A citation-based method for searching scientific literature

Christopher Y Park, Jian Zhou, Aaron K Wong, Kathleen M Chen, Chandra L Theesfeld, Robert B Darnell, Olga G Troyanskaya. Nat Genet 2021
Times Cited: 2







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



Times Cited
  Times     Co-cited
Similarity


The Kipoi repository accelerates community exchange and reuse of predictive models for genomics.
Žiga Avsec, Roman Kreuzhuber, Johnny Israeli, Nancy Xu, Jun Cheng, Avanti Shrikumar, Abhimanyu Banerjee, Daniel S Kim, Thorsten Beier, Lara Urban,[...]. Nat Biotechnol 2019
39
100

MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect.
Daniel Esposito, Jochen Weile, Jay Shendure, Lea M Starita, Anthony T Papenfuss, Frederick P Roth, Douglas M Fowler, Alan F Rubin. Genome Biol 2019
18
100


Selene: a PyTorch-based deep learning library for sequence data.
Kathleen M Chen, Evan M Cofer, Jian Zhou, Olga G Troyanskaya. Nat Methods 2019
24
100

Base-resolution models of transcription-factor binding reveal soft motif syntax.
Žiga Avsec, Melanie Weilert, Avanti Shrikumar, Sabrina Krueger, Amr Alexandari, Khyati Dalal, Robin Fropf, Charles McAnany, Julien Gagneur, Anshul Kundaje,[...]. Nat Genet 2021
17
100

Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk.
Jian Zhou, Chandra L Theesfeld, Kevin Yao, Kathleen M Chen, Aaron K Wong, Olga G Troyanskaya. Nat Genet 2018
102
100


Predicting Splicing from Primary Sequence with Deep Learning.
Kishore Jaganathan, Sofia Kyriazopoulou Panagiotopoulou, Jeremy F McRae, Siavash Fazel Darbandi, David Knowles, Yang I Li, Jack A Kosmicki, Juan Arbelaez, Wenwu Cui, Grace B Schwartz,[...]. Cell 2019
283
100

Deep learning.
Yann LeCun, Yoshua Bengio, Geoffrey Hinton. Nature 2015
100

Sequential regulatory activity prediction across chromosomes with convolutional neural networks.
David R Kelley, Yakir A Reshef, Maxwell Bileschi, David Belanger, Cory Y McLean, Jasper Snoek. Genome Res 2018
67
100

Opportunities and obstacles for deep learning in biology and medicine.
Travers Ching, Daniel S Himmelstein, Brett K Beaulieu-Jones, Alexandr A Kalinin, Brian T Do, Gregory P Way, Enrico Ferrero, Paul-Michael Agapow, Michael Zietz, Michael M Hoffman,[...]. J R Soc Interface 2018
420
100


A method to predict the impact of regulatory variants from DNA sequence.
Dongwon Lee, David U Gorkin, Maggie Baker, Benjamin J Strober, Alessandro L Asoni, Andrew S McCallion, Michael A Beer. Nat Genet 2015
209
100

FIMO: scanning for occurrences of a given motif.
Charles E Grant, Timothy L Bailey, William Stafford Noble. Bioinformatics 2011
50

The zebrafish reference genome sequence and its relationship to the human genome.
Kerstin Howe, Matthew D Clark, Carlos F Torroja, James Torrance, Camille Berthelot, Matthieu Muffato, John E Collins, Sean Humphray, Karen McLaren, Lucy Matthews,[...]. Nature 2013
50

Amphioxus functional genomics and the origins of vertebrate gene regulation.
Ferdinand Marlétaz, Panos N Firbas, Ignacio Maeso, Juan J Tena, Ozren Bogdanovic, Malcolm Perry, Christopher D R Wyatt, Elisa de la Calle-Mustienes, Stephanie Bertrand, Demian Burguera,[...]. Nature 2018
82
50

Cross-species regulatory sequence activity prediction.
David R Kelley. PLoS Comput Biol 2020
9
50

Deep learning of the regulatory grammar of yeast 5' untranslated regions from 500,000 random sequences.
Josh T Cuperus, Benjamin Groves, Anna Kuchina, Alexander B Rosenberg, Nebojsa Jojic, Stanley Fields, Georg Seelig. Genome Res 2017
59
50

ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data.
Shinya Oki, Tazro Ohta, Go Shioi, Hideki Hatanaka, Osamu Ogasawara, Yoshihiro Okuda, Hideya Kawaji, Ryo Nakaki, Jun Sese, Chikara Meno. EMBO Rep 2018
151
50

Clustered DNA motifs mark X chromosomes for repression by a dosage compensation complex.
Patrick McDonel, Judith Jans, Brant K Peterson, Barbara J Meyer. Nature 2006
75
50

Control of Drosophila gastrulation by apical localization of adherens junctions and RhoGEF2.
Verena Kölsch, Thomas Seher, Gregorio J Fernandez-Ballester, Luis Serrano, Maria Leptin. Science 2007
224
50

The medaka draft genome and insights into vertebrate genome evolution.
Masahiro Kasahara, Kiyoshi Naruse, Shin Sasaki, Yoichiro Nakatani, Wei Qu, Budrul Ahsan, Tomoyuki Yamada, Yukinobu Nagayasu, Koichiro Doi, Yasuhiro Kasai,[...]. Nature 2007
690
50

Recruitment and spreading of the C. elegans dosage compensation complex along X chromosomes.
Györgyi Csankovszki, Patrick McDonel, Barbara J Meyer. Science 2004
86
50

The cis-regulatory dynamics of embryonic development at single-cell resolution.
Darren A Cusanovich, James P Reddington, David A Garfield, Riza M Daza, Delasa Aghamirzaie, Raquel Marco-Ferreres, Hannah A Pliner, Lena Christiansen, Xiaojie Qiu, Frank J Steemers,[...]. Nature 2018
123
50

A condensin-like dosage compensation complex acts at a distance to control expression throughout the genome.
Judith Jans, John M Gladden, Edward J Ralston, Catherine S Pickle, Agnès H Michel, Rebecca R Pferdehirt, Michael B Eisen, Barbara J Meyer. Genes Dev 2009
76
50

The UCSC Genome Browser database: 2019 update.
Maximilian Haeussler, Ann S Zweig, Cath Tyner, Matthew L Speir, Kate R Rosenbloom, Brian J Raney, Christopher M Lee, Brian T Lee, Angie S Hinrichs, Jairo Navarro Gonzalez,[...]. Nucleic Acids Res 2019
318
50

Predicting 3D genome folding from DNA sequence with Akita.
Geoff Fudenberg, David R Kelley, Katherine S Pollard. Nat Methods 2020
20
50

Deletion of ultraconserved elements yields viable mice.
Nadav Ahituv, Yiwen Zhu, Axel Visel, Amy Holt, Veena Afzal, Len A Pennacchio, Edward M Rubin. PLoS Biol 2007
207
50

Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period.
Juan J Tena, Cristina González-Aguilera, Ana Fernández-Miñán, Javier Vázquez-Marín, Helena Parra-Acero, Joe W Cross, Peter W J Rigby, Jaime J Carvajal, Joachim Wittbrodt, José L Gómez-Skarmeta,[...]. Genome Res 2014
27
50

Bedside Back to Bench: Building Bridges between Basic and Clinical Genomic Research.
Teri A Manolio, Douglas M Fowler, Lea M Starita, Melissa A Haendel, Daniel G MacArthur, Leslie G Biesecker, Elizabeth Worthey, Rex L Chisholm, Eric D Green, Howard J Jacob,[...]. Cell 2017
64
50

Enhancer Control of Transcriptional Bursting.
Takashi Fukaya, Bomyi Lim, Michael Levine. Cell 2016
281
50

DANIO-CODE: Toward an Encyclopedia of DNA Elements in Zebrafish.
Haihan Tan, Daria Onichtchouk, Cecilia Winata. Zebrafish 2016
6
50

Temporal control of gene expression by the pioneer factor Zelda through transient interactions in hubs.
Jeremy Dufourt, Antonio Trullo, Jennifer Hunter, Carola Fernandez, Jorge Lazaro, Matthieu Dejean, Lucas Morales, Saida Nait-Amer, Katharine N Schulz, Melissa M Harrison,[...]. Nat Commun 2018
50
50

