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10.1186/1741-7007-5-37

The DNA binding parvulin Par17 is targeted to the mitochondrial matrix by a recently evolved prepeptide uniquely present in Hominidae
Cited by: 31
Author(s): Daniel S. Kessler, Panagiotis Papatheodorou, Tina Stratmann, Elke A. Dian, Cristina Hartmann-Fatu, Joachim Rassow, Peter Bayer, Jonathan Wolf Mueller
Software Mentions: 3
Published: almost 19 years ago

10.3390/cells10092375

Transcriptome and Methylome Analysis Reveal Complex Cross-Talks between Thyroid Hormone and Glucocorticoid Signaling at Xenopus Metamorphosis
Cited by: 10
Author(s): Nicolas Buisine, Alexis Grimaldi, Vincent Jonchère, Muriel Rigolet, Corinne Blugeon, Juliette Hamroune, Laurent M. Sachs
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12915-019-0674-0

RNA-Seq in 296 phased trios provides a high-resolution map of genomic imprinting
Cited by: 24
Author(s): Bharati Jadhav, Ramin Monajemi, Kristina K. Gagalova, Daniel J. Ho, Harmen H.M. Draisma, Mark A. van de Wiel, Lude Franke, Bastiaan T. Heijmans, Joyce B. J. van Meurs, Rick Jansen, Peter A.C. ’t Hoen, Andrew J. Sharp, Szymon M. Kiełbasa
Software Mentions: 3
Published: about 7 years ago

10.18632/aging.202353

Cell lineage-specific methylome and genome alterations in gout
Cited by: 6
Author(s): Chia‐Chun Tseng, Wei‐Ting Liao, Man-Chun Wong, Chung‐Jen Chen, Su-Chen Lee, Jeng-Hsien Yen, Shun‐Jen Chang
Software Mentions: 3
Published: over 5 years ago

10.1016/j.cell.2019.04.038

SCAF4 and SCAF8, mRNA Anti-Terminator Proteins
Cited by: 78
Author(s): Lea H. Gregersen, Richard Mitter, Alejandro P. Ugalde, Takayuki Nojima, Nick J. Proudfoot, Reuven Agami, Aengus Stewart, Jesper Q. Svejstrup
Software Mentions: 3
Published: about 7 years ago

10.1038/s41419-019-1892-7

Epigenetic re-wiring of breast cancer by pharmacological targeting of C-terminal binding protein
Cited by: 7
Author(s): Jung S. Byun, Samson Park, Dae Ik Yi, Jee-Hye Shin, Sara Gil Hernandez, Stephen M. Hewitt, Marc C. Nicklaus, Megan L. Peach, Laura Guasch, Binwu Tang, Lalage M. Wakefield, Tingfen Yan, Ambar Caban, Alana Jones, Mohamed Kabbout, Nasreen A. Vohra, Anna María Nápoles, Sandeep K. Singhal, Ryan Yancey, Adriana De Siervi, Kevin Gardner
Software Mentions: 3
Published: almost 7 years ago

10.3390/cancers12030764

Global DNA Hypomethylation in Epithelial Ovarian Cancer: Passive Demethylation and Association with Genomic Instability
Cited by: 41
Author(s): Wa Zhang, David Klinkebiel, Carter J. Barger, Sanjit Pandey, Chittibabu Guda, Austin Miller, Stacey N. Akers, Kunle Odunsi, Adam R. Karpf
Software Mentions: 3
Published: over 6 years ago

10.3390/cancers13133176

Epigenetic Upregulation of MAGE-A Isoforms Promotes Breast Cancer Cell Aggressiveness
Cited by: 4
Author(s): Chaeun Oh, Hwa Ryeon Kim, Seungmin Oh, Je Yeong Ko, Yesol Kim, Keunsoo Kang, Young Yang, Jongmin Kim, Jae Seok Roe, Kyung Hyun Yoo
Software Mentions: 3
Published: about 5 years ago

10.1242/bio.031245

KDM5B decommissions the H3K4 methylation landscape of self-renewal genes during trophoblast stem cell differentiation
Cited by: 18
Author(s): Jian Xu, Benjamin L. Kidder
Software Mentions: 3
Published: over 8 years ago

10.1186/1745-6150-3-22

Classifying transcription factor targets and discovering relevant biological features
Cited by: 10
Author(s): Dustin T. Holloway, Mark A. Kon, Charles DeLisi
Software Mentions: 3
Published: about 18 years ago

10.1371/journal.pone.0190992

HAfTs are novel lncRNA transcripts from aflatoxin exposure
Cited by: 9
Author(s): B. Alex Merrick, Justin Chang, Dhiral Phadke, Meredith A. Bostrom, Ruchir Shah, Xinguo Wang, Oksana Gordon, Garron M. Wright
Software Mentions: 3
Published: over 8 years ago

10.1186/s13040-018-0190-8

Use case driven evaluation of open databases for pediatric cancer research
Cited by: 13
Author(s): Fleur Jeanquartier, Claire Jean-Quartier, Andreas Holzinger
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0233191

