Cell types and ontologies of the Human Cell Atlas

Authors: Osumi-Sutherland, David, Xu, Chuan, Keays, Maria, Kharchenko, Peter V., Regev, Aviv, Lein, Ed, Teichmann, Sarah A.

Source: Nat Cell Biol 23, 1129-1135 (2021)

Subject Terms: Quantitative Biology - Cell Behavior

Access URL: http://arxiv.org/abs/2106.14443

ZNF683 marks a CD8+ T cell population associated with anti-tumor immunity following anti-PD-1 therapy for Richter syndrome

Authors: Parry, Erin M., Lemvigh, Camilla K., Deng, Stephanie, Dangle, Nathan, Ruthen, Neil, Knisbacher, Binyamin A., Broséus, Julien, Hergalant, Sébastien, Guièze, Romain, Li, Shuqiang, Zhang, Wandi, Johnson, Connor, Long, Jaclyn M., Yin, Shanye, Werner, Lillian, Anandappa, Annabelle, Purroy, Noelia, Gohil, Satyen, Oliveira, Giacomo, Bachireddy, Pavan, Shukla, Sachet A., Huang, Teddy, Khoury, Joseph D., Thakral, Beenu, Dickinson, Michael, Tam, Constantine, Livak, Kenneth J., Getz, Gad, Neuberg, Donna, Feugier, Pierre, Kharchenko, Peter, Wierda, William, Olsen, Lars Rønn, Jain, Nitin, Wu, Catherine J.

Source: In Cancer Cell 9 October 2023 41(10):1803-1816

Single-cell analysis reveals immune dysfunction from the earliest stages of CLL that can be reversed by ibrutinib

Authors: Purroy, Noelia, Tong, Yuzhou Evelyn, Lemvigh, Camilla K., Cieri, Nicoletta, Li, Shuqiang, Parry, Erin M., Zhang, Wandi, Rassenti, Laura Z., Kipps, Thomas J., Slager, Susan L., Kay, Neil E., Lesnick, Connie, Shanafelt, Tait D., Ghia, Paolo, Scarfò, Lydia, Livak, Kenneth J., Kharchenko, Peter V., Neuberg, Donna S., Olsen, Lars Rønn, Fan, Jean, Gohil, Satyen H., Wu, Catherine J.

Source: Blood. 139(14):2252-2256

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100183256005.0x000001&indx=1&recIds=ETOCvdc_100183256005.0x000001

Liver stromal cells restrict macrophage maturation and stromal IL-6 limits the differentiation of cirrhosis-linked macrophages

Authors: Buonomo, Erica L., Mei, Shenglin, Guinn, Samantha R., Leo, Isabelle R., Peluso, Michael J., Nolan, Mei-An, Schildberg, Frank A., Zhao, Lei, Lian, Christine, Xu, Shuyun, Misdraji, Joseph, Kharchenko, Peter V., Sharpe, Arlene H.

Source: Journal of hepatology. 76(5):1127-1137

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100179671478.0x000001&indx=1&recIds=ETOCvdc_100179671478.0x000001

Human prostate cancer bone metastases have an actionable immunosuppressive microenvironment

Authors: Kfoury, Youmna, Baryawno, Ninib, Severe, Nicolas, Mei, Shenglin, Gustafsson, Karin, Hirz, Taghreed, Brouse, Thomas, Scadden, Elizabeth W., Igolkina, Anna A., Kokkaliaris, Konstantinos, Choi, Bryan D., Barkas, Nikolas, Randolph, Mark A., Shin, John H., Saylor, Philip J., Scadden, David T., Sykes, David B., Kharchenko, Peter V.

Source: In Cancer Cell 8 November 2021 39(11):1464-1478

Rewiring of human neurodevelopmental gene regulatory programs by human accelerated regions

Authors: Girskis, Kelly M., Stergachis, Andrew B., DeGennaro, Ellen M., Doan, Ryan N., Qian, Xuyu, Johnson, Matthew B., Wang, Peter P., Sejourne, Gabrielle M., Nagy, M. Aurel, Pollina, Elizabeth A., Sousa, André M.M., Shin, Taehwan, Kenny, Connor J., Scotellaro, Julia L., Debo, Brian M., Gonzalez, Dilenny M., Rento, Lariza M., Yeh, Rebecca C., Song, Janet H.T., Beaudin, Marc, Fan, Jean, Kharchenko, Peter V., Sestan, Nenad, Greenberg, Michael E., Walsh, Christopher A.

