A citation-based method for searching scientific literature

Justin B Kinney, Gurinder S Atwal. Neural Comput 2014
Times Cited: 5







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



Times Cited
  Times     Co-cited
Similarity


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
152
80

Precise physical models of protein-DNA interaction from high-throughput data.
Justin B Kinney, Gasper Tkacik, Curtis G Callan. Proc Natl Acad Sci U S A 2007
42
60

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
177
60

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
344
60

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
258
60

Complex effects of nucleotide variants in a mammalian cis-regulatory element.
Jamie C Kwasnieski, Ilaria Mogno, Connie A Myers, Joseph C Corbo, Barak A Cohen. Proc Natl Acad Sci U S A 2012
137
40

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
297
40

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
219
40

Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria.
Nathan M Belliveau, Stephanie L Barnes, William T Ireland, Daniel L Jones, Michael J Sweredoski, Annie Moradian, Sonja Hess, Justin B Kinney, Rob Phillips. Proc Natl Acad Sci U S A 2018
34
40

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
24
40

Sequence logos: a new way to display consensus sequences.
T D Schneider, R M Stephens. Nucleic Acids Res 1990
40

Tuning Transcriptional Regulation through Signaling: A Predictive Theory of Allosteric Induction.
Manuel Razo-Mejia, Stephanie L Barnes, Nathan M Belliveau, Griffin Chure, Tal Einav, Mitchell Lewis, Rob Phillips. Cell Syst 2018
24
40

Transcriptional regulation by the numbers: models.
Lacramioara Bintu, Nicolas E Buchler, Hernan G Garcia, Ulrich Gerland, Terence Hwa, Jané Kondev, Rob Phillips. Curr Opin Genet Dev 2005
431
40

Tuning promoter strength through RNA polymerase binding site design in Escherichia coli.
Robert C Brewster, Daniel L Jones, Rob Phillips. PLoS Comput Biol 2012
95
40


RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond.
Socorro Gama-Castro, Heladia Salgado, Alberto Santos-Zavaleta, Daniela Ledezma-Tejeida, Luis Muñiz-Rascado, Jair Santiago García-Sotelo, Kevin Alquicira-Hernández, Irma Martínez-Flores, Lucia Pannier, Jaime Abraham Castro-Mondragón,[...]. Nucleic Acids Res 2016
258
40

Quantitative dissection of the simple repression input-output function.
Hernan G Garcia, Rob Phillips. Proc Natl Acad Sci U S A 2011
66
40


The quantitative and condition-dependent Escherichia coli proteome.
Alexander Schmidt, Karl Kochanowski, Silke Vedelaar, Erik Ahrné, Benjamin Volkmer, Luciano Callipo, Kèvin Knoops, Manuel Bauer, Ruedi Aebersold, Matthias Heinemann. Nat Biotechnol 2016
312
40


Mutual-information-based registration of medical images: a survey.
Josien P W Pluim, J B Antoine Maintz, Max A Viergever. IEEE Trans Med Imaging 2003
875
20


Analyzing neural responses to natural signals: maximally informative dimensions.
Tatyana Sharpee, Nicole C Rust, William Bialek. Neural Comput 2004
179
20

ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context.
Adam A Margolin, Ilya Nemenman, Katia Basso, Chris Wiggins, Gustavo Stolovitzky, Riccardo Dalla Favera, Andrea Califano. BMC Bioinformatics 2006
20

Detecting novel associations in large data sets.
David N Reshef, Yakir A Reshef, Hilary K Finucane, Sharon R Grossman, Gilean McVean, Peter J Turnbaugh, Eric S Lander, Michael Mitzenmacher, Pardis C Sabeti. Science 2011
513
20

A universal framework for regulatory element discovery across all genomes and data types.
Olivier Elemento, Noam Slonim, Saeed Tavazoie. Mol Cell 2007
219
20

Correcting for the sampling bias problem in spike train information measures.
Stefano Panzeri, Riccardo Senatore, Marcelo A Montemurro, Rasmus S Petersen. J Neurophysiol 2007
226
20

