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10.3390/genes12081249

Proof of Gene Doping in a Mouse Model with a Human Erythropoietin Gene Transferred Using an Adenoviral Vector
Cited by: 7
Author(s): Takehito Sugasawa, Takuro Nakano, Shin‐ichiro Fujita, Yuki Matsumoto, Genki Ishihara, Kai Aoki, Koki Yanazawa, S. Ono, Shinsuke Tamai, Lev Manevich, Hiroshi Ueda, Noriyo Ishibashi, Kenshirou Tamai, Yasuharu Kanki, Yasuko Yoshida, Koichi Watanabe, Tohru Takemasa, Yasushi Kawakami, Kazuhiro Takekoshi
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0017125

Ontogenetic De Novo Copy Number Variations (CNVs) as a Source of Genetic Individuality: Studies on Two Families with MZD Twins for Schizophrenia
Cited by: 66
Author(s): Sujit Maiti, Kiran Kumar, Christina A Castellani, Richard O’Reilly, Shiva M. Singh
Software Mentions: 2
Published: over 15 years ago

10.3390/genes12091388

A Recurrent De Novo Terminal Duplication of 14q32 in Korean Siblings Associated with Developmental Delay and Intellectual Disability, Growth Retardation, Facial Dysmorphism, and Cerebral Infarction: A Case Report and Literature Review
Cited by: 2
Author(s): Ji Yoon Han, Joonhong Park
Software Mentions: 2
Published: almost 5 years ago

10.18632/genesandcancer.113

Pathway analysis of bladder cancer genome-wide association study identifies novel pathways involved in bladder cancer development
Cited by: 12
Author(s): Meng Chen, Nathaniel Rothman, Yuanqing Ye, Jian Gu, Paul Scheet, Maosheng Huang, David W. Chang, Colin P.N. Dinney, Debra T. Silverman, Jonine D. Figueroa, Stephen J. Chanock, Xifeng Wu
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0243791

PEREGRINE: A genome-wide prediction of enhancer to gene relationships supported by experimental evidence
Cited by: 9
Author(s): Caitlin Mills, Anushya Muruganujan, Dustin Ebert, Crystal N. Marconett, Juan Pablo Lewinger, Paul D. Thomas
Software Mentions: 2
Published: over 5 years ago

10.1002/dvg.22963

Transcriptional regulation of the proto‐oncogeneZfp521by SPI1 (PU.1) and HOXC13
Cited by: 11
Author(s): Ming Yu, Salma Aldallal, Latifa Al‐Haj, Shiraj Panjwani, Akina S. McCartney, Sarah Edwards, Pooja Manjunath, Catherine Walker, Alexander Awgulewitsch, Kathryn E. Hentges
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0082499

Metabolomics Coupled with Multivariate Data and Pathway Analysis on Potential Biomarkers in Gastric Ulcer and Intervention Effects of Corydalis yanhusuo Alkaloid
Cited by: 30
Author(s): Tianjiao Li, Shuai Wang, Xin-He Meng, Yong-Rui Bao, Shanshan Guan, Bo Liu, Chen Lü, Lei Wang, Xiaorong Ran
Software Mentions: 2
Published: over 12 years ago

10.1186/s12711-020-0528-9

pCADD: SNV prioritisation in Sus scrofa
Cited by: 16
Author(s): Christian Groß, Martijn F.L. Derks, Hendrik Jan Megens, Mirte Bosse, M.A.M. Groenen, Marcel J. T. Reinders, Dick de Ridder
Software Mentions: 2
Published: over 6 years ago

10.1534/genetics.115.185363

Novel Intronic RNA Structures Contribute to Maintenance of Phenotype in Saccharomyces cerevisiae
Cited by: 27
Author(s): Katarzyna B. Hooks, Samina Naseeb, Steven J. Parker, Sam Griffiths-Jones, Daniela Delneri
Software Mentions: 2
Published: about 10 years ago

10.1186/gb-2006-7-7-r58

Cited by: 22
Author(s): Matthew D. Wilkerson, Shannon D. Schlueter, Volker Brendel
Software Mentions: 2
Published: over 20 years ago

10.1186/gb-2006-7-s1-s9

Cited by: 59
Author(s): Jonathan Allen, William H. Majoros, Mihaela Pertea, Steven L. Salzberg
Software Mentions: 2
Published: over 20 years ago

10.1371/journal.pone.0006146

Molecular Profiling of Breast Cancer Cell Lines Defines Relevant Tumor Models and Provides a Resource for Cancer Gene Discovery
Cited by: 647
Author(s): Jennifer L. Kao, Keyan Salari, Melanie Bocanegra, Yoon‐La Choi, Luc Girard, Jeet Gandhi, Kevin Kwei, Tina Hernandez‐Boussard, Pei Wang, Adi F. Gazdar, John D. Minna, Jonathan R. Pollack
Software Mentions: 2
Published: about 17 years ago

