer

Bailey, P., Chang, D. K., Nones, K., Johns, A. L., Patch, A.-M., Gingras, M.-C., Miller, D. K., Christ, A. N., Bruxner, T. J. C., Quinn, M. C., et al. (2016) · Nature · doi:10.1038/nature16965 · Cited by 3,621 · see citing works

ilastik: interactive machine learning for (bio)image analysis

Berg, S., Kutra, D., Kroeger, T., Straehle, C., Kausler, B. X., Haubold, C., Schiegg, M., Aleš, J., Beier, T., Rudy, M., et al. (2019) · Nature Methods · doi:10.1038/s41592-019-0582-9 · Cited by 3,277 · see citing works

The prognostic landscape of genes and infiltrating immune cells across human cancers

Gentles, A. J., Newman, A. M., Liu, C. L., Bratman, S. V., Feng, W., Kim, D., Nair, V. S., Xu, Y., Khuong, A., Hoang, C. D., et al. (2015) · Nature Medicine · doi:10.1038/nm.3909 · Cited by 3,097 · see citing works

FOLFIRINOX or Gemcitabine as Adjuvant Therapy for Pancreatic Cancer

Conroy, T., Hammel, P., Hebbar, M., Ben Abdelghani, M., Wei, A. C., Raoul, J.-L., Choné, L., Francois, E., Artru, P., Biagi, J. J., et al. (2018) · New England Journal of Medicine · doi:10.1056/nejmoa1809775 · Cited by 2,874 · see citing works

Pancreatic cancer

Mizrahi, J. D., Surana, R., Valle, J. W., & Shroff, R. T. (2020) · The Lancet · doi:10.1016/s0140-6736(20)30974-0 · Cited by 2,559 · see citing works

Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer

Puram, S. V., Tirosh, I., Parikh, A. S., Patel, A. P., Yizhak, K., Gillespie, S., Rodman, C., Luo, C. L., Mroz, E. A., Emerick, K. S., et al. (2017) · Cell · doi:10.1016/j.cell.2017.10.044 · Cited by 2,557 · see citing works

Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer

Robertson, A. G., Kim, J., Al‐Ahmadie, H. A., Joaquim Bellmunt, B., Guo, G., Cherniack, A. D., Hinoue, T., Laird, P. W., Hoadley, K. A., Akbani, R., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.007 · Cited by 2,435 · see citing works

Cross-species single-cell analysis of pancreatic ductal adenocarcinoma reveals antigen-presenting cancer-associated fibroblasts

Elyada, E., Bolisetty, M., Laise, P., Flynn, W. F., Courtois, E. T., Burkhart, R. A., Teinor, J. A., Belleau, P., Biffi, G., Lucito, M. S., et al. (2019) · Cancer Discovery · doi:10.1158/2159-8290.cd-19-0094 · Cited by 2,241 · see citing works

Virtual microdissection identifies distinct tumor- and stroma-specific subtypes of pancreatic ductal adenocarcinoma

Moffitt, R. A., Marayati, R., Flate, E. L., Volmar, K. E., Loeza, S. G. H., Hoadley, K. A., Rashid, N. U., Williams, L. A., Eaton, S. C., Chung, A. H., et al. (2015) · Nature Genetics · doi:10.1038/ng.3398 · Cited by 2,194 · see citing works

Organoid models of human and mouse ductal pancreatic cancer

Boj, S. F., Hwang, C.-I., Baker, L. A., Chio, I. I. C., Engle, D. D., Corbo, V., Jager, M., Ponz-Sarvise, M., Tiriac, H., Spector, M. S., et al. (2015) · Cell · doi:10.1016/j.cell.2014.12.021 · Cited by 2,150 · see citing works

Defining CD8+ T cells that provide the proliferative burst after PD-1 therapy

Im, S. J., Hashimoto, M., Gerner, M. Y., Lee, J., Kissick, H. T., Burger, M. C., Shan, Q., Hale, J. S., Lee, J., Nasti, T. H., et al. (2016) · Nature · doi:10.1038/nature19330 · Cited by 2,070 · see citing works

Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes

Initiative, A. P. C. G., Biankin, A. V., Waddell, N., Kassahn, K. S., Gingras, M.-C., Muthuswamy, L. B., Johns, A. L., Miller, D. K., Wilson, P. J., Patch, A.-M., et al. (2012) · Nature · doi:10.1038/nature11547 · Cited by 2,058 · see citing works

Integrated genomic characterization of pancreatic ductal adenocarcinoma

Raphael, B. J., Hruban, R. H., Aguirre, A. J., Moffitt, R. A., Yeh, J. J., Stewart, C., Robertson, A. G., Cherniack, A. D., Gupta, M., Getz, G., et al. (2017) · Cancer Cell · doi:10.1016/j.ccell.2017.07.007 · Cited by 2,019 · see citing works

Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy

Collisson, E. A., Sadanandam, A., Olson, P., Gibb, W. J., Truitt, M., Gu, S., Cooc, J., Weinkle, J., Kim, G. E., Jakkula, L., et al. (2011) · Nature Medicine · doi:10.1038/nm.2344 · Cited by 1,967 · see citing works

