pypi: picard | Projects | Ecosyste.ms: Papers

10.1186/s40659-020-00282-7

Functional and genomic characterization of three novel cell lines derived from a metastatic gallbladder cancer tumor
Cited by: 4
Author(s): Patricia García, Carolina Bizama, Lorena Rosa, Jaime A. Espinoza, Helga Weber, Javier Cerda‐Infante, Marianela Sánchez, Viviana P. Montecinos, Justo Lorenzo Bermejo, Felix Boekstegers, Marcela Dávila-López, Francisca Alfaro, Claudia Leiva-Acevedo, Zasha Parra, Diego Romero, Sumie Kato, Pamela Leal, Marcela Lagos, Juan Carlos Roa
Software Mentions: 3
Published: over 4 years ago

10.1002/cam4.436

Feasibility of implementing molecular‐guided therapy for the treatment of patients with relapsed or refractory neuroblastoma
Cited by: 24
Author(s): Giselle L. Saulnier Sholler, Jeffrey P. Bond, Genevieve Bergendahl, Akshita Dutta, Julie A. Dragon, Kathleen Neville, William S. Ferguson, William Roberts, Don Eslin, Jacqueline M. Kraveka, Joel A. Kaplan, Deanna Mitchell, Nehal S. Parikh, Melinda S. Merchant, Takamaru Ashikaga, Gina Hanna, Pamela J. Lescault, Ashley L. Siniard, Jason J. Corneveaux, Matthew J. Huentelman, Jeffrey M. Trent
Software Mentions: 3
Published: over 9 years ago

10.1111/mec.15367

Temporal dynamics of migration‐linked genetic variation are driven by streamflows and riverscape permeability
Cited by: 18
Author(s): Suzanne J. Kelson, Michael R. Miller, Tasha Q. Thompson, Sean O’Rourke, Stephanie M. Carlson
Software Mentions: 3
Published: almost 5 years ago

10.1111/1755-0998.12328

Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among<scp>H</scp>ymenoptera
Cited by: 221
Author(s): Brant C. Faircloth, Michael G. Branstetter, Noor D. White, Seán G. Brady
Software Mentions: 3
Published: about 10 years ago

10.1093/ve/veaa010

Linking influenza virus evolution within and between human hosts
Cited by: 39
Author(s): Katherine S Xue, Jesse D. Bloom
Software Mentions: 3
Published: almost 5 years ago

10.3390/v13050836

Phylogenetic Analysis of the 2020 West Nile Virus (WNV) Outbreak in Andalusia (Spain)
Cited by: 12
Author(s): Carlos S. Casimiro-Soriguer, Javier Pérez-Florido, Jose L. Fernández-Rueda, Irene Pedrosa-Corral, Vicente Guillot-Sulay, Nicola Lorusso, Luis Javier Martínez-González, José María Navarro-Marí, Joaquı́n Dopazo, Sara Sanbonmatsu‐Gámez
Software Mentions: 3
Published: over 3 years ago

10.3390/plants9101390

Prediction of Dhurrin Metabolism by Transcriptome and Metabolome Analyses in Sorghum
Cited by: 5
Author(s): Sang Chul Choi, Yong‐Suk Chung, Yun Gyeong Lee, Yuna Kang, Yun Ji Park, Sang Un Park, Changsoo Kim
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pbio.2002039

Dual role of starvation signaling in promoting growth and recovery
Cited by: 17
Author(s): Yonat Gurvich, Dena Leshkowitz, Naama Barkai
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0207936

Gene expression is implicated in the ability of pikas to occupy Himalayan elevational gradient
Cited by: 9
Author(s): Katherine A. Solari, Uma Ramakrishnan, Elizabeth A. Hadly
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0098187

Next-Generation Sequencing of RNA and DNA Isolated from Paired Fresh-Frozen and Formalin-Fixed Paraffin-Embedded Samples of Human Cancer and Normal Tissue
Cited by: 277
Author(s): Jakob Hedegaard, Kasper Thorsen, Mette K. Lund, Anne-Mette K. Hein, Stephen Hamilton-Dutoit, Søren Vang, Iver Nordentoft, Karin Birkenkamp‐Demtröder, Mogens Kruhøffer, Henrik Hager, Bjarne Knudsen, Claus Lindbjerg Andersen, Karina D. Sørensen, Jakob Skou Pedersen, Torben F. Ørntoft, Lars Dyrskjøt
Software Mentions: 3
Published: over 10 years ago

