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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

10.1038/cr.2017.134

Derivation of hypermethylated pluripotent embryonic stem cells with high potency
Cited by: 39
Author(s): Siqin Bao, Walfred W.C. Tang, Baojiang Wu, Shinseog Kim, Jingyun Li, Lin Li, Toshihiro Kobayashi, Caroline Lee, Yanglin Chen, Mengyi Wei, Shudong Li, Sabine Dietmann, Fuchou Tang, Xihe Li, M. Azim Surani
Software Mentions: 3
Published: almost 9 years ago

10.3390/ijms21165743

Premature Activation of Immune Transcription Programs in Autoimmune-Predisposed Mouse Embryonic Stem Cells and Blastocysts
Cited by: 0
Author(s): Oktay Kirak, Eugene Ke, Kevin Yi Yang, Anna Schwarz, Lars Plate, Amy Nham, Justin R. Abadejos, Anna Valencia, R. Luke Wiseman, Kathy O. Lui, Manching Ku
Software Mentions: 3
Published: about 6 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

10.3390/ijms21218383

Trans-Ancestral Fine-Mapping and Epigenetic Annotation as Tools to Delineate Functionally Relevant Risk Alleles at IKZF1 and IKZF3 in Systemic Lupus Erythematosus
Cited by: 6
Author(s): Timothy J. Vyse, Deborah S. Cunninghame Graham
Software Mentions: 3
Published: almost 6 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

10.1093/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

10.3390/ijms19030738

The Coordinated Activities of nAChR and Wnt Signaling Regulate Intestinal Stem Cell Function in Mice
Cited by: 25
Author(s): Toshio Takahashi, Akira Shiraishi, Jun Murata
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0102968

Role of Polycomb Group Proteins in the DNA Damage Response – A Reassessment
Cited by: 12
Author(s): Hollie Chandler, Harshil Patel, Richard D. Palermo, Sharon Brookes, Nik Matthews, Gordon Peters
Software Mentions: 3
Published: about 12 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

10.1371/journal.pone.0247402

DeepSRE: Identification of sterol responsive elements and nuclear transcription factors Y proximity in human DNA by Convolutional Neural Network analysis
Cited by: 0
Author(s): Davide Noto, Antonina Giammanco, Rossella Spina, Francesca Fayer, Angelo B. Cefalù, Maurizio Averna
Software Mentions: 3
Published: over 5 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

10.1007/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

10.3390/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

10.3390/ijms22105335

INTACT vs. FANS for Cell-Type-Specific Nuclei Sorting: A Comprehensive Qualitative and Quantitative Comparison
Cited by: 11
Author(s): Monika Chanu Chongtham, Tamer Butto, Kanak Mungikar, Susanne Gerber, Jennifer Winter
Software Mentions: 3
Published: over 5 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.0222432

The intermediate proteasome is constitutively expressed in pancreatic beta cells and upregulated by stimulatory, low concentrations of interleukin 1 β
Cited by: 13
Author(s): Muhammad Saad Khilji, Danielle Verstappen, Tina Dahlby, Michala Prause, Celina Pihl, Sophie Emilie Bresson, Tenna Holgersen Bryde, Phillip Alexander Keller Andersen, Kristian Klindt, Dušan Živković, Marie‐Pierre Bousquet, Björn Tyrberg, Thomas Mandrup‐Poulsen, Michał Marzec
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0193614

A common copy-number variant within SIRPB1 correlates with human Out-of-Africa migration after genetic drift correction
Cited by: 5
Author(s): José Luis Royo, Joan Valls, Rafael D. Acemel, Carlos Gómez-Marín, Mariona Pascual-Pons, Arantxa Lupiañez, José Luis Gómez-Skármeta, Joan Fibla
Software Mentions: 3
Published: over 8 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

10.1371/journal.pone.0105685

Analysis of Papaya Cell Wall-Related Genes during Fruit Ripening Indicates a Central Role of Polygalacturonases during Pulp Softening
Cited by: 56
Author(s): João Paulo Fabi, Sabrina Garcia Broetto, Sarah Lígia Garcia Leme da Silva, Silin Zhong, Franco Maria Lajolo, João Roberto Oliveira do Nascimento
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0015392