CellProfiler 3.0: Next-generation image processing for biology

McQuin, C., Goodman, A., Chernyshev, V. S., Kamentsky, L. D., Cimini, B. A., Karhohs, K. W., Doan, M., Ding, L., Rafelski, S. M., Thirstrup, D. J., et al. (2018) · PLoS Biology · doi:10.1371/journal.pbio.2005970 · Cited by 1,835 · see citing works

PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells

Wolf, F. A., Hamey, F. K., Plass, M., Solana, J., Dahlin, J. S., Göttgens, B., Rajewsky, N., Simon, L., & Theis, F. J. (2019) · Genome Biology · doi:10.1186/s13059-019-1663-x · Cited by 1,698 · see citing works

Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species

Žilionis, R., Engblom, C., Pfirschke, C., Savova, V., Zemmour, D., Saatcioglu, H. D., Krishnan, I., Maroni, G., Meyerovitz, C. V., Kerwin, C. M., et al. (2019) · Immunity · doi:10.1016/j.immuni.2019.03.009 · Cited by 1,483 · see citing works

Single-cell RNA-seq highlights intra-tumoral heterogeneity and malignant progression in pancreatic ductal adenocarcinoma

Peng, J., Sun, B.-F., Chen, C.-Y., Zhou, J.-Y., Chen, Y.-S., Chen, H., Liu, L., Huang, D., Jiang, J., Cui, G.-S., et al. (2019) · Cell Research · doi:10.1038/s41422-019-0195-y · Cited by 1,321 · see citing works

A Single-Cell Transcriptome Atlas of the Human Pancreas

Muraro, M. J., Dharmadhikari, G., Grün, D., Gröen, N., Dielen, T., Jansen, E., van Gurp, L., Engelse, M. A., Carlotti, F., de Koning, E. J. P., et al. (2016) · Cell Systems · doi:10.1016/j.cels.2016.09.002 · Cited by 1,288 · see citing works

Chronic pancreatitis is essential for induction of pancreatic ductal adenocarcinoma by K-Ras oncogenes in adult mice

Guerra, C., Schuhmacher, A. J., Cañamero, M., Grippo, P. J., Verdaguer, L., Pérez-Gallego, L., Dubus, P., Sandgren, E. P., & Barbacid, M. (2007) · Cancer Cell · doi:10.1016/j.ccr.2007.01.012 · Cited by 1,224 · see citing works

The Immunoreceptor TIGIT Regulates Antitumor and Antiviral CD8 + T Cell Effector Function

Johnston, R. J., Comps‐Agrar, L., Hackney, J. A., Yu, X., Huseni, M. A., Yang, Y., Park, S., Javinal, V., Chiu, H. H., Irving, B. A., et al. (2014) · Cancer Cell · doi:10.1016/j.ccell.2014.10.018 · Cited by 1,191 · see citing works

An atlas of the protein-coding genes in the human, pig, and mouse brain

Sjöstedt, E., Zhong, W., Fagerberg, L., Karlsson, M., Mitsios, N., Adori, C., Oksvold, P., Edfors, F., Limiszewska, A., Hikmet, F., et al. (2020) · Science · doi:10.1126/science.aay5947 · Cited by 1,151 · see citing works

Cross-tissue organization of the fibroblast lineage

Buechler, M. B., Pradhan, R., Krishnamurty, A. T., Cox, C. B., Calviello, A. K., Wang, A. W., Yang, Y. A., Tam, L., Caothien, R. H., Roose‐Girma, M., et al. (2021) · Nature · doi:10.1038/s41586-021-03549-5 · Cited by 1,073 · see citing works

Multiplex digital spatial profiling of proteins and RNA in fixed tissue

Merritt, C. R., Ong, G. T., Church, S. E., Barker, K., Danaher, P., Geiss, G., Hoang, M., Jung, J., Liang, Y., McKay-Fleisch, J., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0472-9 · Cited by 1,072 · see citing works

Massively parallel single-nucleus RNA-seq with DroNc-seq

Habib, N., Avraham-Davidi, I., Basu, A., Burks, T., Shekhar, K., Hofree, M., Choudhury, S. R., Aguet, F., Gelfand, E., Ardlie, K., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4407 · Cited by 1,069 · see citing works

Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas

Moncada, R., Barkley, D., Wagner, F., Chiodin, M., Devlin, J. C., Baron, M., Hajdu, C. H., Simeone, D. M., & Yanai, I. (2020) · Nature Biotechnology · doi:10.1038/s41587-019-0392-8 · Cited by 1,045 · see citing works

Pancreatic cancer stroma: an update on therapeutic targeting strategies

Hosein, A. N., Brekken, R. A., & Maitra, A. (2020) · Nature Reviews Gastroenterology &amp; Hepatology · doi:10.1038/s41575-020-0300-1 · Cited by 950 · see citing works

Molecular subtypes of pancreatic cancer

Collisson, E. A., Bailey, P., Chang, D. K., & Biankin, A. V. (2019) · Nature Reviews Gastroenterology &amp; Hepatology · doi:10.1038/s41575-019-0109-y · Cited by 892 · see citing works

