pypi: browser | Projects | Ecosyste.ms: Papers

10.7554/eLife.08904

Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals
Cited by: 57
Author(s): Alex de Mendoza, Hiroshi Suga, Joan Permanyer, Manuel Irimia, Iñaki Ruiz‐Trillo
Software Mentions: 4
Published: about 9 years ago

10.18632/oncotarget.9535

Alterations of androgen receptor-regulated enhancer RNAs (eRNAs) contribute to enzalutamide resistance in castration-resistant prostate cancer
Cited by: 35
Author(s): Jingwen Zhao, Yu Zhao, Liguo Wang, Jun Zhang, Jeffrey Karnes, Manish Kohli, Guixia Wang, Haojie Huang
Software Mentions: 4
Published: over 8 years ago

10.7554/eLife.29005

Conserved noncoding transcription and core promoter regulatory code in early Drosophila development
Cited by: 10
Author(s): Philippe Batut, T Gingeras
Software Mentions: 4
Published: almost 7 years ago

10.7554/eLife.39658

Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome
Cited by: 33
Author(s): Srivarsha Rajshekar, Jun Yao, Paige K. Arnold, Sara G. Payne, Yinwen Zhang, Teresa V. Bowman, Robert J. Schmitz, John Edwards, Mary Goll
Software Mentions: 4
Published: almost 6 years ago

10.7554/eLife.62438

Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping
Cited by: 52
Author(s): Philip P. Adams, Gabriele Baniulyte, Caroline Esnault, Kavya Chegireddy, Navjot Singh, Molly Monge, Ryan Dale, Gisela Storz, Joseph T. Wade
Software Mentions: 4
Published: almost 4 years ago

10.7554/eLife.50895

Partial loss of CFIm25 causes learning deficits and aberrant neuronal alternative polyadenylation
Cited by: 23
Author(s): Callison E Alcott, Hari Krishna Yalamanchili, Ping Ji, Meike E van der Heijden, Alexander B. Saltzman, Nathan D. Elrod, Lin Ai, Mei Leng, Bhoomi Bhatt, Shuang Hao, Qi Wang, Afaf Saliba, Jianrong Tang, Anna Malovannaya, Eric J. Wagner, Zhandong Liu, Huda Y. Zoghbi
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0238546

MITF and TFEB cross-regulation in melanoma cells
Cited by: 12
Author(s): Josué Ballesteros‐Álvarez, Ramile Dilshat, Valerie Fock, Katrín Möller, Ludwig Karl, Lionel Larue, Margrét H. Ögmundsdóttir, Eirı́kur Steingrı́msson
Software Mentions: 4
Published: about 4 years ago

10.1126/sciadv.abe3516

Genomic profiling of native R loops with a DNA-RNA hybrid recognition sensor
Cited by: 37
Author(s): Kang Wang, Honghong Wang, Conghui Li, Zhenggang Yin, Ran Xiao, Qiuzi Li, Xiaofang Ying, Wen Wang, Jian Huang, Liang Chen, Pingping Fang, Kaiwei Liang
Software Mentions: 4
Published: almost 4 years ago

10.7554/eLife.43922

Dynamic repression by BCL6 controls the genome-wide liver response to fasting and steatosis
Cited by: 38
Author(s): Meredith A Sommars, Krithika Ramachandran, Madhavi D. Senagolage, Christopher R. Futtner, Derrik M Germain, Amanda L. Allred, Yasuhiro Omura, Ilya Bederman, Grant D. Barish
Software Mentions: 4
Published: over 5 years ago

10.1186/s12915-019-0659-z

Biological and RNA regulatory function of MOV10 in mammalian germ cells
Cited by: 18
Author(s): Kaiqiang Fu, Suwen Tian, Huanhuan Tan, Caifeng Wang, Hanben Wang, Min Wang, Yuan‐Yuan Wang, Zhen Chen, Yanfeng Wang, Qiuling Yue, Qiushi Xu, Shuya Zhang, Haixin Li, Jie Xie, Mingyan Lin, Mengcheng Luo, Feng Chen, Lan Ye, Ke Zheng
Software Mentions: 4
Published: over 5 years ago