Estimating mutual information.
Alexander Kraskov, Harald Stögbauer, Peter Grassberger. Phys Rev E Stat Nonlin Soft Matter Phys 2004
557
20

Relative performance of mutual information estimation methods for quantifying the dependence among short and noisy data.
Shiraj Khan, Sharba Bandyopadhyay, Auroop R Ganguly, Sunil Saigal, David J Erickson, Vladimir Protopopescu, George Ostrouchov. Phys Rev E Stat Nonlin Soft Matter Phys 2007
39
20



Adaptive filtering enhances information transmission in visual cortex.
Tatyana O Sharpee, Hiroki Sugihara, Andrei V Kurgansky, Sergei P Rebrik, Michael P Stryker, Kenneth D Miller. Nature 2006
199
20

Minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers.
Davide Albanese, Michele Filosi, Roberto Visintainer, Samantha Riccadonna, Giuseppe Jurman, Cesare Furlanello. Bioinformatics 2013
50
20

Systematic discovery of structural elements governing stability of mammalian messenger RNAs.
Hani Goodarzi, Hamed S Najafabadi, Panos Oikonomou, Todd M Greco, Lisa Fish, Reza Salavati, Ileana M Cristea, Saeed Tavazoie. Nature 2012
103
20

Occam factors and model independent Bayesian learning of continuous distributions.
Ilya Nemenman, William Bialek. Phys Rev E Stat Nonlin Soft Matter Phys 2002
15
20


A SIGNIFICANCE TEST FOR THE LASSO.
Richard Lockhart, Jonathan Taylor, Ryan J Tibshirani, Robert Tibshirani. Ann Stat 2014
156
20

Universal protein fluctuations in populations of microorganisms.
Hanna Salman, Naama Brenner, Chih-kuan Tung, Noa Elyahu, Elad Stolovicki, Lindsay Moore, Albert Libchaber, Erez Braun. Phys Rev Lett 2012
48
20

Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos.
Stephen S Gisselbrecht, Luis A Barrera, Martin Porsch, Anton Aboukhalil, Preston W Estep, Anastasia Vedenko, Alexandre Palagi, Yongsok Kim, Xianmin Zhu, Brian W Busser,[...]. Nat Methods 2013
40
20

Evolvability as a function of purifying selection in TEM-1 β-lactamase.
Michael A Stiffler, Doeke R Hekstra, Rama Ranganathan. Cell 2015
120
20

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
131
20

A systematic survey of an intragenic epistatic landscape.
Claudia Bank, Ryan T Hietpas, Jeffrey D Jensen, Daniel N A Bolon. Mol Biol Evol 2015
66
20

The spatial architecture of protein function and adaptation.
Richard N McLaughlin, Frank J Poelwijk, Arjun Raman, Walraj S Gosal, Rama Ranganathan. Nature 2012
265
20

In pursuit of design principles of regulatory sequences.
Michal Levo, Eran Segal. Nat Rev Genet 2014
126
20

Comprehensive mutational scanning of a kinase in vivo reveals substrate-dependent fitness landscapes.
Alexandre Melnikov, Peter Rogov, Li Wang, Andreas Gnirke, Tarjei S Mikkelsen. Nucleic Acids Res 2014
79
20

Gene expression. MicroRNA control of protein expression noise.
Jörn M Schmiedel, Sandy L Klemm, Yannan Zheng, Apratim Sahay, Nils Blüthgen, Debora S Marks, Alexander van Oudenaarden. Science 2015
197
20

High-throughput cellular RNA device engineering.
Brent Townshend, Andrew B Kennedy, Joy S Xiang, Christina D Smolke. Nat Methods 2015
56
20

Rapid construction of empirical RNA fitness landscapes.
Jason N Pitt, Adrian R Ferré-D'Amaré. Science 2010
104
20

Saturation editing of genomic regions by multiplex homology-directed repair.
Gregory M Findlay, Evan A Boyle, Ronald J Hause, Jason C Klein, Jay Shendure. Nature 2014
180
20

Large-scale de novo DNA synthesis: technologies and applications.
Sriram Kosuri, George M Church. Nat Methods 2014
310
20


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.