A citation-based method for searching scientific literature

Mehran Karimzadeh, Michael M Hoffman. Genome Biol 2022
Times Cited: 2







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



Times Cited
  Times     Co-cited
Similarity


FIMO: scanning for occurrences of a given motif.
Charles E Grant, Timothy L Bailey, William Stafford Noble. Bioinformatics 2011
100

The Human Transcription Factors.
Samuel A Lambert, Arttu Jolma, Laura F Campitelli, Pratyush K Das, Yimeng Yin, Mihai Albu, Xiaoting Chen, Jussi Taipale, Timothy R Hughes, Matthew T Weirauch. Cell 2018
881
100


TIGRESS: Trustful Inference of Gene REgulation using Stability Selection.
Anne-Claire Haury, Fantine Mordelet, Paola Vera-Licona, Jean-Philippe Vert. BMC Syst Biol 2012
186
50

Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism.
Camila M Lopes-Ramos, Marieke L Kuijjer, Shuji Ogino, Charles S Fuchs, Dawn L DeMeo, Kimberly Glass, John Quackenbush. Cancer Res 2018
45
50

Passing messages between biological networks to refine predicted interactions.
Kimberly Glass, Curtis Huttenhower, John Quackenbush, Guo-Cheng Yuan. PLoS One 2013
90
50

Sparse inverse covariance estimation with the graphical lasso.
Jerome Friedman, Trevor Hastie, Robert Tibshirani. Biostatistics 2008
50

A general framework for weighted gene co-expression network analysis.
Bin Zhang, Steve Horvath. Stat Appl Genet Mol Biol 2005
50

Differential connectivity of gene regulatory networks distinguishes corticosteroid response in asthma.
Weiliang Qiu, Feng Guo, Kimberly Glass, Guo Cheng Yuan, John Quackenbush, Xiaobo Zhou, Kelan G Tantisira. J Allergy Clin Immunol 2018
21
50

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
50

Exploiting transfer learning for the reconstruction of the human gene regulatory network.
Paolo Mignone, Gianvito Pio, Domenica D'Elia, Michelangelo Ceci. Bioinformatics 2020
23
50

Haploinsufficiency of Hedgehog interacting protein causes increased emphysema induced by cigarette smoke through network rewiring.
Taotao Lao, Kimberly Glass, Weiliang Qiu, Francesca Polverino, Kushagra Gupta, Jarrett Morrow, John Dominic Mancini, Linh Vuong, Mark A Perrella, Craig P Hersh,[...]. Genome Med 2015
41
50

On convex relaxation of graph isomorphism.
Yonathan Aflalo, Alexander Bronstein, Ron Kimmel. Proc Natl Acad Sci U S A 2015
5
50

The Genetics of Transcription Factor DNA Binding Variation.
Bart Deplancke, Daniel Alpern, Vincent Gardeux. Cell 2016
186
50

Selective Transfer Machine for Personalized Facial Action Unit Detection.
Wen-Sheng Chu, Fernando De la Torre, Jeffery F Cohn. Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit 2013
34
50

ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information.
Alexander Lachmann, Federico M Giorgi, Gonzalo Lopez, Andrea Califano. Bioinformatics 2016
128
50

Factorized Graph Matching.
Feng Zhou, Fernando de la Torre. IEEE Trans Pattern Anal Mach Intell 2016
17
50

Resolving noise-control conflict by gene duplication.
Michal Chapal, Sefi Mintzer, Sagie Brodsky, Miri Carmi, Naama Barkai. PLoS Biol 2019
21
50

Sufu- and Spop-mediated downregulation of Hedgehog signaling promotes beta cell differentiation through organ-specific niche signals.
Theodora Yung, Frankie Poon, Minggao Liang, Sabrina Coquenlorge, Emily C McGaugh, Chi-Chung Hui, Michael D Wilson, M Cristina Nostro, Tae-Hee Kim. Nat Commun 2019
19
50



Reproducible RNA-seq analysis using recount2.
Leonardo Collado-Torres, Abhinav Nellore, Kai Kammers, Shannon E Ellis, Margaret A Taub, Kasper D Hansen, Andrew E Jaffe, Ben Langmead, Jeffrey T Leek. Nat Biotechnol 2017
184
50

Inferring regulatory networks from expression data using tree-based methods.
Vân Anh Huynh-Thu, Alexandre Irrthum, Louis Wehenkel, Pierre Geurts. PLoS One 2010
684
50

Software for computing and annotating genomic ranges.
Michael Lawrence, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin T Morgan, Vincent J Carey. PLoS Comput Biol 2013
50

ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells.
Zhengqing Ouyang, Qing Zhou, Wing Hung Wong. Proc Natl Acad Sci U S A 2009
218
50

Structural perspective of cooperative transcription factor binding.
Ekaterina Morgunova, Jussi Taipale. Curr Opin Struct Biol 2017
92
50

Transcription factors: from enhancer binding to developmental control.
François Spitz, Eileen E M Furlong. Nat Rev Genet 2012
50

The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge.
Katarzyna Tomczak, Patrycja Czerwińska, Maciej Wiznerowicz. Contemp Oncol (Pozn) 2015
50

ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments.
Jeanne Chèneby, Marius Gheorghe, Marie Artufel, Anthony Mathelier, Benoit Ballester. Nucleic Acids Res 2018
128
50

Gene regulatory network inference as relaxed graph matching.
Deborah Weighill, Marouen Ben Guebila, Camila Lopes-Ramos, Kimberly Glass, John Quackenbush, John Platig, Rebekka Burkholz. Proc Conf AAAI Artif Intell 2021
2
50

Understanding Tissue-Specific Gene Regulation.
Abhijeet Rajendra Sonawane, John Platig, Maud Fagny, Cho-Yi Chen, Joseph Nathaniel Paulson, Camila Miranda Lopes-Ramos, Dawn Lisa DeMeo, John Quackenbush, Kimberly Glass, Marieke Lydia Kuijjer. Cell Rep 2017
158
50

Deep learning for inferring gene relationships from single-cell expression data.
Ye Yuan, Ziv Bar-Joseph. Proc Natl Acad Sci U S A 2019
54
50

WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder, Steve Horvath. BMC Bioinformatics 2008
50

Transcription factors: specific DNA binding and specific gene regulation.
Anne-Laure Todeschini, Adrien Georges, Reiner A Veitia. Trends Genet 2014
94
50

Wisdom of crowds for robust gene network inference.
Daniel Marbach, James C Costello, Robert Küffner, Nicole M Vega, Robert J Prill, Diogo M Camacho, Kyle R Allison, Manolis Kellis, James J Collins, Gustavo Stolovitzky. Nat Methods 2012
850
50

GRAND: a database of gene regulatory network models across human conditions.
Marouen Ben Guebila, Camila M Lopes-Ramos, Deborah Weighill, Abhijeet Rajendra Sonawane, Rebekka Burkholz, Behrouz Shamsaei, John Platig, Kimberly Glass, Marieke L Kuijjer, John Quackenbush. Nucleic Acids Res 2022
7
50

ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data.
Scott M Lundberg, William B Tu, Brian Raught, Linda Z Penn, Michael M Hoffman, Su-In Lee. Genome Biol 2016
21
50

Transcription factors Elk-1 and SRF are engaged in IL1-dependent regulation of ZC3H12A expression.
Aneta Kasza, Paulina Wyrzykowska, Irena Horwacik, Piotr Tymoszuk, Danuta Mizgalska, Karren Palmer, Hanna Rokita, Andrew D Sharrocks, Jolanta Jura. BMC Mol Biol 2010
61
50

Integrative analysis of 111 reference human epigenomes.
Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller,[...]. Nature 2015
50


The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.
Jordi Barretina, Giordano Caponigro, Nicolas Stransky, Kavitha Venkatesan, Adam A Margolin, Sungjoon Kim, Christopher J Wilson, Joseph Lehár, Gregory V Kryukov, Dmitriy Sonkin,[...]. Nature 2012
50



Genetic expression profile of olfactory ensheathing cells is distinct from that of Schwann cells and astrocytes.
Adele J Vincent, Jennifer M Taylor, Derek L Choi-Lundberg, Adrian K West, Meng Inn Chuah. Glia 2005
82
50

BET Bromodomain Suppression Inhibits VEGF-induced Angiogenesis and Vascular Permeability by Blocking VEGFR2-mediated Activation of PAK1 and eNOS.
Mingcheng Huang, Qian Qiu, Youjun Xiao, Shan Zeng, Mingying Zhan, Maohua Shi, Yaoyao Zou, Yujin Ye, Liuqin Liang, Xiuyan Yang,[...]. Sci Rep 2016
35
50




Regulation of transcription factor activity by interconnected post-translational modifications.
Theresa M Filtz, Walter K Vogel, Mark Leid. Trends Pharmacol Sci 2014
126
50

Completing the ENCODE3 compendium yields accurate imputations across a variety of assays and human biosamples.
Jacob Schreiber, Jeffrey Bilmes, William Stafford Noble. Genome Biol 2020
12
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.