Identification of De Novo Copy Number Variants Associated with Human Disorders of Sexual Development
Cited by: 133
Author(s): Mounia Tannour‐Louet, Shuo Han, Sean T. Corbett, Jean-François Louet, Svetlana A. Yatsenko, Lindsay Meyers, Chad A. Shaw, Sung-Hae L. Kang, Sau Wai Cheung, Dolores J. Lamb
Software Mentions: 3
Published: almost 16 years ago

10.7554/eLife.44642

Thermosensitive alternative splicing senses and mediates temperature adaptation in Drosophila
Cited by: 51
Author(s): Ane Martín Anduaga, Naveh Evantal, Inés Lucía Patop, Osnat Bartok, Ron Weiss, Sebastián Kadener
Software Mentions: 3
Published: almost 7 years ago

10.7554/eLife.15635

Sox9 and Sox8 protect the adult testis from male-to-female genetic reprogramming and complete degeneration
Cited by: 65
Author(s): Francisco Barrionuevo, Alicia Hurtado, Gwang-Jin Kim, Francisca M. Real, Mohammed Bakkali, Janel L. Kopp, Maike Sander, Gerd Scherer, Miguel Burgos, Rafael Jiménez
Software Mentions: 3
Published: about 10 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

10.7554/eLife.25787

Repression by PRDM13 is critical for generating precision in neuronal identity
Cited by: 34
Author(s): Bishakha Mona, Ana Uruena, Rahul K. Kollipara, Zhenzhong Ma, Mark D. Borromeo, Joshua C. Chang, Jane E. Johnson
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0085648

RNA Polymerase III Transcriptomes in Human Embryonic Stem Cells and Induced Pluripotent Stem Cells, and Relationships with Pluripotency Transcription Factors
Cited by: 32
Author(s): Ravi Alla, Bradley R. Cairns
Software Mentions: 3
Published: over 12 years ago

10.7554/eLife.20851

Age-dependent diastolic heart failure in an in vivo Drosophila model
Cited by: 32
Author(s): Matthew P. Klassen, Christian J. Peters, Shiwei Zhou, Hannah H Williams, Yuh Nung Jan
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0133751

Smooth Muscle Cell Genome Browser: Enabling the Identification of Novel Serum Response Factor Target Genes
Cited by: 43
Author(s): Moon Young Lee, Chanjae Park, Robyn M. Berent, Paul J. Park, Robert Fuchs, Syn Hannah, Chin Albert, Jared Townsend, Craig C. Benson, Doug Redelman, Tong Shen, Sang-Youel Park, Joseph M. Miano, Kenton M. Sanders, Seungil Ro
Software Mentions: 3
Published: about 11 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.0239627

Swimming under elevated hydrostatic pressure increases glycolytic activity in gas gland cells of the European eel
Cited by: 5
Author(s): Gabriel Schneebauer, Constantin Lindemann, Victoria Drechsel, Lasse Marohn, Klaus Wysujack, Elena Santidrian, Ron P. Dirks, Reinhold Hanel, Bernd Pelster
Software Mentions: 3
Published: almost 6 years ago

10.7554/eLife.07860

Quantitative and functional interrogation of parent-of-origin allelic expression biases in the brain
Cited by: 71
Author(s): Julio Pérez, Nimrod D. Rubinstein, Daniel E. Fernandez, Stephen Santoro, Leigh A. Needleman, Olivia Ho-Shing, John J Choi, Mariela Zirlinger, Shau-Kwaun Chen, Jun S. Liu, Catherine Dulac
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0020042

A Locus on Chromosome 5 Is Associated with Dilated Cardiomyopathy in Doberman Pinschers
Cited by: 44
Author(s): Theresa-Bernadette Mausberg, Gerhard Wess, Julia Simak, Lena Keller, Michaela Drögemüller, Cord Drögemüller, Matthew T. Webster, Hannah Stephenson, J. Dukes‐McEwan, Tosso Leeb
Software Mentions: 3
Published: about 15 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

10.1186/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

10.7554/eLife.19272

Combinatorial bZIP dimers display complex DNA-binding specificity landscapes
Cited by: 101
Author(s): José A. Rodríguez‐Martínez, Aaron W. Reinke, Devesh Bhimsaria, Amy E. Keating, Aseem Z. Ansari
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0018880

