A citation-based method for searching scientific literature

Jae-Seok Roe, Chang-Il Hwang, Tim D D Somerville, Joseph P Milazzo, Eun Jung Lee, Brandon Da Silva, Laura Maiorino, Hervé Tiriac, C Megan Young, Koji Miyabayashi, Dea Filippini, Brianna Creighton, Richard A Burkhart, Jonathan M Buscaglia, Edward J Kim, Jean L Grem, Audrey J Lazenby, James A Grunkemeyer, Michael A Hollingsworth, Paul M Grandgenett, Mikala Egeblad, Youngkyu Park, David A Tuveson, Christopher R Vakoc. Cell 2017
Times Cited: 209







List of co-cited articles
1177 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


Epigenomic reprogramming during pancreatic cancer progression links anabolic glucose metabolism to distant metastasis.
Oliver G McDonald, Xin Li, Tyler Saunders, Rakel Tryggvadottir, Samantha J Mentch, Marc O Warmoes, Anna E Word, Alessandro Carrer, Tal H Salz, Sonoko Natsume,[...]. Nat Genet 2017
237
24

Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer.
Alvin P Makohon-Moore, Ming Zhang, Johannes G Reiter, Ivana Bozic, Benjamin Allen, Deepanjan Kundu, Krishnendu Chatterjee, Fay Wong, Yuchen Jiao, Zachary A Kohutek,[...]. Nat Genet 2017
217
22

Virtual microdissection identifies distinct tumor- and stroma-specific subtypes of pancreatic ductal adenocarcinoma.
Richard A Moffitt, Raoud Marayati, Elizabeth L Flate, Keith E Volmar, S Gabriela Herrera Loeza, Katherine A Hoadley, Naim U Rashid, Lindsay A Williams, Samuel C Eaton, Alexander H Chung,[...]. Nat Genet 2015
880
22

Super-enhancers in the control of cell identity and disease.
Denes Hnisz, Brian J Abraham, Tong Ihn Lee, Ashley Lau, Violaine Saint-André, Alla A Sigova, Heather A Hoke, Richard A Young. Cell 2013
21

Selective inhibition of tumor oncogenes by disruption of super-enhancers.
Jakob Lovén, Heather A Hoke, Charles Y Lin, Ashley Lau, David A Orlando, Christopher R Vakoc, James E Bradner, Tong Ihn Lee, Richard A Young. Cell 2013
21

Genomic analyses identify molecular subtypes of pancreatic cancer.
Peter Bailey, David K Chang, Katia Nones, Amber L Johns, Ann-Marie Patch, Marie-Claude Gingras, David K Miller, Angelika N Christ, Tim J C Bruxner, Michael C Quinn,[...]. Nature 2016
21

Master transcription factors and mediator establish super-enhancers at key cell identity genes.
Warren A Whyte, David A Orlando, Denes Hnisz, Brian J Abraham, Charles Y Lin, Michael H Kagey, Peter B Rahl, Tong Ihn Lee, Richard A Young. Cell 2013
20

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
17

Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy.
Eric A Collisson, Anguraj Sadanandam, Peter Olson, William J Gibb, Morgan Truitt, Shenda Gu, Janine Cooc, Jennifer Weinkle, Grace E Kim, Lakshmi Jakkula,[...]. Nat Med 2011
948
15


TP63-Mediated Enhancer Reprogramming Drives the Squamous Subtype of Pancreatic Ductal Adenocarcinoma.
Tim D D Somerville, Yali Xu, Koji Miyabayashi, Hervé Tiriac, Cristian R Cleary, Diogo Maia-Silva, Joseph P Milazzo, David A Tuveson, Christopher R Vakoc. Cell Rep 2018
80
18

Whole genomes redefine the mutational landscape of pancreatic cancer.
Nicola Waddell, Marina Pajic, Ann-Marie Patch, David K Chang, Karin S Kassahn, Peter Bailey, Amber L Johns, David Miller, Katia Nones, Kelly Quek,[...]. Nature 2015
14

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
14

Organoid models of human and mouse ductal pancreatic cancer.
Sylvia F Boj, Chang-Il Hwang, Lindsey A Baker, Iok In Christine Chio, Dannielle D Engle, Vincenzo Corbo, Myrthe Jager, Mariano Ponz-Sarvise, Hervé Tiriac, Mona S Spector,[...]. Cell 2015
13

Loss of KDM6A Activates Super-Enhancers to Induce Gender-Specific Squamous-like Pancreatic Cancer and Confers Sensitivity to BET Inhibitors.
Jaclyn Andricovich, Stephanie Perkail, Yan Kai, Nicole Casasanta, Weiqun Peng, Alexandros Tzatsos. Cancer Cell 2018
136
13

