pypi: browser | Projects | Ecosyste.ms: Papers

10.1186/gb-2008-9-12-r170

FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease
Cited by: 75
Author(s): Rongrong Chen, Alex Morgan, Joel T. Dudley, Tarangini Deshpande, Li Li, Keiichi Kodama, An‐Jen Chiang, Atul J. Butte
Software Mentions: 2
Published: almost 17 years ago

10.1371/journal.pgen.1001116

Identifying Signatures of Natural Selection in Tibetan and Andean Populations Using Dense Genome Scan Data
Cited by: 484
Author(s): Abigail W. Bigham, Marc Bauchet, Dalila Pinto, Xiaole Mao, Joshua M. Akey, Rui Mei, Stephen W. Scherer, Colleen G. Julian, Megan J. Wilson, David López Herráez, Tom D. Brutsaert, Esteban J. Parra, Lorna G. Moore, Mark D. Shriver
Software Mentions: 2
Published: about 14 years ago

10.1186/gb-2010-11-3-r34

Global and unbiased detection of splice junctions from RNA-seq data
Cited by: 87
Author(s): Adam Ameur, Anna Wetterbom, Lars Feuk, Ulf Gyllensten
Software Mentions: 2
Published: almost 15 years ago

10.1186/gb-2010-11-2-r22

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing
Cited by: 254
Author(s): Guoliang Li, Melissa J. Fullwood, Xu Han, Fabianus Hendriyan Mulawadi, Stoyan Velkov, Vinsensius B. Vega, Pramila Ariyaratne, Yusoff Bin Mohamed, Hong Ooi, Chandana Tennakoon, Chia Lin Wei, Yijun Ruan, Wing-Kin Sung
Software Mentions: 2
Published: almost 15 years ago

10.1186/gb-2010-11-4-r36

Optimized design and data analysis of tag-based cytosine methylation assays
Cited by: 76
Author(s): Masako Suzuki, Jun Qiang, Daniel Lia, Marién Pascual, Andrew McLellan, John M. Greally
Software Mentions: 2
Published: almost 15 years ago

10.1186/gb-2010-11-4-r42

Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis
Cited by: 66
Author(s): Qiang Gan, Dustin E. Schones, Suk Ho Eun, Gang Wei, Kairong Cui, Keji Zhao, Xin Chen
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pgen.1008694

WHIMP links the actin nucleation machinery to Src-family kinase signaling during protrusion and motility
Cited by: 7
Author(s): Shail Kabrawala, Margaret D. Zimmer, Kenneth Campellone
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-017-04642-4

Korean Variant Archive (KOVA): a reference database of genetic variations in the Korean population
Cited by: 56
Author(s): Sang Moon Lee, Jihae Seo, Jinman Park, Jae Yong Nam, Ahyoung Choi, Jason S. Ignatius, Robert Bjornson, Jong Hee Chae, In Jin Jang, Sanghyuk Lee, Woong-Yang Park, Daehyun Baek, Murim Choi
Software Mentions: 2
Published: over 7 years ago

10.1186/gb-2013-14-6-r59

Hyperosmotic priming of Arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome
Cited by: 251
Author(s): Emanuela Sani, Paweł Herzyk, Giorgio Perrella, Vincent Colot, Anna Amtmann
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pgen.1008977

Systematic identification of functional SNPs interrupting 3’UTR polyadenylation signals
Cited by: 21
Author(s): Eldad D. Shulman, Ran Elkon
Software Mentions: 2
Published: over 4 years ago

10.1186/1471-2172-9-7

The Innate Immune Database (IIDB)
Cited by: 44
Author(s): Martin Korb, Alistair G. Rust, Vésteinn Thórsson, Christophe Battail, Bin Li, Daehee Hwang, Kathleen A. Kennedy, Jared C. Roach, Carrie M. Rosenberger, Mark Gilchrist, Daniel E. Zak, Carrie D. Johnson, Bruz Marzolf, Alan Aderem, Ilya Shmulevich, Hamid Bolouri
Software Mentions: 2
Published: over 16 years ago

10.1186/gb-2014-15-1-r8

PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast
Cited by: 153
Author(s): Shaun Webb, Ralph D. Hector, Grzegorz Kudla, Sander Granneman
Software Mentions: 2
Published: almost 11 years ago

10.1186/gb-2014-15-1-r1

Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis
Cited by: 1,195
Author(s): Peng Cui, Shoudong Zhang, Feng Ding, Shahjahan Ali, Liming Xiong
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pgen.1005050

Complex Genomic Rearrangements at the PLP1 Locus Include Triplication and Quadruplication
Cited by: 52
Author(s): Christine R. Beck, Claudia M.B. Carvalho, Linda Banser, Tomasz Gambin, Danielle Stubbolo, Bo Yuan, Karen Sperle, Suzanne M. McCahan, Marco Henneke, Pavel Seeman, James Garbern, Grace M. Hobson, James R. Lupski
Software Mentions: 2
Published: over 9 years ago