Neoadjuvant chemoradiotherapy versus upfront surgery for resectable and borderline resectable pancreatic cancer: long-term results of the Dutch randomized PREOPANC trial

Versteijne, E., van Dam, J. L., Suker, M., Janssen, Q. P., Groothuis, K., Akkermans-Vogelaar, J. M., Besselink, M. G., Bonsing, B. A., Buijsen, J., Busch, O. R., et al. (2022) · Journal of Clinical Oncology · doi:10.1200/jco.21.02233 · Cited by 786 · see citing works

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

Slyper, M., Porter, C. B. M., Ashenberg, O., Waldman, J., Drokhlyansky, E., Wakiro, I., Smillie, C. S., Smith-Rosario, G., Wu, J., Dionne, D. A., et al. (2020) · Nature Medicine · doi:10.1038/s41591-020-0844-1 · Cited by 739 · see citing works

EMT Subtype Influences Epithelial Plasticity and Mode of Cell Migration

Aiello, N. M., Maddipati, R., Norgard, R. J., Balli, D., Li, J., Yuan, S., Yamazoe, T., Black, T. A., Sahmoud, A., Furth, E. E., et al. (2018) · Developmental Cell · doi:10.1016/j.devcel.2018.05.027 · Cited by 708 · see citing works

Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution

Chan-Seng-Yue, M., Kim, J. C., Wilson, G. W., Ng, K., Figueroa, E. F., O’Kane, G. M., Connor, A. A., Denroche, R. E., Grant, R. C., McLeod, J., et al. (2020) · Nature Genetics · doi:10.1038/s41588-019-0566-9 · Cited by 669 · see citing works

histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data

Schapiro, D., Jackson, H. W., Raghuraman, S., Fischer, J. R., Zanotelli, V. R., Schulz, D., Giesen, C., Catena, R., Varga, Z., & Bodenmiller, B. (2017) · Nature Methods · doi:10.1038/nmeth.4391 · Cited by 643 · see citing works

Identifying gene expression programs of cell-type identity and cellular activity with single-cell RNA-Seq

Kotliar, D., Veres, A., Nagy, M. A., Tabrizi, S., Hodis, E., Melton, D. A., & Sabeti, P. C. (2019) · eLife · doi:10.7554/elife.43803 · Cited by 638 · see citing works

Genomics-driven precision medicine for advanced pancreatic cancer: early results from the COMPASS trial

Aung, K. L., Fischer, S. E., Denroche, R. E., Jang, G.-H., Dodd, A., Creighton, S., Southwood, B., Liang, S.-B., Chadwick, D., Zhang, A., et al. (2018) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-17-2994 · Cited by 618 · see citing works

Kruppel-like factor 2 regulates thymocyte and T-cell migration

Carlson, C. M., Endrizzi, B. T., Wu, J., Ding, X., Weinreich, M. A., Walsh, E. R., Wani, M. A., Lingrel, J. B., Hogquist, K. A., & Jameson, S. C. (2006) · Nature · doi:10.1038/nature04882 · Cited by 593 · see citing works

Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer

Raghavan, S., Winter, P. S., Navia, A. W., Williams, H. L., DenAdel, A., Lowder, K. E., Galvez-Reyes, J., Kalekar, R. L., Mulugeta, N., Kapner, K. S., et al. (2021) · Cell · doi:10.1016/j.cell.2021.11.017 · Cited by 592 · see citing works

The Human and Mouse Enteric Nervous System at Single-Cell Resolution

Drokhlyansky, E., Smillie, C. S., Wittenberghe, N. V., Ericsson, M., Griffin, G. K., Eraslan, G., Dionne, D. A., Cuoco, M. S., Goder-Reiser, M. N., Sharova, T. Y., et al. (2020) · Cell · doi:10.1016/j.cell.2020.08.003 · Cited by 585 · see citing works

N-Myc Induces an EZH2-Mediated Transcriptional Program Driving Neuroendocrine Prostate Cancer

Dardenne, É., Beltran, H., Benelli, M., Gayvert, K. M., Berger, A., Puca, L., Cyrta, J., Sboner, A., Noorzad, Z., MacDonald, T. Y., et al. (2016) · Cancer Cell · doi:10.1016/j.ccell.2016.09.005 · Cited by 561 · see citing works

Multimodal mapping of the tumor and peripheral blood immune landscape in human pancreatic cancer

Steele, N. G., Carpenter, E. S., Kemp, S. B., Sirihorachai, V. R., The, S., Delrosario, L., Lazarus, J., Amir, E.-A. D., Gunchick, V., Espinoza, C. E., et al. (2020) · Nature Cancer · doi:10.1038/s43018-020-00121-4 · Cited by 546 · see citing works

Stromal Microenvironment Shapes the Intratumoral Architecture of Pancreatic Cancer

Ligorio, M., Sil, S., Malagon-Lopez, J., Nieman, L. T., Misale, S., Pilato, M. D., Ebright, R. Y., Karabacak, M., Kulkarni, A. S., Liu, A., et al. (2018) · Cell · doi:10.1016/j.cell.2019.05.012 · Cited by 534 · see citing works

