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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

10.1186/1471-2105-10-215

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

10.3390/ijms19061722

Systematic Analysis of Long Non-Coding RNAs and mRNAs in the Ovaries of Duroc Pigs During Different Follicular Stages Using RNA Sequencing
Cited by: 30
Author(s): Yi Liu, Mengxun Li, Xiaochen Bo, Tao Li, Ligeng Ma, Tenjiao Zhai, Tao Huang
Software Mentions: 2
Published: about 8 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

10.3390/ijms21061908

Peripheral Circulating Exosomal miRNAs Potentially Contribute to the Regulation of Molecular Signaling Networks in Aging
Cited by: 13
Author(s): Hongxia Zhang, Kunlin Jin
Software Mentions: 2
Published: over 6 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

10.3390/ijms21165831

BrassicaEDB: A Gene Expression Database for Brassica Crops
Cited by: 37
Author(s): Haoyu Chao, Li Tian, Chaoyu Luo, Hualei Huang, Yingfei Ruan, Xiaodong Li, Yue Niu, Yonghai Fan, Wei Sun, Kai Zhang, Jiana Li, Cunmin Qu, Kun Lü
Software Mentions: 2
Published: about 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

10.3390/ijms21249701

Origin and Evolution of the Human Bcl2-Associated Athanogene-1 (BAG-1)
Cited by: 4
Author(s): Peter Q. Nguyen, Kyle Hess, Larissa Smulders, Dat Le, Carolina Briseno, Christina M Chavez, Nikolas Nikolaidis
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22020602

Transposable Elements and Teleost Migratory Behaviour
Cited by: 8
Author(s): Elisa Carotti, Federica Carducci, Adriana Canapa, Marco Barucca, Samuele Greco, Marco Gerdol, Maria Assunta Biscotti
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22168646

PPARγ-Induced Global H3K27 Acetylation Maintains Osteo/Cementogenic Abilities of Periodontal Ligament Fibroblasts
Cited by: 7
Author(s): Hang Yuan, Shigeki Suzuki, Shizu Hirata-Tsuchiya, Akiko Satô, Eiji Nemoto, Masahiro Saito, Hideki Shiba, Satoru Yamada
Software Mentions: 2
Published: about 5 years ago

10.2196/jmir.9644

Online Information Infrastructure Increases Inter-Rater Reliability of Medical Coders: A Quasi-Experimental Study (Preprint)
Cited by: 6
Author(s): Julian Varghese, Sarah Sandmann, Martin Dugas
Software Mentions: 2
Published: over 8 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

10.2196/10227

What People “Like”: Analysis of Social Media Strategies Used by Food Industry Brands, Lifestyle Brands, and Health Promotion Organizations on Facebook and Instagram
Cited by: 106
Author(s): Karen Klassen, Emily S. Borleis, Louis Brennan, Mike Reid, Tracy A. McCaffrey, Megan S C Lim
Software Mentions: 2
Published: about 8 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

10.1371/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

10.1186/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

10.1016/j.isci.2020.101741

The PWWP2A Histone Deacetylase Complex Represses Intragenic Spurious Transcription Initiation in mESCs
Cited by: 8
Author(s): Guifeng Wei, Neil Brockdorff, Tianyi Zhang
Software Mentions: 2
Published: almost 6 years ago

10.18632/oncotarget.8612

Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress
Cited by: 57
Author(s): Seajin Oh, Ryan A. Flynn, Stephen N. Floor, James Purzner, Lance Martin, T. Brian, Simone Schubert, Dedeepya Vaka, A. Sorana Morrissy, Yisu Li, Marcel Kool, Volker Hovestadt, David Jones, Paul A. Northcott, Thomas S. Risch, Hans Jörg Warnatz, Marie Laure Yaspo, Christopher M. Adams, Ryan D. Leib, Marcus R. Breese, Marco A. Marra, David Malkin, Peter Lichter, Jennifer A. Doudna, Stefan M. Pfister, Michael D. Taylor, Howard Y. Chang, Yoon Jae Cho
Software Mentions: 2
Published: over 10 years ago