Genome-wide association study of behavioral, physiological and gene expression traits in outbred CFW mice.
Clarissa C Parker, Shyam Gopalakrishnan, Peter Carbonetto, Natalia M Gonzales, Emily Leung, Yeonhee J Park, Emmanuel Aryee, Joe Davis, David A Blizard, Cheryl L Ackert-Bicknell,[...]. Nat Genet 2016
47
50

deepTools2: a next generation web server for deep-sequencing data analysis.
Fidel Ramírez, Devon P Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S Richter, Steffen Heyne, Friederike Dündar, Thomas Manke. Nucleic Acids Res 2016
50

Massively parallel functional dissection of mammalian enhancers in vivo.
Rupali P Patwardhan, Joseph B Hiatt, Daniela M Witten, Mee J Kim, Robin P Smith, Dalit May, Choli Lee, Jennifer M Andrie, Su-In Lee, Gregory M Cooper,[...]. Nat Biotechnol 2012
302
50

The Drosophila Pioneer Factor Zelda Modulates the Nuclear Microenvironment of a Dorsal Target Enhancer to Potentiate Transcriptional Output.
Shigehiro Yamada, Peter H Whitney, Shao-Kuei Huang, Elizabeth C Eck, Hernan G Garcia, Christine A Rushlow. Curr Biol 2019
26
50

Signatures of Recent Positive Selection in Enhancers Across 41 Human Tissues.
Jiyun M Moon, John A Capra, Patrick Abbot, Antonis Rokas. G3 (Bethesda) 2019
5
50

Transcriptional Pre-patterning of Drosophila Gastrulation.
Bomyi Lim, Michael Levine, Yuji Yamazaki. Curr Biol 2017
23
50

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype.
Daehwan Kim, Joseph M Paggi, Chanhee Park, Christopher Bennett, Steven L Salzberg. Nat Biotechnol 2019
855
50

The ENCODE Blacklist: Identification of Problematic Regions of the Genome.
Haley M Amemiya, Anshul Kundaje, Alan P Boyle. Sci Rep 2019
171
50

Predicting the clinical impact of human mutation with deep neural networks.
Laksshman Sundaram, Hong Gao, Samskruthi Reddy Padigepati, Jeremy F McRae, Yanjun Li, Jack A Kosmicki, Nondas Fritzilas, Jörg Hakenberg, Anindita Dutta, John Shon,[...]. Nat Genet 2018
88
50

Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes.
Timothy J Durham, Riza M Daza, Louis Gevirtzman, Darren A Cusanovich, Olubusayo Bolonduro, William Stafford Noble, Jay Shendure, Robert H Waterston. Genome Res 2021
1
100

Visualization of Transvection in Living Drosophila Embryos.
Bomyi Lim, Tyler Heist, Michael Levine, Takashi Fukaya. Mol Cell 2018
63
50

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
50

Genomic Medicine-Progress, Pitfalls, and Promise.
Jay Shendure, Gregory M Findlay, Matthew W Snyder. Cell 2019
44
50

Comprehensive Characterization of Cancer Driver Genes and Mutations.
Matthew H Bailey, Collin Tokheim, Eduard Porta-Pardo, Sohini Sengupta, Denis Bertrand, Amila Weerasinghe, Antonio Colaprico, Michael C Wendl, Jaegil Kim, Brendan Reardon,[...]. Cell 2018
614
50

Defining the role of common variation in the genomic and biological architecture of adult human height.
Andrew R Wood, Tonu Esko, Jian Yang, Sailaja Vedantam, Tune H Pers, Stefan Gustafsson, Audrey Y Chu, Karol Estrada, Jian'an Luan, Zoltán Kutalik,[...]. Nat Genet 2014
985
50

Accurate quantification of functional analogy among close homologs.
Maria D Chikina, Olga G Troyanskaya. PLoS Comput Biol 2011
22
50

Genic intolerance to functional variation and the interpretation of personal genomes.
Slavé Petrovski, Quanli Wang, Erin L Heinzen, Andrew S Allen, David B Goldstein. PLoS Genet 2013
562
50


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.