10.1038/srep33779

SMAR1 binds to T(C/G) repeat and inhibits tumor progression by regulating miR-371-373 cluster
Cited by: 12
Author(s): Jinumary Mathai, Smriti Mittal, Aftab Alam, Payal Ranade, Devraj Mogare, Sonal Patel, Smita Saxena, Suvankar Ghorai, Abhijeet Kulkarni, Samit Chattopadhyay
Software Mentions: 2
Published: almost 10 years ago

10.1186/1471-2164-16-S8-S2

Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction
Cited by: 68
Author(s): Adam Frankish, Barbara Uszczyńska, Graham R. S. Ritchie, Jose M. Gonzalez, Dmitri D. Pervouchine, Robert Petryszak, Jonathan M. Mudge, Nuno A. Fonseca, Alvis Brāzma, Roderic Guigó, Jennifer Harrow
Software Mentions: 2
Published: about 11 years ago

10.1186/1471-2148-11-267

Visualization and Exploration of Conserved Regulatory Modules Using ReXSpecies 2
Cited by: 4
Author(s): Stephan Struckmann, Daniel Esch, Hans R. Schöler, Georg Fuellen
Software Mentions: 2
Published: almost 15 years ago

10.1038/srep41598

Genome-wide Regulatory Roles of the C2H2-type Zinc Finger Protein ZNF764 on the Glucocorticoid Receptor
Cited by: 14
Author(s): Abeer A. Fadda, Najeeb Syed, Rafah Mackeh, Anna Papadopoulou, Shigeru Suzuki, Puthen V. Jithesh, Tomoshige Kino
Software Mentions: 2
Published: over 9 years ago

10.1038/srep41474

Genome-wide DNA methylation reprogramming in response to inorganic arsenic links inhibition of CTCF binding, DNMT expression and cellular transformation
Cited by: 29
Author(s): Matthew Rea, Meredith Eckstein, Rebekah Eleazer, Caroline N. Smith, Yvonne Fondufe‐Mittendorf
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pgen.1006754

Transcription facilitated genome-wide recruitment of topoisomerase I and DNA gyrase
Cited by: 52
Author(s): Wareed Ahmed, Claudia Sala, Shubhada R. Hegde, Rajiv Kumar Jha, Stewart T. Cole, Valakunja Nagaraja
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pgen.1000081

Genomic Profiling Identifies GATA6 as a Candidate Oncogene Amplified in Pancreatobiliary Cancer
Cited by: 94
Author(s): Kevin Kwei, Murali D. Bashyam, Jennifer L. Kao, Raman Ratheesh, E. Chandrakanth Reddy, Young H. Kim, Kelli Montgomery, Craig P. Giacomini, Yoon La Choi, Sreejata Chatterjee, Collins Karikari, Keyan Salari, Pei Wang, Tina Hernandez‐Boussard, G Swarnalata, Matt van de Rijn, Anirban Maitra, Jonathan R. Pollack
Software Mentions: 2
Published: about 18 years ago

10.1371/journal.pgen.1002641

Patterns of Ancestry, Signatures of Natural Selection, and Genetic Association with Stature in Western African Pygmies
Cited by: 121
Author(s): Joseph P. Jarvis, Laura B. Scheinfeldt, Sameer Soi, Charla Lambert, Larsson Omberg, Bart Ferwerda, Alain Froment, Jean-Marie Bodo, William Beggs, Gabriel E. Hoffman, Jason G. Mezey, Sarah A. Tishkoff
Software Mentions: 2
Published: over 14 years ago

10.1038/s41598-017-14336-6

Unravelling pathways downstream Sox6 induction in K562 erythroid cells by proteomic analysis
Cited by: 6
Author(s): Gloria Barbarani, Antonella Ronchi, Margherita Ruoppolo, Lucia Santorelli, Robert S. Steinfelder, Sudharshan Elangovan, Cristina Fugazza, Marianna Caterino
Software Mentions: 2
Published: almost 9 years ago

10.18632/oncotarget.27806

CPEB1 orchestrates a fine-tuning of miR-145-5p tumor-suppressive activity on TWIST1 translation in prostate cancer cells
Cited by: 5
Author(s): Fatemeh Rajabi, Win Yan Liu-Bordes, Marina Pinskaya, Dominika Foretek, Gueorgui Kratassiouk, Guillaume Pinna, Simona Nanni, Antonella Farsetti, Christian Gespach, Arturo Londoño-Vallejo, Irina Groisman
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-018-37294-z

STAT3 is activated in multicellular spheroids of colon carcinoma cells and mediates expression of IRF9 and interferon stimulated genes
Cited by: 7
Author(s): Elin Edsbäcker, Jason T. Serviss, Iryna Kolosenko, Caroline Palm-Apergi, Angelo De Milito, Katja Pokrovskaja Tamm
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-018-36927-7