10.18632/oncotarget.9674

Expression and functional characterization of CD33 transcript variants in human acute myeloid leukemia
Cited by: 37
Author(s): George S. Laszlo, Kimberly H. Harrington, Chelsea J. Gudgeon, Mary E. Beddoe, Matthew Fitzgibbon, Rhonda E. Ries, Jatinder K. Lamba, Martin W. McIntosh, Soheil Meshinchi, Roland B. Walter
Software Mentions: 2
Published: over 10 years ago

10.18632/oncotarget.11506

AIRE polymorphism, melanoma antigen-specific T cell immunity, and susceptibility to melanoma
Cited by: 8
Author(s): Giuseppina Conteduca, Daniela Fenoglio, Alessia Parodi, Florinda Battaglia, Francesca Kalli, Simone Negrini, Samuele Tardito, Francesca Ferrera, Annalisa Salis, Enrico Millo, Giuseppe Pasquale, Giusi Barra, Gianluca Damonte, Francesco Indiveri, Soldano Ferrone, Gilberto Filaci
Software Mentions: 2
Published: about 10 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

10.18632/oncotarget.12508

ZSCAN5B and primate-specific paralogs bind RNA polymerase III genes and extra-TFIIIC (ETC) sites to modulate mitotic progression
Cited by: 4
Author(s): Younguk Sun, Huimin Zhang, Majid Kazemian, Joseph M. Troy, Christopher H. Seward, Xing Lü, Lisa Stubbs
Software Mentions: 2
Published: almost 10 years ago

10.18632/oncotarget.14098

Cervical small cell neuroendocrine tumor mutation profiles via whole exome sequencing
Cited by: 24
Author(s): Soo Young Cho, Minhye Choi, Hyo Jeong Ban, Chang Hyeon Lee, Soojun Park, Han Kyeom Kim, Young Sik Kim, Young Seek Lee, Ji Yun Lee
Software Mentions: 2
Published: over 9 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

10.18632/oncotarget.14150

AML associated oncofusion proteins PML-RARA, AML1-ETO and CBFB-MYH11 target RUNX/ETS-factor binding sites to modulate H3ac levels and drive leukemogenesis
Cited by: 23
Author(s): Abhishek A. Singh, Amit Mandoli, K.H.M. Prange, Marko Laakso, Joost H.A. Martens
Software Mentions: 2
Published: over 9 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

10.18632/oncotarget.17107

Epigenetic silencing of triple negative breast cancer hallmarks by Withaferin A
Cited by: 49
Author(s): Katarzyna Szarc vel Szic, Ken Declerck, René A. J. Crans, Jolien Diddens, David Scherf, Clarissa Gerhäuser, Wim Vanden Berghe
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pgen.1009290

Natural variation in temperature-modulated immunity uncovers transcription factor bHLH059 as a thermoresponsive regulator in Arabidopsis thaliana
Cited by: 19
Author(s): Friederike Bruessow, Jaqueline Bautor, Gesa Hoffmann, Ipek Yildiz, Jürgen Zeier, Jane E. Parker
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1008026

Quantitative mapping of DNA phosphorothioatome reveals phosphorothioate heterogeneity of low modification frequency
Cited by: 13
Author(s): Jinli Li, Yi Chen, Tao Zheng, Lingxin Kong, Sucheng Zhu, Yihua Sun, Zixin Deng, Litao Yang, Delin You
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1007581

Cooperation, cis-interactions, versatility and evolutionary plasticity of multiple cis-acting elements underlie krox20 hindbrain regulation
Cited by: 20
Author(s): Patrick Torbey, Elodie Thierion, Samuel Collombet, Anne De Cian, Carole Desmarquet-Trin-Dinh, Mathilde Dura, Jean-Paul Concordet, Patrick Charnay, Pascale Gilardi-Hebenstreit
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pgen.1005709

Reciprocal Effects on Neurocognitive and Metabolic Phenotypes in Mouse Models of 16p11.2 Deletion and Duplication Syndromes
Cited by: 110
Author(s): Thomas Arbogast, Abdel‐Mouttalib Ouagazzal, Claire Chevalier, Maksym V. Kopanitsa, Nurudeen O. Afinowi, Eugenia Migliavacca, Belinda S. Cowling, Marie‐Christine Birling, Marie‐France Champy, Alexandre Reymond, Yann Hérault
Software Mentions: 2
Published: over 10 years ago