10.1186/s13072-019-0286-5

BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity
Cited by: 20
Author(s): Pierre Khoueiry, Aoife Ward Gahlawat, Massimo Petretich, Anne-Marie Michon, Daniel F. Simola, Enid Y.N. Lam, Eileen E. M. Furlong, Vladimı́r Beneš, Mark A. Dawson, Rab K. Prinjha, Gerard Drewes, Paola Grandi
Software Mentions: 4
Published: over 5 years ago

10.1111/acel.13178

The inherited methylome landscape is directly altered with paternal aging and associated with offspring neurodevelopmental disorders
Cited by: 27
Author(s): Michelle M. Denomme, Mary E. Haywood, Jason C. Parks, William B. Schoolcraft, Mandy G. Katz‐Jaffe
Software Mentions: 4
Published: over 4 years ago

10.7554/eLife.38340

The origin of the odorant receptor gene family in insects
Cited by: 88
Author(s): Philipp Brand, Hugh M. Robertson, Wei Lin, Ratnasri Pothula, William E. Klingeman, Juan Luís Jurat-Fuentes, Brian R. Johnson
Software Mentions: 4
Published: over 6 years ago

10.1186/s12915-019-0679-8

Mechanistic interpretation of non-coding variants for discovering transcriptional regulators of drug response
Cited by: 13
Author(s): Xiaoman Xie, Casey Hanson, Saurabh Sinha
Software Mentions: 3
Published: over 5 years ago

10.18632/aging.101485

Regulatory RNA binding proteins contribute to the transcriptome-wide splicing alterations in human cellular senescence
Cited by: 13
Author(s): Qiongye Dong, Lei Wei, Michael Q. Zhang, Xiaowo Wang
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pgen.1000404

Selection at a Single Locus Leads to Widespread Expansion of Toxoplasma gondii Lineages That Are Virulent in Mice
Cited by: 116
Author(s): Asis Khan, Sonya Taylor, James W. Ajioka, Benjamin M. Rosenthal, L. David Sibley
Software Mentions: 3
Published: over 15 years ago

10.1038/s41598-017-00176-x

Identifying Novel Transcriptional and Epigenetic Features of Nuclear Lamina-associated Genes
Cited by: 28
Author(s): Feinan Wu, Jie Yao
Software Mentions: 3
Published: over 7 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: over 7 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: almost 6 years ago

10.1186/1741-7007-10-107

Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi: a new view of ctenophore photocytes
Cited by: 106
Author(s): Christine E. Schnitzler, Kevin Pang, Meghan L. Powers, Adam M. Reitzel, Joseph F. Ryan, David Simmons, Takeshi Tada, Morgan Park, Jyoti Gupta, Shelise Brooks, Robert W. Blakesley, Shozo Yokoyama, Steven H. D. Haddock, Mark Q. Martindale, Andreas D. Baxevanis
Software Mentions: 3
Published: almost 12 years ago

10.1038/srep22851

An integrative approach to investigate the respective roles of single-nucleotide variants and copy-number variants in Attention-Deficit/Hyperactivity Disorder
Cited by: 17
Author(s): Leandro Lima, Ana Cecília Feio-dos-Santos, Síntia Belangero, Ary Gadelha, Rodrigo A. Bressan, Giovanni Abrahão Salum, Pedro Mário Pan, Tais Moriyama, Ana Soledade Graeff‐Martins, Ana Carina Tamanaha, Pedro Gomes de Alvarenga, Fernanda Valle Krieger, Bacy Fleitlich-Bilyk, Andrea Parolin Jackowski, Elisa Brietzke, João Ricardo Sato, Guilherme Polanczyk, Jair de Jesus Mari, Gisele Gus Manfro, Maria Conceição do Rosário, Eurípedes Constantino Miguel, Renato Puga, Ana Carolina Tahira, Viviane Neri Souza, Thais Chile, Gisele Rodrigues Gouveia, Sérgio Nery Simões, Xiao Chang, Renata Pellegrino, Lifeng Tian, Joseph T. Glessner, Ronaldo Fumio Hashimoto, Luís Augusto Rohde, Patrick Sleiman, Hákon Hákonarson, Helena Brentani
Software Mentions: 3
Published: over 8 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: about 7 years ago

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: about 17 years ago

10.1038/srep19615

Overlapping signatures of chronic pain in the DNA methylation landscape of prefrontal cortex and peripheral T cells
Cited by: 67
Author(s): Renaud Massart, Sergiy Dymov, Magali Millecamps, Matthew Suderman, Stéphanie Grégoire, Kevin Koenigs, Sebastian Alvarado, Maral Tajerian, Laura S. Stone, Moshe Szyf
Software Mentions: 3
Published: almost 9 years ago

