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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

10.1038/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

10.1186/1471-2164-13-412

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: about 14 years ago

10.1016/j.stemcr.2020.01.004

Activin A and BMP4 Signaling Expands Potency of Mouse Embryonic Stem Cells in Serum-Free Media
Cited by: 13
Author(s): Baojiang Wu, Lin Li, Bojiang Li, Junpeng Gao, Yanglin Chen, Mengyi Wei, Zhiqing Yang, Baojing Zhang, Shudong Li, Kexin Li, Changshan Wang, M. Azim Surani, Xihe Li, Fuchou Tang, Siqin Bao
Software Mentions: 3
Published: over 6 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 10 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: about 10 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 9 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

10.1371/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

10.1038/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 10 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

10.1038/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: almost 8 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: almost 13 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: about 12 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: about 11 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: about 8 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 12 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: about 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: almost 7 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: about 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 7 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 12 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: 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: almost 11 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: about 6 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: over 5 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: over 6 years ago

10.1186/1471-2164-15-86

Finding the missing honey bee genes: lessons learned from a genome upgrade
Cited by: 349
Author(s): Christine G. Elsik, Kim C. Worley, Anna Bennett, Martin Beye, Francisco Câmara, Christopher P. Childers, Dirk C. de Graaf, Griet Debyser, Jixin Deng, Bart Devreese, Eran Elhaik, Jay D. Evans, Leonard J. Foster, Dan Graur, Roderic Guigó, Katharina J. Hoff, Michael Holder, Matthew E. Hudson, Greg J. Hunt, Huaiyang Jiang, Vandita Joshi, Radhika S. Khetani, Peter Kosarev, Christie Kovar, Jian Ma, Ryszard Maleszka, Robin F. A. Moritz, Monica Muñoz-Torres, Terence Murphy, Donna M. Muzny, Irene Newsham, Justin Reese, Hugh M. Robertson, Gene E. Robinson, Olav Rueppell, Victor Solovyev, Mario Stanke, Eckart Stolle, Jennifer M. Tsuruda, Matthias Van Vaerenbergh, Robert M. Waterhouse, Daniel Weaver, Charles W. Whitfield, Yuanqing Wu, Evgeny M. Zdobnov, Lan Zhang, Dianhui Zhu, Richard A. Gibbs
Software Mentions: 3
Published: over 12 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 7 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: about 11 years ago

10.1186/s12859-016-1227-y

PGen: large-scale genomic variations analysis workflow and browser in SoyKB
Cited by: 25
Author(s): Yang Liu, Saad Khan, Juexin Wang, Mats Rynge, Yuanxun Zhang, Shuai Zeng, Shiyuan Chen, João Vitor Maldonado dos Santos, Babu Valliyodan, Prasad Calyam, Nirav Merchant, Henry T. Nguyen, Dong Xu, Trupti Joshi
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12864-018-4556-6

The deregulated microRNAome contributes to the cellular response to aneuploidy
Cited by: 12
Author(s): Milena Dürrbaum, Christine Kruse, K. Julia Nieken, Bianca Habermann, Zuzana Storchová
Software Mentions: 3
Published: over 8 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: over 6 years ago

10.1186/1471-2148-10-90

Exon-primed intron-crossing (EPIC) markers for non-model teleost fishes
Cited by: 56
Author(s): Chenhong Li, Jean-Jack M. Riethoven, Lan Ma
Software Mentions: 3
Published: over 16 years ago

10.1371/journal.pbio.1000238

Concordant Regulation of Translation and mRNA Abundance for Hundreds of Targets of a Human microRNA
Cited by: 376
Author(s): David G. Hendrickson, Daniel J. Hogan, Heather McCullough, Jason W. Myers, Daniel Herschlag, James E. Ferrell, Patrick O. Brown
Software Mentions: 3
Published: almost 17 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: about 8 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: about 8 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: over 5 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

10.1038/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/s12864-016-2539-z

A novel enrichment strategy reveals unprecedented number of novel transcription start sites at single base resolution in a model prokaryote and the gut microbiome
Cited by: 117
Author(s): Laurence Ettwiller, John A. Buswell, Erbay Yigit, Ira Schildkraut
Software Mentions: 3
Published: over 10 years ago