10.1186/s13059-014-0469-0

Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes
Cited by: 137
Author(s): Adam Blattler, Lijing Yao, Heather Witt, Yu Guo, Charles M. Nicolet, Benjamin P. Berman, Peggy J. Farnham
Software Mentions: 2
Published: about 10 years ago

10.1186/s13059-014-0578-9

Using the canary genome to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds
Cited by: 51
Author(s): Carolina Frankl-Vilches, Heiner Kuhl, Martin Werber, Sven Klages, Martin Kerick, Antje Bakker, Edivaldo Herculano Corrêa de Oliveira, Christina Reusch, Floriana Capuano, Jakob Vowinckel, Stefan Leitner, Markus Ralser, Bernd Timmermann, Manfred Gahr
Software Mentions: 2
Published: almost 10 years ago

10.1186/s13059-015-0727-9

Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution
Cited by: 107
Author(s): Pelin Sahlén, Ilgar Abdullayev, Daniel Ramsköld, Liudmila Matskova, Nemanja Rilakovic, Britta Lötstedt, Thomas Albert, Joakim Lundeberg, Rickard Sandberg
Software Mentions: 2
Published: over 9 years ago

10.1186/s13059-015-0736-8

Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions
Cited by: 83
Author(s): Elena M. Pugacheva, Samuel Rivero-Hinojosa, Celso A. Espinoza, Claudia Fabiola Méndez-Catalá, Sungyun Kang, Tomohiko Suzuki, Natsuki Kosaka-Suzuki, Susan Robinson, Vijayaraj Nagarajan, Zhen Ye, Abdelhalim Boukaba, John E.J. Rasko, Alexander Strunnikov, Dmitri Loukinov, Bing Ren, Victor Lobanenkov
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pgen.1001134

Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome
Cited by: 461
Author(s): Robert S. Illingworth, Ulrike Gruenewald-Schneider, Shaun Webb, Alastair Kerr, Keith James, Daniel J. Turner, Colin Smith, David J. Harrison, Robert Andrews, Adrian Bird
Software Mentions: 2
Published: about 14 years ago

10.1186/s13059-015-0835-6

Liver ChIP-seq analysis in FGF19-treated mice reveals SHP as a global transcriptional partner of SREBP-2
Cited by: 30
Author(s): Young Chae Kim, Sangwon Byun, Yang Zhang, Sunmi Seok, Byron Kemper, Jian Ma, Jongsook Kim Kemper
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12859-021-04359-2

Anomaly detection in genomic catalogues using unsupervised multi-view autoencoders
Cited by: 0
Author(s): Quentin Ferré, Jeanne Chèneby, Denis Puthier, Cécile Capponi, Benoît Ballester
Software Mentions: 2
Published: about 3 years ago

10.1186/s13059-016-1142-6

Integrated genome-wide analysis of expression quantitative trait loci aids interpretation of genomic association studies
Cited by: 145
Author(s): Roby Joehanes, Xiaoling Zhang, Tianxiao Huan, Chen Yao, Saixia Ying, Quang Tri Nguyen, Cumhur Yusuf Demirkale, Michael Feolo, Nataliya Sharopova, Anne Sturcke, Alejandro A. Schäffer, Nancy L. Heard‐Costa, Han Chen, Poching Liu, Thomas J. Wang, Kimberly A. Woodhouse, Kahraman Tanrıverdi, Jane E. Freedman, Nalini Raghavachari, Josée Dupuis, Andrew D. Johnson, Christopher J. O’Donnell, Daniel Levy, Peter J. Munson
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13059-017-1161-y

Software tools for visualizing Hi-C data
Cited by: 49
Author(s): Galip Gürkan Yardımcı
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pgen.1004885

Interactions of Chromatin Context, Binding Site Sequence Content, and Sequence Evolution in Stress-Induced p53 Occupancy and Transactivation
Cited by: 49
Author(s): Dan Su, Xuting Wang, Michelle R. Campbell, Lingyun Song, Alexias Safi, Gregory E. Crawford, Douglas A. Bell
Software Mentions: 2
Published: almost 10 years ago

10.1186/1471-2105-13-253

G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes
Cited by: 15
Author(s): Danielle G. Lemay, William Martin, Angie S. Hinrichs, Monique Rijnkels, J. Bruce German, Ian F Korf, Katherine S. Pollard
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pgen.1004507

KDM6 Demethylase Independent Loss of Histone H3 Lysine 27 Trimethylation during Early Embryonic Development
Cited by: 94
Author(s): Karl B. Shpargel, Joshua Starmer, Della Yee, Michael Pohlers, Terry Magnuson
Software Mentions: 2
Published: over 10 years ago

10.1186/s13059-019-1893-y

OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries
Cited by: 44
Author(s): Lin An, Tao Yang, Jingquan Yang, Johannes Nuebler, Guanjue Xiang, R Hardison, Qunhua Li, Yu Zhang
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pgen.1009290