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
12

The EMT-activator Zeb1 is a key factor for cell plasticity and promotes metastasis in pancreatic cancer.
Angela M Krebs, Julia Mitschke, María Lasierra Losada, Otto Schmalhofer, Melanie Boerries, Hauke Busch, Martin Boettcher, Dimitrios Mougiakakos, Wilfried Reichardt, Peter Bronsert,[...]. Nat Cell Biol 2017
511
12

Dissection of transcriptional and cis-regulatory control of differentiation in human pancreatic cancer.
Giuseppe R Diaferia, Chiara Balestrieri, Elena Prosperini, Paola Nicoli, Paola Spaggiari, Alessandro Zerbi, Gioacchino Natoli. EMBO J 2016
77
15

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander,[...]. Proc Natl Acad Sci U S A 2005
12

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
12

Nfib Promotes Metastasis through a Widespread Increase in Chromatin Accessibility.
Sarah K Denny, Dian Yang, Chen-Hua Chuang, Jennifer J Brady, Jing Shan Lim, Barbara M Grüner, Shin-Heng Chiou, Alicia N Schep, Jessika Baral, Cécile Hamard,[...]. Cell 2016
197
12

Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution.
Michelle Chan-Seng-Yue, Jaeseung C Kim, Gavin W Wilson, Karen Ng, Eugenia Flores Figueroa, Grainne M O'Kane, Ashton A Connor, Robert E Denroche, Robert C Grant, Jessica McLeod,[...]. Nat Genet 2020
171
12

Organoid Profiling Identifies Common Responders to Chemotherapy in Pancreatic Cancer.
Hervé Tiriac, Pascal Belleau, Dannielle D Engle, Dennis Plenker, Astrid Deschênes, Tim D D Somerville, Fieke E M Froeling, Richard A Burkhart, Robert E Denroche, Gun-Ho Jang,[...]. Cancer Discov 2018
402
11

Histone H3K27ac separates active from poised enhancers and predicts developmental state.
Menno P Creyghton, Albert W Cheng, G Grant Welstead, Tristan Kooistra, Bryce W Carey, Eveline J Steine, Jacob Hanna, Michael A Lodato, Garrett M Frampton, Phillip A Sharp,[...]. Proc Natl Acad Sci U S A 2010
11

Trp53R172H and KrasG12D cooperate to promote chromosomal instability and widely metastatic pancreatic ductal adenocarcinoma in mice.
Sunil R Hingorani, Lifu Wang, Asha S Multani, Chelsea Combs, Therese B Deramaudt, Ralph H Hruban, Anil K Rustgi, Sandy Chang, David A Tuveson. Cancer Cell 2005
11

Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element.
Marc R Mansour, Brian J Abraham, Lars Anders, Alla Berezovskaya, Alejandro Gutierrez, Adam D Durbin, Julia Etchin, Lee Lawton, Stephen E Sallan, Lewis B Silverman,[...]. Science 2014
453
10

Emerging Biological Principles of Metastasis.
Arthur W Lambert, Diwakar R Pattabiraman, Robert A Weinberg. Cell 2017
10

EMT and dissemination precede pancreatic tumor formation.
Andrew D Rhim, Emily T Mirek, Nicole M Aiello, Anirban Maitra, Jennifer M Bailey, Florencia McAllister, Maximilian Reichert, Gregory L Beatty, Anil K Rustgi, Robert H Vonderheide,[...]. Cell 2012
10

Distant metastasis occurs late during the genetic evolution of pancreatic cancer.
Shinichi Yachida, Siân Jones, Ivana Bozic, Tibor Antal, Rebecca Leary, Baojin Fu, Mihoko Kamiyama, Ralph H Hruban, James R Eshleman, Martin A Nowak,[...]. Nature 2010
10

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
10

Distinct populations of inflammatory fibroblasts and myofibroblasts in pancreatic cancer.
Daniel Öhlund, Abram Handly-Santana, Giulia Biffi, Ela Elyada, Ana S Almeida, Mariano Ponz-Sarvise, Vincenzo Corbo, Tobiloba E Oni, Stephen A Hearn, Eun Jung Lee,[...]. J Exp Med 2017
898
10

Minimal functional driver gene heterogeneity among untreated metastases.
Johannes G Reiter, Alvin P Makohon-Moore, Jeffrey M Gerold, Alexander Heyde, Marc A Attiyeh, Zachary A Kohutek, Collin J Tokheim, Alexia Brown, Rayne M DeBlasio, Juliana Niyazov,[...]. Science 2018
149
10