10.3390/cells9010090

PP2A Deficiency Enhances Carcinogenesis of Lgr5+ Intestinal Stem Cells Both in Organoids and In Vivo
Cited by: 3
Author(s): Yu–Ting Yen, May B. Chien, Yung-Chih Lai, Dao-Peng Chen, Cheng‐Ming Chuong, Mien‐Chie Hung, Shih‐Chieh Hung
Software Mentions: 3
Published: almost 5 years ago

10.3390/cells10061349

Targeting Mitochondrial Damage as a Therapeutic for Ileal Crohn’s Disease
Cited by: 11
Author(s): Kibrom M. Alula, Dakota N. Jackson, Andrew D. Smith, Daniel S. Kim, Kevin Turner, Elizabeth Odstrcil, Benny Abraham Kaipparettu, Themistocles Dassopoulos, K. Venuprasad, Linda A. Feagins, Arianne L. Theiss
Software Mentions: 3
Published: over 3 years ago

10.1016/j.cub.2021.06.023

Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment
Cited by: 21
Author(s): Pere Gelabert, Susanna Sawyer, Anders Bergström, Ashot Margaryan, Thomas C. Collin, Tengiz Meshveliani, Anna Belfer‐Cohen, David Lordkipanidze, Nino Jakeli, Zinovi Matskevich, Guy Bar-Oz, Daniel Fernandes, Olivia Cheronet, Kadir T. Özdoğan, Victoria Oberreiter, Robin N. M. Feeney, Mareike Cordula Stahlschmidt, Pontus Skoglund, Ron Pinhasi
Software Mentions: 3
Published: over 3 years ago

10.1186/s13072-016-0105-1

Targeted bisulfite sequencing of the dynamic DNA methylome
Cited by: 21
Author(s): Michael J. Ziller, Elena K. Stamenova, Hongcang Gu, Andreas Gnirke, Alexander Meissner
Software Mentions: 3
Published: almost 8 years ago

10.2807/1560-7917.ES.2019.24.50.1900130

Towards standardisation: comparison of five whole genome sequencing (WGS) analysis pipelines for detection of epidemiologically linked tuberculosis cases
Cited by: 32
Author(s): Rana Jajou, Thomas A. Kohl, Timothy M Walker, Anders Norman, Daniela María Cirillo, Elisa Tagliani, Stefan Niemann, Albert J. de Neeling, Troels Lillebæk, Richard Anthony, Dick van Soolingen
Software Mentions: 3
Published: almost 5 years ago

10.3389/fgene.2019.00508

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

10.3389/fimmu.2018.02985

CD47 Expression in Natural Killer Cells Regulates Homeostasis and Modulates Immune Response to Lymphocytic Choriomeningitis Virus
Cited by: 43
Author(s): Pulak Nath, Arunakumar Gangaplara, Dipasmita Pal-Nath, Ajeet Mandal, Dragan Maric, John M. Sipes, Maggie Cam, Ethan M. Shevach, D. A. Roberts
Software Mentions: 3
Published: almost 6 years ago

10.3389/fmicb.2020.01994

Phenotypic Variability in a Coinfection With Three Independent Candida parapsilosis Lineages
Cited by: 10
Author(s): Emilia Gómez-Molero, Jesse R. Willis, Anna Dudakova, Laia Carreté, Michael Weig, Uwe Groß, Attila Gácser, Toni Gabaldón, Oliver Bader
Software Mentions: 3
Published: about 4 years ago

10.3389/fmicb.2020.01579

Contribution of Viral Genomic Diversity to Oyster Susceptibility in the Pacific Oyster Mortality Syndrome
Cited by: 12
Author(s): Jean Delmotte, Cristian Chaparro, Richard Galinier, Julien de Lorgeril, Bruno Petton, Pierre‐Louis Stenger, Jérémie Vidal-Dupiol, D. Destoumieux-Garzón, Yannick Gueguen, Caroline Montagnani, Jean-Michel Escoubas, Guillaume Mitta
Software Mentions: 3
Published: over 4 years ago