Integration of high-throughput reporter assays identify a critical enhancer of the Ikzf1 gene
Cited by: 3
Author(s): Jaafar Alomairi, Anne Molitor, Nori Sadouni, Saadat Hussain, Magali Torres, Wiam Saadi, Lan T M Dao, Guillaume Charbonnier, David Santiago-Algarra, Jean-Christophe Andrau, Denis Puthier, Tom Sexton, Salvatore Spicuglia
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0185678

A tissue-specific promoter derived from a SINE retrotransposon drives biallelic expression of PLAGL1 in human lymphocytes
Cited by: 5
Author(s): Claire E. L. Smith, Alexia Alexandraki, Sarah F. Cordery, Rekha Parmar, David T. Bonthron, Elizabeth M. A. Valleley
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12859-016-1139-x

CerealsDB 3.0: expansion of resources and data integration
Cited by: 38
Author(s): Paul Wilkinson, Mark Winfield, Gary Barker, Simon Tyrrell, Xingdong Bian, Alexandra M. Allen, Amanda Burridge, Jane A. Coghill, Christy Waterfall, Mario Cáccamo, Robert P. Davey, Keith J. Edwards
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pone.0254444

Using Assessment Design Decision Framework in understanding the impact of rapid transition to remote education on student assessment in health-related colleges: A qualitative study
Cited by: 8
Author(s): Myriam Jaam, Zachariah Nazar, Daniel Rainkie, Diana Alsayed Hassan, Farhat Hussain, Salah Kassab, Abdelali Agouni
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0165395

TCGA Expedition: A Data Acquisition and Management System for TCGA Data
Cited by: 56
Author(s): Uma Chandran, Olga Medvedeva, M. Michael Barmada, Philip D. Blood, Anish Chakka, Soumya Luthra, Antonio M. Ferreira, Kim F. Wong, Adrian V. Lee, Zhihui Zhang, Robert Budden, James R. Scott, Annerose Berndt, Jeremy M. Berg, Rebecca S. Jacobson
Software Mentions: 3
Published: almost 10 years ago

10.3390/cells9061435

Altered Transcription Factor Binding and Gene Bivalency in Islets of Intrauterine Growth Retarded Rats
Cited by: 13
Author(s): Yu‐Chin Lien, Paul Zhiping Wang, Xueqing Maggie Lu, Rebecca A. Simmons
Software Mentions: 3
Published: about 6 years ago

10.1007/s10522-017-9741-5

A network-based meta-analysis for characterizing the genetic landscape of human aging
Cited by: 15
Author(s): Hagen Blankenburg, Peter P. Pramstaller, Francisco S. Domingues
Software Mentions: 3
Published: over 8 years ago

10.1093/bioinformatics/btw672

Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning
Cited by: 25
Author(s): Toby Dylan Hocking, Patricia Goerner-Potvin, Andréanne Morin, Xiaojian Shao, Tomi Pastinen, Guillaume Bourque
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2105-13-85

DIPSBC - data integration platform for systems biology collaborations
Cited by: 13
Author(s): Felix Dreher, Thomas Kreitler, Christopher Hardt, Atanas Kamburov, Reha Yildirimman, K. Schellander, Hans Lehrach, Bodo Lange, Ralf Herwig
Software Mentions: 3
Published: over 14 years ago

10.1186/s12864-016-2457-0

Integrating RNA-seq and ChIP-seq data to characterize long non-coding RNAs in Drosophila melanogaster
Cited by: 18
Author(s): Mei-Ju May Chen, Li-Kai Chen, Yu-Shing Lai, Yu-Yu Lin, Dung-Chi Wu, Yi-Chung Tung, Kwei-Yan Liu, Hsueh‐Tzu Shih, Yi-Jyun Chen, Yen‐Ting Lin, Li‐Ting Ma, Jun Huang, Po-Chun Wu, Hong Mei, Fang-Hua Chu, June‐Tai Wu, Wen-Hsiung Li, Chien‐Yu Chen
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0031915

3T3 Cell Lines Stably Expressing Pax6 or Pax6(5a) – A New Tool Used for Identification of Common and Isoform Specific Target Genes
Cited by: 32
Author(s): Yury Kiselev, Tonje Engevik Eriksen, Siri Forsdahl, Lan Huong Nguyen, Ingvild Mikkola
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0022046

Spliceosomal Intron Insertions in Genome Compacted Ray-Finned Fishes as Evident from Phylogeny of MC Receptors, Also Supported by a Few Other GPCRs
Cited by: 18
Author(s): Abhishek Kumar, Anita Bhandari, Rahul Sinha, Pankaj Goyal, Alessandro Grapputo
Software Mentions: 3
Published: about 15 years ago

10.1186/s12859-014-0422-y

YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia
Cited by: 9
Author(s): Shi Tan, Avirup Dutta, Nicholas S. Jakubovics, Mia Yang Ang, Cheuk Chuen Siow, Naresh V.R. Mutha, Hamed Heydari, Wei Yee Wee, George T.F. Wong, Siew Woh Choo
Software Mentions: 3
Published: over 11 years ago

10.1186/1745-6150-2-34

Systematic analysis of mRNA 5' coding sequence incompleteness in Danio rerio: an automated EST-based approach
Cited by: 5
Author(s): Flavia Frabetti, Raffaella Casadei, Luca Lenzi, Silvia Canaider, Lorenza Vitale, Federica Facchin, Paolo Carinci, Maria Zannotti, Pierluigi Strippoli
Software Mentions: 3
Published: over 18 years ago