Total Neoadjuvant Therapy With FOLFIRINOX in Combination With Losartan Followed by Chemoradiotherapy for Locally Advanced Pancreatic Cancer

Murphy, J. E., Wo, J. Y.-L., Ryan, D. P., Clark, J. W., Jiang, W., Yeap, B. Y., Drapek, L. C., Ly, L., Baglini, C. V., Blaszkowsky, L. S., et al. (2019) · JAMA Oncology · doi:10.1001/jamaoncol.2019.0892 · Cited by 525 · see citing works

Integrated Single-Cell Atlas of Endothelial Cells of the Human Lung

Schupp, J. C., Adams, T. S., Cosme, C., Raredon, M. S. B., Yuan, Y., Omote, N., Poli, S., Chioccioli, M., Rose, K.-A., Manning, E. P., et al. (2021) · Circulation · doi:10.1161/circulationaha.120.052318 · Cited by 453 · see citing works

Spatially confined sub-tumor microenvironments in pancreatic cancer

Grünwald, B. T., Devisme, A., Andrieux, G., Vyas, F., Aliar, K., McCloskey, C. W., Macklin, A., Jang, G. H., Denroche, R., Romero, J. M., et al. (2021) · Cell · doi:10.1016/j.cell.2021.09.022 · Cited by 433 · see citing works

Individualization of Irinotecan Treatment: A Review of Pharmacokinetics, Pharmacodynamics, and Pharmacogenetics

de Man, F. M., Goey, A. K. L., van Schaik, R. H. N., Mathijssen, R. H. J., & Bins, S. (2018) · Clinical Pharmacokinetics · doi:10.1007/s40262-018-0644-7 · Cited by 421 · see citing works

Notch and Kras reprogram pancreatic acinar cells to ductal intraepithelial neoplasia

Jean–Paul De La, O., Emerson, L. L., Goodman, J. L., Froebe, S. C., Illum, B. E., Curtis, A. B., & Murtaugh, L. C. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0810111105 · Cited by 396 · see citing works

Beta-catenin blocks Kras-dependent reprogramming of acini into pancreatic cancer precursor lesions in mice.

Morris, J. P., Cano, D., Sekine, S., Wang, S. C., & Hebrok, M. (2010) · Journal of Clinical Investigation · doi:10.1172/jci40045 · Cited by 391 · see citing works

scCODA is a Bayesian model for compositional single-cell data analysis

Büttner, M., Ostner, J., Müller, C. L., Theis, F. J., & Schubert, B. (2021) · Nature Communications · doi:10.1038/s41467-021-27150-6 · Cited by 388 · see citing works

Single-Cell Transcriptomics of Pancreatic Cancer Precursors Demonstrates Epithelial and Microenvironmental Heterogeneity as an Early Event in Neoplastic Progression

Bernard, V., Semaan, A., Huang, J. H., Lucas, F. A. S., Mulu, F. C., Stephens, B. M., Guerrero, P. A., Huang, Y., Zhao, J., Kamyabi, N., et al. (2018) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-18-1955 · Cited by 387 · see citing works

Semaphorin 5A Is a Bifunctional Axon Guidance Cue Regulated by Heparan and Chondroitin Sulfate Proteoglycans

Kantor, D. B., Chivatakarn, O., Thompson-Peer, K. L., Oster, S. F., Inatani, M., Hansen, M. J., Flanagan, J. G., Yamaguchi, Y., Sretavan, D. W., Giger, R. J., et al. (2004) · Neuron · doi:10.1016/j.neuron.2004.12.002 · Cited by 380 · see citing works

Nfib Promotes Metastasis through a Widespread Increase in Chromatin Accessibility

Denny, S. K., Yang, D., Chuang, C.-H., Brady Jennifer, J., Lim, J. S., Grüner, B. M., Chiou, S., Schep, A. N., Baral, J., Hamard, C., et al. (2016) · Cell · doi:10.1016/j.cell.2016.05.052 · Cited by 358 · see citing works

Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics

Muus, C., Luecken, M. D., Eraslan, G., Sikkema, L., Waghray, A., Heimberg, G., Kobayashi, Y., Vaishnav, E. D., Subramanian, A., Smillie, C. S., et al. (2021) · Nature Medicine · doi:10.1038/s41591-020-01227-z · Cited by 336 · see citing works

Runx2, A multifunctional transcription factor in skeletal development

Komori, T. (2002) · Journal of Cellular Biochemistry · doi:10.1002/jcb.10276 · Cited by 326 · see citing works

The CD155/TIGIT axis promotes and maintains immune evasion in neoantigen-expressing pancreatic cancer

Freed-Pastor, W. A., Lambert, L. J., Ely, Z. A., Pattada, N. B., Bhutkar, A., Eng, G., Mercer, K. L., Garcia, A. P., Lin, L., Rideout, W. M., et al. (2021) · Cancer Cell · doi:10.1016/j.ccell.2021.07.007 · Cited by 273 · see citing works

CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response

Biasci, D., Smoragiewicz, M., Connell, C. M., Wang, Z., Gao, Y., Thaventhiran, J. E. D., Basu, B., Magiera, Ł., Johnson, T. I., Bax, L., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2013644117 · Cited by 264 · see citing works