Natural variation in temperature-modulated immunity uncovers transcription factor bHLH059 as a thermoresponsive regulator in Arabidopsis thaliana
Cited by: 19
Author(s): Friederike Bruessow, Jaqueline Bautor, Gesa Hoffmann, Ipek Yildiz, Jürgen Zeier, Jane E. Parker
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pgen.1008026

Quantitative mapping of DNA phosphorothioatome reveals phosphorothioate heterogeneity of low modification frequency
Cited by: 13
Author(s): Jinli Li, Yi Chen, Tao Zheng, Lingxin Kong, Sucheng Zhu, Yihua Sun, Zixin Deng, Litao Yang, Delin You
Software Mentions: 2
Published: over 5 years ago

10.1093/gbe/evu142

Sequence-Level Mechanisms of Human Epigenome Evolution
Cited by: 17
Author(s): James Prendergast, Emily Chambers, Colin A. Semple
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pgen.1007581

Cooperation, cis-interactions, versatility and evolutionary plasticity of multiple cis-acting elements underlie krox20 hindbrain regulation
Cited by: 20
Author(s): Patrick Torbey, Elodie Thierion, Samuel Collombet, Anne De Cian, Carole Desmarquet-Trin-Dinh, Mathilde Dura, Jean-Paul Concordet, Patrick Charnay, Pascale Gilardi-Hebenstreit
Software Mentions: 2
Published: over 6 years ago

10.1093/gbe/evy029

Genomic Architecture of the Two Cold-Adapted Genera Exiguobacterium and Psychrobacter: Evidence of Functional Reduction in the Exiguobacterium antarcticum B7 Genome
Cited by: 15
Author(s): Larissa Maranhão Dias, Adriana Ribeiro Carneiro Folador, Amanda M.S. Oliveira, Rommel Thiago Jucá Ramos, Artur M. S. Silva, Rafael Azevedo Baraúna
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pgen.1005709

Reciprocal Effects on Neurocognitive and Metabolic Phenotypes in Mouse Models of 16p11.2 Deletion and Duplication Syndromes
Cited by: 110
Author(s): Thomas Arbogast, Abdel‐Mouttalib Ouagazzal, Claire Chevalier, Maksym V. Kopanitsa, Nurudeen O. Afinowi, Eugenia Migliavacca, Belinda S. Cowling, Marie‐Christine Birling, Marie‐France Champy, Alexandre Reymond, Yann Hérault
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41598-017-06351-4

Integrin α6β4 Upregulates Amphiregulin and Epiregulin through Base Excision Repair-Mediated DNA Demethylation and Promotes Genome-wide DNA Hypomethylation
Cited by: 9
Author(s): Brittany L. Carpenter, Jinpeng Liu, Lei Qi, Chi Wang, Kathleen L. O’Connor
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2105-11-119

Prodigal: prokaryotic gene recognition and translation initiation site identification
Cited by: 7,098
Author(s): Doreene R. Hyatt, Gwo Liang Chen, Philip F. LoCascio, Miriam Land, Frank W. Larimer, Loren Hauser
Software Mentions: 2
Published: over 14 years ago

10.1093/gbe/evab183

nf-LO: A Scalable, Containerized Workflow for Genome-to-Genome Lift Over
Cited by: 7
Author(s): Andrea Talenti, James Prendergast
Software Mentions: 2
Published: over 3 years ago

10.1186/s12881-016-0359-2

Sacral agenesis: a pilot whole exome sequencing and copy number study
Cited by: 15
Author(s): Robert M. Porsch, Elisa Merello, Patrizia De Marco, Gregory Yin Ming Cheng, Laura Rodriguez, Man-Ting So, Pak C. Sham, Paul Kwong Hang Tam, Valeria Capra, Stacey S. Cherny, Maria Mercè García-Barceló, Desmond Campbell
Software Mentions: 2
Published: almost 8 years ago

10.1186/gm486

BAIT: Organizing genomes and mapping rearrangements in single cells
Cited by: 31
Author(s): Matthew J. Hills, Kieran O’Neill, Ester Falconer, Ryan R. Brinkman, Peter M. Lansdorp
Software Mentions: 2
Published: almost 12 years ago

10.1186/s13073-016-0320-1

Comprehensive promoter level expression quantitative trait loci analysis of the human frontal lobe
Cited by: 19
Author(s): Cornelis Blauwendraat, Margherita Francescatto, J. Raphael Gibbs, Iris E. Jansen, Javier Simón‐Sánchez, Dena G. Hernandez, Allissa Dillman, Andrew B. Singleton, Mark Cookson, Patrizia Rizzu, Peter Heutink
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pgen.1009613

A combinatorial cis-regulatory logic restricts color-sensing Rhodopsins to specific photoreceptor subsets in Drosophila
Cited by: 4
Author(s): Clara Poupault, Diane Choi, Khanh Lam-Kamath, Deepshe Dewett, Ansa Razzaq, Joseph Bunker, Alexis Perry, Irene Cho, Jens Rister
Software Mentions: 2
Published: over 3 years ago