Source: In Neuron 20 October 2021 109(20):3239-3251

Diversity of developing peripheral glia revealed by single-cell RNA sequencing

Authors: Tasdemir-Yilmaz, Ozge E., Druckenbrod, Noah R., Olukoya, Olubusola O., Dong, Weixiu, Yung, Andrea R., Bastille, Isle, Pazyra-Murphy, Maria F., Sitko, Austen A., Hale, Evan B., Vigneau, Sébastien, Gimelbrant, Alexander A., Kharchenko, Peter V., Goodrich, Lisa V., Segal, Rosalind A.

Source: In Developmental Cell 13 September 2021 56(17):2516-2535

Vitessce: integrative visualization of multimodal and spatially resolved single-cell data

Authors: Keller, Mark S., Gold, Ilan, McCallum, Chuck, Manz, Trevor, Kharchenko, Peter V., Gehlenborg, Nils

Source: Nature Methods; January 2025, Vol. 22 Issue: 1 p63-67, 5p

Spatiotemporal structure of cell fate decisions in murine neural crest

Authors: Soldatov, Ruslan, Kaucka, Marketa, Kastriti, Maria Eleni, Petersen, Julian, Chontorotzea, Tatiana, Englmaier, Lukas, Akkuratova, Natalia, Yang, Yunshi, Häring, Martin, Dyachuk, Viacheslav, Bock, Christoph, Farlik, Matthias, Piacentino, Michael L., Boismoreau, Franck, Hilscher, Markus M., Yokota, Chika, Qian, Xiaoyan, Nilsson, Mats, Bronner, Marianne E., Croci, Laura, Hsiao, Wen-Yu, Guertin, David A., Brunet, Jean-Francois, Consalez, Gian Giacomo, Ernfors, Patrik, Fried, Kaj, Kharchenko, Peter V., Adameyko, Igor

Source: Science, 2019 Jun 01. 364(6444), 971-971.

Access URL: https://www.jstor.org/stable/26681537

National Cancer Institute Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions

Authors: Kagan, Jacob, Moritz, Robert L., Mazurchuk, Richard, Lee, Je Hyuk, Kharchenko, Peter Vasili, Rozenblatt-Rosen, Orit, Ruppin, Eytan, Edfors, Fredrik, Ginty, Fiona, Goltsev, Yury

Source: Journal of proteome research. 19(5):1900-1912

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN624008207&indx=1&recIds=ETOCRN624008207

Rapid Mobilization Reveals a Highly Engraftable Hematopoietic Stem Cell

Authors: Hoggatt, Jonathan, Singh, Pratibha, Tate, Tiffany A., Chou, Bin-Kuan, Datari, Shruti R., Fukuda, Seiji, Liu, Liqiong, Kharchenko, Peter V., Schajnovitz, Amir, Baryawno, Ninib, Mercier, Francois E., Boyer, Joseph, Gardner, Jason, Morrow, Dwight M., Scadden, David T., Pelus, Louis M.

Source: In Cell 11 January 2018 172(1-2):191-204

Cell Kinetics in the Adult Neurogenic Niche and Impact of Diet-Induced Accelerated Aging

Authors: Stankiewicz, Alexander J., Mortazavi, Farzad, Kharchenko, Peter V., McGowan, Erin M., Kharchenko, Vasili, Zhdanova, Irina V.

Source: Journal of neuroscience. 39(15):2810-2822

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN619625650&indx=1&recIds=ETOCRN619625650

Joint analysis of heterogeneous single-cell RNA-seq dataset collections

Authors: Barkas, Nikolas, Petukhov, Viktor, Nikolaeva, Daria, Lozinsky, Yaroslav, Demharter, Samuel, Khodosevich, Konstantin, Kharchenko, Peter

Source: Nature methods. 16(8):695-698

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100187168556.0x000001&indx=1&recIds=ETOCvdc_100187168556.0x000001

Multipotent peripheral glial cells generate neuroendocrine cells of the adrenal medulla

Authors: Furlan, Alessandro, Dyachuk, Vyacheslav, Kastriti, Maria Eleni, Calvo-Enrique, Laura, Abdo, Hind, Hadjab, Saida, Chontorotzea, Tatiana, Akkuratova, Natalia, Usoskin, Dmitry, Kamenev, Dmitry, Petersen, Julian, Sunadome, Kazunori, Memic, Fatima, Marklund, Ulrika, Fried, Kaj, Topilko, Piotr, Lallemend, Francois, Kharchenko, Peter V., Ernfors, Patrik, Adameyko, Igor

Source: Science, 2017 Jul 01. 357(6346), 46-46.