10.1038/srep28396

Identification of long non-coding RNAs involved in neuronal development and intellectual disability
Cited by: 42
Author(s): Eva D’haene, Eva Jacobs, Pieter-Jan Volders, Tim De Meyer, Björn Menten, Sarah Vergult
Software Mentions: 3
Published: over 8 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: over 5 years ago

10.1038/srep02962

Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network
Cited by: 17
Author(s): Jianliang Li, Joseph Mazar, Cuncong Zhong, Geoffrey J. Faulkner, Subramaniam S. Govindarajan, Zhan Zhang, Marcel E. Dinger, Gavin Meredith, Christopher M. Adams, Shaojie Zhang, John S. Mattick, Animesh Ray, Ranjan J. Perera
Software Mentions: 3
Published: about 11 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: almost 4 years ago

10.1038/srep12062

Differential and coherent processing patterns from small RNAs
Cited by: 21
Author(s): Sachin Pundhir, Jan Gorodkin
Software Mentions: 3
Published: over 9 years ago

10.1038/srep37622

HMGA1P7-pseudogene regulates H19 and Igf2 expression by a competitive endogenous RNA mechanism
Cited by: 33
Author(s): Marco De Martino, Floriana Forzati, Marianna Marfella, Simona Pellecchia, Claudio Arra, Luigi Terracciano, Alfredo Fusco, Francesco Esposito
Software Mentions: 3
Published: almost 8 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 8 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: almost 5 years ago

10.1038/sdata.2018.240

Meta-mining of copy number profiles of high-risk neuroblastoma tumors
Cited by: 26
Author(s): Pauline Depuydt, Jan Koster, Valentina Boeva, Toby Dylan Hocking, Frank Speleman, Gudrun Schleiermacher, Katleen De Preter
Software Mentions: 3
Published: about 6 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: about 6 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: almost 7 years ago

10.1371/journal.ppat.1007948

The fitness landscape of the African Salmonella Typhimurium ST313 strain D23580 reveals unique properties of the pBT1 plasmid
Cited by: 19
Author(s): Rocı́o Canals, Roy R. Chaudhuri, Rebecca E. Steiner, Siân V. Owen, Natalia Quinones-Olvera, Michael A. Gordon, Michael Baym, Michael Ibba, Jay C. D. Hinton
Software Mentions: 3
Published: about 5 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 12 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 8 years ago

10.1371/journal.ppat.1007875

Global analysis of polysome-associated mRNA in vesicular stomatitis virus infected cells
Cited by: 20
Author(s): William J. Neidermyer, Sean P. J. Whelan
Software Mentions: 3
Published: over 5 years ago

10.1530/REP-18-0270

Dynamic changes in gene expression and signalling during trophoblast development in the horse
Cited by: 10
Author(s): Jordan E. Read, Victoria Cabrera-Sharp, Victoria Offord, Samantha Mirczuk, Steve Allen, Robert C. Fowkes, Amanda M. de Mestre
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 3 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 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: over 8 years ago

10.1371/journal.pgen.1005652

Conserved piRNA Expression from a Distinct Set of piRNA Cluster Loci in Eutherian Mammals
Cited by: 69
Author(s): Gung Wei Chirn, Reazur Rahman, Yuliya A. Sytnikova, Jessica Matts, Mei Zeng, Daniel Gerlach, Michael Yu, Bonnie Berger, Mayumi Naramura, Benjamin T. Kile, Nelson C. Lau
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.ppat.1005166

Global Analysis of Mouse Polyomavirus Infection Reveals Dynamic Regulation of Viral and Host Gene Expression and Promiscuous Viral RNA Editing
Cited by: 12
Author(s): Seth B. Garren, Yuvabharath Kondaveeti, Michael O. Duff, Gordon G. Carmichael
Software Mentions: 3
Published: about 9 years ago

10.1007/978-3-030-58948-6_4

Cross Reality (XR): Challenges and Opportunities Across the Spectrum
Cited by: 25
Author(s): Cindy Ziker, Barbara Truman, Heather Dodds
Software Mentions: 3
Published: almost 4 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: over 3 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: almost 10 years ago