10.1186/s13073-018-0562-1

Epigenomic profiling of non-small cell lung cancer xenografts uncover LRP12 DNA methylation as predictive biomarker for carboplatin resistance
Cited by: 36
Author(s): Sabrina Grasse, Matthias Lienhard, Steffen Frese, Martin Kerick, Anne Steinbach, Christina Grimm, Michelle Hussong, Jana Rolff, Michael W. Becker, Felix Dreher, Uwe Schirmer, Stefan Boerno, Anna Ramisch, Gunda Leschber, Bernd Timmermann, Christian Grohé, H Lüders, Martin Vingron, Iduna Fichtner, Sebastian Klein, Margarete Odenthal, Reinhard Büttner, Hans Lehrach, Holger Sültmann, Ralf Herwig, Michal R. Schweiger
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2105-13-2

ABrowse - a customizable next-generation genome browser framework
Cited by: 18
Author(s): Lei Kong, Jun Wang, Shuqi Zhao, Xiaocheng Gu, Jianxun Luo, Ge Gao
Software Mentions: 2
Published: almost 13 years ago

10.1186/1471-2105-9-21

LeARN: a platform for detecting, clustering and annotating non-coding RNAs
Cited by: 10
Author(s): Céline Noirot, Christine Gaspin, Thomas Schiex, Jérôme Gouzy
Software Mentions: 2
Published: almost 17 years ago

10.1371/journal.pgen.1005946

MiR144/451 Expression Is Repressed by RUNX1 During Megakaryopoiesis and Disturbed by RUNX1/ETO
Cited by: 17
Author(s): Nicole Kohrs, Stephan Kolodziej, Olga N. Kuvardina, Julia Herglotz, Jasmin Yillah, Stefanie Herkt, Alexander Piechatzek, Gabriela Salinas Riester, Thomas Lingner, Christian Wichmann, Halvard Bönig, Erhard Seifried, Uwe Platzbecker, Hind Medyouf, Manuel Grez, Jörn Lausen
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-19494-9

Cell Type-Specific Survey of Epigenetic Modifications by Tandem Chromatin Immunoprecipitation Sequencing
Cited by: 5
Author(s): Mari Mito, Mitsutaka Kadota, Kaori Tanaka, Yasuhide Furuta, Kuniya Abe, Shigeo Iwasaki, Shinichi Nakagawa
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pgen.1008036

LINE-2 transposable elements are a source of functional human microRNAs and target sites
Cited by: 42
Author(s): Rebecca Petri, Per Ludvik Brattås, Yogita Sharma, Marie E. Jönsson, Karolina Pircs, Johan Bengzon, Johan Jakobsson
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1005702

Fmrp Interacts with Adar and Regulates RNA Editing, Synaptic Density and Locomotor Activity in Zebrafish
Cited by: 70
Author(s): Adi Shamay-Ramot, Khen Khermesh, Hagit T. Porath, Michal Barák, Yishay Pinto, Chaim Wachtel, Alona Zilberberg, Tali Lerer-Goldshtein, Sol Efroni, Erez Y. Levanon, Lior Appelbaum
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pgen.1002384

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome
Cited by: 892
Author(s): A. P. Jason de Koning, Wanjun Gu, Todd A. Castoe, Mark A. Batzer, David D. Pollock
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pgen.1006682

Wnt/Tcf1 pathway restricts embryonic stem cell cycle through activation of the Ink4/Arf locus
Cited by: 37
Author(s): Anchel de Jaime-Soguero, Francesco Aulicino, Gökhan Ertaylan, Anna Griego, Aniello Cerrato, Aravind Tallam, Antonio del Sol, María Pía Cosma, Frederic Lluı́s
Software Mentions: 2
Published: over 7 years ago

10.1186/1755-8794-2-31

Identification of gene co-regulatory modules and associated cis-elements involved in degenerative heart disease
Cited by: 8
Author(s): Charles G. Danko, Arkady M. Pertsov
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pgen.1006296

Genome-Wide Interaction Analyses between Genetic Variants and Alcohol Consumption and Smoking for Risk of Colorectal Cancer
Cited by: 37
Author(s): Jian Gong, Carolyn M. Hutter, Polly A. Newcomb, Cornelia M. Ulrich, Stephanie A. Bien, Peter T. Campbell, John A. Baron, Sonja I. Berndt, Stéphane Bézieau, Hermann Brenner, Graham Casey, Andrew T. Chan, Jenny Chang–Claude, Mengmeng Du, David Duggan, Jane C. Figueiredo, Steven Gallinger, Edward Giovannucci, Robert W. Haile, Tabitha A. Harrison, Richard B. Hayes, Michael Hoffmeister, John L. Hopper, Thomas J. Hudson, Jihyoun Jeon, Mark A. Jenkins, Jonathan Kocarnik, Sébastien Küry, Loı̈c Le Marchand, Yi Lin, Noralane M. Lindor, Reiko Nishihara, Shuji Ogino, John D. Potter, Anja Rudolph, Robert E. Schoen, Petra Schrotz‐King, Daniela Seminara, Martha L. Slattery, Stephen N. Thibodeau, Mark Thornquist, Réka Tóth, Robert B. Wallace, Emily White, Shuo Jiao, Mathieu Lemire, Li Hsu, Ulrike Peters
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pgen.1000672