Gating of Sema3E/PlexinD1 Signaling by Neuropilin-1 Switches Axonal Repulsion to Attraction during Brain Development

Chauvet, S., Cohen, S., Yoshida, Y., Fekrane, L., Livet, J., Gayet, O., Ségu, L., Buhot, M.-C., Jessell, T. M., Henderson, C. E., et al. (2007) · Neuron · doi:10.1016/j.neuron.2007.10.019 · Cited by 251 · see citing works

The molecular functions of hepatocyte nuclear factors – In and beyond the liver

Lau, H. H., Ng, N. H. J., Loo, L. S. W., Jasmen, J. B., & Teo, A. K. K. (2018) · Journal of Hepatology · doi:10.1016/j.jhep.2017.11.026 · Cited by 250 · see citing works

Single-nucleus and in situ RNA-sequencing reveal cell topographies in the human pancreas

Tosti, L., Hang, Y., Debnath, O., Tiesmeyer, S., Trefzer, T., Steiger, K., Ten, F. W., Lukassen, S., Ballke, S., Kühl, A. A., et al. (2021) · Gastroenterology · doi:10.1053/j.gastro.2020.11.010 · Cited by 228 · see citing works

Stem cell and neurogenic gene-expression profiles link prostate basal cells to aggressive prostate cancer

Zhang, D., Park, D., Zhong, Y., Lu, Y., Rycaj, K., Gong, S., Chen, X., Liu, X., Chao, H., Whitney, P., et al. (2016) · Nature Communications · doi:10.1038/ncomms10798 · Cited by 223 · see citing works

Bcl-2 Antiapoptotic Family Proteins and Chemoresistance in Cancer

Maji, S., Panda, S., Samal, S. K., Shriwas, O., Rath, R., Pellecchia, M., Emdad, L., Das, S. K., Fisher, P. B., & Dash, R. (2017) · Advances in cancer research · doi:10.1016/bs.acr.2017.11.001 · Cited by 216 · see citing works

IL-34 and CSF-1 display an equivalent macrophage differentiation ability but a different polarization potential

Boulakirba, S., Pfeifer, A., Mhaidly, R., Obba, S., Goulard, M., Schmitt, T., Chaintreuil, P., Calleja, A., Furstoss, N., Orange, F., et al. (2018) · Scientific Reports · doi:10.1038/s41598-017-18433-4 · Cited by 199 · see citing works

Multiple ABCB1 transcriptional fusions in drug resistant high-grade serous ovarian and breast cancer

Christie, E. L., Pattnaik, S., Beach, J. A., Copeland, A., Rashoo, N., Fereday, S., Hendley, J., Alsop, K., Brady, S. W., Lamb, G., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09312-9 · Cited by 193 · see citing works

Multicentre phase II trial of trastuzumab and capecitabine in patients with HER2 overexpressing metastatic pancreatic cancer

Harder, J., Ihorst, G., Heinemann, V., Hofheinz, R., Moehler, M. H., Buechler, P., Kloeppel, G., Röcken, C., Bitzer, M., Boeck, S. H., et al. (2012) · British Journal of Cancer · doi:10.1038/bjc.2012.18 · Cited by 188 · see citing works

Emerging roles of the CXCL12/CXCR4 axis in pancreatic cancer progression and therapy

Sleightholm, R. L., Neilsen, B. K., Li, J., Steele, M. M., Singh, R. K., Hollingsworth, M. A., & Oupický, D. (2017) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2017.05.012 · Cited by 172 · see citing works

Unsupervised removal of systematic background noise from droplet-based single-cell experiments using <tt>CellBender</tt>

Fleming, S. J., Chaffin, M. D., Arduini, A., Akkad, A.-D., Banks, E., Marioni, J. C., Philippakis, A. A., Ellinor, P. T., & Babadi, M. (2019) · doi:10.1101/791699 · Cited by 164 · see citing works

Leukocyte heterogeneity in pancreatic ductal adenocarcinoma: phenotypic and spatial features associated with clinical outcome

Liudahl, S. M., Betts, C. B., Sivagnanam, S., Morales-Oyarvide, V., da Silva, A., Yuan, C., Hwang, S., Grossblatt-Wait, A., Leis, K. R., Larson, W., et al. (2021) · Cancer Discovery · doi:10.1158/2159-8290.cd-20-0841 · Cited by 164 · see citing works

CXCL10 and CCL21 Promote Migration of Pancreatic Cancer Cells Toward Sensory Neurons and Neural Remodeling in Tumors in Mice, Associated With Pain in Patients

Hirth, M., Gandla, J., Höper, C., Gaida, M. M., Agarwal, N. K., Simonetti, M., Demir, A., Xie, Y., Weiss, C., Michalski, C. W., et al. (2020) · Gastroenterology · doi:10.1053/j.gastro.2020.04.037 · Cited by 162 · see citing works

Composition, Spatial Characteristics, and Prognostic Significance of Myeloid Cell Infiltration in Pancreatic Cancer

