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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

10.1371/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

10.1371/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

10.1371/journal.pone.0015688

High-Definition Mapping of Retroviral Integration Sites Defines the Fate of Allogeneic T Cells After Donor Lymphocyte Infusion
Cited by: 40
Author(s): Claudia Cattoglio, Giulietta Maruggi, Cynthia C. Bartholomae, Nirav Malani, Danilo Pellin, Fabienne Cocchiarella, Zulma Magnani, Fabio Ciceri, Alessandro Ambrosi, Christof von Kalle, Frederic D. Bushman, Chiara Bonini, Manfred Schmidt, Fulvio Mavilio, Alessandra Recchia
Software Mentions: 3
Published: over 15 years ago

10.1371/journal.pone.0094101

Deep Investigation of Arabidopsis thaliana Junk DNA Reveals a Continuum between Repetitive Elements and Genomic Dark Matter
Cited by: 52
Author(s): Florian Maumus, Hadi Quesneville
Software Mentions: 3
Published: over 12 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

10.1186/1756-8722-6-25

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/s12915-019-0674-0

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

10.1186/1471-2164-15-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.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

10.1038/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

10.1371/journal.pone.0233044

Runx3 prevents spontaneous colitis by directing the differentiation of anti-inflammatory mononuclear phagocytes
Cited by: 13
Author(s): Shay Hantisteanu, Yosef Dicken, Varda Negreanu, Dalia Goldenberg, Ori Brenner, Dena Leshkowitz, Joseph Lotem, Ditsa Levanon, Yoram Groner
Software Mentions: 3
Published: about 6 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

10.1371/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

10.1038/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

10.1186/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

10.1038/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

10.1038/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

10.1371/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

10.1038/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

10.1128/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

10.1186/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/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

10.1038/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

10.1186/1471-2164-15-86

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

10.1038/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

10.1186/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

10.1186/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

10.1038/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

10.1101/2021.07.09.21260221

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

10.1186/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

10.1186/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

10.1186/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

10.1186/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: over 10 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/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

10.1186/1471-2164-14-648

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: almost 9 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: over 8 years ago

10.1093/gbe/evaa228

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

10.1186/1471-2148-9-252

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

10.1186/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/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/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

10.1186/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

10.3390/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

10.1186/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

10.1186/1471-2164-7-42

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

10.1186/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/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: over 5 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/gb-2012-13-11-r102

Evidence for conserved post-transcriptional roles of unitary pseudogenes and for frequent bifunctionality of mRNAs
Cited by: 63
Author(s): Ana C. Marques, Jennifer Y. Tan, Sheena Lee, Lesheng Kong, Andreas Heger, Chris P. Ponting
Software Mentions: 3
Published: over 14 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/gb-2007-8-12-r269

CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction
Cited by: 90
Author(s): Samuel S. Gross, B. Chuong, Marina Sirota, Serafim Batzoglou
Software Mentions: 3
Published: over 19 years ago

10.1186/gb-2009-10-4-r38

Transcriptional features of genomic regulatory blocks
Cited by: 100
Author(s): Altuna Akalin, David Fredman, Erik Arner, Xianjun Dong, Jan Christian Bryne, Harukazu Suzuki, Carsten O. Daub, Yoshihide Hayashizaki, Boris Lenhard
Software Mentions: 3
Published: over 17 years ago

10.1186/gb-2009-10-4-r39

FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions
Cited by: 64
Author(s): Jessica Severin, Andrew Waterhouse, Hideya Kawaji, Timo Lassmann, Erik van Nimwegen, Piotr J. Balwierz, Michiel de Hoon, David Hume, Piero Carninci, Yoshihide Hayashizaki, Harukazu Suzuki, Carsten O. Daub, Alistair R.R. Forrest
Software Mentions: 3
Published: over 17 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: over 6 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

10.3389/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 8 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

10.1371/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

10.3390/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

10.3389/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: over 6 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

10.1186/1471-2164-14-818

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

10.3389/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: almost 6 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

10.3389/fgene.2019.00007

A New Panel-Based Next-Generation Sequencing Method for ADME Genes Reveals Novel Associations of Common and Rare Variants With Expression in a Human Liver Cohort
Cited by: 35
Author(s): Kathrin Klein, Roman Tremmel, Stefan Winter, Sarah Fehr, Florian Battke, Tim Scheurenbrand, Elke Schaeffeler, Saskia Biskup, Matthias Schwab, Ulrich M. Zanger
Software Mentions: 3
Published: over 7 years ago

10.1097/MD.0000000000012679

Comprehensive assessment gene signatures for clear cell renal cell carcinoma prognosis
Cited by: 11
Author(s): Po-Ya Chang, Zhitong Bing, Jinhui Tian, Jingyun Zhang, Xiuxia Li, Long Ge, Juan Ling, Kun Yang, Yumin Li
Software Mentions: 3
Published: almost 8 years ago

