A citation-based method for searching scientific literature

Carl G de Boer, Eeshit Dhaval Vaishnav, Ronen Sadeh, Esteban Luis Abeyta, Nir Friedman, Aviv Regev. Nat Biotechnol 2020
Times Cited: 71







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



Times Cited
  Times     Co-cited
Similarity


Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters.
Eilon Sharon, Yael Kalma, Ayala Sharp, Tali Raveh-Sadka, Michal Levo, Danny Zeevi, Leeat Keren, Zohar Yakhini, Adina Weinberger, Eran Segal. Nat Biotechnol 2012
294
29

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
82
21



Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning.
Babak Alipanahi, Andrew Delong, Matthew T Weirauch, Brendan J Frey. Nat Biotechnol 2015
983
15

Design of synthetic yeast promoters via tuning of nucleosome architecture.
Kathleen A Curran, Nathan C Crook, Ashty S Karim, Akash Gupta, Allison M Wagman, Hal S Alper. Nat Commun 2014
89
14

Model-driven generation of artificial yeast promoters.
Benjamin J Kotopka, Christina D Smolke. Nat Commun 2020
37
27



Core promoter sequence in yeast is a major determinant of expression level.
Shai Lubliner, Ifat Regev, Maya Lotan-Pompan, Sarit Edelheit, Adina Weinberger, Eran Segal. Genome Res 2015
58
15

Enzymatic assembly of DNA molecules up to several hundred kilobases.
Daniel G Gibson, Lei Young, Ray-Yuan Chuang, J Craig Venter, Clyde A Hutchison, Hamilton O Smith. Nat Methods 2009
12

Systematic interrogation of human promoters.
Shira Weingarten-Gabbay, Ronit Nir, Shai Lubliner, Eilon Sharon, Yael Kalma, Adina Weinberger, Eran Segal. Genome Res 2019
46
19

High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis.
Rupali P Patwardhan, Choli Lee, Oren Litvin, David L Young, Dana Pe'er, Jay Shendure. Nat Biotechnol 2009
203
12

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
124
11

Tuning genetic control through promoter engineering.
Hal Alper, Curt Fischer, Elke Nevoigt, Gregory Stephanopoulos. Proc Natl Acad Sci U S A 2005
560
11

Composability of regulatory sequences controlling transcription and translation in Escherichia coli.
Sriram Kosuri, Daniel B Goodman, Guillaume Cambray, Vivek K Mutalik, Yuan Gao, Adam P Arkin, Drew Endy, George M Church. Proc Natl Acad Sci U S A 2013
240
11


Random sequences rapidly evolve into de novo promoters.
Avihu H Yona, Eric J Alm, Jeff Gore. Nat Commun 2018
54
14

FIMO: scanning for occurrences of a given motif.
Charles E Grant, Timothy L Bailey, William Stafford Noble. Bioinformatics 2011
9

Human 5' UTR design and variant effect prediction from a massively parallel translation assay.
Paul J Sample, Ban Wang, David W Reid, Vlad Presnyak, Iain J McFadyen, David R Morris, Georg Seelig. Nat Biotechnol 2019
79
9

Unraveling determinants of transcription factor binding outside the core binding site.
Michal Levo, Einat Zalckvar, Eilon Sharon, Ana Carolina Dantas Machado, Yael Kalma, Maya Lotam-Pompan, Adina Weinberger, Zohar Yakhini, Remo Rohs, Eran Segal. Genome Res 2015
95
9

Systematic Dissection of Sequence Elements Controlling σ70 Promoters Using a Genomically Encoded Multiplexed Reporter Assay in Escherichia coli.
Guillaume Urtecho, Arielle D Tripp, Kimberly D Insigne, Hwangbeom Kim, Sriram Kosuri. Biochemistry 2019
38
18

Automated design of synthetic ribosome binding sites to control protein expression.
Howard M Salis, Ethan A Mirsky, Christopher A Voigt. Nat Biotechnol 2009
9

Low affinity binding site clusters confer hox specificity and regulatory robustness.
Justin Crocker, Namiko Abe, Lucrezia Rinaldi, Alistair P McGregor, Nicolás Frankel, Shu Wang, Ahmad Alsawadi, Philippe Valenti, Serge Plaza, François Payre,[...]. Cell 2015
197
9

Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution.
Martin Kircher, Chenling Xiong, Beth Martin, Max Schubach, Fumitaka Inoue, Robert J A Bell, Joseph F Costello, Jay Shendure, Nadav Ahituv. Nat Commun 2019
63
11

Synthetic promoter design in Escherichia coli based on a deep generative network.
Ye Wang, Haochen Wang, Lei Wei, Shuailin Li, Liyang Liu, Xiaowo Wang. Nucleic Acids Res 2020
38
18

Suboptimization of developmental enhancers.
Emma K Farley, Katrina M Olson, Wei Zhang, Alexander J Brandt, Daniel S Rokhsar, Michael S Levine. Science 2015
163
8


Determinants of enhancer and promoter activities of regulatory elements.
Robin Andersson, Albin Sandelin. Nat Rev Genet 2020
194
8

Analysis of combinatorial cis-regulation in synthetic and genomic promoters.
Jason Gertz, Eric D Siggia, Barak A Cohen. Nature 2009
218
8

Short Synthetic Terminators for Improved Heterologous Gene Expression in Yeast.
Kathleen A Curran, Nicholas J Morse, Kelly A Markham, Allison M Wagman, Akash Gupta, Hal S Alper. ACS Synth Biol 2015
115
8

Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence.
Justin B Kinney, Anand Murugan, Curtis G Callan, Edward C Cox. Proc Natl Acad Sci U S A 2010
175
8


Automated design of thousands of nonrepetitive parts for engineering stable genetic systems.
Ayaan Hossain, Eriberto Lopez, Sean M Halper, Daniel P Cetnar, Alexander C Reis, Devin Strickland, Eric Klavins, Howard M Salis. Nat Biotechnol 2020
25
24

Systematic dissection of the sequence determinants of gene 3' end mediated expression control.
Ophir Shalem, Eilon Sharon, Shai Lubliner, Ifat Regev, Maya Lotan-Pompan, Zohar Yakhini, Eran Segal. PLoS Genet 2015
39
15

Determination and inference of eukaryotic transcription factor sequence specificity.
Matthew T Weirauch, Ally Yang, Mihai Albu, Atina G Cote, Alejandro Montenegro-Montero, Philipp Drewe, Hamed S Najafabadi, Samuel A Lambert, Ishminder Mann, Kate Cook,[...]. Cell 2014
831
8


Massively Parallel Interrogation of the Effects of Gene Expression Levels on Fitness.
Leeat Keren, Jean Hausser, Maya Lotan-Pompan, Ilya Vainberg Slutskin, Hadas Alisar, Sivan Kaminski, Adina Weinberger, Uri Alon, Ron Milo, Eran Segal. Cell 2016
93
8

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
8

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
87
8

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution.
Hannah K Long, Sara L Prescott, Joanna Wysocka. Cell 2016
421
7

Deciphering the rules by which 5'-UTR sequences affect protein expression in yeast.
Shlomi Dvir, Lars Velten, Eilon Sharon, Danny Zeevi, Lucas B Carey, Adina Weinberger, Eran Segal. Proc Natl Acad Sci U S A 2013
152
7



MEME SUITE: tools for motif discovery and searching.
Timothy L Bailey, Mikael Boden, Fabian A Buske, Martin Frith, Charles E Grant, Luca Clementi, Jingyuan Ren, Wilfred W Li, William S Noble. Nucleic Acids Res 2009
7


Predictable tuning of protein expression in bacteria.
Mads T Bonde, Margit Pedersen, Michael S Klausen, Sheila I Jensen, Tune Wulff, Scott Harrison, Alex T Nielsen, Markus J Herrgård, Morten O A Sommer. Nat Methods 2016
83
7

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
322
7


Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay.
Alexandre Melnikov, Anand Murugan, Xiaolan Zhang, Tiberiu Tesileanu, Li Wang, Peter Rogov, Soheil Feizi, Andreas Gnirke, Curtis G Callan, Justin B Kinney,[...]. Nat Biotechnol 2012
387
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.