Väyrynen, S. A., Zhang, J., Yuan, C., Väyrynen, J. P., Costa, A. D., Williams, H. L., Morales‐Oyarvide, V., Lau, M. C., Rubinson, D. A., Dunne, R. F., et al. (2020) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-20-3141 · Cited by 159 · see citing works

Basal‐like and classical cells coexist in pancreatic cancer revealed by single‐cell analysis on biopsy‐derived pancreatic cancer organoids from the classical subtype

Juiz, N. A., Kaoutari, A. E., Bigonnet, M., Gayet, O., Roques, J., Nicolle, R., Iovanna, J., & Dusetti, N. (2020) · The FASEB Journal · doi:10.1096/fj.202000363rr · Cited by 150 · see citing works

Therapeutic avenues for cancer neuroscience: translational frontiers and clinical opportunities

Shi, D. D., Guo, J. A., Hoffman, H. I., Su, J., Mino-Kenudson, M. A., Barth, J. L., Schenkel, J. M., Loeffler, J. S., Shih, H. A., Hong, T. S., et al. (2022) · The Lancet Oncology · doi:10.1016/s1470-2045(21)00596-9 · Cited by 146 · see citing works

The role of NrCAM in neural development and disorders—Beyond a simple glue in the brain

Sakurai, T. (2011) · Molecular and Cellular Neuroscience · doi:10.1016/j.mcn.2011.12.002 · Cited by 143 · see citing works

MYC regulates ductal-neuroendocrine lineage plasticity in pancreatic ductal adenocarcinoma associated with poor outcome and chemoresistance

Farrell, A. S., Joly, M. M., Allen-Petersen, B. L., Worth, P. J., Lanciault, C., Sauer, D., Link, J. M., Pelz, C., Heiser, L. M., Morton, J. P., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-01967-6 · Cited by 131 · see citing works

L-WRN conditioned medium for gastrointestinal epithelial stem cell culture shows replicable batch-to-batch activity levels across multiple research teams

VanDussen, K. L., Sonnek, N. M., & Stappenbeck, T. S. (2019) · Stem Cell Research · doi:10.1016/j.scr.2019.101430 · Cited by 117 · see citing works

FOXP1 circular RNA sustains mesenchymal stem cell identity via microRNA inhibition

Cherubini, A., Barilani, M., Rossi, R. L., Jalal, M., Rusconi, F., Buono, G., Ragni, E., Cantarella, G., Simpson, H., Péault, B., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz199 · Cited by 116 · see citing works

Reelin: Neurodevelopmental Architect and Homeostatic Regulator of Excitatory Synapses

Wasser, C. R., & Herz, J. (2017) · Journal of Biological Chemistry · doi:10.1074/jbc.r116.766782 · Cited by 111 · see citing works

A joint model of unpaired data from scRNA-seq and spatial transcriptomics for imputing missing gene expression measurements

Lopez, R., Nazaret, A., Langevin, M., Samaran, J., Regier, J., Jordan, M. I., & Yosef, N. (2019) · arXiv · doi:10.48550/arxiv.1905.02269 · Cited by 105 · see citing works

REG3A accelerates pancreatic cancer cell growth under IL-6-associated inflammatory condition: Involvement of a REG3A–JAK2/STAT3 positive feedback loop

Liu, X., Wang, J., Wang, H., Yin, G., Liu, Y., Xiang, L., & Xiang, M. (2015) · Cancer Letters · doi:10.1016/j.canlet.2015.03.014 · Cited by 96 · see citing works

Use of Angiotensin System Inhibitors Is Associated with Immune Activation and Longer Survival in Nonmetastatic Pancreatic Ductal Adenocarcinoma

Liu, H., Naxerova, K., Pinter, M., Incio, J., Lee, H., Shigeta, K., Ho, W. W., Crain, J. A., Jacobson, A., Michelakos, T., et al. (2017) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-17-0256 · Cited by 96 · see citing works

Wnt5a and Wnt11 regulate mammalian anterior-posterior axis elongation

Andre, P., Song, H., Kim, W., Kispert, A., & Yang, Y. (2015) · Development · doi:10.1242/dev.119065 · Cited by 95 · see citing works

CCL19-producing fibroblastic stromal cells restrain lung carcinoma growth by promoting local antitumor T-cell responses

Cheng, H., Onder, L., Cupovic, J., Boesch, M., Novković, M., Pikor, N. B., Tarantino, I., Rodriguez, R., Schneider, T., Jochum, W., et al. (2018) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2017.12.998 · Cited by 88 · see citing works

Keratin 17 identifies the most lethal molecular subtype of pancreatic cancer

Roa‐Peña, L., Leiton, C. V., Babu, S., Pan, C., Vanner, E. A., Akalin, A., Bandovic, J., Moffitt, R. A., Shroyer, K. R., & Escobar‐Hoyos, L. F. (2019) · Scientific Reports · doi:10.1038/s41598-019-47519-4 · Cited by 85 · see citing works

SPP1 inhibition improves the cisplatin chemo-sensitivity of cervical cancer cell lines

Chen, X., Xiong, D., Ye, L., et al. (2019) · Cancer Chemotherapy and Pharmacology · doi:10.1007/s00280-018-3759-5 · Cited by 83 · see citing works