Genetic Determinants of Circulating Sphingolipid Concentrations in European Populations
Cited by: 185
Author(s): Andrew A. Hicks, Peter P. Pramstaller, Åsa Johansson, Véronique Vitart, Igor Rudan, Péter Ugocsai, Yurii S. Aulchenko, Christopher S. Franklin, Gerhard Liebisch, Jeanette Erdmann, Inger Jonasson, Irina V. Zorkoltseva, Cristian Pattaro, Caroline Hayward, Aaron Isaacs, Christian Hengstenberg, Susan Campbell, Carsten Gnewuch, A. Cecile J.W. Janssens, A. V. Kirichenko, Inke R. König, Fabio Marroni, Ozren Polašek, Ayşe Demirkan, Ivana Kolčić, Christine Schwienbacher, Wilmar Igl, Zrinka Biloglav, Jacqueline C. M. Witteman, Irene Pichler, Ghazal Zaboli, Tatiana I. Axenovich, Annette Peters, Stefan Schreiber, H‐Erich Wichmann, Heribert Schunkert, Nick Hastie, Ben A. Oostra, Sarah H. Wild, Thomas Meitinger, Ulf Gyllensten, Cornelia M. van Duijn, James F. Wilson, Alan F. Wright, Gerd Schmitz, Harry Campbell
Software Mentions: 2
Published: about 15 years ago

10.1038/s41598-018-29074-6

Culture of haploid blastocysts in FGF4 favors the derivation of epiblast stem cells with a primed epigenetic and transcriptional landscape
Cited by: 2
Author(s): Runsheng He, Benjamin L. Kidder
Software Mentions: 2
Published: over 6 years ago

10.1186/s12920-021-01007-9

Epigenetic landscapes of intracranial aneurysm risk haplotypes implicate enhancer function of endothelial cells and fibroblasts in dysregulated gene expression
Cited by: 5
Author(s): Kerry E. Poppenberg, Haley R Zebraski, Naval Avasthi, Muhammad Waqas, Adnan H. Siddiqui, James N. Jarvis, Vincent M. Tutino
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pgen.1005117

Asymmetric Transcript Discovery by RNA-seq in C. elegans Blastomeres Identifies neg-1, a Gene Important for Anterior Morphogenesis
Cited by: 20
Author(s): Erin Osborne Nishimura, Jay C. Zhang, Adam D. Werts, Bob Goldstein, Jason D. Lieb
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-018-33629-y

LncRNA BLAT1 is Upregulated in Basal-like Breast Cancer through Epigenetic Modifications
Cited by: 25
Author(s): Yoo Jane Han, Sonja Boatman, Jing Zhang, Xinxin Du, Albert C. Yeh, Yonglan Zheng, Jeffrey Mueller, Olufunmilayo I. Olopade
Software Mentions: 2
Published: about 6 years ago

10.1186/1471-2164-16-S8-S2

Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction
Cited by: 68
Author(s): Adam Frankish, Barbara Uszczyńska, Graham R. S. Ritchie, Jose M. Gonzalez, Dmitri D. Pervouchine, Robert Petryszak, Jonathan M. Mudge, Nuno A. Fonseca, Alvis Brāzma, Roderic Guigó, Jennifer Harrow
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pgen.1006754

Transcription facilitated genome-wide recruitment of topoisomerase I and DNA gyrase
Cited by: 52
Author(s): Wareed Ahmed, Claudia Sala, Shubhada R. Hegde, Rajiv Kumar Jha, Stewart T. Cole, Valakunja Nagaraja
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-018-37294-z

STAT3 is activated in multicellular spheroids of colon carcinoma cells and mediates expression of IRF9 and interferon stimulated genes
Cited by: 7
Author(s): Elin Edsbäcker, Jason T. Serviss, Iryna Kolosenko, Caroline Palm-Apergi, Angelo De Milito, Katja Pokrovskaja Tamm
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-018-36927-7

High Quality ATAC-Seq Data Recovered from Cryopreserved Breast Cell Lines and Tissue
Cited by: 23
Author(s): Saori Fujiwara, Songjoon Baek, Lyuba Varticovski, Sohyoung Kim, Gordon L. Hager
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-018-37678-1

Intelectin 3 is dispensable for resistance against a mycobacterial infection in zebrafish (Danio rerio)
Cited by: 11
Author(s): Markus Ojanen, Meri Uusi-Mäkelä, Sanna-Kaisa E. Harjula, Anni Saralahti, Kaisa Oksanen, Niklas Kähkönen, Juha Määttä, Vesa P. Hytönen, Marko Pesu, Mika Rämet
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pgen.1002390