10.1186/1751-0473-6-2

SAMMate: a GUI tool for processing short read alignments in SAM/BAM format
Cited by: 55
Author(s): Guiyin Xu, Nan Deng, Zhiyu Zhao, Thair Judeh, Erik K. Flemington, Dongxiao Zhu
Software Mentions: 3
Published: over 15 years ago

10.3389/fendo.2015.00021

Promoter Methylation Status of Ras-Association Domain Family Member in Pheochromocytoma
Cited by: 17
Author(s): Antje Richter, Tobias Zimmermann, Tanja Haag, Sara K. Walesch, Reinhard Dammann
Software Mentions: 3
Published: over 11 years ago

10.1038/s41598-017-04786-3

sRNA and cis-antisense sRNA identification in Staphylococcus aureus highlights an unusual sRNA gene cluster with one encoding a secreted peptide
Cited by: 25
Author(s): Julie Bronsard, Gaëtan Pascreau, Mohamed Sassi, Tony Mauro, Yoann Augagneur, Brice Felden
Software Mentions: 3
Published: about 9 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: about 7 years ago

10.1186/s12864-015-1959-5

Development of ListeriaBase and comparative analysis of Listeria monocytogenes
Cited by: 8
Author(s): Mui Fern Tan, Cheuk Chuen Siow, Avirup Dutta, Naresh V.R. Mutha, Wei Yee Wee, Hamed Heydari, Shi Tan, Mia Yang Ang, George T.F. Wong, Siew Woh Choo
Software Mentions: 3
Published: almost 11 years ago

10.3389/fcell.2021.666303

Lgr4 Regulates Oviductal Epithelial Secretion Through the WNT Signaling Pathway
Cited by: 3
Author(s): Xue Tan, Lingling Zhang, Tianqi Li, Jia Zhan, Kun Qiao, Haili Wu, Shenfei Sun, Meina Huang, Fangxi Zhang, Meixing Zhang, Changwei Li, Li R, Hongjie Pan
Software Mentions: 3
Published: almost 5 years ago

10.3389/fcell.2021.727183

A Novel Pyroptosis-Associated Long Non-coding RNA Signature Predicts Prognosis and Tumor Immune Microenvironment of Patients With Breast Cancer
Cited by: 29
Author(s): Liqin Ping, Kaiming Zhang, Xueqi Ou, Xingsheng Qiu, Xia Xiao
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12915-015-0159-8

Poised chromatin and bivalent domains facilitate the mitosis-to-meiosis transition in the male germline
Cited by: 58
Author(s): Ho-Su Sin, Andrey V. Kartashov, Kazuteru Hasegawa, Artem Barski, Satoshi H. Namekawa
Software Mentions: 3
Published: about 11 years ago

10.1186/1476-511X-13-25

Leptin gene promoter DNA methylation in WNIN obese mutant rats
Cited by: 9
Author(s): Rajender Rao Kalashikam, Padmavathi J. N. Inagadapa, Anju Elizabeth Thomas, Sugeetha Jeyapal, Nappan Veettil Giridharan, Manchala Raghunath
Software Mentions: 3
Published: over 12 years ago

10.26508/lsa.202000663

Splicing of enhancer-associated lincRNAs contributes to enhancer activity
Cited by: 22
Author(s): Jennifer Y. Tan, Adriano Biasini, Robert S. Young, Ana C. Marques
Software Mentions: 3
Published: over 6 years ago

10.1007/s00335-015-9599-2

A mouse informatics platform for phenotypic and translational discovery
Cited by: 28
Author(s): Natalie Ring, Terrence F. Meehan, Judith A. Blake, James M. Brown, Chao-Kung Chen, Nathalie Conte, Armida Di Fenza, Tanja Fiegel, Neil R. Horner, Julius O. B. Jacobsen, Natasha A. Karp, Thomas N. Lawson, Justin C. Mason, Peter Matthews, Hugh W. Morgan, Mike Relac, Luís Santos, Damian Smedley, Duncan Sneddon, Alice Pengelly, Ilinca Tudose, Jonathan Warren, Henrik Westerberg, Gagarine Yaikhom, Helen Parkinson, Ann‐Marie Mallon
Software Mentions: 3
Published: almost 11 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

10.1074/mcp.O115.048777

Galaxy Integrated Omics: Web-based Standards-Compliant Workflows for Proteomics Informed by Transcriptomics*
Cited by: 28
Author(s): Jun Fan, Shyamasree Saha, Gary Barker, Kate J Heesom, Fawaz Ghali, Andrew R. Jones, David A. Matthews, Conrad Bessant
Software Mentions: 3
Published: almost 11 years ago

10.1186/gb-2014-15-1-r3

RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome
Cited by: 76
Author(s): Ian M. Silverman, Liancheng Fan, A Vinogradov Alexander, Loyal A. Goff, Cole Trapnell, John L. Rinn, Brian D. Gregory
Software Mentions: 3
Published: over 12 years ago

10.3390/cancers13133176

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

10.1016/j.celrep.2018.07.104

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

10.1534/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: almost 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

10.1016/j.celrep.2020.108533

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

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