10.1534/g3.120.401149

The Genome Sequence of the Jean-Talon Strain, an Archeological Beer Yeast from Québec, Reveals Traces of Adaptation to Specific Brewing Conditions
Cited by: 2
Author(s): Anna Fijarczyk, Mathieu Hénault, Souhir Marsit, Guillaume Charron, Tobias Fischborn, Luc Nicole-Labrie, Christian R. Landry
Software Mentions: 3
Published: about 4 years ago

10.1093/gigascience/giy084

SL-quant: a fast and flexible pipeline to quantify spliced leader trans-splicing events from RNA-seq data
Cited by: 11
Author(s): Carlo Yague-Sanz, Damien Hermand
Software Mentions: 3
Published: over 6 years ago

10.1093/gigascience/giaa121

Unifying package managers, workflow engines, and containers: Computational reproducibility with BioNix
Cited by: 5
Author(s): Justin Bedő, Leon Di Stefano, Anthony T. Papenfuss
Software Mentions: 3
Published: about 4 years ago

10.1242/jcs.247957

BCAT1 affects mitochondrial metabolism independently of leucine transamination in activated human macrophages
Cited by: 25
Author(s): Jeong‐Hun Ko, Antoni Olona, Adonia E. Papathanassiu, Norzawani Buang, Kwon-Sik Park, Ana S.H. Costa, Claudio Mauro, Christian Frezza, Jacques Behmoaras
Software Mentions: 3
Published: almost 5 years ago

10.1038/sdata.2018.146

BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea
Cited by: 33
Author(s): Johannes Alneberg, John Sundh, Christin M. Bennke, Sara Beier, Daniel Lundin, Luisa W. Hugerth, Jarone Pinhassi, Veljo Kisand, Lasse Riemann, Klaus Jürgens, Matthias Labrenz, Anders F. Andersson
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-019-46756-x

Identification and Characterization of Genetic Determinants of Isoniazid and Rifampicin Resistance in Mycobacterium tuberculosis in Southern India
Cited by: 31
Author(s): Asma Munir, Narender Kumar, Suresh Babu Ramalingam, Sembulingam Tamilzhalagan, Siva Kumar Shanmugam, Alangudi Natarajan Palaniappan, Dina Nair, Padma Priyadarshini, Mohan Natarajan, Srikanth Tripathy, Uma Devi Ranganathan, Sharon J. Peacock, Julian Parkhill, Tom L. Blundell, Sony Malhotra
Software Mentions: 3
Published: over 5 years ago

10.1167/iovs.62.7.16

North Carolina Macular Dystrophy: Phenotypic Variability and Computational Analysis of Disease-Associated Noncoding Variants
Cited by: 9
Author(s): David J. Green, Eva Lenassi, Cerys Manning, David McGaughey, Vinod Sharma, Graeme Black, Jamie M Ellingford, Panagiotis I. Sergouniotis
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.58534

Heterogeneity of murine periosteum progenitors involved in fracture healing
Cited by: 48
Author(s): Brya G. Matthews, Sanja Novak, Francesca Sbrana, Jessica L Funnell, Ye Cao, Emma J. Buckels, Danka Grčević, Ivo Kalajzić
Software Mentions: 3
Published: almost 4 years ago

10.7554/eLife.25787

Repression by PRDM13 is critical for generating precision in neuronal identity
Cited by: 34
Author(s): Bishakha Mona, Ana Uruena, Rahul K. Kollipara, Zhenzhong Ma, Mark D. Borromeo, Joshua C. Chang, Jane E. Johnson
Software Mentions: 3
Published: about 7 years ago

10.18632/oncotarget.11524

Subclones in B-lymphoma cell lines: isogenic models for the study of gene regulation
Cited by: 6
Author(s): Hilmar Quentmeier, Claudia Pommerenke, Ole Ammerpohl, Robert Geffers, Vivien Hauer, Roderick A.F. MacLeod, Stefan Nagel, Julia Romani, Emanuela Rosati, Anders Rosén, Cord C. Uphoff, Margarete Zaborski, Hans Drexler
Software Mentions: 3
Published: about 8 years ago