Identification of Evolutionarily Conserved Exons as Regulated Targets for the Splicing Activator Tra2β in Development
Cited by: 61
Author(s): Sushma Nagaraja Grellscheid, Caroline Dalgliesh, Markus Storbeck, Andrew Best, Yilei Liu, Miriam Jakubik, Ylva Mende, Ingrid Ehrmann, Tomaž Curk, Kristina Roßbach, Cyril F. Bourgeois, James Stévenin, David Grellscheid, Michael S. Jackson, Brunhilde Wirth, David J. Elliott
Software Mentions: 2
Published: almost 13 years ago

10.1038/s41598-019-43292-6

Identification of regulatory variants associated with genetic susceptibility to meningococcal disease
Cited by: 3
Author(s): Lisa Borghini, Eileen Png, Alexander Binder, Victoria J. Wright, Ellie Pinnock, Ronald de Groot, Jan A. Hazelzet, Marieke Emonts, Michiel van der Flier, Luregn J Schlapbach, Suzanne T. Anderson, Fatou Secka, Antonio Salas, Colin G. Fink, Enitan D. Carrol, Andrew J. Pollard, Lachlan Coin, Taco W. Kuijpers, Federico Martinón‐Torres, Werner Zenz, Michael Levin, Martin L. Hibberd, Sonia Dávila
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-019-43403-3

Recognition of 3′-end L1, Alu, processed pseudogenes, and mRNA stem-loops in the human genome using sequence-based and structure-based machine-learning models
Cited by: 0
Author(s): Alexander Shein, Anton Zaikin, Maria Poptsova
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2164-14-611

Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes
Cited by: 159
Author(s): James R. Doroghazi, William W. Metcalf
Software Mentions: 2
Published: almost 12 years ago

10.1186/1471-2105-11-10

MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement
Cited by: 52
Author(s): Guanqun Shi, Liqing Zhang, Tao Jiang
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pntd.0000543

Anti-schistosomal Intervention Targets Identified by Lifecycle Transcriptomic Analyses
Cited by: 117
Author(s): Jennifer M. Fitzpatrick, Emily Peak, Samïrah Perally, Iain W. Chalmers, John Barrett, Timothy P. Yoshino, Alasdair Ivens, Karl F. Hoffmann
Software Mentions: 2
Published: about 15 years ago

10.1186/s12920-015-0087-z

Systems biology of myasthenia gravis, integration of aberrant lncRNA and mRNA expression changes
Cited by: 19
Author(s): Zhaohui Luo, Ye Li, Xiaofang Liu, Mingyao Luo, Liqun Xu, Yue‐Bei Luo, Bo Xiao, Huan Yang
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-020-57753-w

Evolutionary history of DNA methylation related genes in chordates: new insights from multiple whole genome duplications
Cited by: 20
Author(s): Jingwei Liu, Huihua Hu, Stéphane Panserat, Lucie Marandel
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pntd.0007871

GSMN-ML- a genome scale metabolic network reconstruction of the obligate human pathogen Mycobacterium leprae
Cited by: 8
Author(s): Khushboo Borah, Jacque-Lucca Kearney, Ruma Banerjee, Pankaj Vats, Huihai Wu, Sonal Dahale, Sunitha Manjari Kasibhatla, Rajendra Joshi, Bhushan Bonde, Olabisi Ojo, Ramanuj Lahiri, Diana L. Williams, Johnjoe McFadden
Software Mentions: 2
Published: over 4 years ago

10.1186/1755-8794-6-1

Multilocus loss of DNA methylation in individuals with mutations in the histone H3 Lysine 4 Demethylase KDM5C
Cited by: 72
Author(s): Daria Grafodatskaya, Barian H Y Chung, Darci T. Butcher, Andrei L. Turinsky, Sarah J. Goodman, Sana Choufani, Yi‐An Chen, Youliang Lou, Cheng Zhao, Rageen Rajendram, Fatima Abidi, Cindy Skinner, James Stavropoulos, Carolyn A. Bondy, Jill Hamilton, Shoshana J. Wodak, Stephen W. Scherer, Charles E. Schwartz, Rosanna Weksberg
Software Mentions: 2
Published: almost 12 years ago

10.1186/1471-2164-13-636

Genetic analysis of DNA methylation and gene expression levels in whole blood of healthy human subjects
Cited by: 184
Author(s): Kristel R. van Eijk, Simone de Jong, Marco P. Boks, Terry Langeveld, Fabrice Colas, Jan H. Veldink, Carolien G.F. de Kovel, Esther Janson, Eric Strengman, Peter Langfelder, René S. Kahn, Leonard H van den Berg, Steve Horvath, Roel A. Ophoff
Software Mentions: 2
Published: about 12 years ago

10.1038/s41598-020-74687-5

Evaluation of blood gene expression levels in facioscapulohumeral muscular dystrophy patients
Cited by: 10
Author(s): Mirko Signorelli, Amanda G. Mason, Karlien Mul, Teresinha Evangelista, Hailiang Mei, N.C. Voermans, Stephen J. Tapscott, Roula Tsonaka, B.G.M. van Engelen, Silvère M. van der Maarel, Pietro Spitali
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0097568