Neuronal Migration and AUTS2 Syndrome

Hori, K., & Hoshino, M. (2017) · Brain Sciences · doi:10.3390/brainsci7050054 · Cited by 68 · see citing works

Krüppel-like Factor 4 Promotes Esophageal Squamous Cell Carcinoma Differentiation by Up-regulating Keratin 13 Expression

He, H., Li, S., Yuan, H., et al. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.629717 · Cited by 67 · see citing works

Reg proteins promote acinar-to-ductal metaplasia and act as novel diagnostic and prognostic markers in pancreatic ductal adenocarcinoma

Li, Q., Wang, H., Zogopoulos, G., Shao, Q., Dong, K., Lv, F., Nwilati, K., Gui, X. S., Cuggia, A., Liu, J., et al. (2016) · Oncotarget · doi:10.18632/oncotarget.12834 · Cited by 65 · see citing works

Localization of Metallothionein in Hair Follicles of Normal Skin and the Basal Cell Layer of Hyperplastic Epidermis: Possible Association with Cell Proliferation

Karasawa, M., Nishimura, N., Nishimura, H., et al. (1991) · Journal of Investigative Dermatology · doi:10.1111/1523-1747.ep12478393 · Cited by 53 · see citing works

Chemokine Signatures of Pathogen-Specific T Cells I: Effector T Cells

Eberlein, J., Davenport, B., Nguyen, T. T., Victorino, F., Jhun, K., van der Heide, V., Kuleshov, M. V., Ma’ayan, A., Kedl, R. M., & Homann, D. (2020) · The Journal of Immunology · doi:10.4049/jimmunol.2000253 · Cited by 50 · see citing works

MEN1 deficiency leads to neuroendocrine differentiation of lung cancer and disrupts the DNA damage response

Qiu, H., Jin, B., Wang, Z., Xu, B., Zheng, Q., Zhang, L., Zhu, L.-Y., Shi, S., Yuan, J.-B., Lin, X., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-14614-4 · Cited by 48 · see citing works

An Attractive Reelin Gradient Establishes Synaptic Lamination in the Vertebrate Visual System

Donato, V. D., Santis, F. D., Albadri, S., Auer, T. O., Duroure, K., Charpentier, M., Concordet, J., Gebhardt, C., & Bene, F. D. (2018) · Neuron · doi:10.1016/j.neuron.2018.01.030 · Cited by 46 · see citing works

The oncogenic receptor ErbB2 modulates gemcitabine and irinotecan/SN-38 chemoresistance of human pancreatic cancer cells via hCNT1 transporter and multidrug-resistance associated protein MRP-2

Skrypek, N., Vasseur, R., Vincent, A., et al. (2015) · Oncotarget · doi:10.18632/oncotarget.3414 · Cited by 42 · see citing works

Contactin-1/F3 Regulates Neuronal Migration and Morphogenesis Through Modulating RhoA Activity

Chen, Y., Lu, I.-L., & Tsai, J. (2018) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2018.00422 · Cited by 41 · see citing works

Complement in Pancreatic Disease—Perpetrator or Savior?

Bettac, L., Denk, S., Seufferlein, T. T. W., & Huber-Lang, M. S. (2017) · Frontiers in Immunology · doi:10.3389/fimmu.2017.00015 · Cited by 39 · see citing works

<i>Sall4</i> regulates neuromesodermal progenitors and their descendants during body elongation in mouse embryos

Tahara, N., Kawakami, H., Chen, K. Q., Anderson, A., Yamashita Peterson, M., Gong, W., Shah, P., Hayashi, S., Nishinakamura, R., Nakagawa, Y., et al. (2019) · Development · doi:10.1242/dev.177659 · Cited by 35 · see citing works

Gene Characterization of Sciellin (SCEL) and Protein Localization in Vertebrate Epithelia Displaying Barrier Properties

Champliaud, M.-F., Baden, H. P., Koch, M., et al. (2000) · Genomics · doi:10.1006/geno.2000.6390 · Cited by 32 · see citing works

RNA Isolation from Mouse Pancreas: A Ribonuclease-rich Tissue

Azevedo‐Pouly, A. C. P., Elgamal, O. A., & Schmittgen, T. D. (2014) · Journal of Visualized Experiments · doi:10.3791/51779 · Cited by 31 · see citing works

Pan-cancer Transcriptomic Predictors of Perineural Invasion Improve Occult Histopathologic Detection

Guo, J. A., Hoffman, H. I., Shroff, S. G., et al. (2021) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-20-4382 · Cited by 30 · see citing works

AMD3100/Plerixafor overcomes immune inhibition by the CXCL12–KRT19 coating on pancreatic and colorectal cancer cells

Fearon, D. T., & Janowitz, T. (2021) · British Journal of Cancer · doi:10.1038/s41416-021-01315-y · Cited by 24 · see citing works

Platelet-Derived Growth Factor D Is a Prognostic Biomarker and Is Associated with Platinum Resistance in Epithelial Ovarian Cancer

Zhang, M., Liu, T., Xia, B., et al. (2017) · International Journal of Gynecological Cancer · doi:10.1097/igc.0000000000001171 · Cited by 23 · see citing works