10.1038/s41598-017-06351-4

Integrin α6β4 Upregulates Amphiregulin and Epiregulin through Base Excision Repair-Mediated DNA Demethylation and Promotes Genome-wide DNA Hypomethylation
Cited by: 9
Author(s): Brittany L. Carpenter, Jinpeng Liu, Lei Qi, Chi Wang, Kathleen L. O’Connor
Software Mentions: 2
Published: about 9 years ago

10.1186/1471-2105-11-119

Prodigal: prokaryotic gene recognition and translation initiation site identification
Cited by: 7,098
Author(s): Doreene R. Hyatt, Gwo Liang Chen, Philip F. LoCascio, Miriam Land, Frank W. Larimer, Loren Hauser
Software Mentions: 2
Published: over 16 years ago

10.18632/oncotarget.25536

Prostate cancer susceptibility gene HIST1H1A is a modulator of androgen receptor signaling and epithelial to mesenchymal transition
Cited by: 6
Author(s): Kendra A. Williams, Minnkyong Lee, Jean M. Winter, Derek Gildea, Carla Calagua, Natasha Curry, Jens Lichtenberg, Huihui Ye, Nigel P.S. Crawford
Software Mentions: 2
Published: about 8 years ago

10.1186/s12881-016-0359-2

Sacral agenesis: a pilot whole exome sequencing and copy number study
Cited by: 15
Author(s): Robert M. Porsch, Elisa Merello, Patrizia De Marco, Gregory Yin Ming Cheng, Laura Rodriguez, Man-Ting So, Pak C. Sham, Paul Kwong Hang Tam, Valeria Capra, Stacey S. Cherny, Maria Mercè García-Barceló, Desmond Campbell
Software Mentions: 2
Published: almost 10 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

10.1371/journal.pgen.1009613

A combinatorial cis-regulatory logic restricts color-sensing Rhodopsins to specific photoreceptor subsets in Drosophila
Cited by: 4
Author(s): Clara Poupault, Diane Choi, Khanh Lam-Kamath, Deepshe Dewett, Ansa Razzaq, Joseph Bunker, Alexis Perry, Irene Cho, Jens Rister
Software Mentions: 2
Published: about 5 years ago

10.1186/1471-2105-13-2

ABrowse - a customizable next-generation genome browser framework
Cited by: 18
Author(s): Lei Kong, Jun Wang, Shuqi Zhao, Xiaocheng Gu, Jianxun Luo, Ge Gao
Software Mentions: 2
Published: over 14 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

10.1186/1471-2105-9-21

LeARN: a platform for detecting, clustering and annotating non-coding RNAs
Cited by: 10
Author(s): Céline Noirot, Christine Gaspin, Thomas Schiex, Jérôme Gouzy
Software Mentions: 2
Published: over 18 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: almost 7 years ago

10.1371/journal.pgen.1005946

MiR144/451 Expression Is Repressed by RUNX1 During Megakaryopoiesis and Disturbed by RUNX1/ETO
Cited by: 17
Author(s): Nicole Kohrs, Stephan Kolodziej, Olga N. Kuvardina, Julia Herglotz, Jasmin Yillah, Stefanie Herkt, Alexander Piechatzek, Gabriela Salinas Riester, Thomas Lingner, Christian Wichmann, Halvard Bönig, Erhard Seifried, Uwe Platzbecker, Hind Medyouf, Manuel Grez, Jörn Lausen
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pgen.1008036

LINE-2 transposable elements are a source of functional human microRNAs and target sites
Cited by: 42
Author(s): Rebecca Petri, Per Ludvik Brattås, Yogita Sharma, Marie E. Jönsson, Karolina Pircs, Johan Bengzon, Johan Jakobsson
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1005702

Fmrp Interacts with Adar and Regulates RNA Editing, Synaptic Density and Locomotor Activity in Zebrafish
Cited by: 70
Author(s): Adi Shamay-Ramot, Khen Khermesh, Hagit T. Porath, Michal Barák, Yishay Pinto, Chaim Wachtel, Alona Zilberberg, Tali Lerer-Goldshtein, Sol Efroni, Erez Y. Levanon, Lior Appelbaum
Software Mentions: 2
Published: almost 11 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: about 12 years ago