High Quality ATAC-Seq Data Recovered from Cryopreserved Breast Cell Lines and Tissue
Cited by: 23
Author(s): Saori Fujiwara, Songjoon Baek, Lyuba Varticovski, Sohyoung Kim, Gordon L. Hager
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-018-37678-1

Intelectin 3 is dispensable for resistance against a mycobacterial infection in zebrafish (Danio rerio)
Cited by: 11
Author(s): Markus Ojanen, Meri Uusi-Mäkelä, Sanna-Kaisa E. Harjula, Anni Saralahti, Kaisa Oksanen, Niklas Kähkönen, Juha Määttä, Vesa P. Hytönen, Marko Pesu, Mika Rämet
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1002390

Identification of Evolutionarily Conserved Exons as Regulated Targets for the Splicing Activator Tra2β in Development
Cited by: 61
Author(s): Sushma Nagaraja Grellscheid, Caroline Dalgliesh, Markus Storbeck, Andrew Best, Yilei Liu, Miriam Jakubik, Ylva Mende, Ingrid Ehrmann, Tomaž Curk, Kristina Roßbach, Cyril F. Bourgeois, James Stévenin, David Grellscheid, Michael S. Jackson, Brunhilde Wirth, David J. Elliott
Software Mentions: 2
Published: over 14 years ago

10.1038/s41598-019-43292-6

Identification of regulatory variants associated with genetic susceptibility to meningococcal disease
Cited by: 3
Author(s): Lisa Borghini, Eileen Png, Alexander Binder, Victoria J. Wright, Ellie Pinnock, Ronald de Groot, Jan A. Hazelzet, Marieke Emonts, Michiel van der Flier, Luregn J Schlapbach, Suzanne T. Anderson, Fatou Secka, Antonio Salas, Colin G. Fink, Enitan D. Carrol, Andrew J. Pollard, Lachlan Coin, Taco W. Kuijpers, Federico Martinón‐Torres, Werner Zenz, Michael Levin, Martin L. Hibberd, Sonia Dávila
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-43403-3

Recognition of 3′-end L1, Alu, processed pseudogenes, and mRNA stem-loops in the human genome using sequence-based and structure-based machine-learning models
Cited by: 0
Author(s): Alexander Shein, Anton Zaikin, Maria Poptsova
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2164-14-611

Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes
Cited by: 159
Author(s): James R. Doroghazi, William W. Metcalf
Software Mentions: 2
Published: over 13 years ago

10.1186/1748-7188-6-4

Fast local fragment chaining using sum-of-pair gap costs
Cited by: 14
Author(s): Christian Otto, Steve Hoffmann, Jan Gorodkin, Peter F. Stadler
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0005008

Transcriptional Network of p63 in Human Keratinocytes
Cited by: 42
Author(s): Silvia Pozzi, Federico Zambelli, Daniele Merico, Giulio Pavesi, Amélie Robert, Peggy Maltère, Xavier Gidrol, Roberto Mantovani, M. Alessandra Viganò
Software Mentions: 2
Published: over 17 years ago

10.1371/journal.pone.0074132

Evolutionary Genomics and Adaptive Evolution of the Hedgehog Gene Family (Shh, Ihh and Dhh) in Vertebrates
Cited by: 25
Author(s): Joana Pereira, Warren E. Johnson, Stephen J. O’Brien, Erich D. Jarvis, Guojie Zhang, M. Thomas P. Gilbert, Vı́tor Vasconcelos, Agostinho Antunes
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pgen.1000163

Deep Sequencing Analysis of Small Noncoding RNA and mRNA Targets of the Global Post-Transcriptional Regulator, Hfq
Cited by: 518
Author(s): Alexandra Sittka, Sacha Lucchini, Kai Papenfort, Cynthia M. Sharma, Katarzyna Rolle, Tim T. Binnewies, Jay C. D. Hinton, Jörg Vogel
Software Mentions: 2
Published: almost 18 years ago

10.1038/s41598-020-57753-w

Evolutionary history of DNA methylation related genes in chordates: new insights from multiple whole genome duplications
Cited by: 20
Author(s): Jingwei Liu, Huihua Hu, Stéphane Panserat, Lucie Marandel
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2164-15-765

Liver transcriptome analysis in gilthead sea bream upon exposure to low temperature
Cited by: 80
Author(s): Alba Nicoletta Mininni, Massimo Milan, Serena Ferraresso, T. Petochi, Patrizia Di Marco, G. Marino, Silvia Livi, Chiara Romualdi, Luca Bargelloni, Tomaso Patarnello
Software Mentions: 2
Published: almost 12 years ago

10.1186/1471-2148-9-85

Origin and evolution of the RIG-I like RNA helicase gene family
Cited by: 224
Author(s): Jun Zou, Ming Chang, Pin Nie, Chris J. Secombes
Software Mentions: 2
Published: over 17 years ago