10.1186/s12915-018-0580-x

Identification of cell types in a mouse brain single-cell atlas using low sampling coverage
Cited by: 15
Author(s): Aparna Bhaduri, Tomasz J. Nowakowski, Alex A. Pollen, Arnold R. Kriegstein
Software Mentions: 3
Published: almost 8 years ago

10.3390/cancers11030284

Gliosarcoma Is Driven by Alterations in PI3K/Akt, RAS/MAPK Pathways and Characterized by Collagen Gene Expression Signature
Cited by: 15
Author(s): Bartosz Wojtaś, Bartłomiej Gielniewski, Kamil Wojnicki, Marta Maleszewska, Shamba S. Mondal, Paweł Nauman, Wiesława Grajkowska, Rainer Glaß, Ulrich Schüller, Christel Herold‐Mende, Bożena Kamińska
Software Mentions: 3
Published: over 7 years ago

10.3390/biology9090295

Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing
Cited by: 33
Author(s): Girum Fitihamlak Ejigu, Jaehee Jung
Software Mentions: 3
Published: almost 6 years ago

10.1186/1471-2229-11-63

OryzaPG-DB: Rice Proteome Database based on Shotgun Proteogenomics
Cited by: 62
Author(s): Mohamed Helmy, Masaru Tomita, Yasushi Ishihama
Software Mentions: 3
Published: over 15 years ago

10.1186/s12870-020-02576-0

Genome-wide identification, phylogeny and expression analysis of the SPL gene family in wheat
Cited by: 33
Author(s): Ting Zhu, Yue Liu, Liting Ma, Xiaoying Wang, Dazhong Zhang, Yuyan Han, Qin Ding, Lingjian Ma
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0073953

Human Melanoma Cells Over-Express Extracellular Matrix 1 (ECM1) Which Is Regulated by TFAP2C
Cited by: 18
Author(s): Geeta Lal, Piedad Gómez Contreras, Mikhail V. Kulak, George W. Woodfield, Thomas B. Bair, Frederick E. Domann, Ronald J. Weigel
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pone.0193790

Ribosome profiling uncovers selective mRNA translation associated with eIF2 phosphorylation in erythroid progenitors
Cited by: 13
Author(s): Nahuel A. Paolini, Kat Moore, Franca M. di Summa, Ivo F.A.C. Fokkema, Peter A.C. ’t Hoen, Marieke von Lindern
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0013020

Genome-Wide DNA Methylation Maps in Follicular Lymphoma Cells Determined by Methylation-Enriched Bisulfite Sequencing
Cited by: 36
Author(s): Jeong-Hyeon Choi, Yajun Li, Jiangtao Guo, Lirong Pei, Tibor A. Rauch, Robin Kramer, Simone Macmil, Graham B. Wiley, Lynda Bennett, Jennifer Schnabel, Kristen H. Taylor, Sun Il Kim, Dong Xu, Arun Sreekumar, Gerd P. Pfeifer, Bruce A. Roe, Charles W. Caldwell, Kapil N. Bhalla, Huidong Shi
Software Mentions: 3
Published: almost 16 years ago

10.1186/s12864-015-2214-9

Analysis of nucleosome positioning landscapes enables gene discovery in the human malaria parasite Plasmodium falciparum
Cited by: 5
Author(s): Xueqing Maggie Lu, Evelien M. Bunnik, Neeti Pokhriyal, Sara Nasseri, Stefano Lonardi, Karine G. Le Roch
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0159024

Functional Characterization of the Osteoarthritis Susceptibility Mapping to CHST11—A Bioinformatics and Molecular Study
Cited by: 10
Author(s): Louise N. Reynard, Madhushika Ratnayake, Mauro Santibanez‐Koref, John Loughlin
Software Mentions: 3
Published: about 10 years ago

10.1186/1471-2105-10-26

Identifying differential exon splicing using linear models and correlation coefficients
Cited by: 19
Author(s): Sonia Shah, Jacqueline A. Pallas
Software Mentions: 3
Published: over 17 years ago

10.1371/journal.pone.0043652

Pitfalls of Establishing DNA Barcoding Systems in Protists: The Cryptophyceae as a Test Case
Cited by: 26
Author(s): Kerstin Hoef‐Emden
Software Mentions: 3
Published: almost 14 years ago

10.1186/s12870-021-02894-x

A gene expression atlas for kiwifruit (Actinidia chinensis) and network analysis of transcription factors
Cited by: 14
Author(s): Lara Brian, Ben Warren, Peter A. McAtee, Jessica A. Rodrigues, Niels J. Nieuwenhuizen, Asher Pasha, Karine David, Annette Richardson, Nicholas J. Provart, Andrew C. Allan, Erika Varkonyi‐Gasic, Robert J. Schaffer
Software Mentions: 3
Published: over 5 years ago

10.1038/celldisc.2015.8

The PRC2-associated factor C17orf96 is a novel CpG island regulator in mouse ES cells
Cited by: 26
Author(s): Robert Liefke, Yang Shi
Software Mentions: 3
Published: over 11 years ago