Arabidopsis Plasmodesmal Proteome
Cited by: 222
Author(s): Lourdes Fernández‐Calvino, Christine Faulkner, John Walshaw, Gerhard Saalbach, Emmanuelle Bayer, Yoselin Benitez‐Alfonso, Andrew J. Maule
Software Mentions: 3
Published: over 15 years ago

10.7554/eLife.35989

Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation
Cited by: 129
Author(s): Daniel Fuentes, Tomek Swigut, Joanna Wysocka
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0169687

Recessive coding and regulatory mutations in FBLIM1 underlie the pathogenesis of chronic recurrent multifocal osteomyelitis (CRMO)
Cited by: 59
Author(s): Allison Cox, Benjamin W. Darbro, Ronald M. Laxer, Gabriel Vélez, Xinyu Bing, Alexis L. Finer, Albert Erives, Vinit B. Mahajan, Alexander G. Bassuk, Polly J. Ferguson
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0078032

Fine-Mapping an Association of FSHR with Preterm Birth in a Finnish Population
Cited by: 16
Author(s): Sung Chun, Jevon Plunkett, Kari Teramo, Louis J. Muglia, Justin C. Fay
Software Mentions: 3
Published: almost 13 years ago

10.7554/eLife.11469

An experimentally validated network of nine haematopoietic transcription factors reveals mechanisms of cell state stability
Cited by: 55
Author(s): Judith Schütte, Huange Wang, Stella Antoniou, Andrew Jarratt, Nicola K. Wilson, Joey Riepsaame, Fernando J. Calero-Nieto, Victoria Moignard, Silvia Basilico, Sarah Kinston, Rebecca Hannah, Mun Chiang Chan, Sylvia Nürnberg, Willem H. Ouwehand, Nicola Bonzanni, Marella Ftr de Bruijn, Berthold Göttgens
Software Mentions: 3
Published: over 10 years ago

10.7554/eLife.26129

FXR1 regulates transcription and is required for growth of human cancer cells with TP53/FXR2 homozygous deletion
Cited by: 25
Author(s): Yichao Fan, Yue Jiao, Mengtao Xiao, Han Han‐Zhang, Yao Vickie Wang, Chun Ma, Zhilin Deng, Yingxiang Li, Yanyan Yu, Xinghao Wang, Shen Niu, Youjia Hua, Zhiping Weng, Peter Atadja, En Li, Bin Xiang
Software Mentions: 3
Published: about 9 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

10.1038/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

10.1186/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

10.7554/eLife.40364

PLZF targets developmental enhancers for activation during osteogenic differentiation of human mesenchymal stem cells
Cited by: 27
Author(s): Shuchi Agrawal-Singh, Mads Lerdrup, Ana-Luisa R Gomes, Harmen J.G. van de Werken, Jens Vilstrup Johansen, Robin Andersson, Albin Sandelin, Kristian Helin, Klaus Hansen
Software Mentions: 3
Published: over 7 years ago

10.1101/2021.07.09.21260221

Genetic regulation of<i>OAS1</i>nonsense-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

10.1186/1756-8722-6-25

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

10.1186/1471-2164-10-148

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

10.1128/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

10.1186/1471-2105-14-18

JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison
Cited by: 9
Author(s): Phillip Seitzer, Tu Anh Ngoc Huynh, Marc T. Facciotti
Software Mentions: 3
Published: over 13 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

10.1186/s12920-017-0301-2

Analysis of viral diversity for vaccine target discovery
Cited by: 12
Author(s): Mohammad Asif Khan, Yongli Hu, Olivo Miotto, Natascha May Thevasagayam, Rashmi Sukumaran, Hadia Syahirah Abd Raman, Vladimir Brusic, Tin Wee Tan, J. Thomas August
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0047216

A Hybrid Distance Measure for Clustering Expressed Sequence Tags Originating from the Same Gene Family
Cited by: 5
Author(s): Keng-Hoong Ng, Chin-Kuan Ho, Somnuk Phon-Amnuaisuk
Software Mentions: 3
Published: almost 14 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

10.3390/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

10.2196/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

10.7554/eLife.08954

The splicing regulators Esrp1 and Esrp2 direct an epithelial splicing program essential for mammalian development
Cited by: 110
Author(s): Thomas W. Bebee, Juw Won Park, Katherine I Sheridan, Claude C. Warzecha, Benjamin Cieply, Alex M Rohacek, Yi Xing, Russ P. Carstens
Software Mentions: 3
Published: almost 11 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