10.1371/journal.pone.0086822

DNA Methylation Signature of Childhood Chronic Physical Aggression in T Cells of Both Men and Women
Cited by: 80
Author(s): Claire Guillemin, Nadine Provençal, Matthew Suderman, Sylvana M. Côté, Frank Vitaro, Michael Hallett, Richard E. Tremblay, Moshe Szyf
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0209096

Genome-wide association study (GWAS) of ovarian cancer in Japanese predicted regulatory variants in 22q13.1
Cited by: 8
Author(s): Varalee Yodsurang, Yaqi Tang, Yusuke Takahashi, Chizu Tanikawa, Yoichiro Kamatani, Atsushi Takahashi, Yukihide Momozawa, Nobuo Fuse, Junichi Sugawara, Atsushi Shimizu, Akimune Fukushima, Asahi Hishida, Norihiro Furusyo, Mariko Naito, Kenji Wakai, Taiki Yamaji, Norie Sawada, Motoki Iwasaki, Shoichiro Tsugane, Makoto Hirata, Yoshinori Murakami, Michiaki Kubo, Koichi Matsuda
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2105-8-320

Apollo2Go: a web service adapter for the Apollo genome viewer to enable distributed genome annotation
Cited by: 6
Author(s): Kathrin Klee, Rebecca Ernst, Manuel Spannagl, Klaus Mayer
Software Mentions: 2
Published: almost 19 years ago

10.1038/s41598-020-74687-5

Evaluation of blood gene expression levels in facioscapulohumeral muscular dystrophy patients
Cited by: 10
Author(s): Mirko Signorelli, Amanda G. Mason, Karlien Mul, Teresinha Evangelista, Hailiang Mei, N.C. Voermans, Stephen J. Tapscott, Roula Tsonaka, B.G.M. van Engelen, Silvère M. van der Maarel, Pietro Spitali
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pgen.1008827

Population genetic models of GERP scores suggest pervasive turnover of constrained sites across mammalian evolution
Cited by: 53
Author(s): Christian D. Huber, Bernard Kim, Kirk E. Lohmueller
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pgen.1005947

Integrative Tissue-Specific Functional Annotations in the Human Genome Provide Novel Insights on Many Complex Traits and Improve Signal Prioritization in Genome Wide Association Studies
Cited by: 91
Author(s): Qiongshi Lu, Ryan L. Powles, Qian Wang, B. Julie He, Hongyu Zhao
Software Mentions: 2
Published: over 10 years ago

10.1098/rsob.160197

SBE6: a novel long-range enhancer involved in driving sonic hedgehog expression in neural progenitor cells
Cited by: 15
Author(s): Nezha S. Benabdallah, Philippe Gautier, Betül Hekimoglu-Balkan, Laura A. Lettice, Shipra Bhatia, Wendy A. Bickmore
Software Mentions: 2
Published: almost 10 years ago

10.1038/s41598-020-78907-w

Genome-wide association identifies several QTLs controlling cysteine and methionine content in soybean seed including some promising candidate genes
Cited by: 11
Author(s): Sidiki Malle, Milad Eskandari, Malcolm J. Morrison, François Belzile
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2105-11-10

MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement
Cited by: 52
Author(s): Guanqun Shi, Liqing Zhang, Tao Jiang
Software Mentions: 2
Published: over 16 years ago

10.1038/s41598-021-81387-1

Analysis of ovarian transcriptomes reveals thousands of novel genes in the insect vector Rhodnius prolixus
Cited by: 17
Author(s): Vitor Lima Coelho, Tarcísio Fontenele de Brito, Ingrid Alexandre de Abreu Brito, Maira Arruda Cardoso, Mateus Berni, Helena Araujo, Michael Sammeth, Andrea Pane
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-015-1533-1

Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea
Cited by: 17
Author(s): Gustavo Rodríguez-Esteban, Alejandro González-Sastre, José Ignacio Rojo-Laguna, Emili Saló, Josep F. Abril
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2148-9-207

Whole genome duplications and expansion of the vertebrate GATA transcription factor gene family
Cited by: 47
Author(s): William J. Gillis, John St. John, Bruce Bowerman, Stephan Schneider
Software Mentions: 2
Published: about 17 years ago

10.1038/s41598-021-90422-0

Simplification of culture conditions and feeder-free expansion of bovine embryonic stem cells
Cited by: 24
Author(s): Delia Alba Soto, Micaela Navarro, Canbin Zheng, Michelle M. Halstead, Chuan Zhou, Carly Guiltinan, Jun Wu, Pablo J. Ross
Software Mentions: 2
Published: about 5 years ago

10.1186/s12864-015-1414-7

The salinity tolerant poplar database (STPD): a comprehensive database for studying tree salt-tolerant adaption and poplar genomics
Cited by: 7
Author(s): Ying Ma, Ting Xu, Dongshi Wan, Tao Ma, Shengjun Shi, Jianquan Liu, Quanjun Hu
Software Mentions: 2
Published: over 11 years ago