10.1186/s12870-019-1672-7

Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume
Cited by: 35
Author(s): Xinxin Wu, Ting Shi, Shahid Iqbal, Yong Zhang, Lin Liu, Zhihong Gao
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-8-113

Discovery and characterization of 91 novel transcripts expressed in cattle placenta
Cited by: 9
Author(s): Charu G. Kumar, Joshua H. Larson, Mark Band, Harris A. Lewin
Software Mentions: 3
Published: over 19 years ago

10.18632/aging.102652

Integrated transcriptome expression profiling reveals a novel lncRNA associated with L-DOPA-induced dyskinesia in a rat model of Parkinson’s disease
Cited by: 8
Author(s): Chunlei Han, Yunpeng Liu, Yun‐Peng Sui, Ning Chen, Tingting Du, Ying Jiang, Chenjia Guo, Kailiang Wang, Qiao Wang, Shiying Fan, Michio Shimabukuro, Fangang Meng, Yuan Fang, Jianguo Zhang
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-021-07478-5

Global analysis of expression, maturation and subcellular localization of mouse liver transcriptome identifies novel sex-biased and TCPOBOP-responsive long non-coding RNAs
Cited by: 13
Author(s): Christine N Goldfarb, David J. Waxman
Software Mentions: 3
Published: over 5 years ago

10.1016/j.celrep.2018.07.104

Simultaneous Measurement of Transcriptional and Post-transcriptional Parameters by 3′ End RNA-Seq
Cited by: 9
Author(s): Manfred Schmid, Agnieszka Tudek, Torben Heick Jensen
Software Mentions: 3
Published: about 8 years ago

10.3390/cells8060623

Functionally Significant Features in the 5′ Untranslated Region of the ABCA1 Gene and Their Comparison in Vertebrates
Cited by: 10
Author(s): Pavel Dvořák, Sarah Leupen, Pavel Souček
Software Mentions: 3
Published: about 7 years ago

10.3791/57633

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
Cited by: 3
Author(s): Christoph N. Schlaffner, Georg J. Pirklbauer, Andreas Bender, Judith A. Steen, Jyoti S. Choudhary
Software Mentions: 3
Published: about 8 years ago

10.1523/ENEURO.0108-21.2021

Forebrain Neural Precursor Cells Are Differentially Vulnerable to Zika Virus Infection
Cited by: 1
Author(s): Samantha M Shelton, Alexandra R Soucy, Ronni Kurzion, Ella Zeldich, John H. Connor, Tarik F. Haydar
Software Mentions: 3
Published: about 5 years ago

10.1016/j.celrep.2020.108533

USP15 Deubiquitinase Safeguards Hematopoiesis and Genome Integrity in Hematopoietic Stem Cells and Leukemia Cells
Cited by: 10
Author(s): Paul van den Berk, Cesare Lancini, Michela Serresi, María Pilar Sánchez-Bailón, Danielle Hulsman, Colin C. Pritchard, Ji‐Ying Song, Matthias Jürgen Schmitt, Ellen Tanger, Oliver Popp, Philipp Mertins, Ivo J. Huijbers, Heinz Jacobs, Maarten van Lohuizen, Gaetano Gargiulo, Elisabetta Citterio
Software Mentions: 3
Published: over 5 years ago

10.18632/oncotarget.24361

Integrative proteomic and transcriptomic analysis provides evidence for TrkB (NTRK2) as a therapeutic target in combination with tyrosine kinase inhibitors for non-small cell lung cancer
Cited by: 12
Author(s): Daniel R. Gomez, Lauren A. Byers, Monique B. Nilsson, Lixia Diao, Jing Wang, Lerong Li, Pan Tong, Mia Hofstad, Babita Saigal, Ignacio I. Wistuba, Neda Kalhor, Stephen G. Swisher, You-Hong Fan, Waun Ki Hong, Milind Suraokar, Carmen Behrens, César A. Moran, John V. Heymach
Software Mentions: 3
Published: over 8 years ago

10.18632/oncotarget.14843

Relationship between LINC00341 expression and cancer prognosis
Cited by: 13
Author(s): Meijian Liao, Bing Li, Shikuan Zhang, Qing Liu, Weijie Liao, Weidong Xie, Yaou Zhang
Software Mentions: 3
Published: over 9 years ago

10.1016/j.jsb.2016.02.012

Web-based volume slicer for 3D electron-microscopy data from EMDB
Cited by: 14
Author(s): José Salavert-Torres, A. Iudin, Ingvar Lagerstedt, Eduardo Sanz-García, Gerard J. Kleywegt, Ardan Patwardhan
Software Mentions: 3
Published: over 10 years ago

10.1523/JNEUROSCI.2836-16.2016

LHX2 Interacts with the NuRD Complex and Regulates Cortical Neuron Subtype DeterminantsFezf2andSox11
Cited by: 52
Author(s): Bhavana Muralidharan, Zeba Khatri, Upasana Maheshwari, Rupesh Gupta, Basabdatta Roy, Saurabh J. Pradhan, Krishanpal Karmodiya, Hari Padmanabhan, Ashwin S. Shetty, Chinthapalli Balaji, Ullas Kolthur‐Seetharam, Jeffrey D. Macklis, Sanjeev Galande, Shubha Tole
Software Mentions: 3
Published: over 9 years ago

