A citation-based method for searching scientific literature

Povilas Gibas, Milda Narmontė, Zdislav Staševskij, Juozas Gordevičius, Saulius Klimašauskas, Edita Kriukienė. PLoS Biol 2020
Times Cited: 11







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



Times Cited
  Times     Co-cited
Similarity


Tethered Oligonucleotide-Primed Sequencing, TOP-Seq: A High-Resolution Economical Approach for DNA Epigenome Profiling.
Zdislav Staševskij, Povilas Gibas, Juozas Gordevičius, Edita Kriukienė, Saulius Klimašauskas. Mol Cell 2017
17
81

Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine.
Chun-Xiao Song, Keith E Szulwach, Ye Fu, Qing Dai, Chengqi Yi, Xuekun Li, Yujing Li, Chih-Hsin Chen, Wen Zhang, Xing Jian,[...]. Nat Biotechnol 2011
721
54

Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1.
Mamta Tahiliani, Kian Peng Koh, Yinghua Shen, William A Pastor, Hozefa Bandukwala, Yevgeny Brudno, Suneet Agarwal, Lakshminarayan M Iyer, David R Liu, L Aravind,[...]. Science 2009
45

Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome.
Miao Yu, Gary C Hon, Keith E Szulwach, Chun-Xiao Song, Liang Zhang, Audrey Kim, Xuekun Li, Qing Dai, Yin Shen, Beomseok Park,[...]. Cell 2012
702
36

DNA unmethylome profiling by covalent capture of CpG sites.
Edita Kriukienė, Viviane Labrie, Tarang Khare, Giedrė Urbanavičiūtė, Audronė Lapinaitė, Karolis Koncevičius, Daofeng Li, Ting Wang, Shraddha Pai, Carolyn Ptak,[...]. Nat Commun 2013
37
36

GENCODE reference annotation for the human and mouse genomes.
Adam Frankish, Mark Diekhans, Anne-Maud Ferreira, Rory Johnson, Irwin Jungreis, Jane Loveland, Jonathan M Mudge, Cristina Sisu, James Wright, Joel Armstrong,[...]. Nucleic Acids Res 2019
36

Human DNA methylomes at base resolution show widespread epigenomic differences.
Ryan Lister, Mattia Pelizzola, Robert H Dowen, R David Hawkins, Gary Hon, Julian Tonti-Filippini, Joseph R Nery, Leonard Lee, Zhen Ye, Que-Minh Ngo,[...]. Nature 2009
36



Single-Base Resolution Analysis of 5-Formyl and 5-Carboxyl Cytosine Reveals Promoter DNA Methylation Dynamics.
Francesco Neri, Danny Incarnato, Anna Krepelova, Stefania Rapelli, Francesca Anselmi, Caterina Parlato, Claudio Medana, Federica Dal Bello, Salvatore Oliviero. Cell Rep 2015
77
27

Enhanced chemical stability of adomet analogues for improved methyltransferase-directed labeling of DNA.
Gražvydas Lukinavičius, Miglė Tomkuvienė, Viktoras Masevičius, Saulius Klimašauskas. ACS Chem Biol 2013
40
27

Synthesis of S-Adenosyl-L-Methionine Analogs with Extended Transferable Groups for Methyltransferase-Directed Labeling of DNA and RNA.
Viktoras Masevičius, Milda Nainytė, Saulius Klimašauskas. Curr Protoc Nucleic Acid Chem 2016
9
33

Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution.
Yibin Liu, Paulina Siejka-Zielińska, Gergana Velikova, Ying Bi, Fang Yuan, Marketa Tomkova, Chunsen Bai, Lei Chen, Benjamin Schuster-Böckler, Chun-Xiao Song. Nat Biotechnol 2019
137
27

Engineering the DNA cytosine-5 methyltransferase reaction for sequence-specific labeling of DNA.
Grazvydas Lukinavicius, Audrone Lapinaite, Giedre Urbanaviciute, Ruta Gerasimaite, Saulius Klimasauskas. Nucleic Acids Res 2012
34
27

Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine.
Shinsuke Ito, Li Shen, Qing Dai, Susan C Wu, Leonard B Collins, James A Swenberg, Chuan He, Yi Zhang. Science 2011
27