10.1038/s41438-020-00347-4

Major-effect candidate genes identified in cultivated strawberry (Fragaria × ananassa Duch.) for ellagic acid deoxyhexoside and pelargonidin-3-O-malonylglucoside biosynthesis, key polyphenolic compounds
Cited by: 17
Author(s): Jahn Davik, Kjersti Aaby, Matteo Buti, Muath Alsheikh, Nada Šurbanovski, Stefan Martens, D. Røen, Daniel J. Sargent
Software Mentions: 3
Published: over 4 years ago

10.1186/s40537-015-0018-z

SOCR data dashboard: an integrated big data archive mashing medicare, labor, census and econometric information
Cited by: 23
Author(s): Syed Sameed Husain, Alexandr A. Kalinin, Anh Truong, Ivo D. Dinov
Software Mentions: 3
Published: over 9 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: about 10 years ago

10.1016/j.jbc.2021.100784

Generation of an isoform-level transcriptome atlas of macrophage activation
Cited by: 14
Author(s): Apple Cortez Vollmers, Honey Mekonen, Sophia Campos, Susan Carpenter, Christopher Vollmers
Software Mentions: 3
Published: almost 4 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 10 years ago

10.1093/gigascience/giaa001

A highly contiguous genome assembly of the bat hawkmoth Hyles vespertilio (Lepidoptera: Sphingidae)
Cited by: 8
Author(s): Martin Pippel, David Jebb, Franziska Patzold, Sylke Winkler, Heiko Vogel, Gene Myers, Michael Hiller, Anna K. Hundsdoerfer
Software Mentions: 3
Published: almost 5 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: almost 9 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: almost 16 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 17 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: about 4 years ago

10.1093/gigascience/giz073

A large interactive visual database of copy number variants discovered in taurine cattle
Cited by: 21
Author(s): Arun Kommadath, Jason R. Grant, Kirill Krivushin, Adrien M. Butty, C.F. Baes, Tara R. Carthy, D.P. Berry, Paul Stothard
Software Mentions: 3
Published: over 5 years ago

10.1111/jcmm.15568

A functional genomics approach to investigate the differentiation of iPSCs into lung epithelium at air‐liquid interface
Cited by: 10
Author(s): Jenny L. Kerschner, Alekh Paranjapye, Shiyi Yin, Dannielle L. Skander, Gürkan Bebek, Shih Hsing Leir, Ann Harris
Software Mentions: 3
Published: over 4 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: over 14 years ago

10.1093/g3journal/jkab163

Nuku, a family of primate retrocopies derived from KU70
Cited by: 0
Author(s): Paul A. Rowley, Aisha Ellahi, Kyudong Han, Jagdish Suresh Patel, James T. Van Leuven, Sara L. Sawyer
Software Mentions: 3
Published: over 3 years ago

10.1534/g3.117.043752

Constraints on eQTL Fine Mapping in the Presence of Multisite Local Regulation of Gene Expression
Cited by: 23
Author(s): Biao Zeng, Luke R. Lloyd‐Jones, Alexander Holloway, Urko M. Marigorta, Andres Metspalu, Grant W. Montgomery, Tõnu Esko, Kenneth L. Brigham, Arshed A Quyyumi, Youssef Idaghdour, Jian Yang, Peter M. Visscher, Joseph E. Powell, Greg Gibson
Software Mentions: 3
Published: over 7 years ago

10.1534/g3.115.019828

Enrichment of H3K9me2 on Unsynapsed Chromatin in<i>Caenorhabditis elegans</i>Does Not Target<i>de Novo</i>Sites
Cited by: 14
Author(s): Yiqing Guo, Bing Yang, Yini Li, Xia Xu, Eleanor M. Maine
Software Mentions: 3
Published: about 9 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 12 years ago

10.3390/genes9090424

Human Age Prediction Based on DNA Methylation Using a Gradient Boosting Regressor
Cited by: 41
Author(s): Xingyan Li, Weidong Li, Yan Xu
Software Mentions: 3
Published: over 6 years ago

10.3389/fphar.2019.00050

Semantic Queries Expedite MedDRA Terms Selection Thanks to a Dedicated User Interface: A Pilot Study on Five Medical Conditions
Cited by: 3
Author(s): Julien Souvignet, Gunnar Declerck, Béatrice Trombert-Paviot, Hadyl Asfari, Marie-Christine Jaulent, Cédric Bousquet
Software Mentions: 3
Published: almost 6 years ago