Structural and biochemical changes underlying a keratoderma-like phenotype in mice lacking suprabasal AP1 transcription factor function

Rorke, E. A., Adhikary, G., Young, C. A., Rice, R. H., Elias, P. M., Crumrine, D., Meyer, J. M., Blumenberg, M., & Eckert, R. L. (2015) · Cell Death and Disease · doi:10.1038/cddis.2015.21 · Cited by 21 · see citing works

scCODA: A Bayesian model for compositional single-cell data analysisPreprint

Büttner, M., Ostner, J., Müller, C. L., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.12.14.422688 · Cited by 17 · see citing works

Refining the Molecular Framework for Pancreatic Cancer with Single-cell and Spatial Technologies

Guo, J. A., Hoffman, H. I., Weekes, C. D., Zheng, L., Ting, D. T., & Hwang, W. L. (2021) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-20-4712 · Cited by 14 · see citing works

Lef1 plays a role in patterning the mesoderm and ectoderm in Xenopus tropicalis

Rol, G., Gent, Y. Y. J., Peterson-Maduro, J., et al. (2009) · The International Journal of Developmental Biology · doi:10.1387/ijdb.072395gr · Cited by 10 · see citing works

Pancreatic cancer: Advances and challenges

Halbrook, C. J., Lyssiotis, C. A., Pasca di Magliano, M., & Maitra, A. (2023) · Cell · doi:10.1016/j.cell.2023.02.014 · Cited by 1,321 · see citing works

Neoadjuvant therapy for pancreatic cancer

Springfeld, C., Ferrone, C. R., Katz, M. H. G., Philip, P. A., Hong, T. S., Hackert, T., Büchler, M. W., & Neoptolemos, J. (2023) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-023-00746-1 · Cited by 377 · see citing works

Mechanisms of Resistance to Oncogenic KRAS Inhibition in Pancreatic Cancer

Dilly, J., Hoffman, M. T., Abbassi, L., Li, Z., Paradiso, F., Parent, B. D., Hennessey, C. J., Jordan, A. C., Morgado, M., Dasgupta, S., et al. (2024) · Cancer Discovery · doi:10.1158/2159-8290.cd-24-0177 · Cited by 276 · see citing works

Impact of the Human Cell Atlas on medicine

Rood, J. E., Maartens, A., Hupalowska, A., Teichmann, S. A., & Regev, A. (2022) · Nature Medicine · doi:10.1038/s41591-022-02104-7 · Cited by 222 · see citing works

Epithelial-to-mesenchymal transition (EMT) and cancer metastasis: the status quo of methods and experimental models 2025

Allgayer, H., Mahapatra, S., Mishra, B., Swain, B., Saha, S., Khanra, S., Kumari, K., Panda, V. K., Malhotra, D., Patil, N. S., et al. (2025) · Molecular Cancer · doi:10.1186/s12943-025-02338-2 · Cited by 127 · see citing works

Perspectives on single-nucleus RNA sequencing in different cell types and tissues

Kim, N., Kang, H., Jo, A., Yoo, S.-A., & Lee, H.-O. (2023) · Journal of Pathology and Translational Medicine · doi:10.4132/jptm.2022.12.19 · Cited by 97 · see citing works

A Classical Epithelial State Drives Acute Resistance to KRAS Inhibition in Pancreatic Cancer

Singhal, A., Styers, H. C., Rub, J., Li, Z., Torborg, S. R., Kim, J. Y., Grbovic-Huezo, O., Feng, H., Tarcan, Z. C., Sahin Ozkan, H., et al. (2024) · Cancer Discovery · doi:10.1158/2159-8290.cd-24-0740 · Cited by 84 · see citing works

Transition from one- to two-dimensional development facilitates maintenance of multicellularity

Manjarrez-Casas, A. M., Bagheri, H. C., & Dobay, A. (2016) · Royal Society Open Science · doi:10.1098/rsos.160554

Bacterial solutions to multicellularity: a tale of biofilms, filaments and fruiting bodies

Claessen, D., Rozen, D. E., Kuipers, O. P., Søgaard‐Andersen, L., & van Wezel, G. P. (2014) · Nature Reviews Microbiology · doi:10.1038/nrmicro3178 · Cited by 476 · see citing works

Building a Multicellular Organism

Kaiser, D. (2001) · Annual Review of Genetics · doi:10.1146/annurev.genet.35.102401.090145 · Cited by 205 · see citing works

Varied solutions to multicellularity: The biophysical and evolutionary consequences of diverse intercellular bonds

Day, T. C., Márquez-Zacarías, P., Bravo, P., Pokhrel, A. R., MacGillivray, K. A., Ratcliff, W. C., & Yunker, P. J. (2022) · Biophysics Reviews · doi:10.1063/5.0080845 · Cited by 25 · see citing works

Multicellular Life Cycles as an Emergent Property in Filamentous Bacteria

Rossetti, V., & Bagheri, H. C. (2015) · Advances in marine genomics · doi:10.1007/978-94-017-9642-2_10 · Cited by 15 · see citing works