Direct decarboxylation of 5-carboxylcytosine by DNA C5-methyltransferases.
Zita Liutkevičiūtė, Edita Kriukienė, Janina Ličytė, Milda Rudytė, Giedrė Urbanavičiūtė, Saulius Klimašauskas. J Am Chem Soc 2014
42
27

Repurposing enzymatic transferase reactions for targeted labeling and analysis of DNA and RNA.
Miglė Tomkuvienė, Milda Mickutė, Giedrius Vilkaitis, Saulius Klimašauskas. Curr Opin Biotechnol 2019
15
27

Direct transfer of extended groups from synthetic cofactors by DNA methyltransferases.
Christian Dalhoff, Grazvydas Lukinavicius, Saulius Klimasăuskas, Elmar Weinhold. Nat Chem Biol 2006
148
27

Jump-seq: Genome-Wide Capture and Amplification of 5-Hydroxymethylcytosine Sites.
Lulu Hu, Yuwen Liu, Shengtong Han, Lei Yang, Xiaolong Cui, Yawei Gao, Qing Dai, Xingyu Lu, Xiaochen Kou, Yanhong Zhao,[...]. J Am Chem Soc 2019
14
27

A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands.
M Frommer, L E McDonald, D S Millar, C M Collis, F Watt, G W Grigg, P L Molloy, C L Paul. Proc Natl Acad Sci U S A 1992
18

The advantages of SMRT sequencing.
Richard J Roberts, Mauricio O Carneiro, Michael C Schatz. Genome Biol 2013
331
18

Model-based analysis of ChIP-Seq (MACS).
Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li,[...]. Genome Biol 2008
18

Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain.
Lu Wen, Xianlong Li, Liying Yan, Yuexi Tan, Rong Li, Yangyu Zhao, Yan Wang, Jingcheng Xie, Yan Zhang, Chunxiao Song,[...]. Genome Biol 2014
179
18

Chemical modification-assisted bisulfite sequencing (CAB-Seq) for 5-carboxylcytosine detection in DNA.
Xingyu Lu, Chun-Xiao Song, Keith Szulwach, Zhipeng Wang, Payton Weidenbacher, Peng Jin, Chuan He. J Am Chem Soc 2013
72
18

Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution.
Michael J Booth, Miguel R Branco, Gabriella Ficz, David Oxley, Felix Krueger, Wolf Reik, Shankar Balasubramanian. Science 2012
600
18


GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists.
Eran Eden, Roy Navon, Israel Steinfeld, Doron Lipson, Zohar Yakhini. BMC Bioinformatics 2009
18

Distinctive epigenomes characterize glioma stem cells and their response to differentiation cues.
Dan Zhou, Bonnie M Alver, Shuang Li, Ryan A Hlady, Joyce J Thompson, Mark A Schroeder, Jeong-Heon Lee, Jingxin Qiu, Philip H Schwartz, Jann N Sarkaria,[...]. Genome Biol 2018
49
18

5-Hydroxymethylcytosine signatures in cell-free DNA provide information about tumor types and stages.
Chun-Xiao Song, Senlin Yin, Li Ma, Amanda Wheeler, Yu Chen, Yan Zhang, Bin Liu, Junjie Xiong, Weihan Zhang, Jiankun Hu,[...]. Cell Res 2017
124
18

Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics.
Li Shen, Hao Wu, Dinh Diep, Shinpei Yamaguchi, Ana C D'Alessio, Ho-Lim Fung, Kun Zhang, Yi Zhang. Cell 2013
348
18

Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming.
Chun-Xiao Song, Keith E Szulwach, Qing Dai, Ye Fu, Shi-Qing Mao, Li Lin, Craig Street, Yujing Li, Mickael Poidevin, Hao Wu,[...]. Cell 2013
378
18

Naive pluripotency is associated with global DNA hypomethylation.
Harry G Leitch, Kirsten R McEwen, Aleksandra Turp, Vesela Encheva, Tom Carroll, Nils Grabole, William Mansfield, Buhe Nashun, Jaysen G Knezovich, Austin Smith,[...]. Nat Struct Mol Biol 2013
348
18


A sensitive approach to map genome-wide 5-hydroxymethylcytosine and 5-formylcytosine at single-base resolution.
Zhiyi Sun, Nan Dai, Janine G Borgaro, Aine Quimby, Dapeng Sun, Ivan R Corrêa, Yu Zheng, Zhenyu Zhu, Shengxi Guan. Mol Cell 2015
55
18