Genome-Wide Quantitative Analysis of Histone H3 Lysine 4 Trimethylation in Wild House Mouse Liver: Environmental Change Causes Epigenetic Plasticity
Cited by: 12
Author(s): Angelika Börsch-Haubold, Inka Montero, Kathryn Konrad, Bernhard Haubold
Software Mentions: 2
Published: over 10 years ago

10.1186/s12874-016-0164-9

ODMedit: uniform semantic annotation for data integration in medicine based on a public metadata repository
Cited by: 28
Author(s): Martin Dugas, Alexandra Meidt, Philipp Neuhaus, Michael Storck, Julian Varghese
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-020-78907-w

Genome-wide association identifies several QTLs controlling cysteine and methionine content in soybean seed including some promising candidate genes
Cited by: 11
Author(s): Sidiki Malle, Milad Eskandari, Malcolm J. Morrison, François Belzile
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-021-81387-1

Analysis of ovarian transcriptomes reveals thousands of novel genes in the insect vector Rhodnius prolixus
Cited by: 17
Author(s): Vitor Lima Coelho, Tarcísio Fontenele de Brito, Ingrid Alexandre de Abreu Brito, Maira Arruda Cardoso, Mateus Berni, Helena Araujo, Michael Sammeth, Andrea Pane
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0005008

Transcriptional Network of p63 in Human Keratinocytes
Cited by: 42
Author(s): Silvia Pozzi, Federico Zambelli, Daniele Merico, Giulio Pavesi, Amélie Robert, Peggy Maltère, Xavier Gidrol, Roberto Mantovani, M. Alessandra Viganò
Software Mentions: 2
Published: over 15 years ago

10.1186/1471-2164-12-165

Rice-Map: a new-generation rice genome browser
Cited by: 12
Author(s): Jun Wang, Lei Kong, Shuqi Zhao, He Zhang, Liang Tang, Zhe Li, Xiaocheng Gu, Jianxun Luo, Ge Gao
Software Mentions: 2
Published: over 13 years ago

10.1038/s41598-021-90422-0

Simplification of culture conditions and feeder-free expansion of bovine embryonic stem cells
Cited by: 24
Author(s): Delia Alba Soto, Micaela Navarro, Canbin Zheng, Michelle M. Halstead, Chuan Zhou, Carly Guiltinan, Jun Wu, Pablo J. Ross
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-016-2794-z

MBDDiff: an R package designed specifically for processing MBDcap-seq datasets
Cited by: 3
Author(s): Yuanhang Liu, Desiree Wilson, Robin J. Leach, Yidong Chen
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0006074

More than 9,000,000 Unique Genes in Human Gut Bacterial Community: Estimating Gene Numbers Inside a Human Body
Cited by: 127
Author(s): Xing Yang, Lu Xie, Yixue Li, Chaochun Wei
Software Mentions: 2
Published: over 15 years ago

10.1186/1471-2164-12-305

A tissue-specific landscape of sense/antisense transcription in the mouse intestine
Cited by: 19
Author(s): Ulrich C. Klostermeier, Matthias Barann, Michael Wittig, Robert Häsler, André Franke, Olga Gavrilova, Benjamin Kreck, Christian Sina, Markus B. Schilhabel, Stefan Schreiber, Philip Rosenstiel
Software Mentions: 2
Published: over 13 years ago

10.3390/s18082633

PHAROS—PHysical Assistant RObot System
Cited by: 42
Author(s): Ângelo Costa, Ester Martínez-Martín, Miguel Cazorla, Vicente Julián
Software Mentions: 2
Published: over 6 years ago

10.1186/s13029-015-0032-8

LocusTrack: Integrated visualization of GWAS results and genomic annotation
Cited by: 28
Author(s): Gabriel Cuéllar-Partida, Miguel E. Renteriá, Stuart MacGregor
Software Mentions: 2
Published: almost 10 years ago

10.1038/s41598-017-07514-z

Assessment of imprinting- and genetic variation-dependent monoallelic expression using reciprocal allele descendants between human family trios
Cited by: 7
Author(s): Trees‐Juen Chuang, Yu-Hsiang Tseng, Chia-Ying Chen, Yi-Da Wang
Software Mentions: 2
Published: over 7 years ago

10.1186/s12860-021-00378-2

Construction and characterization of EGFP reporter plasmid harboring putative human RAX promoter for in vitro monitoring of retinal progenitor cells identity
Cited by: 2
Author(s): Atefeh Atefi, Pendar Shojaei kojouri, Fereshteh Karamali, Shiva Irani, Mohammad Hossein Nasr-Esfahani
Software Mentions: 2
Published: over 3 years ago

10.1186/s13287-019-1270-5

The long non-coding RNA Snhg3 is essential for mouse embryonic stem cell self-renewal and pluripotency
Cited by: 16
Author(s): Weisi Lu, Jianping Yu, Fang Shi, Jianing Zhang, Rui Huang, Shanshan Yin, Zhou Songyang, Junjiu Huang
Software Mentions: 2
Published: over 5 years ago