10.1534/g3.115.019828

Enrichment of H3K9me2 on Unsynapsed Chromatin inCaenorhabditis elegansDoes Not Targetde NovoSites
Cited by: 14
Author(s): Yiqing Guo, Bing Yang, Yini Li, Xia Xu, Eleanor M. Maine
Software Mentions: 3
Published: about 11 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: about 9 years ago

10.1186/s12864-015-2285-7

cChIP-seq: a robust small-scale method for investigation of histone modifications
Cited by: 13
Author(s): Cristina Valensisi, Jo Ling Liao, Colin Andrus, Stephanie L. Battle, R. David Hawkins
Software Mentions: 3
Published: almost 11 years ago

10.1186/s12864-021-07934-2

CAMPAREE: a robust and configurable RNA expression simulator
Cited by: 1
Author(s): Nicholas F. Lahens, Thomas G. Brooks, Dimitra Sarantopoulou, Soumyashant Nayak, Cris Lawrence, Antonijo Mrčela, Anand Srinivasan, Jonathan Schug, John B. Hogenesch, Yoseph Barash, Gregory R. Grant
Software Mentions: 3
Published: almost 5 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

10.1186/1471-2164-14-818

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

10.1186/1471-2164-14-648

Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs
Cited by: 80
Author(s): Jeroen Crappé, Wim Van Criekinge, Geert Trooskens, Eisuke Hayakawa, Walter Luyten, Geert Baggerman, Gerben Menschaert
Software Mentions: 3
Published: over 13 years ago

10.1186/s12864-021-07512-6

Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing
Cited by: 15
Author(s): Aleksandra Bliznina, Aki Masunaga, Michael J. Mansfield, Yongkai Tan, Andrew W. Liu, Charlotte West, Tanmay Rustagi, Hsiao-Chiao Chien, Saurabh Kumar, Julien Pichon, Charles Plessy, Nicholas M. Luscombe
Software Mentions: 3
Published: over 5 years ago

10.7717/peerj.1310

Expression of temperature-sensitive ion channel TRPM8 in sperm cells correlates with vertebrate evolution
Cited by: 25
Author(s): Rakesh Kumar Majhi, S. K. Saha, Ashutosh Kumar, Arijit Ghosh, Nirlipta Swain, Luna Goswami, Pratyush P. Mohapatra, Apratim Maity, Vivek Kumar Sahoo, Abhishek Kumar, Chandan Goswami
Software Mentions: 3
Published: almost 11 years ago

10.1186/s12864-020-6697-7

iMarmot: an integrative platform for comparative and functional genomics of marmots
Cited by: 3
Author(s): Baoning Liu, Liang Bai, Qingqing Yu, Fang Hu, Jing Wu, Zhao Song, Rong Wang, Weirong Wang, Yuanqing Tao, Jianglin Fan, Enqi Liu
Software Mentions: 3
Published: over 6 years ago

10.7717/peerj.8592

fRNAkenseq: a fully powered-by-CyVerse cloud integrated RNA-sequencing analysis tool
Cited by: 2
Author(s): Allen Hubbard, Matthew Bomhoff, Carl J. Schmidt
Software Mentions: 3
Published: over 6 years ago

10.7717/peerj.3640

Expression differences inAphidius ervi(Hymenoptera: Braconidae) females reared on different aphid host species
Cited by: 11
Author(s): Gabriel I. Ballesteros, Juergen Gadau, Fabrice Legeai, Angélica González-González, Blas Lavandero, Jean Simon, Christian C. Figueroa
Software Mentions: 3
Published: about 9 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: almost 6 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: almost 12 years ago

10.7717/peerj.5067

Horizontally transferred genes in the ctenophoreMnemiopsis leidyi
Cited by: 7
Author(s): Alexandra M. Hernandez, Joseph F. Ryan
Software Mentions: 3
Published: about 8 years ago

10.12688/wellcomeopenres.15355.2

GeneDB and Wikidata
Cited by: 2
Author(s): Magnus Manske, Ulrike Böhme, Christoph Püthe, Matthew Berriman
Software Mentions: 3
Published: almost 7 years ago