10.1186/s12859-020-03806-w

oposSOM-Browser: an interactive tool to explore omics data landscapes in health science
Cited by: 10
Author(s): Henry Loeffler‐Wirth, Jasmin Reikowski, Siras Hakobyan, Jonas Wagner, Hans Binder
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0012315

A Critical Analysis of Atoh7 (Math5) mRNA Splicing in the Developing Mouse Retina
Cited by: 15
Author(s): Lev Prasov, Nadean L. Brown, Thomas Gläser
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.pgen.0020024

SPA: A Probabilistic Algorithm for Spliced Alignment
Cited by: 25
Author(s): Erik van Nimwegen, Nicodème Paul, Robert P. Sheridan, Mihaela Zavolan
Software Mentions: 2
Published: over 20 years ago

10.1098/rsob.190150

Multivariable regulation of gene expression plasticity in metazoans
Cited by: 11
Author(s): Long Xiao, Zhiguang Zhao, Fei He, Zhuo Du
Software Mentions: 2
Published: over 6 years ago

10.3390/s18082633

PHAROS—PHysical Assistant RObot System
Cited by: 42
Author(s): Ângelo Costa, Ester Martínez-Martín, Miguel Cazorla, Vicente Julián
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pgen.1006700

Probing the canonicity of the Wnt/Wingless signaling pathway
Cited by: 37
Author(s): Alexandra Franz, Daria Shlyueva, Erich Brunner, Alexander Stark, Konrad Basler
Software Mentions: 2
Published: over 9 years ago

10.1186/s13029-015-0032-8

LocusTrack: Integrated visualization of GWAS results and genomic annotation
Cited by: 28
Author(s): Gabriel Cuéllar-Partida, Miguel E. Renteriá, Stuart MacGregor
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2105-10-215

Regression based predictor for p53 transactivation
Cited by: 7
Author(s): Sivakumar Gowrisankar, Anil G. Jegga
Software Mentions: 2
Published: about 17 years ago

10.1186/1471-2156-12-27

PoPoolation DB: a user-friendly web-based database for the retrieval of natural polymorphisms in Drosophila
Cited by: 10
Author(s): Ram Vinay Pandey, Robert Kofler, Pablo Orozco‐terWengel, Viola Nolte, Christian Schlötterer
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pgen.1001116

Identifying Signatures of Natural Selection in Tibetan and Andean Populations Using Dense Genome Scan Data
Cited by: 484
Author(s): Abigail W. Bigham, Marc Bauchet, Dalila Pinto, Xiaole Mao, Joshua M. Akey, Rui Mei, Stephen W. Scherer, Colleen G. Julian, Megan J. Wilson, David López Herráez, Tom D. Brutsaert, Esteban J. Parra, Lorna G. Moore, Mark D. Shriver
Software Mentions: 2
Published: almost 16 years ago

10.1186/s13287-019-1270-5

The long non-coding RNA Snhg3 is essential for mouse embryonic stem cell self-renewal and pluripotency
Cited by: 16
Author(s): Weisi Lu, Jianping Yu, Fang Shi, Jianing Zhang, Rui Huang, Shanshan Yin, Zhou Songyang, Junjiu Huang
Software Mentions: 2
Published: about 7 years ago

10.1002/stem.2294

Jun-Mediated Changes in Cell Adhesion Contribute to Mouse Embryonic Stem Cell Exit from Ground State Pluripotency
Cited by: 16
Author(s): Giulia Veluscek, Yaoyong Li, Shen-Hsi Yang, Andrew D. Sharrocks
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2105-13-206

CaPSID: A bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes
Cited by: 39
Author(s): Ivan Borozan, Shane Wilson, Paola Blanchette, Philippe Laflamme, Stuart Watt, Paul M. Krzyzanowski, Fabrice Sircoulomb, Robert Rottapel, Philip E. Branton, Vincent Ferretti
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pntd.0000543

Anti-schistosomal Intervention Targets Identified by Lifecycle Transcriptomic Analyses
Cited by: 117
Author(s): Jennifer M. Fitzpatrick, Emily Peak, Samïrah Perally, Iain W. Chalmers, John Barrett, Timothy P. Yoshino, Alasdair Ivens, Karl F. Hoffmann
Software Mentions: 2
Published: almost 17 years ago

10.7150/thno.47039

Comprehensive characterization of functional eRNAs in lung adenocarcinoma reveals novel regulators and a prognosis-related molecular subtype
Cited by: 18
Author(s): Na Qin, Zijuan Ma, Cheng Wang, Erbao Zhang, Yuancheng Li, Mingtao Huang, Congcong Chen, Chang Zhang, Jingyi Fan, Yayun Gu, Xin Xu, Yang Liu, Xiaoxia Wei, Rong Yin, Yue Jiang, Juncheng Dai, Guangfu Jin, Lin Xu, Hongbing Shen, Hongxia Ma
Software Mentions: 2
Published: over 6 years ago