10.1371/journal.pgen.1002384

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome
Cited by: 892
Author(s): A. P. Jason de Koning, Wanjun Gu, Todd A. Castoe, Mark A. Batzer, David D. Pollock
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pgen.1006682

Wnt/Tcf1 pathway restricts embryonic stem cell cycle through activation of the Ink4/Arf locus
Cited by: 37
Author(s): Anchel de Jaime-Soguero, Francesco Aulicino, Gökhan Ertaylan, Anna Griego, Aniello Cerrato, Aravind Tallam, Antonio del Sol, María Pía Cosma, Frederic Lluı́s
Software Mentions: 2
Published: over 9 years ago

10.1186/1755-8794-2-31

Identification of gene co-regulatory modules and associated cis-elements involved in degenerative heart disease
Cited by: 8
Author(s): Charles G. Danko, Arkady M. Pertsov
Software Mentions: 2
Published: over 17 years ago

10.1371/journal.pgen.1006296

Genome-Wide Interaction Analyses between Genetic Variants and Alcohol Consumption and Smoking for Risk of Colorectal Cancer
Cited by: 37
Author(s): Jian Gong, Carolyn M. Hutter, Polly A. Newcomb, Cornelia M. Ulrich, Stephanie A. Bien, Peter T. Campbell, John A. Baron, Sonja I. Berndt, Stéphane Bézieau, Hermann Brenner, Graham Casey, Andrew T. Chan, Jenny Chang–Claude, Mengmeng Du, David Duggan, Jane C. Figueiredo, Steven Gallinger, Edward Giovannucci, Robert W. Haile, Tabitha A. Harrison, Richard B. Hayes, Michael Hoffmeister, John L. Hopper, Thomas J. Hudson, Jihyoun Jeon, Mark A. Jenkins, Jonathan Kocarnik, Sébastien Küry, Loı̈c Le Marchand, Yi Lin, Noralane M. Lindor, Reiko Nishihara, Shuji Ogino, John D. Potter, Anja Rudolph, Robert E. Schoen, Petra Schrotz‐King, Daniela Seminara, Martha L. Slattery, Stephen N. Thibodeau, Mark Thornquist, Réka Tóth, Robert B. Wallace, Emily White, Shuo Jiao, Mathieu Lemire, Li Hsu, Ulrike Peters
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pgen.1000672

Genetic Determinants of Circulating Sphingolipid Concentrations in European Populations
Cited by: 185
Author(s): Andrew A. Hicks, Peter P. Pramstaller, Åsa Johansson, Véronique Vitart, Igor Rudan, Péter Ugocsai, Yurii S. Aulchenko, Christopher S. Franklin, Gerhard Liebisch, Jeanette Erdmann, Inger Jonasson, Irina V. Zorkoltseva, Cristian Pattaro, Caroline Hayward, Aaron Isaacs, Christian Hengstenberg, Susan Campbell, Carsten Gnewuch, A. Cecile J.W. Janssens, A. V. Kirichenko, Inke R. König, Fabio Marroni, Ozren Polašek, Ayşe Demirkan, Ivana Kolčić, Christine Schwienbacher, Wilmar Igl, Zrinka Biloglav, Jacqueline C. M. Witteman, Irene Pichler, Ghazal Zaboli, Tatiana I. Axenovich, Annette Peters, Stefan Schreiber, H‐Erich Wichmann, Heribert Schunkert, Nick Hastie, Ben A. Oostra, Sarah H. Wild, Thomas Meitinger, Ulf Gyllensten, Cornelia M. van Duijn, James F. Wilson, Alan F. Wright, Gerd Schmitz, Harry Campbell
Software Mentions: 2
Published: almost 17 years ago

10.1186/s12920-021-01007-9

Epigenetic landscapes of intracranial aneurysm risk haplotypes implicate enhancer function of endothelial cells and fibroblasts in dysregulated gene expression
Cited by: 5
Author(s): Kerry E. Poppenberg, Haley R Zebraski, Naval Avasthi, Muhammad Waqas, Adnan H. Siddiqui, James N. Jarvis, Vincent M. Tutino
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pgen.1005117