Access URL: https://www.jstor.org/stable/26399379

Ectopic protein interactions within BRD4–chromatin complexes drive oncogenic megadomain formation in NUT midline carcinoma

Authors: Alekseyenko, Artyom A., Walsh, Erica M., Zee, Barry M., Pakozdi, Tibor, Hsi, Peter, Lemieux, Madeleine E., Dal Cin, Paola, Ince, Tan A., Kharchenko, Peter V., Kuroda, Mitzi I., French, Christopher A.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2017 May . 114(21), E4184-E4192.

Access URL: https://www.jstor.org/stable/26483329

RNA velocity of single cells

Authors: La Manno, Gioele, Soldatov, Ruslan, Zeisel, Amit, Braun, Emelie, Hochgerner, Hannah, Petukhov, Viktor, Lidschreiber, Katja, Kastriti, Maria, Lönnerberg, Peter, Furlan, Alessandro, Fan, Jean, Borm, Lars, Liu, Zehua, Bruggen, David, Guo, Jimin, He, Xiaoling, Barker, Roger, Sundström, Erik, Castelo-Branco, Gonçalo, Cramer, Patrick, Adameyko, Igor, Linnarsson, Sten, Kharchenko, Peter

Source: Nature. 560(7719):494-498

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100175726711.0x000001&indx=1&recIds=ETOCvdc_100175726711.0x000001

DropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments

Authors: Petukhov, Viktor, Guo, Jimin, Baryawno, Ninib, Severe, Nicolas, Scadden, David, Samsonova, Maria, Kharchenko, Peter

Source: Genome biology. 19(1):1-16

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100165709676.0x000001&indx=1&recIds=ETOCvdc_100165709676.0x000001

Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells

Authors: Yu, Vionnie W.C., Yusuf, Rushdia Z., Oki, Toshihiko, Wu, Juwell, Saez, Borja, Wang, Xin, Cook, Colleen, Baryawno, Ninib, Ziller, Michael J., Lee, Eunjung, Gu, Hongcang, Meissner, Alexander, Lin, Charles P., Kharchenko, Peter V., Scadden, David T.

Source: In Cell 17 November 2016 167(5):1310-1322

Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia

Authors: Wang, Lili, Brooks, Angela N., Fan, Jean, Wan, Youzhong, Gambe, Rutendo, Li, Shuqiang, Hergert, Sarah, Yin, Shanye, Freeman, Samuel S., Levin, Joshua Z., Fan, Lin, Seiler, Michael, Buonamici, Silvia, Smith, Peter G., Chau, Kevin F., Cibulskis, Carrie L., Zhang, Wandi, Rassenti, Laura Z., Ghia, Emanuela M., Kipps, Thomas J., Fernandes, Stacey, Bloch, Donald B., Kotliar, Dylan, Landau, Dan A., Shukla, Sachet A., Aster, Jon C., Reed, Robin, DeLuca, David S., Brown, Jennifer R., Neuberg, Donna, Getz, Gad, Livak, Kenneth J., Meyerson, Matthew M., Kharchenko, Peter V., Wu, Catherine J.

Source: In Cancer Cell 14 November 2016 30(5):750-763

Proximity-Based Differential Single-Cell Analysis of the Niche to Identify Stem/Progenitor Cell Regulators

Authors: Silberstein, Lev, Goncalves, Kevin A., Kharchenko, Peter V., Turcotte, Raphael, Kfoury, Youmna, Mercier, Francois, Baryawno, Ninib, Severe, Nicolas, Bachand, Jacqueline, Spencer, Joel A., Papazian, Ani, Lee, Dongjun, Chitteti, Brahmananda Reddy, Srour, Edward F., Hoggatt, Jonathan, Tate, Tiffany, Lo Celso, Cristina, Ono, Noriaki, Nutt, Stephen, Heino, Jyrki, Sipilä, Kalle, Shioda, Toshihiro, Osawa, Masatake, Lin, Charles P., Hu, Guo-fu, Scadden, David T.

Source: In Cell Stem Cell 6 October 2016 19(4):530-543