A citation-based method for searching scientific literature

Zeyu Chen, Eri Arai, Omar Khan, Zhen Zhang, Shin Foong Ngiow, Yuan He, Hua Huang, Sasikanth Manne, Zhendong Cao, Amy E Baxter, Zhangying Cai, Elizabeth Freilich, Mohammed A Ali, Josephine R Giles, Jennifer E Wu, Allison R Greenplate, Mohamed A Hakeem, Qingzhou Chen, Makoto Kurachi, Kito Nzingha, Viktoriya Ekshyyan, Divij Mathew, Zhuoyu Wen, Nancy A Speck, Alexis Battle, Shelley L Berger, E John Wherry, Junwei Shi. Cell 2021
Times Cited: 31







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



Times Cited
  Times     Co-cited
Similarity


Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
35

Genome-wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function.
Eric Shifrut, Julia Carnevale, Victoria Tobin, Theodore L Roth, Jonathan M Woo, Christina T Bui, P Jonathan Li, Morgan E Diolaiti, Alan Ashworth, Alexander Marson. Cell 2018
192
35

Systematic Immunotherapy Target Discovery Using Genome-Scale In Vivo CRISPR Screens in CD8 T Cells.
Matthew B Dong, Guangchuan Wang, Ryan D Chow, Lupeng Ye, Lvyun Zhu, Xiaoyun Dai, Jonathan J Park, Hyunu R Kim, Youssef Errami, Christopher D Guzman,[...]. Cell 2019
105
35

Model-based analysis of ChIP-Seq (MACS).
Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li,[...]. Genome Biol 2008
29

Targeting REGNASE-1 programs long-lived effector T cells for cancer therapy.
Jun Wei, Lingyun Long, Wenting Zheng, Yogesh Dhungana, Seon Ah Lim, Cliff Guy, Yanyan Wang, Yong-Dong Wang, Chenxi Qian, Beisi Xu,[...]. Nature 2019
138
29

In vivo CRISPR screening reveals nutrient signaling processes underpinning CD8+ T cell fate decisions.
Hongling Huang, Peipei Zhou, Jun Wei, Lingyun Long, Hao Shi, Yogesh Dhungana, Nicole M Chapman, Guotong Fu, Jordy Saravia, Jana L Raynor,[...]. Cell 2021
31
29

Epigenetic stability of exhausted T cells limits durability of reinvigoration by PD-1 blockade.
Kristen E Pauken, Morgan A Sammons, Pamela M Odorizzi, Sasikanth Manne, Jernej Godec, Omar Khan, Adam M Drake, Zeyu Chen, Debattama R Sen, Makoto Kurachi,[...]. Science 2016
631
25

CRISPR-engineered T cells in patients with refractory cancer.
Edward A Stadtmauer, Joseph A Fraietta, Megan M Davis, Adam D Cohen, Kristy L Weber, Eric Lancaster, Patricia A Mangan, Irina Kulikovskaya, Minnal Gupta, Fang Chen,[...]. Science 2020
515
25

STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
25

CRISPR-Cas9 knockin mice for genome editing and cancer modeling.
Randall J Platt, Sidi Chen, Yang Zhou, Michael J Yim, Lukasz Swiech, Hannah R Kempton, James E Dahlman, Oren Parnas, Thomas M Eisenhaure, Marko Jovanovic,[...]. Cell 2014
22

Inflammation directs memory precursor and short-lived effector CD8(+) T cell fates via the graded expression of T-bet transcription factor.
Nikhil S Joshi, Weiguo Cui, Anmol Chandele, Heung Kyu Lee, David R Urso, James Hagman, Laurent Gapin, Susan M Kaech. Immunity 2007
22

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.
Sven Heinz, Christopher Benner, Nathanael Spann, Eric Bertolino, Yin C Lin, Peter Laslo, Jason X Cheng, Cornelis Murre, Harinder Singh, Christopher K Glass. Mol Cell 2010
19



Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.
Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang, William J Greenleaf. Nat Methods 2013
19

Selective expression of the interleukin 7 receptor identifies effector CD8 T cells that give rise to long-lived memory cells.
Susan M Kaech, Joyce T Tan, E John Wherry, Bogumila T Konieczny, Charles D Surh, Rafi Ahmed. Nat Immunol 2003
19

CD8 T Cell Exhaustion During Chronic Viral Infection and Cancer.
Laura M McLane, Mohamed S Abdel-Hakeem, E John Wherry. Annu Rev Immunol 2019
583
19

Tumor-Specific T Cell Dysfunction Is a Dynamic Antigen-Driven Differentiation Program Initiated Early during Tumorigenesis.
Andrea Schietinger, Mary Philip, Varintra E Krisnawan, Edison Y Chiu, Jeffrey J Delrow, Ryan S Basom, Peter Lauer, Dirk G Brockstedt, Sue E Knoblaugh, Günter J Hämmerling,[...]. Immunity 2016
324
19

TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion.
Omar Khan, Josephine R Giles, Sierra McDonald, Sasikanth Manne, Shin Foong Ngiow, Kunal P Patel, Michael T Werner, Alexander C Huang, Katherine A Alexander, Jennifer E Wu,[...]. Nature 2019
494
19

Chromatin states define tumour-specific T cell dysfunction and reprogramming.
Mary Philip, Lauren Fairchild, Liping Sun, Ellen L Horste, Steven Camara, Mojdeh Shakiba, Andrew C Scott, Agnes Viale, Peter Lauer, Taha Merghoub,[...]. Nature 2017
425
19

The epigenetic landscape of T cell exhaustion.
Debattama R Sen, James Kaminski, R Anthony Barnitz, Makoto Kurachi, Ulrike Gerdemann, Kathleen B Yates, Hsiao-Wei Tsao, Jernej Godec, Martin W LaFleur, Flavian D Brown,[...]. Science 2016
489
19

Pooled Knockin Targeting for Genome Engineering of Cellular Immunotherapies.
Theodore L Roth, P Jonathan Li, Franziska Blaeschke, Jasper F Nies, Ryan Apathy, Cody Mowery, Ruby Yu, Michelle L T Nguyen, Youjin Lee, Anna Truong,[...]. Cell 2020
66
19

A CRISPR-Cas9 delivery system for in vivo screening of genes in the immune system.
Martin W LaFleur, Thao H Nguyen, Matthew A Coxe, Kathleen B Yates, Justin D Trombley, Sarah A Weiss, Flavian D Brown, Jacob E Gillis, Daniel J Coxe, John G Doench,[...]. Nat Commun 2019
50
19

Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation.
Johan Henriksson, Xi Chen, Tomás Gomes, Ubaid Ullah, Kerstin B Meyer, Ricardo Miragaia, Graham Duddy, Jhuma Pramanik, Kosuke Yusa, Riitta Lahesmaa,[...]. Cell 2019
73
19

Multiplex genome engineering using CRISPR/Cas systems.
Le Cong, F Ann Ran, David Cox, Shuailiang Lin, Robert Barretto, Naomi Habib, Patrick D Hsu, Xuebing Wu, Wenyan Jiang, Luciano A Marraffini,[...]. Science 2013
19

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response.
Britt Adamson, Thomas M Norman, Marco Jost, Min Y Cho, James K Nuñez, Yuwen Chen, Jacqueline E Villalta, Luke A Gilbert, Max A Horlbeck, Marco Y Hein,[...]. Cell 2016
437
19

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
19

c-Jun overexpression in CAR T cells induces exhaustion resistance.
Rachel C Lynn, Evan W Weber, Elena Sotillo, David Gennert, Peng Xu, Zinaida Good, Hima Anbunathan, John Lattin, Robert Jones, Victor Tieu,[...]. Nature 2019
242
19

Defining CD8+ T cells that provide the proliferative burst after PD-1 therapy.
Se Jin Im, Masao Hashimoto, Michael Y Gerner, Junghwa Lee, Haydn T Kissick, Matheus C Burger, Qiang Shan, J Scott Hale, Judong Lee, Tahseen H Nasti,[...]. Nature 2016
867
16

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma.
Moshe Sade-Feldman, Keren Yizhak, Stacey L Bjorgaard, John P Ray, Carl G de Boer, Russell W Jenkins, David J Lieb, Jonathan H Chen, Dennie T Frederick, Michal Barzily-Rokni,[...]. Cell 2018
646
16

The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
16

Dynamic Changes in Chromatin Accessibility Occur in CD8+ T Cells Responding to Viral Infection.
James P Scott-Browne, Isaac F López-Moyado, Sara Trifari, Victor Wong, Lukas Chavez, Anjana Rao, Renata M Pereira. Immunity 2016
163
16

Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade.
Brian C Miller, Debattama R Sen, Rose Al Abosy, Kevin Bi, Yamini V Virkud, Martin W LaFleur, Kathleen B Yates, Ana Lako, Kristen Felt, Girish S Naik,[...]. Nat Immunol 2019
575
16

TOX reinforces the phenotype and longevity of exhausted T cells in chronic viral infection.
Francesca Alfei, Kristiyan Kanev, Maike Hofmann, Ming Wu, Hazem E Ghoneim, Patrick Roelli, Daniel T Utzschneider, Madlaina von Hoesslin, Jolie G Cullen, Yiping Fan,[...]. Nature 2019
333
16

TOX is a critical regulator of tumour-specific T cell differentiation.
Andrew C Scott, Friederike Dündar, Paul Zumbo, Smita S Chandran, Christopher A Klebanoff, Mojdeh Shakiba, Prerak Trivedi, Laura Menocal, Heather Appleby, Steven Camara,[...]. Nature 2019
388
16