Asymmetric Transcript Discovery by RNA-seq in C. elegans Blastomeres Identifies neg-1, a Gene Important for Anterior Morphogenesis
Cited by: 20
Author(s): Erin Osborne Nishimura, Jay C. Zhang, Adam D. Werts, Bob Goldstein, Jason D. Lieb
Software Mentions: 2
Published: over 11 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

10.1371/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.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

10.3390/nu5051706

Genome-Wide Association Study of Serum Selenium Concentrations
Cited by: 9
Author(s): Jian Gong, Li Hsu, Tabitha A. Harrison, Irena B. King, Stefan Stürup, Xiaoling Song, David Duggan, Yan Liu, Carolyn M. Hutter, Stephen J. Chanock, Charles B. Eaton, James R. Marshall, Ulrike Peters
Software Mentions: 1
Published: over 13 years ago

10.1038/s41598-017-03067-3

Identification of the functional variant driving ORMDL3 and GSDMB expression in human chromosome 17q12-21 in primary biliary cholangitis
Cited by: 23
Author(s): Yuki Hitomi, Kazuyuki Kojima, M. Kawashima, Yosuke Kawai, Nao Nishida, Yoshihiro Aiba, Michio Yasunami, Masao Nagasaki, Minoru Nakamura, Katsushi Tokunaga
Software Mentions: 1
Published: about 9 years ago

10.1038/s41598-017-04657-x

Genetic targeting and anatomical registration of neuronal populations in the zebrafish brain with a new set of BAC transgenic tools
Cited by: 56
Author(s): Dominique Förster, Irene Arnold-Ammer, Eva Laurell, Alison J. Barker, António M. Fernandes, Karin Finger‐Baier, Alessandro Filosa, Thomas O. Helmbrecht, Yvonne Kölsch, Enrico Kühn, Estuardo Robles, Krasimir Slanchev, Tod R. Thiele, Herwig Baier, Fumi Kubo
Software Mentions: 1
Published: about 9 years ago

10.1038/s41598-017-10339-5

The PDK1 Inhibitor Dichloroacetate Controls Cholesterol Homeostasis Through the ERK5/MEF2 Pathway
Cited by: 23
Author(s): Asaad Khan, Nerea Allende-Vega, Delphine Gitenay, Sabine Gerbal‐Chaloin, Claire Gondeau, Dang Nghiem Vo, Sana Belkahla, Stefania Orecchioni, Giovanna Talarico, Francesco Bertolini, Milica Božić, José M. Valdivielso, Fabienne Bejjani, Isabelle Jariel, Isabel C. López-Mejía, Lluís Fajas, Charles-Henri Lecellier, Javier Hernandez, Martine Daujat, Martín Villalba
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-017-12532-y

SHH signaling directed by two oral epithelium-specific enhancers controls tooth and oral development
Cited by: 22
Author(s): Tomoko Sagai, Takanori Amano, Akiteru Maeno, Hiroshi Kanazawa, Hye-Jin Seo, Sung Won Cho, Toshihiko Shiroishi
Software Mentions: 1
Published: almost 9 years ago

10.1007/s13205-012-0063-7

Vertebrate patatin-like phospholipase domain-containing protein 4 (PNPLA4) genes and proteins: a gene with a role in retinol metabolism
Cited by: 7
Author(s): Roger S. Holmes
Software Mentions: 1
Published: over 14 years ago

10.1007/s13205-011-0013-9

Genomics and proteomics of vertebrate cholesterol ester lipase (LIPA) and cholesterol 25-hydroxylase (CH25H)
Cited by: 32
Author(s): Roger S. Holmes, John L. VandeBerg, Laura A. Cox
Software Mentions: 1
Published: about 15 years ago

10.1042/AN20130029

Increased Binding of Stroke-Induced Long Non-Coding RNAs to the Transcriptional Corepressors Sin3A and coREST
Cited by: 67
Author(s): Ashutosh Dharap, Courtney Pokrzywa, Raghu Vemuganti
Software Mentions: 1
Published: about 13 years ago