10.3389/fphar.2021.634956

Association Between NR3C1 Mutations and Glucocorticoid Resistance in Children With Acute Lymphoblastic Leukemia
Cited by: 6
Author(s): Haiyan Liu, Ziping Li, Fei Qiu, Chunjie Li, Xiaojing Lin, Yingyi He, Maoxiang Qian, Yuanbin Song, Hui Zhang
Software Mentions: 2
Published: over 3 years ago

10.3389/fpls.2021.642631

Epigenetic Variability Among Saffron Crocus (Crocus sativus L.) Accessions Characterized by Different Phenotypes
Cited by: 13
Author(s): Matteo Busconi, Elisabeth Wischnitzki, Marcello Del Corvo, Licia Colli, Giovanna Soffritti, Lorenzo Stagnati, Silvia Fluch, Eva Maria Sehr, Marcelino de los Mozos Pascual, José Antonio Fernández
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2020.00482

Long-Term Dynamics Among Wolbachia Strains During Thermal Adaptation of Their Drosophila melanogaster Hosts
Cited by: 7
Author(s): Rupert Mazzucco, Viola Nolte, Thapasya Vijayan, Christian Schlötterer
Software Mentions: 2
Published: over 4 years ago

10.1242/jcs.239871

Ciliary proteins specify the cell inflammatory response by tuning NFκB signaling, independently of primary cilia
Cited by: 15
Author(s): Megan Mc Fie, Lada A. Koneva, I. Collins, Clarissa Coveney, Aisling M Clube, Anastasios Chanalaris, Tonia L. Vincent, Jelena S. Bezbradica, Stephen N. Sansom, Angus K. T. Wann
Software Mentions: 2
Published: almost 5 years ago

10.1002/jcla.23896

Application of high‐throughput sequencing for hereditary thrombocytopenia in southwestern China
Cited by: 2
Author(s): Luying Zhang, Juanjuan Yu, Ying Xian, Xiaohong Wen, Xianmin Guan, Yuxia Guo, Ming Luo, Dou Yu
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0241137

Genomic variations and signatures of selection in Wuhua yellow chicken
Cited by: 13
Author(s): Zhuoxian Weng, Yongjie Xu, Weina Li, Jiebo Chen, Ming Zhong, Zhong Fang, Bin Du, Bin Zhang, Xunhe Huang
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.ppat.1007008

Atrophy of skin-draining lymph nodes predisposes for impaired immune responses to secondary infection in mice with chronic intestinal nematode infection
Cited by: 13
Author(s): Xiaogang Feng, Cajsa Classon, Graciela Terán, Yunlong Yang, Lei Li, Sherwin Chan, Ulf Ribacke, Antonio Gigliotti Rothfuchs, Jonathan M. Coquet, Susanne Nylén
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.ppat.1007881

Oxamniquine resistance alleles are widespread in Old World Schistosoma mansoni and predate drug deployment
Cited by: 27
Author(s): Frédéric D. Chevalier, Winka Le Clec’h, Marina McDew-White, Vinay Menon, Meghan A. Guzman, S. Holloway, Xiaoguang Cao, Alexander B. Taylor, Safari Kinung’hi, Anouk N. Gouvras, Bonnie L. Webster, Joanne P. Webster, Aidan M. Emery, David Rollinson, Amadou Garba Djirmay, Khalid M. Al Mashikhi, Salem Al Yafae, Mohamed A. Idris, Hélène Moné, Gabriel Mouahid, P. John Hart, Philip T. LoVerde, Timothy J. Anderson
Software Mentions: 2
Published: about 5 years ago

10.1038/s41416-018-0089-7

Somatic mutations in benign breast disease tissue and risk of subsequent invasive breast cancer
Cited by: 8
Author(s): Thomas E. Rohan, Christopher A. Miller, Tiandao Li, Yihong Wang, Olivier Loudig, Mindy Ginsberg, Andrew G. Glass, Elaine R. Mardis
Software Mentions: 2
Published: over 6 years ago