Base-resolution maps of 5-formylcytosine and 5-carboxylcytosine reveal genome-wide DNA demethylation dynamics.
Xingyu Lu, Dali Han, Boxuan Simen Zhao, Chun-Xiao Song, Li-Sheng Zhang, Louis C Doré, Chuan He. Cell Res 2015
51
18

Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution.
Michael J Booth, Giovanni Marsico, Martin Bachman, Dario Beraldi, Shankar Balasubramanian. Nat Chem 2014
137
18

Presence of fetal DNA in maternal plasma and serum.
Y M Lo, N Corbetta, P F Chamberlain, V Rai, I L Sargent, C W Redman, J S Wainscoat. Lancet 1997
18

Determination of fetal DNA fraction from the plasma of pregnant women using sequence read counts.
Sung K Kim, Gregory Hannum, Jennifer Geis, John Tynan, Grant Hogg, Chen Zhao, Taylor J Jensen, Amin R Mazloom, Paul Oeth, Mathias Ehrich,[...]. Prenat Diagn 2015
127
18

Detection of the placental epigenetic signature of the maspin gene in maternal plasma.
Stephen S C Chim, Yu K Tong, Rossa W K Chiu, Tze K Lau, Tse N Leung, Lisa Y S Chan, Cees B M Oudejans, Chunming Ding, Y M Dennis Lo. Proc Natl Acad Sci U S A 2005
251
18

Noninvasive prenatal methylomic analysis by genomewide bisulfite sequencing of maternal plasma DNA.
Fiona M F Lun, Rossa W K Chiu, Kun Sun, Tak Y Leung, Peiyong Jiang, K C Allen Chan, Hao Sun, Y M Dennis Lo. Clin Chem 2013
102
18

EnhancerAtlas: a resource for enhancer annotation and analysis in 105 human cell/tissue types.
Tianshun Gao, Bing He, Sheng Liu, Heng Zhu, Kai Tan, Jiang Qian. Bioinformatics 2016
98
18

Comparing methods for fetal fraction determination and quality control of NIPT samples.
Daphne M van Beek, Roy Straver, Marian M Weiss, Elles M J Boon, Karin Huijsdens-van Amsterdam, Cees B M Oudejans, Marcel J T Reinders, Erik A Sistermans. Prenat Diagn 2017
36
18

Enzymatic or In Vivo Installation of Propargyl Groups in Combination with Click Chemistry for the Enrichment and Detection of Methyltransferase Target Sites in RNA.
Katja Hartstock, Benedikt S Nilges, Anna Ovcharenko, Nicolas V Cornelissen, Nikolai Püllen, Ann-Marie Lawrence-Dörner, Sebastian A Leidel, Andrea Rentmeister. Angew Chem Int Ed Engl 2018
55
18

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
18

Oligonucleotide-Addressed Covalent 3'-Terminal Derivatization of Small RNA Strands for Enrichment and Visualization.
Aleksandr Osipenko, Alexandra Plotnikova, Milda Nainytė, Viktoras Masevičius, Saulius Klimašauskas, Giedrius Vilkaitis. Angew Chem Int Ed Engl 2017
11
18

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
18

Functional mapping of the plant small RNA methyltransferase: HEN1 physically interacts with HYL1 and DICER-LIKE 1 proteins.
Simona Baranauskė, Milda Mickutė, Alexandra Plotnikova, Andreas Finke, Česlovas Venclovas, Saulius Klimašauskas, Giedrius Vilkaitis. Nucleic Acids Res 2015
41
18

Selective covalent labeling of miRNA and siRNA duplexes using HEN1 methyltransferase.
Alexandra Plotnikova, Aleksandr Osipenko, Viktoras Masevičius, Giedrius Vilkaitis, Saulius Klimašauskas. J Am Chem Soc 2014
28
18

A Highly Sensitive and Robust Method for Genome-wide 5hmC Profiling of Rare Cell Populations.
Dali Han, Xingyu Lu, Alan H Shih, Ji Nie, Qiancheng You, Meng Michelle Xu, Ari M Melnick, Ross L Levine, Chuan He. Mol Cell 2016
77
18


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.