10.1155/2014/259382

Structural Differences Observed in Arboviruses of the Alphavirus and Flavivirus Genera
Cited by: 18
Author(s): Raquel Hernandez, Dennis T. Brown, Angel Paredes
Software Mentions: 1
Published: over 12 years ago

10.18632/aging.101671

A CREB1/miR-433 reciprocal feedback loop modulates proliferation and metastasis in colorectal cancer
Cited by: 31
Author(s): Yan Li, Weiqiang You, Nengquan Sheng, Jianfeng Gong, Landian Hu, Gewen Tan, Hongqi Chen, Zhigang Wang
Software Mentions: 1
Published: over 7 years ago

10.18632/aging.101470

Integrated DNA methylation and gene expression analysis identifies SLAMF7 as a key regulator of atherosclerosis
Cited by: 13
Author(s): Zhangyong Xia, Minghong Gu, Xiaodong Jia, Xiaoting Wang, Chunxia Wu, Jiangwen Guo, Liyong Zhang, Yifeng Du, Jiyue Wang
Software Mentions: 1
Published: about 8 years ago

10.1111/acel.12607

The PPARγ-SETD8 axis constitutes an epigenetic, p53-independent checkpoint on p21-mediated cellular senescence
Cited by: 21
Author(s): Chieh Tien Shih, Ian Yi‐Feng Chang, Yi Tung Chen, Chung Pei, Hui-Wen Chen, Chang Ching Yang, Juu Chin Lu, Yau Sheng Tsai, Hua Chien Chen, Bertrand Chin‐Ming Tan
Software Mentions: 1
Published: over 9 years ago

10.1186/s13015-019-0158-3

TMRS: an algorithm for computing the time to the most recent substitution event from a multiple alignment column
Cited by: 0
Author(s): Hisanori Kiryu, Yuto Ichikawa, Yasuhiro Kojima
Software Mentions: 1
Published: almost 7 years ago

10.1186/1748-7188-6-2

WordCluster: detecting clusters of DNA words and genomic elements
Cited by: 19
Author(s): Michael Hackenberg, Pedro Carpena, Pedro Bernaola‐Galván, Guillermo Barturen, Ángel M. Alganza, José Luis Tejera Oliver
Software Mentions: 1
Published: over 15 years ago

10.1016/j.ajhg.2018.11.004

GWAS Identifies Risk Locus for Erectile Dysfunction and Implicates Hypothalamic Neurobiology and Diabetes in Etiology
Cited by: 36
Author(s): Jonas Bovijn, Leigh Jackson, Jenny C Censin, Chia‐Yen Chen, Triin Laisk, Samantha Laber, Teresa Ferreira, Sara L. Pulit, Craig A. Glastonbury, Jordan W. Smoller, Jamie Harrison, Katherine S. Ruth, Robin N Beaumont, Samuel E. Jones, Jessica Tyrrell, Andrew R. Wood, Michael N. Weedon, Reedik Mägi, Benjamin M. Neale, Cecilia M. Lindgren, Anna Murray, Michael V. Holmes
Software Mentions: 1
Published: over 7 years ago

10.1152/ajpendo.00580.2012

Decreased expression of the satiety signal receptor CCKAR is responsible for increased growth and body weight during the domestication of chickens
Cited by: 59
Author(s): Ian Dunn, Simone Meddle, Peter W.F. Wilson, Chloe A. Wardle, Andy Law, Valerie Bishop, Camilla Hindar, Gavin Robertson, David W. Burt, Stephanie J. Ellison, David Morrice, Paul Hocking
Software Mentions: 1
Published: over 13 years ago

10.4269/ajtmh.15-0049

Population Genetics, Evolutionary Genomics, and Genome-Wide Studies of Malaria: A View Across the International Centers of Excellence for Malaria Research
Cited by: 13
Author(s): Jane M. Carlton, Sarah K. Volkman, Swapna Uplekar, Daniel Hupalo, João M. P. Alves, Liwang Cui, Martin J. Donnelly, David S. Roos, Omar S. Harb, Mónica Mancero Acosta, Andrew C. Read, Paulo Eduardo Martins Ribolla, O. P. Singh, Neena Valecha, Samuel C. Wassmer, Marcelo U. Ferreira, Ananías A. Escalante
Software Mentions: 1
Published: about 11 years ago