10.1186/s12918-018-0608-4

The synthetic histone-binding regulator protein PcTF activates interferon genes in breast cancer cells
Cited by: 10
Author(s): Kimberly C. Olney, David B. Nyer, Daniel A. Vargas, Melissa A. Wilson Sayres, Karmella A. Haynes
Software Mentions: 2
Published: about 6 years ago

10.1038/sdata.2017.184

Verification of Arabidopsis stock collections using SNPmatch, a tool for genotyping high-plexed samples
Cited by: 25
Author(s): Rahul Pisupati, Ilka Reichardt, Ümit Seren, Pamela Korte, Viktoria Nizhynska, Envel Kerdaffrec, Kristina Uzunova, Fernando A. Rabanal, Daniele Filiault, Magnus Nordborg
Software Mentions: 2
Published: almost 7 years ago

10.7554/eLife.23813

Human biallelic MFN2 mutations induce mitochondrial dysfunction, upper body adipose hyperplasia, and suppression of leptin expression
Cited by: 56
Author(s): Nuno Rocha, David A Bulger, Andrea Frontini, Hannah Titheradge, Sigrid Bjerge Gribsholt, Rachel Knox, Matthew J. Page, Julie Harris, Felicity Payne, Claire Adams, Alison Sleigh, John R. Crawford, Anette P. Gjesing, Jette Bork-Jensen, Oluf Pedersen, Inês Barroso, Torben Hansen, Helen Cox, Mary Reilly, Rebecca J. Brown, Simeon I. Taylor, Duncan McHale, Martin Armstrong, Elif A Oral, Vladimı́r Saudek, Stephen O’Rahilly, Eamonn R. Maher, Bjørn Richelsen, David B. Savage, Robert K. Semple
Software Mentions: 2
Published: over 7 years ago

10.3389/fgene.2021.625564

Case Report: Whole Exome Sequencing Revealed Disease-Causing Variants in Two Genes in a Patient With Autism Spectrum Disorder, Intellectual Disability, Hyperactivity, Sleep and Gastrointestinal Disturbances
Cited by: 8
Author(s): Maria Cerminara, Giovanni Spirito, Livia Pisciotta, Margherita Squillario, Martina Servetti, Maria Teresa Divizia, Margherita Lerone, Bianca Berloco, Silvia Boeri, Lino Nobili, Diego Vozzi, Remo Sanges, Stefano Gustincich, Aldamaria Puliti
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pgen.1006455

Extremely Rare Polymorphisms in Saccharomyces cerevisiae Allow Inference of the Mutational Spectrum
Cited by: 13
Author(s): Yuan Zhu, Gavin Sherlock, Dmitri A. Petrov
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pgen.1006537

Genomes of Fasciola hepatica from the Americas Reveal Colonization with Neorickettsia Endobacteria Related to the Agents of Potomac Horse and Human Sennetsu Fevers
Cited by: 91
Author(s): Samantha N. McNulty, José F. Tort, Gabriel Rinaldi, Kerstin Fischer, Bruce A. Rosa, Pablo Smircich, Santiago Fontenla, Young Jun Choi, Rahul Tyagi, Kymberlie Hallsworth-Pepin, Victoria H. Mann, Lakshmi Kammili, Patricia S. Latham, Nicolás Dell’Oca, Fernanda Domínguez, Carlos Carmona, Peter U. Fischer, Paul J. Brindley, Makedonka Mitreva
Software Mentions: 2
Published: almost 8 years ago

10.1093/g3journal/jkaa009

Fast and inexpensive whole-genome sequencing library preparation from intact yeast cells
Cited by: 2
Author(s): Sibylle C. Vonesch, Shengdi Li, Chelsea Szu-Tu, Bianca P. Hennig, Nikolay Dobrev, Lars M. Steinmetz, M Steinmetz Lars
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pgen.1003475

Genome-Wide Analysis in German Shepherd Dogs Reveals Association of a Locus on CFA 27 with Atopic Dermatitis
Cited by: 56
Author(s): Katarina Tengvall, Marcin Kierczak, Kerstin Bergvall, Mia Olsson, Marcel Frankowiack, Fabiana H.G. Farias, Gerli Pielberg, Örjan Carlborg, Tosso Leeb, Gerhard Andersson, Lennart Hammarström, Åke Hedhammar, Kerstin Lindblad‐Toh
Software Mentions: 2
Published: over 11 years ago