10.1002/stem.2294

Jun-Mediated Changes in Cell Adhesion Contribute to Mouse Embryonic Stem Cell Exit from Ground State Pluripotency
Cited by: 16
Author(s): Giulia Veluscek, Yaoyong Li, Shen-Hsi Yang, Andrew D. Sharrocks
Software Mentions: 2
Published: almost 9 years ago

10.7150/thno.47039

Comprehensive characterization of functional eRNAs in lung adenocarcinoma reveals novel regulators and a prognosis-related molecular subtype
Cited by: 18
Author(s): Na Qin, Zijuan Ma, Cheng Wang, Erbao Zhang, Yuancheng Li, Mingtao Huang, Congcong Chen, Chang Zhang, Jingyi Fan, Yayun Gu, Xin Xu, Yang Liu, Xiaoxia Wei, Rong Yin, Yue Jiang, Juncheng Dai, Guangfu Jin, Lin Xu, Hongbing Shen, Hongxia Ma
Software Mentions: 2
Published: almost 5 years ago

10.7150/thno.48744

Proteasome activator PA200 maintains stability of histone marks during transcription and aging
Cited by: 14
Author(s): Tiancai Jiang, Shuang Ma, Xia Han, Zi-Yu Luo, Qianqian Zhu, Tomoki Chiba, Wei Xie, Kui Lin, Xiao‐Bo Qiu
Software Mentions: 2
Published: almost 4 years ago

10.7150/thno.51931

Functional roles of antisense enhancer RNA for promoting prostate cancer progression
Cited by: 22
Author(s): Chun-Wu Pan, Simeng Wen, Lei Chen, Yulei Wei, Yuanjie Niu, Yu Zhao
Software Mentions: 2
Published: almost 4 years ago

10.7150/thno.53170

Tanshinone I, a new EZH2 inhibitor restricts normal and malignant hematopoiesis through upregulation of MMP9 and ABCG2
Cited by: 22
Author(s): Ying Huang, Shanhe Yu, Wenxuan Zhen, Cheng Tien, Dan Wang, Jiebo Lin, Yuxin Wu, Yifan Wang, Yi Chen, Liping Shu, Yi Wang, Xiao Jian Sun, Yi Zhou, Fan Yang, Chih-Hung Hsu, Pengfei Xu
Software Mentions: 2
Published: almost 4 years ago

10.1186/1471-2105-13-206

CaPSID: A bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes
Cited by: 39
Author(s): Ivan Borozan, Shane Wilson, Paola Blanchette, Philippe Laflamme, Stuart Watt, Paul M. Krzyzanowski, Fabrice Sircoulomb, Robert Rottapel, Philip E. Branton, Vincent Ferretti
Software Mentions: 2
Published: over 12 years ago

10.1186/s12859-020-03806-w

oposSOM-Browser: an interactive tool to explore omics data landscapes in health science
Cited by: 10
Author(s): Henry Loeffler‐Wirth, Jasmin Reikowski, Siras Hakobyan, Jonas Wagner, Hans Binder
Software Mentions: 2
Published: about 4 years ago

10.1186/s12864-015-1414-7

The salinity tolerant poplar database (STPD): a comprehensive database for studying tree salt-tolerant adaption and poplar genomics
Cited by: 7
Author(s): Ying Ma, Ting Xu, Dongshi Wan, Tao Ma, Shengjun Shi, Jianquan Liu, Quanjun Hu
Software Mentions: 2
Published: over 9 years ago

10.1038/s41398-020-00966-4

Integration of postmortem amygdala expression profiling, GWAS, and functional cell culture assays: neuroticism-associated synaptic vesicle glycoprotein 2A (SV2A) gene is regulated by miR-133a and miR-218
Cited by: 9
Author(s): Magdalena Jurkiewicz, Dirk Moser, Antonius Koller, Lei Yu, Emily I. Chen, David A. Bennett, Turhan Canli
Software Mentions: 2
Published: about 4 years ago

10.1038/s41398-020-01056-1

Identification of candidate genetic variants and altered protein expression in neural stem and mature neural cells support altered microtubule function to be an essential component in bipolar disorder
Cited by: 12
Author(s): Katarina Truvé, Toshima Z. Parris, Dzeneta Vizlin‐Hodzic, Susanne Salmela, Evelin Berger, Hans Ǻgren, Keiko Funa
Software Mentions: 2
Published: about 4 years ago

10.1186/1471-2105-8-320

Apollo2Go: a web service adapter for the Apollo genome viewer to enable distributed genome annotation
Cited by: 6
Author(s): Kathrin Klee, Rebecca Ernst, Manuel Spannagl, Klaus Mayer
Software Mentions: 2
Published: about 17 years ago

10.1128/mBio.02367-19

Combination of Proteogenomics with Peptide De Novo Sequencing Identifies New Genes and Hidden Posttranscriptional Modifications
Cited by: 37
Author(s): Bernhard Blank‐Landeshammer, Ines Teichert, Ramona Märker, Minou Nowrousian, Ulrich Kück, Albert Sickmann
Software Mentions: 2
Published: about 5 years ago

Projects: pypi: browser

Papers Mentioning browser 2,125