Hallmarks of cancer: the next generation.
Douglas Hanahan, Robert A Weinberg. Cell 2011
9

Cancer statistics, 2019.
Rebecca L Siegel, Kimberly D Miller, Ahmedin Jemal. CA Cancer J Clin 2019
9

Human Pancreatic Tumor Organoids Reveal Loss of Stem Cell Niche Factor Dependence during Disease Progression.
Takashi Seino, Shintaro Kawasaki, Mariko Shimokawa, Hiroki Tamagawa, Kohta Toshimitsu, Masayuki Fujii, Yuki Ohta, Mami Matano, Kosaku Nanki, Kenta Kawasaki,[...]. Cell Stem Cell 2018
277
9

The chromatin accessibility landscape of primary human cancers.
M Ryan Corces, Jeffrey M Granja, Shadi Shams, Bryan H Louie, Jose A Seoane, Wanding Zhou, Tiago C Silva, Clarice Groeneveld, Christopher K Wong, Seung Woo Cho,[...]. Science 2018
387
9


Epigenetic plasticity and the hallmarks of cancer.
William A Flavahan, Elizabeth Gaskell, Bradley E Bernstein. Science 2017
549
9

Core signaling pathways in human pancreatic cancers revealed by global genomic analyses.
Siân Jones, Xiaosong Zhang, D Williams Parsons, Jimmy Cheng-Ho Lin, Rebecca J Leary, Philipp Angenendt, Parminder Mankoo, Hannah Carter, Hirohiko Kamiyama, Antonio Jimeno,[...]. Science 2008
8

Projecting cancer incidence and deaths to 2030: the unexpected burden of thyroid, liver, and pancreas cancers in the United States.
Lola Rahib, Benjamin D Smith, Rhonda Aizenberg, Allison B Rosenzweig, Julie M Fleshman, Lynn M Matrisian. Cancer Res 2014
8

Epithelial-to-mesenchymal transition is dispensable for metastasis but induces chemoresistance in pancreatic cancer.
Xiaofeng Zheng, Julienne L Carstens, Jiha Kim, Matthew Scheible, Judith Kaye, Hikaru Sugimoto, Chia-Chin Wu, Valerie S LeBleu, Raghu Kalluri. Nature 2015
8

Genomics-Driven Precision Medicine for Advanced Pancreatic Cancer: Early Results from the COMPASS Trial.
Kyaw L Aung, Sandra E Fischer, Robert E Denroche, Gun-Ho Jang, Anna Dodd, Sean Creighton, Bernadette Southwood, Sheng-Ben Liang, Dianne Chadwick, Amy Zhang,[...]. Clin Cancer Res 2018
238
8

Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes.
Andrew V Biankin, Nicola Waddell, Karin S Kassahn, Marie-Claude Gingras, Lakshmi B Muthuswamy, Amber L Johns, David K Miller, Peter J Wilson, Ann-Marie Patch, Jianmin Wu,[...]. Nature 2012
8

Transcriptional Addiction in Cancer.
James E Bradner, Denes Hnisz, Richard A Young. Cell 2017
499
8

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
8

Preinvasive and invasive ductal pancreatic cancer and its early detection in the mouse.
Sunil R Hingorani, Emanuel F Petricoin, Anirban Maitra, Vinodh Rajapakse, Catrina King, Michael A Jacobetz, Sally Ross, Thomas P Conrads, Timothy D Veenstra, Ben A Hitt,[...]. Cancer Cell 2003
8

Cancer statistics, 2020.
Rebecca L Siegel, Kimberly D Miller, Ahmedin Jemal. CA Cancer J Clin 2020
8

Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers.
Xiaoyang Zhang, Peter S Choi, Joshua M Francis, Marcin Imielinski, Hideo Watanabe, Andrew D Cherniack, Matthew Meyerson. Nat Genet 2016
209
8

Enhancer reprogramming in tumor progression: a new route towards cancer cell plasticity.
Luca Fagnocchi, Vittoria Poli, Alessio Zippo. Cell Mol Life Sci 2018
24
29

Therapeutic targeting of ependymoma as informed by oncogenic enhancer profiling.
Stephen C Mack, Kristian W Pajtler, Lukas Chavez, Konstantin Okonechnikov, Kelsey C Bertrand, Xiuxing Wang, Serap Erkek, Alexander Federation, Anne Song, Christine Lee,[...]. Nature 2018
118
7


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.