10.7717/peerj.4106

Transcriptomic profiling of mTOR and ryanodine receptor signaling molecules in developing zebrafish in the absence and presence of PCB 95
Cited by: 6
Author(s): Daniel F. Frank, Galen W. Miller, Richard E. Connon, Juergen Geist, Pamela J. Lein
Software Mentions: 3
Published: almost 9 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: almost 7 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: almost 6 years ago

10.1186/1471-2148-9-252

Positive selection for the male functionality of a co-retroposed gene in the hominoids
Cited by: 13
Author(s): Yong Zhang, Shujuan Lu, Shuqi Zhao, Xiaofeng Zheng, Manyuan Long, Liping Wei
Software Mentions: 3
Published: almost 17 years ago

10.1186/1471-2164-13-147

Genome-wide analysis of Pax8 binding provides new insights into thyroid functions
Cited by: 40
Author(s): Sergio Ruiz‐Llorente, Enrique Carrillo Santa de Pau, Ana Sastre-Perona, Cristina Montero‐Conde, Gonzalo Goméz-López, James A. Fagin, Alfonso Valencia, David G. Pisano, Pilar Santisteban
Software Mentions: 3
Published: over 14 years ago

10.3390/v12070783

Inter-Strain Epigenomic Profiling Reveals a Candidate IAP Master Copy in C3H Mice
Cited by: 9
Author(s): Rita Rebollo, Mariana Galvão Ferrarini, Liane Gagnier, Ying Zhang, Ardian Ferraj, Christine R. Beck, Matthew C. Lorincz, Dixie L. Mager
Software Mentions: 3
Published: about 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: almost 9 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 7 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 7 years ago

10.1186/s13567-020-00850-5

Integrated time-serial transcriptome networks reveal common innate and tissue-specific adaptive immune responses to PRRSV infection
Cited by: 18
Author(s): Bee-Oh Lim, Sang–Wook Kim, kyu sang lim, Chang Gi Jeong, Seung Chai Kim, Sang Myeong Lee, Choi Kyu Park, M.F.W. te Pas, Haesu Gho, Tae Hun Kim, Kyung Tai Lee, Won Il Kim, Jun Mo Kim
Software Mentions: 3
Published: almost 6 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: over 10 years ago

10.1186/s13015-018-0133-4

Coordinate systems for supergenomes
Cited by: 10
Author(s): Fabian Gärtner, Christian Höner zu Siederdissen, Lydia Müller, Peter F. Stadler
Software Mentions: 3
Published: almost 8 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: about 10 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

10.1371/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

10.3390/v13040544

Detection of H3K4me3 Identifies NeuroHIV Signatures, Genomic Effects of Methamphetamine and Addiction Pathways in Postmortem HIV+ Brain Specimens that Are Not Amenable to Transcriptome Analysis
Cited by: 4
Author(s): Liana V. Basova, Alexander Lindsey, Anne Marie McGovern, Ronald J. Ellis, Maria Cecília Garibaldi Marcondes
Software Mentions: 3
Published: over 5 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: over 7 years ago

10.3389/fimmu.2019.02016

Continuous Developmental and Early Life Trichloroethylene Exposure Promoted DNA Methylation Alterations in Polycomb Protein Binding Sites in Effector/Memory CD4+ T Cells
Cited by: 10
Author(s): Stephanie D. Byrum, Charity L. Washam, John M. Patterson, Kanan K. Vyas, Kathleen M. Gilbert, Sarah J. Blossom
Software Mentions: 3
Published: about 7 years ago

10.1186/1471-2164-7-42

Gene expression profiling of Naïve sheep genetically resistant and susceptible to gastrointestinal nematodes
Cited by: 87
Author(s): Orla M. Keane, Amonida Zadissa, Theresa Wilson, D. L. Hyndman, G. J. Greer, David Baird, Alan McCulloch, A. M. Crawford, John C. McEwan
Software Mentions: 3
Published: over 20 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 8 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 5 years ago