10.7150/thno.48744

Proteasome activator PA200 maintains stability of histone marks during transcription and aging
Cited by: 14
Author(s): Tiancai Jiang, Shuang Ma, Xia Han, Zi-Yu Luo, Qianqian Zhu, Tomoki Chiba, Wei Xie, Kui Lin, Xiao‐Bo Qiu
Software Mentions: 2
Published: over 5 years ago

10.7150/thno.51931

Functional roles of antisense enhancer RNA for promoting prostate cancer progression
Cited by: 22
Author(s): Chun-Wu Pan, Simeng Wen, Lei Chen, Yulei Wei, Yuanjie Niu, Yu Zhao
Software Mentions: 2
Published: over 5 years ago

10.7150/thno.53170

Tanshinone I, a new EZH2 inhibitor restricts normal and malignant hematopoiesis through upregulation of MMP9 and ABCG2
Cited by: 22
Author(s): Ying Huang, Shanhe Yu, Wenxuan Zhen, Cheng Tien, Dan Wang, Jiebo Lin, Yuxin Wu, Yifan Wang, Yi Chen, Liping Shu, Yi Wang, Xiao Jian Sun, Yi Zhou, Fan Yang, Chih-Hung Hsu, Pengfei Xu
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1008694

WHIMP links the actin nucleation machinery to Src-family kinase signaling during protrusion and motility
Cited by: 7
Author(s): Shail Kabrawala, Margaret D. Zimmer, Kenneth Campellone
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-017-04642-4

Korean Variant Archive (KOVA): a reference database of genetic variations in the Korean population
Cited by: 56
Author(s): Sang Moon Lee, Jihae Seo, Jinman Park, Jae Yong Nam, Ahyoung Choi, Jason S. Ignatius, Robert Bjornson, Jong Hee Chae, In Jin Jang, Sanghyuk Lee, Woong-Yang Park, Daehyun Baek, Murim Choi
Software Mentions: 2
Published: about 9 years ago

10.1038/s41398-020-00966-4

Integration of postmortem amygdala expression profiling, GWAS, and functional cell culture assays: neuroticism-associated synaptic vesicle glycoprotein 2A (SV2A) gene is regulated by miR-133a and miR-218
Cited by: 9
Author(s): Magdalena Jurkiewicz, Dirk Moser, Antonius Koller, Lei Yu, Emily I. Chen, David A. Bennett, Turhan Canli
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41398-020-01056-1

Identification of candidate genetic variants and altered protein expression in neural stem and mature neural cells support altered microtubule function to be an essential component in bipolar disorder
Cited by: 12
Author(s): Katarina Truvé, Toshima Z. Parris, Dzeneta Vizlin‐Hodzic, Susanne Salmela, Evelin Berger, Hans Ǻgren, Keiko Funa
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0202369

Genome-wide identification of clusters of predicted microRNA binding sites as microRNA sponge candidates
Cited by: 13
Author(s): Xiaoyong Pan, Anne Wenzel, Lars Juhl Jensen, Jan Gorodkin
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0063925

Comprehensive Functional Annotation of Seventy-One Breast Cancer Risk Loci
Cited by: 42
Author(s): Suhn Kyong Rhie, Simon Coetzee, Houtan Noushmehr, Chunli Yan, Jae Mun Kim, Christopher A. Haiman
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0031092

The Pseudomonas aeruginosa Transcriptome in Planktonic Cultures and Static Biofilms Using RNA Sequencing
Cited by: 208
Author(s): Andreas Dötsch, Denitsa Eckweiler, Monika Schniederjans, Ariane Zimmermann, Vanessa Jensen, Maren Scharfe, Robert Geffers, Susanne Häußler
Software Mentions: 2
Published: over 14 years ago

10.1186/s12920-015-0087-z

Systems biology of myasthenia gravis, integration of aberrant lncRNA and mRNA expression changes
Cited by: 19
Author(s): Zhaohui Luo, Ye Li, Xiaofang Liu, Mingyao Luo, Liqun Xu, Yue‐Bei Luo, Bo Xiao, Huan Yang
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pntd.0007871

GSMN-ML- a genome scale metabolic network reconstruction of the obligate human pathogen Mycobacterium leprae
Cited by: 8
Author(s): Khushboo Borah, Jacque-Lucca Kearney, Ruma Banerjee, Pankaj Vats, Huihai Wu, Sonal Dahale, Sunitha Manjari Kasibhatla, Rajendra Joshi, Bhushan Bonde, Olabisi Ojo, Ramanuj Lahiri, Diana L. Williams, Johnjoe McFadden
Software Mentions: 2
Published: about 6 years ago

10.1128/mBio.02367-19

Combination of Proteogenomics with Peptide De Novo Sequencing Identifies New Genes and Hidden Posttranscriptional Modifications
Cited by: 37
Author(s): Bernhard Blank‐Landeshammer, Ines Teichert, Ramona Märker, Minou Nowrousian, Ulrich Kück, Albert Sickmann
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pgen.1008977