10.1371/journal.pgen.1006581

Differences in the rare variant spectrum among human populations
Cited by: 90
Author(s): Iain Mathieson, David Reich
Software Mentions: 3
Published: over 9 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.1002728

Target Gene Analysis by Microarrays and Chromatin Immunoprecipitation Identifies HEY Proteins as Highly Redundant bHLH Repressors
Cited by: 66
Author(s): Julia Heisig, D. F. Weber, Eva Englberger, Anja Winkler, Susanne Kneitz, Wing-Kin Sung, Elmar Wolf, Martin Eilers, Wei Chia-Lin, Manfred Gessler
Software Mentions: 3
Published: over 14 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

10.1186/gb-2013-14-7-r72

A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design
Cited by: 18
Author(s): Robin P. Smith, Samantha J. Riesenfeld, Alisha K. Holloway, Qiang Li, Karl K. Murphy, Natalie M. Feliciano, Lorenzo Orecchia, Nir Oksenberg, Katherine S. Pollard, Nadav Ahituv
Software Mentions: 3
Published: over 13 years ago

10.1186/s13059-016-1023-z

Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells
Cited by: 54
Author(s): Xiaoli Zhang, Jun Wu, Jian Wang, Tingting Shen, Hua Li, Jun Lü, Yunzhao Gu, Yani Kang, Chee-Hong Wong, Chew Yee Ngan, Zongshu Shao, Ji Wu, Xiaodong Zhao
Software Mentions: 3
Published: about 10 years ago

10.1186/gb-2012-13-8-r75

Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers
Cited by: 220
Author(s): Alayne Brunner, Andrew H. Beck, Badreddin Edris, Robert T. Sweeney, Shirley Zhu, Rui Li, Kelli Montgomery, Sushama Varma, Thea Gilks, Xiangqian Guo, Joseph W. Foley, Daniela Witten, Craig P. Giacomini, Ryan A. Flynn, Jonathan R. Pollack, Robert Tibshirani, Howard Y. Chang, Matt van de Rijn, Robert B. West
Software Mentions: 3
Published: over 14 years ago

10.1186/s12864-016-2542-4

Multivariate models from RNA-Seq SNVs yield candidate molecular targets for biomarker discovery: SNV-DA
Cited by: 6
Author(s): Matt R. Paul, Nicholas P. Levitt, David E. Moore, Patricia M. Watson, Robert Wilson, Chadrick E. Denlinger, Dennis K. Watson, Paul E. Anderson
Software Mentions: 3
Published: over 10 years ago

10.1186/1471-2350-12-55

Geographic differences in allele frequencies of susceptibility SNPs for cardiovascular disease
Cited by: 43
Author(s): Keyue Ding, Iftikhar J. Kullo
Software Mentions: 3
Published: over 15 years ago

10.1371/journal.pgen.1006260

Novel Genetic Variants for Cartilage Thickness and Hip Osteoarthritis
Cited by: 73
Author(s): Martha C. Castaño-Betancourt, Dan S. Evans, Yolande F M Ramos, Cindy G. Boer, Sarah Metrustry, Youfang Liu, Wouter den Hollander, Jeroen van Rooij, Virginia B. Kraus, Michelle S. Yau, Braxton D. Mitchell, Kenneth Muir, Albert Hofman, Michael Doherty, Sally Doherty, Weiya Zhang, Robert Kraaij, Fernando Rivadeneira, Elizabeth Barrett‐Connor, Rose A. Maciewicz, N K Arden, Rob G H H Nelissen, Margreet Kloppenburg, Joanne M. Jordan, Michael C. Nevitt, P. Eline Slagboom, Deborah Hart, Floris P. J. G. Lafeber, Unnur Styrkársdóttir, Eleftheria Zeggini, Εvangelos Εvangelou, Tim D. Spector, André G. Uitterlinden, Nancy E Lane, Ingrid Meulenbelt, Ana M. Valdes, Joyce B. J. van Meurs
Software Mentions: 3
Published: almost 10 years ago

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Papers Mentioning browser 2,125