10.1186/s12911-020-01177-z

Implementation of data access and use procedures in clinical data warehouses. A systematic review of literature and publicly available policies
Cited by: 9
Author(s): Elena Pavlenko, Daniel Strech, Holger Langhof
Software Mentions: 3
Published: about 6 years ago

10.1128/JVI.00980-17

ZIC2 Is Essential for Maintenance of Latency and Is a Target of an Immediate Early Protein during Kaposi's Sarcoma-Associated Herpesvirus Lytic Reactivation
Cited by: 10
Author(s): Yuanzhi Lyu, K. Nakano, Ryan R. Davis, Clifford G. Tepper, Mel Campbell, Yoshihiro Izumiya
Software Mentions: 3
Published: almost 9 years ago

10.2196/resprot.9639

A Web-Based Telemanagement System for Patients With Complex Inflammatory Bowel Disease: Protocol for a Randomized Controlled Clinical Trial
Cited by: 9
Author(s): Mariam Aguas, Javier del Hoyo, Raquel Faubel, Diana Muñoz, Dana A. Dominguez, Guillermo Bastida, Belén Navarro, Alejandra Barrios, Bernardo Valdivieso, Marisa Correcher, Pilar Nos
Software Mentions: 3
Published: over 7 years ago

10.1186/1756-8722-6-25

Structurally differentiated cis-elements that interact with PU.1 are functionally distinguishable in acute promyelocytic leukemia
Cited by: 12
Author(s): Maoxiang Qian, Ji Wen, Xuehua Zhu, Xiaohong Jia, Xian‐Wen Yang, Yanzhi Du, Kankan Wang, Ji Zhang
Software Mentions: 3
Published: over 13 years ago

10.1038/s41388-018-0659-4

Histoepigenetic analysis of HPV- and tobacco-associated head and neck cancer identifies both subtype-specific and common therapeutic targets despite divergent microenvironments
Cited by: 20
Author(s): Ivenise Carrero, Hsuan-Chen Liu, Andrew G. Sikora, Aleksandar Milosavljevic
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-10-148

IMGD: an integrated platform supporting comparative genomics and phylogenetics of insect mitochondrial genomes
Cited by: 17
Author(s): Wonhoon Lee, Jongsun Park, Jaeyoung Choi, Ki Won Jung, Bong Soo Park, Donghan Kim, Jae-Young Lee, Kyohun Ahn, Wonho Song, Seogchan Kang, Yong Hwan Lee, Seung Hwan Lee
Software Mentions: 3
Published: over 17 years ago

10.1128/AEM.01741-18

Response of the Biocontrol Agent Pseudomonas pseudoalcaligenes AVO110 to Rosellinia necatrix Exudate
Cited by: 5
Author(s): Clara Pliego, José Ignacio Crespo-Gómez, Adrián Pintado, Isabel Pérez‐Martínez, Antonio de Vicente, Francisco M. Cazorla, Cayo Ramos
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pgen.1005154

Genome-Wide Negative Feedback Drives Transgenerational DNA Methylation Dynamics in Arabidopsis
Cited by: 49
Author(s): Tasuku Ito, Yoshiaki Tarutani, Taiko Kim To, Mohamed Kassam, Evelyne Duvernois-Berthet, Sandra Cortijo, Kazuya Takashima, Hidetoshi Saze, Atsushi Toyoda, Asao Fujiyama, Vincent Colot, Tetsuji Kakutani
Software Mentions: 3
Published: over 11 years ago

10.1186/s12920-018-0453-8

Identification of exon skipping events associated with Alzheimer’s disease in the human hippocampus
Cited by: 17
Author(s): Seonggyun Han, Jason E. Miller, Seyoun Byun, Dokyoon Kim, Shannon L. Risacher, Andrew J. Saykin, Younghee Lee, Kwangsik Nho
Software Mentions: 3
Published: over 7 years ago

10.1128/mBio.00768-21

Duplication and Functional Divergence of Branched-Chain Amino Acid Biosynthesis Genes in Aspergillus nidulans
Cited by: 7
Author(s): Joel T Steyer, Damien J. Downes, Cameron C. Hunter, Pierre Migeon, Richard B. Todd
Software Mentions: 3
Published: about 5 years ago

10.1038/s41398-021-01360-4

Genome wide association study identifies four loci for early onset schizophrenia
Cited by: 12
Author(s): Shuxia Guo, Jiewei Liu, Wenqiang Li, Yongfeng Yang, Luxian Lv, Xiao Xiao, Ming Li, Fanglin Guan, Xiong‐Jian Luo
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2350-7-18

Breakpoint Associated with a novel 2.3 Mb deletion in the VCFS region of 22q11 and the role of Alu (SINE) in recurring microdeletions
Cited by: 24
Author(s): Raihan K. Uddin, Yang Zhang, Victoria Mok Siu, Yao Shan Fan, Richard O’Reilly, Jay Rao, Shiva M. Singh
Software Mentions: 3
Published: over 20 years ago