Systematic identification of functional SNPs interrupting 3’UTR polyadenylation signals
Cited by: 21
Author(s): Eldad D. Shulman, Ran Elkon
Software Mentions: 2
Published: about 6 years ago

10.1186/1471-2172-9-7

The Innate Immune Database (IIDB)
Cited by: 44
Author(s): Martin Korb, Alistair G. Rust, Vésteinn Thórsson, Christophe Battail, Bin Li, Daehee Hwang, Kathleen A. Kennedy, Jared C. Roach, Carrie M. Rosenberger, Mark Gilchrist, Daniel E. Zak, Carrie D. Johnson, Bruz Marzolf, Alan Aderem, Ilya Shmulevich, Hamid Bolouri
Software Mentions: 2
Published: over 18 years ago

10.1371/journal.pgen.1005050

Complex Genomic Rearrangements at the PLP1 Locus Include Triplication and Quadruplication
Cited by: 52
Author(s): Christine R. Beck, Claudia M.B. Carvalho, Linda Banser, Tomasz Gambin, Danielle Stubbolo, Bo Yuan, Karen Sperle, Suzanne M. McCahan, Marco Henneke, Pavel Seeman, James Garbern, Grace M. Hobson, James R. Lupski
Software Mentions: 2
Published: over 11 years ago

10.1007/s00439-017-1838-z

Enrichment of putatively damaging rare variants in the DYX2 locus and the reading-related genes CCDC136 and FLNC
Cited by: 8
Author(s): Andrew Adams, Shelley D. Smith, Dongnhu T. Truong, Erik G. Willcutt, Richard K. Olson, John C. DeFries, Bruce F. Pennington, Jeffrey R. Gruen
Software Mentions: 2
Published: almost 9 years ago

10.1007/s00439-014-1454-0

A single codon insertion in PICALM is associated with development of familial subvalvular aortic stenosis in Newfoundland dogs
Cited by: 13
Author(s): Joshua A. Stern, Stephen N. White, Linda B. Lehmkuhl, Yamir Reina-Doreste, Jordan L. Ferguson, Nanette Nascone‐Yoder, Kathryn M. Meurs
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pgen.1001134

Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome
Cited by: 461
Author(s): Robert S. Illingworth, Ulrike Gruenewald-Schneider, Shaun Webb, Alastair Kerr, Keith James, Daniel J. Turner, Colin Smith, David J. Harrison, Robert Andrews, Adrian Bird
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.pone.0006971

Genomic Analysis Suggests that mRNA Destabilization by the Microprocessor Is Specialized for the Auto-Regulation of Dgcr8
Cited by: 45
Author(s): Archana Shenoy, Robert Blelloch
Software Mentions: 2
Published: almost 17 years ago

10.1186/s12859-021-04359-2

Anomaly detection in genomic catalogues using unsupervised multi-view autoencoders
Cited by: 0
Author(s): Quentin Ferré, Jeanne Chèneby, Denis Puthier, Cécile Capponi, Benoît Ballester
Software Mentions: 2
Published: almost 5 years ago

10.1186/s40246-021-00342-3

Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism
Cited by: 11
Author(s): Evin M. Padhi, Tristan J. Hayeck, Cheng Zhang, Satadal Chatterjee, Brandon J. Mannion, Marta Byrska-Bishop, Marjolaine Willems, Lucile Pinson, Sylvia Redon, Caroline Bénech, Kévin Uguen, Séverine Audebert‐Bellanger, Cédric Le Marechal, Claude Férec, Stéphanie Efthymiou, Fatima Rahman, Shazia Maqbool, Reza Maroofian, Henry Houlden, Rajeeva Musunuri, Giuseppe Narzisi, Avinash Abhyankar, Riana D Hunter, Jennifer A. Akiyama, Lauren Fries, Jeffrey Ng, Elvisa Mehinovic, Nicholas Stong, Andrew S. Allen, Diane E. Dickel, Raphael Bernier, David U. Gorkin, L Pennacchio, Michael C. Zody, Tychele N. Turner
Software Mentions: 2
Published: about 5 years ago

10.1128/JVI.00919-14

Unfixed Endogenous Retroviral Insertions in the Human Population
Cited by: 110
Author(s): Emanuele Marchi, Alexander Kanapin, Gkikas Magiorkinis, Robert Belshaw
Software Mentions: 2
Published: almost 12 years ago