NR4A transcription factors limit CAR T cell function in solid tumours.
Joyce Chen, Isaac F López-Moyado, Hyungseok Seo, Chan-Wang J Lio, Laura J Hempleman, Takashi Sekiya, Akihiko Yoshimura, James P Scott-Browne, Anjana Rao. Nature 2019
273
16

The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation in response to LCMV viral infection.
Claudia X Dominguez, Robert A Amezquita, Tianxia Guan, Heather D Marshall, Nikhil S Joshi, Steven H Kleinstein, Susan M Kaech. J Exp Med 2015
138
16

Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing.
Joseph M Replogle, Thomas M Norman, Albert Xu, Jeffrey A Hussmann, Jin Chen, J Zachery Cogan, Elliott J Meer, Jessica M Terry, Daniel P Riordan, Niranjan Srinivas,[...]. Nat Biotechnol 2020
76
16

Genetic screens in human cells using the CRISPR-Cas9 system.
Tim Wang, Jenny J Wei, David M Sabatini, Eric S Lander. Science 2014
16

In vivo CRISPR screening in CD8 T cells with AAV-Sleeping Beauty hybrid vectors identifies membrane targets for improving immunotherapy for glioblastoma.
Lupeng Ye, Jonathan J Park, Matthew B Dong, Quanjun Yang, Ryan D Chow, Lei Peng, Yaying Du, Jianjian Guo, Xiaoyun Dai, Guangchuan Wang,[...]. Nat Biotechnol 2019
67
16

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.
Atray Dixit, Oren Parnas, Biyu Li, Jenny Chen, Charles P Fulco, Livnat Jerby-Arnon, Nemanja D Marjanovic, Danielle Dionne, Tyler Burks, Raktima Raychowdhury,[...]. Cell 2016
564
16

Genome-scale CRISPR-Cas9 knockout screening in human cells.
Ophir Shalem, Neville E Sanjana, Ella Hartenian, Xi Shi, David A Scott, Tarjei Mikkelson, Dirk Heckl, Benjamin L Ebert, David E Root, John G Doench,[...]. Science 2014
16

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9.
John G Doench, Nicolo Fusi, Meagan Sullender, Mudra Hegde, Emma W Vaimberg, Katherine F Donovan, Ian Smith, Zuzana Tothova, Craig Wilen, Robert Orchard,[...]. Nat Biotechnol 2016
16

CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes.
Luke A Gilbert, Matthew H Larson, Leonardo Morsut, Zairan Liu, Gloria A Brar, Sandra E Torres, Noam Stern-Ginossar, Onn Brandman, Evan H Whitehead, Jennifer A Doudna,[...]. Cell 2013
16

Targeting a CAR to the TRAC locus with CRISPR/Cas9 enhances tumour rejection.
Justin Eyquem, Jorge Mansilla-Soto, Theodoros Giavridis, Sjoukje J C van der Stegen, Mohamad Hamieh, Kristen M Cunanan, Ashlesha Odak, Mithat Gönen, Michel Sadelain. Nature 2017
847
16

CRISPR screen in regulatory T cells reveals modulators of Foxp3.
Jessica T Cortez, Elena Montauti, Eric Shifrut, Jovylyn Gatchalian, Yusi Zhang, Oren Shaked, Yuanming Xu, Theodore L Roth, Dimitre R Simeonov, Yana Zhang,[...]. Nature 2020
66
16

Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks.
Adam J Rubin, Kevin R Parker, Ansuman T Satpathy, Yanyan Qi, Beijing Wu, Alvin J Ong, Maxwell R Mumbach, Andrew L Ji, Daniel S Kim, Seung Woo Cho,[...]. Cell 2019
111
16

Determinants of response and resistance to CD19 chimeric antigen receptor (CAR) T cell therapy of chronic lymphocytic leukemia.
Joseph A Fraietta, Simon F Lacey, Elena J Orlando, Iulian Pruteanu-Malinici, Mercy Gohil, Stefan Lundh, Alina C Boesteanu, Yan Wang, Roddy S O'Connor, Wei-Ting Hwang,[...]. Nat Med 2018
693
16

The Chemokine Receptor CX3CR1 Defines Three Antigen-Experienced CD8 T Cell Subsets with Distinct Roles in Immune Surveillance and Homeostasis.
Carmen Gerlach, E Ashley Moseman, Scott M Loughhead, David Alvarez, Anthonie J Zwijnenburg, Lisette Waanders, Rohit Garg, Juan C de la Torre, Ulrich H von Andrian. Immunity 2016
271
12

Unraveling the Complex Interplay Between T Cell Metabolism and Function.
Ramon I Klein Geltink, Ryan L Kyle, Erika L Pearce. Annu Rev Immunol 2018
306
12


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.