10.3389/fnmol.2017.00283

RNA-Sequencing Analysis Reveals a Regulatory Role for Transcription Factor Fezf2 in the Mature Motor Cortex
Cited by: 6
Author(s): Alison J Clare, Hollie E. Wicky, Ruth M. Empson, Stephanie M. Hughes
Software Mentions: 3
Published: about 7 years ago

10.3389/fphys.2020.587358

Transcriptional Programs Driving Shear Stress-Induced Differentiation of Kidney Proximal Tubule Cells in Culture
Cited by: 18
Author(s): Hyun Jung Park, Zhenjiang Fan, Yinge Bai, Qidong Ren, Youssef Rbaibi, Kimberly R. Long, Megan L. Gliozzi, Natalie Rittenhouse, Joseph Locker, Amanda C. Poholek, Ora A. Weisz
Software Mentions: 3
Published: about 4 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: almost 16 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: almost 6 years ago

10.3389/fmicb.2020.596626

High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies
Cited by: 3
Author(s): Jared T. Broddrick, Richard Szubin, Charles J. Norsigian, Jonathan M. Monk, Bernhard Ø. Palsson, M. N. Parenteau
Software Mentions: 3
Published: about 4 years ago

10.3389/fpls.2019.01333

AppleMDO: A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States
Cited by: 34
Author(s): Lingling Da, Yue Liu, Jiaotong Yang, Tian Tian, Jiajie She, Xuelian Ma, Wenying Xu, Zhen Su
Software Mentions: 3
Published: about 5 years ago

10.3389/fimmu.2018.00603

Transcriptional Modulation of Human Endogenous Retroviruses in Primary CD4+ T Cells Following Vorinostat Treatment
Cited by: 20
Author(s): Cory H. White, Nadejda Beliakova-Bethell, Steven M. Lada, Michael S. Breen, Tara Hurst, Celsa A. Spina, Douglas D. Richman, John Frater, Gkikas Magiorkinis, Christopher H. Woelk
Software Mentions: 3
Published: over 6 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: almost 6 years ago

10.3389/fimmu.2019.00667

NF-κB Signaling and IL-4 Signaling Regulate SATB1 Expression via Alternative Promoter Usage During Th2 Differentiation
Cited by: 11
Author(s): Satyajeet P. Khare, Ankitha Shetty, Rahul Biradar, Indumathi Patta, Zhi Chen, Ameya Sathe, Puli Chandramouli Reddy, Riitta Lahesmaa, Sanjeev Galande
Software Mentions: 3
Published: over 5 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: almost 8 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: almost 7 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 18 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: about 8 years ago

10.3389/fimmu.2019.00660

High-Quality Library Preparation for NGS-Based Immunoglobulin Germline Gene Inference and Repertoire Expression Analysis
Cited by: 47
Author(s): Néstor Vázquez Bernat, Martin Corcoran, Uta Hardt, Mateusz Kaduk, Ganesh E. Phad, Marcel Martin, Gunilla B. Karlsson Hedestam
Software Mentions: 3
Published: over 5 years ago

10.1093/gigascience/giy095

Draft genome assembly of the invasive cane toad, Rhinella marina
Cited by: 56
Author(s): Richard J. Edwards, Daniel Enosi Tuipulotu, Timothy G. Amos, Denis O’Meally, Mark F. Richardson, Tonia Russell, Marcelo Vallinoto, Miguel Carneiro, Nuno Ferrand, Marc R. Wilkins, Fernando Sequeira, Lee A. Rollins, Edward C. Holmes, Richard Shine
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.ppat.1004183

The PhoP-Dependent ncRNA Mcr7 Modulates the TAT Secretion System in Mycobacterium tuberculosis
Cited by: 116
Author(s): Luis Solans, Jesús Gonzalo-Asensio, Claudia Sala, Andrej Benjak, Swapna Uplekar, Jacques Rougemont, Christophe Guilhot, Wladimir Malaga, Carlos Martı́n, Stewart T. Cole
Software Mentions: 3
Published: over 10 years ago