10.1111/andr.12476

The <scp>SET</scp> protein promotes androgen production in testicular Leydig cells
Cited by: 5
Author(s): B. Zhang, Wei Ma, Qun Zhu, Wei Xu, Lingling Gao, Boqun Xu, Shunqing Xu, Chunfang Gao, J. Liu, Yugui Cui
Software Mentions: 1
Published: over 8 years ago

10.1007/s10456-017-9542-0

RCAN1.4 regulates VEGFR-2 internalisation, cell polarity and migration in human microvascular endothelial cells
Cited by: 51
Author(s): Ahmad F. Alghanem, Emma L. Wilkinson, Maxine S. Emmett, Mohammad Aljasir, Katherine Holmes, Beverley A. Rothermel, Victoria A. Simms, Victoria L. Heath, Michael Cross
Software Mentions: 1
Published: over 9 years ago

10.1093/aobpla/plt011

Microscopic elucidation of abundant endophytic bacteria colonizing the cell wall–plasma membrane peri-space in the shoot-tip tissue of banana
Cited by: 56
Author(s): Pious Thomas, K. Madhavi Reddy
Software Mentions: 1
Published: over 13 years ago

10.1186/ar3515

Interleukin-1, tumor necrosis factor-alpha, and transforming growth factor-beta 1 and integrative meniscal repair: influences on meniscal cell proliferation and migration
Cited by: 52
Author(s): Katherine M. Riera, Nicole E. Rothfusz, Rebecca E. Wilusz, J. Brice Weinberg, Farshid Guilak, Amy L. McNulty
Software Mentions: 1
Published: over 15 years ago

10.1186/ar1700

Cited by: 3
Author(s): Lars Andersson, Greta Petersen, Per Johnson, Fredrik Ståhl
Software Mentions: 1
Published: over 21 years ago

10.1186/1471-2105-15-S1-S8

AnnotateGenomicRegions: a web application
Cited by: 8
Author(s): Luca Zammataro, Rita DeMolfetta, Gabriele Bucci, Arnaud Céol, Heiko Mul̈ler
Software Mentions: 1
Published: over 12 years ago

10.1186/s12859-018-2247-6

CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata
Cited by: 9
Author(s): Syed Ahmad Chan Bukhari, Marcos Martínez-Romero, Martin J. O’ Connor, Attila L. Egyedi, Debra Willrett, John Graybeal, Mark A. Musen, Kei‐Hoi Cheung, Steven H. Kleinstein
Software Mentions: 1
Published: about 8 years ago

10.1186/1471-2105-7-S5-S4

Large-scale analysis of antigenic diversity of T-cell epitopes in dengue virus
Cited by: 35
Author(s): Mohammad Asif Khan, A. T. Heiny, Kenneth X. Lee, Kellathur N. Srinivasan, Tin Wee Tan, J. Thomas August, Vladimir Brusic
Software Mentions: 1
Published: almost 20 years ago

10.1186/1471-2105-10-59

The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation
Cited by: 32
Author(s): Sandra N. Loevenich, Erich Brunner, Nichole L. King, Eric W. Deutsch, Stephen E. Stein, Ruedi Aebersold, Ernst Hafen
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2105-14-167

Identifying cancer mutation targets across thousands of samples: MuteProc, a high throughput mutation analysis pipeline
Cited by: 2
Author(s): Alireza Hadj Khodabakhshi, Anthony P. Fejes, İnanç Birol, Steven J.M. Jones
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2105-10-S15-S3

Gevab: a prototype genome variation analysis browsing server
Cited by: 2
Author(s): Woo-Yeon Kim, Sang Yoon Kim, TaeHyung Kim, Sung‐Min Ahn, Ha Na Byun, Deokhoon Kim, Dae-Soo Kim, Yong Seok Lee, Ho Ghang, Daeui Park, Byoung-Chul Kim, Chulhong Kim, Sung-Hoon Lee, Seong‐Jin Kim, Jong Bhak
Software Mentions: 1
Published: almost 17 years ago