10.1371/journal.pgen.1007156

Regulation of circadian clock transcriptional output by CLOCK:BMAL1
Cited by: 112
Author(s): Alexandra J. Trott, Jérôme S. Menet
Software Mentions: 3
Published: over 8 years ago

10.1101/2021.07.09.21260221

Genetic regulation ofOAS1nonsense-mediated decay underlies association with risk of severe COVID-19
Cited by: 8
Author(s): Abdul Rouf Banday, Megan L. Stanifer, Óscar Flórez-Vargas, Olusegun O. Onabajo, Muhammad Atif Zahoor, Brenen W. Papenberg, Timothy J. Ring, Chia-Han Lee, Evangelos Andreakos, Evgeny Arons, Greg Barsh, Leslie G. Biesecker, David L. Boyle, Andrea N. Burnett‐Hartman, Mary Carrington, Euijin Chang, Pyoeng Gyun Choe, Rex L Chrisholm, Clifton L. Dalgard, Jeff Edberg, Nathan Erdmann, Heather Spencer Feigelson, Gary S. Firestein, Adam J. Gehring, Michelle Ho, Steven M. Holland, Amy Hutchinson, Hogune Im, Michael G. Ison, Hong Bin Kim, Robert J. Kreitman, Bruce R. Korf, Lisa Mirabello, Jennifer A. Pacheco, Michael J. Peluso, Daniel J. Rader, David T. Redden, Marylyn D. Ritchie, Brooke Rosenbloom, Hanaisa P. Sant Anna, Sharon A. Savage, E. Siouti, Vasiliki Triantafyllia, Joselin M. Vargas, Anurag Verma, Vibha Vij, Duane R. Wesemann, Meredith Yeager, Xu G. Yu, Yu Zhang, Steeve Boulant, Stephen J. Chanock, Jordan J. Feld, Ludmila Prokunina–Olsson
Software Mentions: 3
Published: about 5 years ago

10.1038/s41389-020-00285-9

Triptolide targets super-enhancer networks in pancreatic cancer cells and cancer-associated fibroblasts
Cited by: 32
Author(s): Pawan Noel, Shaimaa Hussein, Serina Ng, Corina E. Antal, Wei Lin, Emily Rodela, Priscilla Delgado, Sanna Naveed, Michael Downes, Yin Lin, Ronald M. Evans, Daniel D. Von Hoff, Haiyong Han
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-017-12335-1

Alpha TC1 and Beta-TC-6 genomic profiling uncovers both shared and distinct transcriptional regulatory features with their primary islet counterparts
Cited by: 23
Author(s): Nathan Lawlor, Ahrim Youn, Romy Kursawe, Duygu Ucar, Michael L. Stitzel
Software Mentions: 3
Published: almost 9 years ago

10.1093/bioinformatics/btu072

SegAnnDB: interactive Web-based genomic segmentation
Cited by: 17
Author(s): Toby Dylan Hocking, Valentina Boeva, Guillem Rigaill, Gudrun Schleiermacher, Isabelle Janoueix‐Lerosey, Olivier Delattre, Wilfrid Richer, Franck Bourdeaut, Miyuki Suguro, Masao Seto, Francis Bach, Jean-Philippe Vert
Software Mentions: 3
Published: over 12 years ago

10.1038/s41598-021-91503-w

Colonisation dynamics of Listeria monocytogenes strains isolated from food production environments
Cited by: 12
Author(s): Jessica Gray, P. Scott Chandry, Mandeep Kaur, Chawalit Kocharunchitt, Séamus Fanning, John P. Bowman, Edward M. Fox
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-021-89798-w

Genomic selection signatures in autism spectrum disorder identifies cognitive genomic tradeoff and its relevance in paradoxical phenotypes of deficits versus potentialities
Cited by: 3
Author(s): Anil Prakash, Moinak Banerjee
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-97350-z

Genetic predisposition to tinnitus in the UK Biobank population
Cited by: 1
Author(s): Madeleine E Urbanek, Jian Zuo
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pgen.1009634

Quantitative mapping of mRNA 3’ ends in Pseudomonas aeruginosa reveals a pervasive role for premature 3’ end formation in response to azithromycin
Cited by: 5
Author(s): Salini Konikkat, Michelle R. Scribner, Rory Eutsey, N. Luisa Hiller, Vaughn S. Cooper, C. Joel McManus
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pgen.1004613

Targeted H3R26 Deimination Specifically Facilitates Estrogen Receptor Binding by Modifying Nucleosome Structure
Cited by: 43
Author(s): Michael J. Guertin, Xuesen Zhang, Lynne J. Anguish, Sohyoung Kim, Lyuba Varticovski, John T. Lis, Gordon L. Hager, Scott A. Coonrod
Software Mentions: 3
Published: almost 12 years ago

10.1038/s41598-020-78555-0

Evolutionary divergence of novel open reading frames in cichlids speciation
Cited by: 5
Author(s): Shraddha Puntambekar, Rachel Newhouse, Jaime San-Miguel, Ruchi Chauhan, Grégoire Vernaz, Thomas W. Willis, Matthew T. Wayland, Yagnesh Umrania, Eric A. Miska, Sudhakaran Prabakaran
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-98708-z

