A citation-based method for searching scientific literature

Merve Deniz Abdusselamoglu, Elif Eroglu, Thomas R Burkard, Jürgen A Knoblich. Elife 2019
Times Cited: 9







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



Times Cited
  Times     Co-cited
Similarity


Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
55

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
55



Drosophila neuroblasts: a model for stem cell biology.
Catarina C F Homem, Juergen A Knoblich. Development 2012
251
33


Zic2 is an enhancer-binding factor required for embryonic stem cell specification.
Zhuojuan Luo, Xin Gao, Chengqi Lin, Edwin R Smith, Stacy A Marshall, Selene K Swanson, Laurence Florens, Michael P Washburn, Ali Shilatifard. Mol Cell 2015
56
33



Fiji: an open-source platform for biological-image analysis.
Johannes Schindelin, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Tobias Pietzsch, Stephan Preibisch, Curtis Rueden, Stephan Saalfeld, Benjamin Schmid,[...]. Nat Methods 2012
33

Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation.
Yujia Sun, Chung-Yi Nien, Kai Chen, Hsiao-Yun Liu, Jeff Johnston, Julia Zeitlinger, Christine Rushlow. Genome Res 2015
82
33

The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila.
Hsiao-Lan Liang, Chung-Yi Nien, Hsiao-Yun Liu, Mark M Metzstein, Nikolai Kirov, Christine Rushlow. Nature 2008
293
33

The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
33

Continued Activity of the Pioneer Factor Zelda Is Required to Drive Zygotic Genome Activation.
Stephen L McDaniel, Tyler J Gibson, Katharine N Schulz, Meilin Fernandez Garcia, Markus Nevil, Siddhant U Jain, Peter W Lewis, Kenneth S Zaret, Melissa M Harrison. Mol Cell 2019
39
33

Zelda binding in the early Drosophila melanogaster embryo marks regions subsequently activated at the maternal-to-zygotic transition.
Melissa M Harrison, Xiao-Yong Li, Tommy Kaplan, Michael R Botchan, Michael B Eisen. PLoS Genet 2011
192
33

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
33

Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the early Drosophila embryo.
Katharine N Schulz, Eliana R Bondra, Arbel Moshe, Jacqueline E Villalta, Jason D Lieb, Tommy Kaplan, Daniel J McKay, Melissa M Harrison. Genome Res 2015
82
33

Time-resolved transcriptomics in neural stem cells identifies a v-ATPase/Notch regulatory loop.
Sebastian Wissel, Heike Harzer, François Bonnay, Thomas R Burkard, Ralph A Neumüller, Juergen A Knoblich. J Cell Biol 2018
12
22

FACS purification and transcriptome analysis of drosophila neural stem cells reveals a role for Klumpfuss in self-renewal.
Christian Berger, Heike Harzer, Thomas R Burkard, Jonas Steinmann, Suzanne van der Horst, Anne-Sophie Laurenson, Maria Novatchkova, Heinrich Reichert, Juergen A Knoblich. Cell Rep 2012
89
22

Transcriptomes of lineage-specific Drosophila neuroblasts profiled by genetic targeting and robotic sorting.
Ching-Po Yang, Chi-Cheng Fu, Ken Sugino, Zhiyong Liu, Qingzhong Ren, Ling-Yu Liu, Xiaohao Yao, Luke P Lee, Tzumin Lee. Development 2016
30
22


FACS purification of Drosophila larval neuroblasts for next-generation sequencing.
Heike Harzer, Christian Berger, Ryan Conder, Gerald Schmauss, Juergen A Knoblich. Nat Protoc 2013
37
22

SWI/SNF complex prevents lineage reversion and induces temporal patterning in neural stem cells.
Elif Eroglu, Thomas R Burkard, Yanrui Jiang, Nidhi Saini, Catarina C F Homem, Heinrich Reichert, Juergen A Knoblich. Cell 2014
92
22



The tumor suppressors Brat and Numb regulate transit-amplifying neuroblast lineages in Drosophila.
Sarah K Bowman, Vivien Rolland, Joerg Betschinger, Kaolin A Kinsey, Gregory Emery, Juergen A Knoblich. Dev Cell 2008
276
22


Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4.
Lisa Ann Cirillo, Frank Robert Lin, Isabel Cuesta, Dara Friedman, Michal Jarnik, Kenneth S Zaret. Mol Cell 2002
776
22

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
22


Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.
Sven Heinz, Christopher Benner, Nathanael Spann, Eric Bertolino, Yin C Lin, Peter Laslo, Jason X Cheng, Cornelis Murre, Harinder Singh, Christopher K Glass. Mol Cell 2010
22

Pioneer transcription factors in cell reprogramming.
Makiko Iwafuchi-Doi, Kenneth S Zaret. Genes Dev 2014
315
22

Grainyhead and Zelda compete for binding to the promoters of the earliest-expressed Drosophila genes.
Melissa M Harrison, Michael R Botchan, Thomas W Cline. Dev Biol 2010
57
22


Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.
Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang, William J Greenleaf. Nat Methods 2013
22

Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm.
Xiao-yong Li, Stewart MacArthur, Richard Bourgon, David Nix, Daniel A Pollard, Venky N Iyer, Aaron Hechmer, Lisa Simirenko, Mark Stapleton, Cris L Luengo Hendriks,[...]. PLoS Biol 2008
345
22

Zelda potentiates morphogen activity by increasing chromatin accessibility.
Sun Melody Foo, Yujia Sun, Bomyi Lim, Ruta Ziukaite, Kevin O'Brien, Chung-Yi Nien, Nikolai Kirov, Stanislav Y Shvartsman, Christine A Rushlow. Curr Biol 2014
75
22

Mutations affecting the pattern of the larval cuticle inDrosophila melanogaster : II. Zygotic loci on the third chromosome.
G Jürgens, E Wieschaus, C Nüsslein-Volhard, H Kluding. Wilehm Roux Arch Dev Biol 1984
564
22

ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm.
Marta Bozek, Roberto Cortini, Andrea Ennio Storti, Ulrich Unnerstall, Ulrike Gaul, Nicolas Gompel. Genome Res 2019
18
22


The Drosophila embryo at single-cell transcriptome resolution.
Nikos Karaiskos, Philipp Wahle, Jonathan Alles, Anastasiya Boltengagen, Salah Ayoub, Claudia Kipar, Christine Kocks, Nikolaus Rajewsky, Robert P Zinzen. Science 2017
171
22

Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition.
Xiao-Yong Li, Melissa M Harrison, Jacqueline E Villalta, Tommy Kaplan, Michael B Eisen. Elife 2014
105
22


Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-seq.
Susan E Lott, Jacqueline E Villalta, Gary P Schroth, Shujun Luo, Leath A Tonkin, Michael B Eisen. PLoS Biol 2011
127
22

Odd-Paired: The Drosophila Zic Gene.
Deborah A Hursh, Brian G Stultz. Adv Exp Med Biol 2018
3
66

Genome-scale functional characterization of Drosophila developmental enhancers in vivo.
Evgeny Z Kvon, Tomas Kazmar, Gerald Stampfel, J Omar Yáñez-Cuna, Michaela Pagani, Katharina Schernhuber, Barry J Dickson, Alexander Stark. Nature 2014
229
22

Temporal coordination of gene networks by Zelda in the early Drosophila embryo.
Chung-Yi Nien, Hsiao-Lan Liang, Stephen Butcher, Yujia Sun, Shengbo Fu, Tenzin Gocha, Nikolai Kirov, J Robert Manak, Christine Rushlow. PLoS Genet 2011
157
22

The ZIC gene family encodes multi-functional proteins essential for patterning and morphogenesis.
Rob Houtmeyers, Jacob Souopgui, Sabine Tejpar, Ruth Arkell. Cell Mol Life Sci 2013
59
22

The Heidelberg Screen for Pattern Mutants of Drosophila: A Personal Account.
Eric Wieschaus, Christiane Nüsslein-Volhard. Annu Rev Cell Dev Biol 2016
28
22



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.