10.1186/s12859-017-1846-y

RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement
Cited by: 26
Author(s): Maninder Sandhu, V. Sureshkumar, Chandra Prakash, Rekha Dixit, Amolkumar U. Solanke, Tilak Raj Sharma, Trilochan Mohapatra, S. V. Amitha Mithra
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2105-11-S1-S14

Prediction of novel miRNAs and associated target genes in Glycine max
Cited by: 106
Author(s): Trupti Joshi, Zhe Yan, Marc Libault, Dong‐Hoon Jeong, Sunhee Park, Pamela J. Green, D. Janine Sherrier, Andrew Farmer, Greg May, Blake C. Meyers, Dong Xu, Gary Stacey
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2105-14-S17-A17

FPD2GB2: Automating a transition from a customized genome browser to GBrowse2
Cited by: 1
Author(s): Roger G. Chui, Jerzy W. Jaromczyk, Neil Moore, Christopher L. Schardl
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2105-13-S3-S6

Detection of gene expression changes at chromosomal rearrangement breakpoints in evolution
Cited by: 8
Author(s): Adriana Muñoz, David Sankoff
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2105-11-29

miRMaid: a unified programming interface for microRNA data resources
Cited by: 17
Author(s): Anders Jacobsen, Anders Krogh, Sakari Kauppinen, Morten Lindow
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2105-14-289

Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data
Cited by: 197
Author(s): Thorfinn Sand Korneliussen, Ida Moltke, Anders Albrechtsen, Rasmus Nielsen
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2105-13-187

ParsEval: parallel comparison and analysis of gene structure annotations
Cited by: 24
Author(s): Daniel Standage, Volker Brendel
Software Mentions: 1
Published: about 14 years ago

10.1186/1471-2105-6-S1-S17

An evaluation of GO annotation retrieval for BioCreAtIvE and GOA
Cited by: 153
Author(s): Evelyn Camon, Daniel Barrell, Emily Dimmer, Vivian Lee, Michele Magrane, John Maslen, David Binns, Rolf Apweiler
Software Mentions: 1
Published: over 21 years ago

10.1186/1471-2105-9-549

nGASP – the nematode genome annotation assessment project
Cited by: 65
Author(s): Avril Coghlan, Tristan J. Fiedler, Sheldon McKay, Paul Flicek, Todd W. Harris, Darin Blasiar, Lincoln Stein
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2105-11-238

A database and API for variation, dense genotyping and resequencing data
Cited by: 37
Author(s): Daniel Ríos, William McLaren, Yuan Chen, Ewan Birney, Arne Stabenau, Paul Flicek, Fiona Cunningham
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2105-9-S8-S3

Integrating biological data – the Distributed Annotation System
Cited by: 82
Author(s): Andy Jenkinson, Mario Albrecht, Ewan Birney, Hagen Blankenburg, Thomas A. Down, Alex Bateman, Henning Hermjakob, Tim Hubbard, Rafael C. Jiménez, Philip Jones, Andreas Kähäri, Eugene Kulesha, José Ramón Macías, Gabrielle A. Reeves, Andreas Prlić
Software Mentions: 1
Published: about 18 years ago

10.1186/s12859-021-04090-y

Low-level variant calling for non-matched samples using a position-based and nucleotide-specific approach
Cited by: 0
Author(s): Jeffrey N. Dudley, Celine Hong, Marwan A. Hawari, Jasmine Shwetar, Julie C. Sapp, Justin Lack, Henoke Shiferaw, Jennifer J. Johnston, Leslie G. Biesecker
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2105-16-S13-S1

Proceedings of the 2015 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference
Cited by: 0
Author(s): Jonathan D. Wren, Shraddha Thakkar, Ramin Homayouni, Donald J. Johann, Mikhail G. Dozmorov
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12859-015-0673-2

GESPA: classifying nsSNPs to predict disease association
Cited by: 6
Author(s): Jay K. Khurana, Jay E. Reeder, Antony E. Shrimpton, Juilee Thakar
Software Mentions: 1
Published: about 11 years ago

Projects: pypi: browser

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Papers Mentioning browser 2,125