AGO CLIP-based imputation of potent siRNA sequences targeting SARS-CoV-2 with antifibrotic miRNA-like activity
Cited by: 6
Author(s): Seung Hyun Ahn, Dowoon Gu, Yongjun Koh, Hye-Sook Lee, Sung Wook
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-019-42686-w

Enhanced early-life nutrition upregulates cholesterol biosynthetic gene expression and Sertoli cell maturation in testes of pre-pubertal Holstein bulls
Cited by: 12
Author(s): Chinju Johnson, Alysha Dance, Igor Kovalchuk, John P. Kastelic, Jacob C. Thundathil
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pgen.1004290

Copy Number Variation Is a Fundamental Aspect of the Placental Genome
Cited by: 55
Author(s): Roberta L. Hannibal, Edward B. Chuong, Juan Carlos Rivera-Mulia, David M. Gilbert, Anton Valouev, Julie C. Baker
Software Mentions: 3
Published: over 12 years ago

10.1186/1471-2164-13-412

Detecting transcription of ribosomal protein pseudogenes in diverse human tissues from RNA-seq data
Cited by: 34
Author(s): Peter D. Tonner, Vinodh Srinivasasainagendra, Shaojie Zhang, Degui Zhi
Software Mentions: 3
Published: almost 14 years ago

10.1038/s41598-018-34864-z

Interactome determination of a Long Noncoding RNA implicated in Embryonic Stem Cell Self-Renewal
Cited by: 14
Author(s): Keriayn N. Smith, Joshua Starmer, Terry Magnuson
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pgen.1001029

Ancestry-Shift Refinement Mapping of the C6orf97-ESR1 Breast Cancer Susceptibility Locus
Cited by: 88
Author(s): Simon Stacey, Patrick Sulem, Carlo Zanon, Sigurjon A. Gudjonsson, Guðmar Þorleifsson, Agnar Helgason, Áslaug Jónasdóttir, Søren Besenbacher, Jelena Kostic, James D. Fackenthal, Dezheng Huo, Clement Adebamowo, Temidayo O. Ogundiran, Janet E. Olson, Zachary S. Fredericksen, Xianshu Wang, Maxime P. Look, Anieta M. Sieuwerts, John W.M. Martens, Isabel Pajares, Maria Dolores García-Prats, José Manuel Ramón-Cajal, Ana De Juan, Angeles Panadero, Eugenia Ortega, Katja K.H. Aben, Sita H. Vermeulen, Fatemeh Asadzadeh, K. C. Anton van Engelenburg, Sara Margolin, Chen Shen, Pei Ei Wu, Asta Försti, Per Lenner, Roger Henriksson, Robert Johansson, Kerstin Enquist, Göran Hallmans, Þorvaldur Jónsson, Helgi Sigurðsson, Kristín Alexíusdóttir, Jūlı́us Guðmundsson, Ásgeir Sigurðsson, Michael L. Frigge, Larus J. Gudmundsson, Kristleifur Kristjánsson, Bjarni V. Halldórsson, Unnur Styrkársdóttir, Jeffrey R. Gulcher, Kari Hemminki, Annika Lindblom, Lambertus A. Kiemeney, J. I. Mayordomo, John A. Foekens, Fergus J. Couch, Olufunmilayo I. Olopade, Daníel F. Guðbjartsson, Unnur Þorsteinsdóttir, Thorunn Rafnar, Óskar T. Jóhannsson, Kāri Stefánsson
Software Mentions: 3
Published: about 16 years ago

10.1186/s12864-016-2948-z

Genome-wide association study to identify potential genetic modifiers in a canine model for Duchenne muscular dystrophy
Cited by: 8
Author(s): Candice Brinkmeyer-Langford, Cynthia Balog-Alvarez, James J. Cai, Brian W. Davis, Joe N. Kornegay
Software Mentions: 3
Published: almost 10 years ago

10.1093/gbe/evaa228

Comparative Genomics within and across Bilaterians Illuminates the Evolutionary History of ALK and LTK Proto-Oncogene Origination and Diversification
Cited by: 5
Author(s): Alex Dornburg, Zheng Wang, Junrui Wang, Elizabeth S. Mo, Francesc López-Giráldez, Jeffrey P. Townsend
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13059-021-02409-9

Evolution of mouse circadian enhancers from transposable elements
Cited by: 29
Author(s): Julius Judd, Hayley Sanderson, Cédric Feschotte
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pgen.1009008

Male-biased aganglionic megacolon in the TashT mouse model of Hirschsprung disease involves upregulation of p53 protein activity and Ddx3y gene expression
Cited by: 6
Author(s): Tatiana Cardinal, Karl-F. Bergeron, Rodolphe Soret, Ouliana Souchkova, Christophe Fauré, Amélina Guillon, Nicolas Pilon
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13073-017-0481-6

Nuclear Wiskott–Aldrich syndrome protein co-regulates T cell factor 1-mediated transcription in T cells
Cited by: 16
Author(s): Nikolai V. Kuznetsov, Bader Almuzzaini, Joanna S. Kritikou, Marisa A. P. Baptista, Mariana M.S. Oliveira, Márton Keszei, Scott B. Snapper, Piergiorgio Percipalle, Lisa S. Westerberg
Software Mentions: 3
Published: almost 9 years ago

