A citation-based method for searching scientific literature

Yuping Zhang, Sathiya P Narayanan, Rahul Mannan, Gregory Raskind, Xiaoming Wang, Pankaj Vats, Fengyun Su, Noshad Hosseini, Xuhong Cao, Chandan Kumar-Sinha, Stephanie J Ellison, Thomas J Giordano, Todd M Morgan, Sethuramasundaram Pitchiaya, Ajjai Alva, Rohit Mehra, Marcin Cieslik, Saravana M Dhanasekaran, Arul M Chinnaiyan. Proc Natl Acad Sci U S A 2021
Times Cited: 14







List of co-cited articles
77 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


Eleven grand challenges in single-cell data science.
David Lähnemann, Johannes Köster, Ewa Szczurek, Davis J McCarthy, Stephanie C Hicks, Mark D Robinson, Catalina A Vallejos, Kieran R Campbell, Niko Beerenwinkel, Ahmed Mahfouz,[...]. Genome Biol 2020
225
35

Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma.
Kyu-Tae Kim, Hye Won Lee, Hae-Ock Lee, Hye Jin Song, Da Eun Jeong, Sang Shin, Hyunho Kim, Yoojin Shin, Do-Hyun Nam, Byong Chang Jeong,[...]. Genome Biol 2016
115
35

Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors.
Matthew D Young, Thomas J Mitchell, Felipe A Vieira Braga, Maxine G B Tran, Benjamin J Stewart, John R Ferdinand, Grace Collord, Rachel A Botting, Dorin-Mirel Popescu, Kevin W Loudon,[...]. Science 2018
248
28

Simultaneous epitope and transcriptome measurement in single cells.
Marlon Stoeckius, Christoph Hafemeister, William Stephenson, Brian Houck-Loomis, Pratip K Chattopadhyay, Harold Swerdlow, Rahul Satija, Peter Smibert. Nat Methods 2017
876
21

Kidney Single-Cell Atlas Reveals Myeloid Heterogeneity in Progression and Regression of Kidney Disease.
Bryan R Conway, Eoin D O'Sullivan, Carolynn Cairns, James O'Sullivan, Daniel J Simpson, Angela Salzano, Katie Connor, Peng Ding, Duncan Humphries, Kevin Stewart,[...]. J Am Soc Nephrol 2020
43
21

mRNA-Seq whole-transcriptome analysis of a single cell.
Fuchou Tang, Catalin Barbacioru, Yangzhou Wang, Ellen Nordman, Clarence Lee, Nanlan Xu, Xiaohui Wang, John Bodeau, Brian B Tuch, Asim Siddiqui,[...]. Nat Methods 2009
21

Robust enumeration of cell subsets from tissue expression profiles.
Aaron M Newman, Chih Long Liu, Michael R Green, Andrew J Gentles, Weiguo Feng, Yue Xu, Chuong D Hoang, Maximilian Diehn, Ash A Alizadeh. Nat Methods 2015
21

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.
Evan Z Macosko, Anindita Basu, Rahul Satija, James Nemesh, Karthik Shekhar, Melissa Goldman, Itay Tirosh, Allison R Bialas, Nolan Kamitaki, Emily M Martersteck,[...]. Cell 2015
21

Single-cell dissection of intratumoral heterogeneity and lineage diversity in metastatic gastric adenocarcinoma.
Ruiping Wang, Minghao Dang, Kazuto Harada, Guangchun Han, Fang Wang, Melissa Pool Pizzi, Meina Zhao, Ghia Tatlonghari, Shaojun Zhang, Dapeng Hao,[...]. Nat Med 2021
31
21

Fast, sensitive and accurate integration of single-cell data with Harmony.
Ilya Korsunsky, Nghia Millard, Jean Fan, Kamil Slowikowski, Fan Zhang, Kevin Wei, Yuriy Baglaenko, Michael Brenner, Po-Ru Loh, Soumya Raychaudhuri. Nat Methods 2019
653
21

Single-cell RNA sequencing of human kidney.
Jinling Liao, Zhenyuan Yu, Yang Chen, Mengying Bao, Chunlin Zou, Haiying Zhang, Deyun Liu, Tianyu Li, Qingyun Zhang, Jiaping Li,[...]. Sci Data 2020
59
21

Renal cell carcinoma.
James J Hsieh, Mark P Purdue, Sabina Signoretti, Charles Swanton, Laurence Albiges, Manuela Schmidinger, Daniel Y Heng, James Larkin, Vincenzo Ficarra. Nat Rev Dis Primers 2017
885
21

Progressive immune dysfunction with advancing disease stage in renal cell carcinoma.
David A Braun, Kelly Street, Kelly P Burke, David L Cookmeyer, Thomas Denize, Christina B Pedersen, Satyen H Gohil, Nicholas Schindler, Lucas Pomerance, Laure Hirsch,[...]. Cancer Cell 2021
32
21

Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
21

Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy.
Chirag Krishna, Renzo G DiNatale, Fengshen Kuo, Raghvendra M Srivastava, Lynda Vuong, Diego Chowell, Sounak Gupta, Chad Vanderbilt, Tanaya A Purohit, Ming Liu,[...]. Cancer Cell 2021
20
21

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq.
Itay Tirosh, Benjamin Izar, Sanjay M Prakadan, Marc H Wadsworth, Daniel Treacy, John J Trombetta, Asaf Rotem, Christopher Rodman, Christine Lian, George Murphy,[...]. Science 2016
21

Tumor and immune reprogramming during immunotherapy in advanced renal cell carcinoma.
Kevin Bi, Meng Xiao He, Ziad Bakouny, Abhay Kanodia, Sara Napolitano, Jingyi Wu, Grace Grimaldi, David A Braun, Michael S Cuoco, Angie Mayorga,[...]. Cancer Cell 2021
45
21

Dynamic single-cell RNA sequencing identifies immunotherapy persister cells following PD-1 blockade.
Kartik Sehgal, Andrew Portell, Elena V Ivanova, Patrick H Lizotte, Navin R Mahadevan, Jonathan R Greene, Amir Vajdi, Carino Gurjao, Tyler Teceno, Luke J Taus,[...]. J Clin Invest 2021
13
23

Single-cell RNA sequencing reveals the tumor microenvironment and facilitates strategic choices to circumvent treatment failure in a chemorefractory bladder cancer patient.
Hye Won Lee, Woosung Chung, Hae-Ock Lee, Da Eun Jeong, Areum Jo, Joung Eun Lim, Jeong Hee Hong, Do-Hyun Nam, Byong Chang Jeong, Se Hoon Park,[...]. Genome Med 2020
41
21

Single-cell transcriptomic architecture and intercellular crosstalk of human intrahepatic cholangiocarcinoma.
Min Zhang, Hui Yang, Lingfei Wan, Zhaohai Wang, Haiyang Wang, Chen Ge, Yunhui Liu, Yajing Hao, Dongdong Zhang, Gaona Shi,[...]. J Hepatol 2020
71
21

Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing.
Chunhong Zheng, Liangtao Zheng, Jae-Kwang Yoo, Huahu Guo, Yuanyuan Zhang, Xinyi Guo, Boxi Kang, Ruozhen Hu, Julie Y Huang, Qiming Zhang,[...]. Cell 2017
806
21

Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma.
David A Braun, Yue Hou, Ziad Bakouny, Miriam Ficial, Miriam Sant' Angelo, Juliet Forman, Petra Ross-Macdonald, Ashton C Berger, Opeyemi A Jegede, Liudmilla Elagina,[...]. Nat Med 2020
143
21

An immune-active tumor microenvironment favors clinical response to ipilimumab.
Rui-Ru Ji, Scott D Chasalow, Lisu Wang, Omid Hamid, Henrik Schmidt, John Cogswell, Suresh Alaparthy, David Berman, Maria Jure-Kunkel, Nathan O Siemers,[...]. Cancer Immunol Immunother 2012
534
14

European Association of Urology Guidelines on Renal Cell Carcinoma: The 2019 Update.
Börje Ljungberg, Laurance Albiges, Yasmin Abu-Ghanem, Karim Bensalah, Saeed Dabestani, Sergio Fernández-Pello, Rachel H Giles, Fabian Hofmann, Milan Hora, Markus A Kuczyk,[...]. Eur Urol 2019
572
14

PD-1 blockade induces responses by inhibiting adaptive immune resistance.
Paul C Tumeh, Christina L Harview, Jennifer H Yearley, I Peter Shintaku, Emma J M Taylor, Lidia Robert, Bartosz Chmielowski, Marko Spasic, Gina Henry, Voicu Ciobanu,[...]. Nature 2014
14

Comprehensive Integration of Single-Cell Data.
Tim Stuart, Andrew Butler, Paul Hoffman, Christoph Hafemeister, Efthymia Papalexi, William M Mauck, Yuhan Hao, Marlon Stoeckius, Peter Smibert, Rahul Satija. Cell 2019
14

Clonal evolution in breast cancer revealed by single nucleus genome sequencing.
Yong Wang, Jill Waters, Marco L Leung, Anna Unruh, Whijae Roh, Xiuqing Shi, Ken Chen, Paul Scheet, Selina Vattathil, Han Liang,[...]. Nature 2014
624
14

A systematic evaluation of single-cell RNA-sequencing imputation methods.
Wenpin Hou, Zhicheng Ji, Hongkai Ji, Stephanie C Hicks. Genome Biol 2020
47
14

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics.
Kelly Street, Davide Risso, Russell B Fletcher, Diya Das, John Ngai, Nir Yosef, Elizabeth Purdom, Sandrine Dudoit. BMC Genomics 2018
463
14

A comparison of single-cell trajectory inference methods.
Wouter Saelens, Robrecht Cannoodt, Helena Todorov, Yvan Saeys. Nat Biotechnol 2019
388
14

Deep generative modeling for single-cell transcriptomics.
Romain Lopez, Jeffrey Regier, Michael B Cole, Michael I Jordan, Nir Yosef. Nat Methods 2018
315
14