10.1093/hmg/ddv272

Homozygous loss-of-function variants in European cosmopolitan and isolate populations
Cited by: 25
Author(s): Vera B. Kaiser, Victoria Svinti, James Prendergast, You-Ying Chau, Archie Campbell, Inga Patarčić, Inês Barroso, Peter K. Joshi, Nicholas D. Hastie, Ana Miljković, Martin S. Taylor, Generation Scotland, Uk K, Stefan Enroth, Yasin Memari, Anja Kolb-Kokocinski, Alan F. Wright, Ulf Gyllensten, Richard Durbin, Igor Rudan, Harry Campbell, Ozren Polašek, Åsa Johansson, Sascha Sauer, David J. Porteous, Ross M. Fraser, Camilla Drake, Véronique Vitart, Caroline Hayward, Colin A. Semple, James F. Wilson
Software Mentions: 2
Published: about 11 years ago

10.1002/humu.22842

Facilitating Collaboration in Rare Genetic Disorders Through Effective Matchmaking in DECIPHER
Cited by: 35
Author(s): Eleni A. Chatzimichali, Simon Brent, Benjamin Hutton, Daniel Perrett, Caroline F. Wright, A. Paul Bevan, Matthew E. Hurles, Helen V. Firth, Ganesh Swaminathan
Software Mentions: 2
Published: about 11 years ago

10.1002/humu.22471

A 129-kb Deletion on Chromosome 12 Confers Substantial Protection Against Rheumatoid Arthritis, Implicating the GeneSLC2A3
Cited by: 21
Author(s): Colin Veal, Katherine Reekie, Johnny C. Lorentzen, Peter K. Gregersen, Leonid Padyukov, Anthony J. Brookes
Software Mentions: 2
Published: over 12 years ago

10.1002/humu.22594

Genetic Variations and Diseases in UniProtKB/Swiss‐Prot: The Ins and Outs of Expert Manual Curation
Cited by: 49
Author(s): Maria Livia Famiglietti, Anne Estreicher, Arnaud Gos, Jerven Bolleman, Sébastien Géhant, Lionel Breuza, Alan Bridge, Sylvain Poux, Nicole Redaschi, Lydie Bougueleret, Ioannis Xénarios
Software Mentions: 2
Published: about 12 years ago

10.1093/humrep/deab099

Exome sequencing reveals variants in known and novel candidate genes for severe sperm motility disorders
Cited by: 28
Author(s): Manon S Oud, Brendan J Houston, Ludmila Voložonoka, Francesco K. Mastrorosa, Giles Holt, Bilal Alobaidi, P F deVries, Galuh D.N. Astuti, Liliana Ramos, Robert I McLachlan, Moira K O'Bryan, Joris A. Veltman, H Chemes, Harsh Sheth
Software Mentions: 2
Published: about 5 years ago

10.1186/s12860-021-00378-2

Construction and characterization of EGFP reporter plasmid harboring putative human RAX promoter for in vitro monitoring of retinal progenitor cells identity
Cited by: 2
Author(s): Atefeh Atefi, Pendar Shojaei kojouri, Fereshteh Karamali, Shiva Irani, Mohammad Hossein Nasr-Esfahani
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pgen.1004885

Interactions of Chromatin Context, Binding Site Sequence Content, and Sequence Evolution in Stress-Induced p53 Occupancy and Transactivation
Cited by: 49
Author(s): Dan Su, Xuting Wang, Michelle R. Campbell, Lingyun Song, Alexias Safi, Gregory E. Crawford, Douglas A. Bell
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2105-13-253

G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes
Cited by: 15
Author(s): Danielle G. Lemay, William Martin, Angie S. Hinrichs, Monique Rijnkels, J. Bruce German, Ian F Korf, Katherine S. Pollard
Software Mentions: 2
Published: almost 14 years ago

10.3390/jof7080600

Transcription Factors in the Fungus Aspergillus nidulans: Markers of Genetic Innovation, Network Rewiring and Conflict between Genomics and Transcriptomics
Cited by: 6
Author(s): Oier Etxebeste
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pgen.1004507

KDM6 Demethylase Independent Loss of Histone H3 Lysine 27 Trimethylation during Early Embryonic Development
Cited by: 94
Author(s): Karl B. Shpargel, Joshua Starmer, Della Yee, Michael Pohlers, Terry Magnuson
Software Mentions: 2
Published: about 12 years ago

10.1038/s41598-017-07514-z

Assessment of imprinting- and genetic variation-dependent monoallelic expression using reciprocal allele descendants between human family trios
Cited by: 7
Author(s): Trees‐Juen Chuang, Yu-Hsiang Tseng, Chia-Ying Chen, Yi-Da Wang
Software Mentions: 2
Published: about 9 years ago

10.3892/ijo.2012.1724

Epigenetic silencing of miR-335 and its host gene MEST in hepatocellular carcinoma
Cited by: 70
Author(s): Osamu Dohi, Kohichiroh Yasui, Yasuyuki Gen, Hisashi Takada, Mio Endo, Kazuhiro Tsuji, Chika Konishi, Naotaka Yamada, Hironori Mitsuyoshi, Nobuaki Yagi, Yuji Naito, Shinji Tanaka, Shigeki Arii, Toshikazu Yoshikawa
Software Mentions: 2
Published: over 13 years ago

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