10.1186/s12943-020-01293-4

Long non-coding RNA NEAT1 promotes bone metastasis of prostate cancer through N6-methyladenosine
Cited by: 154
Author(s): Simeng Wen, Yulei Wei, Chong Zen, Wei Xiong, Yuanjie Niu, Yu Zhao
Software Mentions: 3
Published: almost 6 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: about 8 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: over 6 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 6 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

10.1186/1471-2350-12-55

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

10.1093/database/bax009

HopBase: a unified resource for Humulus genomics
Cited by: 27
Author(s): Steven T. Hill, Ramcharan Sudarsanam, Jimmy C. Henning, David A. Hendrix
Software Mentions: 3
Published: over 9 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: almost 11 years ago

10.1186/s12885-017-3252-2

Genome-wide DNA methylation measurements in prostate tissues uncovers novel prostate cancer diagnostic biomarkers and transcription factor binding patterns
Cited by: 47
Author(s): Marie K. Kirby, Ryne C. Ramaker, Brian S. Roberts, Brittany N. Lasseigne, David S. Gunther, Todd C. Burwell, Nicholas S. Davis, Zulfiqar Gulzar, Devin Absher, Sara J. Cooper, James D. Brooks, R Myers
Software Mentions: 3
Published: over 9 years ago

10.1186/s12864-018-4869-5

Limitations of alignment-free tools in total RNA-seq quantification
Cited by: 61
Author(s): Douglas C. Wu, Jun Yao, Kevin S. Ho, Alan M. Lambowitz, Claus O. Wilke
Software Mentions: 3
Published: about 8 years ago

10.1016/j.dib.2015.10.033

Identification of genes escaping X inactivation by allelic expression analysis in a novel hybrid mouse model
Cited by: 6
Author(s): Joel B. Berletch, Wenxiu Ma, Fan Yang, Jay Shendure, William Stafford Noble, Christine M. Distèche, Xinxian Deng
Software Mentions: 3
Published: almost 11 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

10.1186/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 9 years ago

10.1371/journal.pone.0079402

Linear Decay of Retrotransposon Antisense Bias across Genes Is Contingent upon Tissue Specificity
Cited by: 1
Author(s): Sara B. Linker, Dale J. Hedges
Software Mentions: 3
Published: almost 13 years ago

10.1186/s13100-021-00233-3

RIP-seq reveals LINE-1 ORF1p association with p-body enriched mRNAs
Cited by: 17
Author(s): Erica M. Briggs, Wilson McKerrow, Paolo Mita, Jef D. Boeke, Susan K. Logan, David Fenyö
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

10.3390/microorganisms7100420

Reduced Virulence of an Introduced Forest Pathogen over 50 Years
Cited by: 6
Author(s): Rosie E. Bradshaw, Shannon Ormond, Pierre‐Yves Dupont, Pranav Chettri, I. Kutay Ozturk, Rebecca McDougal, L. S. Bulman, Murray P. Cox
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-021-07421-8

Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress
Cited by: 4
Author(s): Junling Dou, F.S. Schenkel, Lirong Hu, Adnan Khan, Muhammad Zahoor Khan, Ying Yu, Yajing Wang
Software Mentions: 3
Published: over 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 5 years ago

10.1186/s12885-021-07900-x

Super-enhancer-associated long noncoding RNA AC005592.2 promotes tumor progression by regulating OLFM4 in colorectal cancer
Cited by: 7
Author(s): Yan Liu, Huanhuan Chen, Li Tang, Pan Jiang, Feng Yan
Software Mentions: 3
Published: over 5 years ago

10.1038/s42003-019-0488-1

Systematic discovery of conservation states for single-nucleotide annotation of the human genome
Cited by: 16
Author(s): Adriana Arneson, Jason Ernst
Software Mentions: 3
Published: about 7 years ago

10.1186/s13148-019-0699-9

Rheumatoid arthritis-relevant DNA methylation changes identified in ACPA-positive asymptomatic individuals using methylome capture sequencing
Cited by: 14
Author(s): Xiaojian Shao, Marie Hudson, Inés Colmegna, Celia Greenwood, Marvin J. Fritzler, Philip Awadalla, Tomi Pastinen, Sasha Bernatsky
Software Mentions: 3
Published: about 7 years ago

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