Modular, efficient and constant-memory single-cell RNA-seq preprocessing.
Páll Melsted, A Sina Booeshaghi, Lauren Liu, Fan Gao, Lambda Lu, Kyung Hoi Joseph Min, Eduardo da Veiga Beltrame, Kristján Eldjárn Hjörleifsson, Jase Gehring, Lior Pachter. Nat Biotechnol 2021
37
14

BBKNN: fast batch alignment of single cell transcriptomes.
Krzysztof Polański, Matthew D Young, Zhichao Miao, Kerstin B Meyer, Sarah A Teichmann, Jong-Eun Park. Bioinformatics 2020
151
14

Tumour evolution inferred by single-cell sequencing.
Nicholas Navin, Jude Kendall, Jennifer Troge, Peter Andrews, Linda Rodgers, Jeanne McIndoo, Kerry Cook, Asya Stepansky, Dan Levy, Diane Esposito,[...]. Nature 2011
14

Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing.
Charissa Kim, Ruli Gao, Emi Sei, Rachel Brandt, Johan Hartman, Thomas Hatschek, Nicola Crosetto, Theodoros Foukakis, Nicholas E Navin. Cell 2018
378
14

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama.
Brian Hie, Bryan Bryson, Bonnie Berger. Nat Biotechnol 2019
169
14

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.
Laleh Haghverdi, Aaron T L Lun, Michael D Morgan, John C Marioni. Nat Biotechnol 2018
585
14

Full-length RNA-seq from single cells using Smart-seq2.
Simone Picelli, Omid R Faridani, Asa K Björklund, Gösta Winberg, Sven Sagasser, Rickard Sandberg. Nat Protoc 2014
14

Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma.
Nayoung Kim, Hong Kwan Kim, Kyungjong Lee, Yourae Hong, Jong Ho Cho, Jung Won Choi, Jung-Il Lee, Yeon-Lim Suh, Bo Mi Ku, Hye Hyeon Eum,[...]. Nat Commun 2020
151
14


Single-Cell RNA-seq Identification of the Cellular Molecular Characteristics of Sporadic Bilateral Clear Cell Renal Cell Carcinoma.
Zhenyuan Yu, Wenhao Lu, Cheng Su, Yufang Lv, Yu Ye, Bingqian Guo, Deyun Liu, Haibiao Yan, Hua Mi, Tianyu Li,[...]. Front Oncol 2021
4
50

An Immune Atlas of Clear Cell Renal Cell Carcinoma.
Stéphane Chevrier, Jacob Harrison Levine, Vito Riccardo Tomaso Zanotelli, Karina Silina, Daniel Schulz, Marina Bacac, Carola Hermine Ries, Laurie Ailles, Michael Alexander Spencer Jewett, Holger Moch,[...]. Cell 2017
475
14

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.
Cole Trapnell, Davide Cacchiarelli, Jonna Grimsby, Prapti Pokharel, Shuqiang Li, Michael Morse, Niall J Lennon, Kenneth J Livak, Tarjei S Mikkelsen, John L Rinn. Nat Biotechnol 2014
14

Cancer incidence and mortality patterns in Europe: Estimates for 40 countries and 25 major cancers in 2018.
J Ferlay, M Colombet, I Soerjomataram, T Dyba, G Randi, M Bettio, A Gavin, O Visser, F Bray. Eur J Cancer 2018
14

Single-cell transcriptomics of the mouse kidney reveals potential cellular targets of kidney disease.
Jihwan Park, Rojesh Shrestha, Chengxiang Qiu, Ayano Kondo, Shizheng Huang, Max Werth, Mingyao Li, Jonathan Barasch, Katalin Suszták. Science 2018
439
14

Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma.
Qiming Zhang, Yao He, Nan Luo, Shashank J Patel, Yanjie Han, Ranran Gao, Madhura Modak, Sebastian Carotta, Christian Haslinger, David Kind,[...]. Cell 2019
330
14


Dissecting transcriptional heterogeneity in primary gastric adenocarcinoma by single cell RNA sequencing.
Min Zhang, Shuofeng Hu, Min Min, Yanli Ni, Zheng Lu, Xiaotian Sun, Jiaqi Wu, Bing Liu, Xiaomin Ying, Yan Liu. Gut 2021
38
14

A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer.
Johanna Wagner, Maria Anna Rapsomaniki, Stéphane Chevrier, Tobias Anzeneder, Claus Langwieder, August Dykgers, Martin Rees, Annette Ramaswamy, Simone Muenst, Savas Deniz Soysal,[...]. Cell 2019
267
14

MYC Drives Temporal Evolution of Small Cell Lung Cancer Subtypes by Reprogramming Neuroendocrine Fate.
Abbie S Ireland, Alexi M Micinski, David W Kastner, Bingqian Guo, Sarah J Wait, Kyle B Spainhower, Christopher C Conley, Opal S Chen, Matthew R Guthrie, Danny Soltero,[...]. Cancer Cell 2020
88
14


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.