A citation-based method for searching scientific literature

Justin B Kinney, Gasper Tkacik, Curtis G Callan. Proc Natl Acad Sci U S A 2007
Times Cited: 42







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



Times Cited
  Times     Co-cited
Similarity




A biophysical approach to transcription factor binding site discovery.
Marko Djordjevic, Anirvan M Sengupta, Boris I Shraiman. Genome Res 2003
139
30

Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE.
Barrett C Foat, Alexandre V Morozov, Harmen J Bussemaker. Bioinformatics 2006
194
28



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
21

Physical constraints and functional characteristics of transcription factor-DNA interaction.
Ulrich Gerland, J David Moroz, Terence Hwa. Proc Natl Acad Sci U S A 2002
172
19

Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities.
Michael F Berger, Anthony A Philippakis, Aaron M Qureshi, Fangxue S He, Preston W Estep, Martha L Bulyk. Nat Biotechnol 2006
422
19

Additivity in protein-DNA interactions: how good an approximation is it?
Panayiotis V Benos, Martha L Bulyk, Gary D Stormo. Nucleic Acids Res 2002
229
16

Predicting transcription factor affinities to DNA from a biophysical model.
Helge G Roider, Aditi Kanhere, Thomas Manke, Martin Vingron. Bioinformatics 2007
139
16

Analyzing neural responses to natural signals: maximally informative dimensions.
Tatyana Sharpee, Nicole C Rust, William Bialek. Neural Comput 2004
179
16

Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays.
Sonali Mukherjee, Michael F Berger, Ghil Jona, Xun S Wang, Dale Muzzey, Michael Snyder, Richard A Young, Martha L Bulyk. Nat Genet 2004
259
14

Transcriptional regulatory code of a eukaryotic genome.
Christopher T Harbison, D Benjamin Gordon, Tong Ihn Lee, Nicola J Rinaldi, Kenzie D Macisaac, Timothy W Danford, Nancy M Hannett, Jean-Bosco Tagne, David B Reynolds, Jane Yoo,[...]. Nature 2004
14

Quantitative specificity of the Mnt repressor.
D S Fields, Y He, A Y Al-Uzri, G D Stormo. J Mol Biol 1997
68
14

Spike-triggered neural characterization.
Odelia Schwartz, Jonathan W Pillow, Nicole C Rust, Eero P Simoncelli. J Vis 2006
238
14

Genome-wide mapping of in vivo protein-DNA interactions.
David S Johnson, Ali Mortazavi, Richard M Myers, Barbara Wold. Science 2007
14

A feature-based approach to modeling protein-DNA interactions.
Eilon Sharon, Shai Lubliner, Eran Segal. PLoS Comput Biol 2008
63
14

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
429
14

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
342
14


An improved map of conserved regulatory sites for Saccharomyces cerevisiae.
Kenzie D MacIsaac, Ting Wang, D Benjamin Gordon, David K Gifford, Gary D Stormo, Ernest Fraenkel. BMC Bioinformatics 2006
487
11

Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity.
Outi Hallikas, Kimmo Palin, Natalia Sinjushina, Reetta Rautiainen, Juha Partanen, Esko Ukkonen, Jussi Taipale. Cell 2006
356
11

The Protein Data Bank.
H M Berman, J Westbrook, Z Feng, G Gilliland, T N Bhat, H Weissig, I N Shindyalov, P E Bourne. Nucleic Acids Res 2000
11


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
198
11

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
11

Inferring binding energies from selected binding sites.
Yue Zhao, David Granas, Gary D Stormo. PLoS Comput Biol 2009
150
11

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
11



On the selection and evolution of regulatory DNA motifs.
Ulrich Gerland, Terence Hwa. J Mol Evol 2002
70
9

Predictive modeling of genome-wide mRNA expression: from modules to molecules.
Harmen J Bussemaker, Barrett C Foat, Lucas D Ward. Annu Rev Biophys Biomol Struct 2007
60
9



Protein-DNA binding specificity predictions with structural models.
Alexandre V Morozov, James J Havranek, David Baker, Eric D Siggia. Nucleic Acids Res 2005
140
9


Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules.
Jean-Valery Turatsinze, Morgane Thomas-Chollier, Matthieu Defrance, Jacques van Helden. Nat Protoc 2008
180
9

Synergy in a neural code.
N Brenner, S P Strong, R Koberle, W Bialek, R R de Ruyter van Steveninck. Neural Comput 2000
187
9


Diversity and complexity in DNA recognition by transcription factors.
Gwenael Badis, Michael F Berger, Anthony A Philippakis, Shaheynoor Talukder, Andrew R Gehrke, Savina A Jaeger, Esther T Chan, Genita Metzler, Anastasia Vedenko, Xiaoyu Chen,[...]. Science 2009
637
9

Predicting expression patterns from regulatory sequence in Drosophila segmentation.
Eran Segal, Tali Raveh-Sadka, Mark Schroeder, Ulrich Unnerstall, Ulrike Gaul. Nature 2008
323
9

Weak pairwise correlations imply strongly correlated network states in a neural population.
Elad Schneidman, Michael J Berry, Ronen Segev, William Bialek. Nature 2006
712
9

Estimating linear-nonlinear models using Renyi divergences.
Minjoon Kouh, Tatyana O Sharpee. Network 2009
21
19


Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins.
Matthew Slattery, Todd Riley, Peng Liu, Namiko Abe, Pilar Gomez-Alcala, Iris Dror, Tianyin Zhou, Remo Rohs, Barry Honig, Harmen J Bussemaker,[...]. Cell 2011
285
9


Evaluation of methods for modeling transcription factor sequence specificity.
Matthew T Weirauch, Atina Cote, Raquel Norel, Matti Annala, Yue Zhao, Todd R Riley, Julio Saez-Rodriguez, Thomas Cokelaer, Anastasia Vedenko, Shaheynoor Talukder,[...]. Nat Biotechnol 2013
206
9

Position specific variation in the rate of evolution in transcription factor binding sites.
Alan M Moses, Derek Y Chiang, Manolis Kellis, Eric S Lander, Michael B Eisen. BMC Evol Biol 2003
107
7

Gene regulation at the single-cell level.
Nitzan Rosenfeld, Jonathan W Young, Uri Alon, Peter S Swain, Michael B Elowitz. Science 2005
681
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.