10.3389/fnhum.2018.00249

Measuring Mindfulness: A Psychophysiological Approach
Cited by: 14
Author(s): Vladimir Bostanov, Lilian Ohlrogge, Rita Britz, Martin Hautzinger, Boris Kotchoubey
Software Mentions: 3
Published: over 6 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: about 5 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 13 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: over 7 years ago

10.3389/fimmu.2020.00538

5-Azacytidine Potentiates Anti-tumor Immunity in a Model of Pancreatic Ductal Adenocarcinoma
Cited by: 11
Author(s): Nancy D. Ebelt, Edith Zuniga, B. Lamar Johnson, Don J. Diamond, Edwin R. Manuel
Software Mentions: 3
Published: over 4 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: over 12 years ago

10.3389/fgene.2019.01348

Long Noncoding RNA RAET1K Enhances CCNE1 Expression and Cell Cycle Arrest of Lung Adenocarcinoma Cell by Sponging miRNA-135a-5p
Cited by: 12
Author(s): Chang Zheng, Xuelian Li, Yong Ren, Zhihua Yin, Baosen Zhou
Software Mentions: 3
Published: almost 5 years ago

10.3389/fimmu.2021.636061

Human β-Defensin 2 Mutations Are Associated With Asthma and Atopy in Children and Its Application Prevents Atopic Asthma in a Mouse Model
Cited by: 10
Author(s): Natascha Borchers, Elisangela Santos-Valente, Antoaneta A. Toncheva, Jan Wehkamp, André Franke, Vincent D. Gaertner, Peter Nordkild, Jon Genuneit, Benjamin Anderschou Holbech Jensen, Michael Kabesch
Software Mentions: 3
Published: over 3 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: over 8 years ago

10.3389/fgene.2018.00132

Chromatin Landscape Distinguishes the Genomic Loci of Hundreds of Androgen-Receptor-Associated LincRNAs From the Loci of Non-associated LincRNAs
Cited by: 10
Author(s): Luis DaSilva, Felipe Beckedorff, Ana C. Ayupe, Murilo Sena Amaral, Vinícius C. Mesel, Alexandre Videira, Eduardo M. Reis, João Carlos Setúbal, Sérgio Verjovski-Almeida
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2020.00003

BedSect: An Integrated Web Server Application to Perform Intersection, Visualization, and Functional Annotation of Genomic Regions From Multiple Datasets
Cited by: 13
Author(s): Gyan Prakash Mishra, Arup Ghosh, Atimukta Jha, Sunil K. Raghav
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pbio.3000580

12-h clock regulation of genetic information flow by XBP1s
Cited by: 34
Author(s): Yinghong Pan, Heather Ballance, Huan Meng, Naomi Gonzalez, Sam-Moon Kim, Leymaan Abdurehman, Brian York, Xi Chen, Yisrael Schnytzer, Oren Levy, Clifford C. Dacso, Colleen A. McClung, Bert W. O’Malley, Silvia Liu, Bokai Zhu
Software Mentions: 3
Published: almost 5 years ago

10.3389/fgene.2020.597943

The Intergenerational Impacts of Paternal Diet on DNA Methylation and Offspring Phenotypes in Sheep
Cited by: 14
Author(s): Nicole Groß, Todd D. Taylor, Thomas D. Crenshaw, Hasan Khatib
Software Mentions: 3
Published: about 4 years ago

10.3389/fgene.2019.01409

LncRNA LUCRC Regulates Colorectal Cancer Cell Growth and Tumorigenesis by Targeting Endoplasmic Reticulum Stress Response
Cited by: 13
Author(s): G.H. Tang, Xue Chen, Jian Ding, Jie Du, Xun Lin, Lu Xia, Jiabian Lian, Yang Feng, Xiu‐Sheng He, Wen Li
Software Mentions: 3
Published: almost 5 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: almost 15 years ago

10.3389/fgene.2019.00508

F8 Inversions at Xq28 Causing Hemophilia A Are Associated With Specific Methylation Changes: Implication for Molecular Epigenetic Diagnosis
Cited by: 14
Author(s): Muhammad Ahmer Jamil, Amit Sharma, Nicole Nuesgen, Behnaz Pezeshkpoor, André Heimbach, A. Pavlova, Johannes Oldenburg, Osman El‐Maarri
Software Mentions: 3
Published: over 5 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: about 10 years ago

Projects: pypi: browser

Papers Mentioning browser 2,125