10.1186/1471-2164-11-42

Evolution and diversity of secretome genes in the apicomplexan parasite Theileria annulata
Cited by: 36
Author(s): William Weir, Tülin Karagenç, Margaret Baird, Andy Tait, Brian Shiels
Software Mentions: 3
Published: over 16 years ago

10.1186/s13059-020-02186-x

Cis-acting lnc-eRNA SEELA directly binds histone H4 to promote histone recognition and leukemia progression
Cited by: 17
Author(s): Ke Fang, Wei Huang, Yu-Meng Sun, Tian-Qi Chen, Zhan-Cheng Zeng, Qianqian Yang, Qi Pan, Cai Han, Lin-Yu Sun, Xue-Qun Luo, Wen-Tao Wang, Yue‐Qin Chen
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pgen.1004562

A Genome-Wide Association Study of the Maize Hypersensitive Defense Response Identifies Genes That Cluster in Related Pathways
Cited by: 60
Author(s): Bode A. Olukolu, Guan‐Feng Wang, Vijay Vontimitta, Bala P. Venkata, Sandeep Marla, Jiabing Ji, Emma W. Gachomo, Kevin Chu, Adisu Negeri, Jacqueline Benson, Rebecca Nelson, Peter J. Bradbury, Dahlia M. Nielsen, James B. Holland, Peter Balint‐Kurti, Gurmukh S. Johal
Software Mentions: 3
Published: almost 12 years ago

10.1186/s13059-020-02201-1

Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription
Cited by: 28
Author(s): Yue Feng, Yao Wang, Xiangnan Wang, Xiaohong He, Chen Yang, Ardalan Naseri, Thoru Pederson, Jing Zheng, Shaojie Zhang, Xiao Xiao, Wei Xie, Hanhui Ma
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-018-22284-y

Genome-wide transcriptome analysis identifies alternative splicing regulatory network and key splicing factors in mouse and human psoriasis
Cited by: 19
Author(s): Li Jin, Peng Yu
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2164-15-S9-S2

TINAGL1 and B3GALNT1 are potential therapy target genes to suppress metastasis in non-small cell lung cancer
Cited by: 60
Author(s): Hideaki Umeyama, Mitsuo Iwadate, Y-h. Taguchi
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pgen.1004566

Histone Methyltransferase MMSET/NSD2 Alters EZH2 Binding and Reprograms the Myeloma Epigenome through Global and Focal Changes in H3K36 and H3K27 Methylation
Cited by: 174
Author(s): Relja Popovic, Eva Martínez-García, Ευγενία Γιαννοπούλου, Quanwei Zhang, Qingyang Zhang, Teresa Ezponda, Mrinal Y. Shah, Yupeng Zheng, Christine M. Will, Eliza C. Small, Youjia Hua, Marinka Bulic, Yanwen Jiang, Matteo Carrara, Raffaele Calogero, William L. Kath, Neil L. Kelleher, Ji Ping Wang, Olivier Elemento, Jonathan D. Licht
Software Mentions: 3
Published: almost 12 years ago

10.1186/s13059-014-0414-2

Discovery of novel transcripts and gametophytic functions via RNA-seq analysis of maize gametophytic transcriptomes
Cited by: 67
Author(s): Antony M. Chettoor, Scott A. Givan, Rex A. Cole, Clayton T Coker, Erica Unger-Wallace, Zuzana Vejlupkova, Erik Vollbrecht, John E. Fowler, Evans Mulenga
Software Mentions: 3
Published: about 12 years ago

10.1186/s13059-016-0924-1

JBrowse: a dynamic web platform for genome visualization and analysis
Cited by: 595
Author(s): Robert Buels, Eric Yao, Colin Diesh, Richard D. Hayes, Monica Muñoz-Torres, Gregg Helt, David Goodstein, Christine G. Elsik, Suzanna Lewis, Lincoln Stein, Ian Holmes
Software Mentions: 3
Published: over 10 years ago

10.1186/1471-2164-14-818

Exploration of the gene fusion landscape of glioblastoma using transcriptome sequencing and copy number data
Cited by: 67
Author(s): Nameeta Shah, Michael Lankerovich, Hwahyung Lee, Jae-Geun Yoon, Brett Schroeder, Greg Foltz
Software Mentions: 3
Published: over 13 years ago

10.1186/s12864-017-4169-5

CGDV: a webtool for circular visualization of genomics and transcriptomics data
Cited by: 3
Author(s): Vineet Jha, Gulzar Singh, Sanjiv Kumar, Amol D. Sonawane, Abhay Jere, Krishanpal Anamika
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pcbi.1007274

A benchmark of computational CRISPR-Cas9 guide design methods
Cited by: 23
Author(s): Jacob Bradford, Dimitri Perrin
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pcbi.1005720

Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb
Cited by: 16
Author(s): Remo Monti, Iros Barozzi, Marco Osterwalder, Elizabeth Lee, Momoe Kato, Tyler Garvin, Ingrid Plajzer-Frick, Catherine S. Pickle, Jennifer A. Akiyama, Veena Afzal, Niko Beerenwinkel, Diane E. Dickel, Axel Visel, Len A. Pennacchio
Software Mentions: 3
Published: almost 9 years ago

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Papers Mentioning browser 2,125