10.3389/fgene.2019.00856

Evaluation of the Performance of AmpliSeq and SureSelect Exome Sequencing Libraries for Ion Proton
Cited by: 8
Author(s): Piyush Gampawar, Yasaman Saba, Ulrike Werner, Reinhold Schmidt, Bertram Müller‐Myhsok, Helena Schmidt
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pgen.1008291

Monitoring the interplay between transposable element families and DNA methylation in maize
Cited by: 49
Author(s): Jaclyn M. Noshay, Sarah N. Anderson, Peng Zhou, Lexiang Ji, William A. Ricci, Zefu Lu, Michelle C. Stitzer, Peter A. Crisp, Candice N. Hirsch, Xiaoyu Zhang, Robert J. Schmitz, Nathan M. Springer
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pntd.0005949

Genomic analyses of African Trypanozoon strains to assess evolutionary relationships and identify markers for strain identification
Cited by: 12
Author(s): Joshua B. Richardson, Kuang‐Yao Lee, Paul O. Mireji, John Enyaru, Mark Sistrom, Serap Aksoy, Hongyu Zhao, Adalgisa Caccone
Software Mentions: 2
Published: about 7 years ago

10.1186/s12916-015-0489-y

RNY-derived small RNAs as a signature of coronary artery disease
Cited by: 32
Author(s): Emanuela Repetto, Laeticia Lichtenstein, Zoheir Hizir, Nedra Tekaya, Mohamed Benahmed, Jean‐Bernard Ruidavets, Laure‐Emmanuelle Zaragosi, Bertrand Fougère, Laura Bouchareychas, Annelise Genoux, Romain Lotte, Raymond Ruimy, Jean Ferrières, Pascal Barbry, Laurent O. Martinez, Michèle Trabucchi
Software Mentions: 2
Published: about 9 years ago

10.1186/s12711-019-0487-1

Genotyping by low-coverage whole-genome sequencing in intercross pedigrees from outbred founders: a cost-efficient approach
Cited by: 38
Author(s): Yanjun Zan, Thibaut Payen, Mette Lillie, Christa F. Honaker, P. B. Siegel, Örjan Carlborg
Software Mentions: 2
Published: over 5 years ago

10.1186/gb-2011-12-9-r90

Exome sequencing identifies a missense mutation in Isl1 associated with low penetrance otitis media in dearisch mice
Cited by: 22
Author(s): Jennifer Hilton, Morag A. Lewis, M’hamed Grati, Neil J. Ingham, Selina Pearson, Roman A. Laskowski, David J. Adams, Karen P. Steel
Software Mentions: 2
Published: almost 14 years ago

10.1186/s12864-020-07125-5

Towards a better understanding of the low recall of insertion variants with short-read based variant callers
Cited by: 12
Author(s): Wesley Delage, Julien Thévenon, Claire Lemaitre
Software Mentions: 2
Published: about 4 years ago

10.1186/gb-2014-15-2-r23

Genome-wide co-localization of Polycomb orthologs and their effects on gene expression in human fibroblasts
Cited by: 46
Author(s): Helen Pemberton, Emma Anderton, Harshil Patel, Sharon Brookes, Hollie Chandler, Richard D. Palermo, Julie Stock, Marc Rodríguez‐Niedenführ, Tomáš Raček, Lucas de Breed, Aengus Stewart, Nik Matthews, Gordon Peters
Software Mentions: 2
Published: almost 11 years ago

10.1002/advs.202002602

Protein Arginine Methyltransferase PRMT5 Regulates Fatty Acid Metabolism and Lipid Droplet Biogenesis in White Adipose Tissues
Cited by: 20
Author(s): Zhihao Jia, Yue Feng, Xiyue Chen, Narayanan Narayanan, Jiamin Qiu, Sabriya A. Syed, Anthony N. Imbalzano, Meng Deng, Peng Yu, Chang‐Deng Hu, Shihuan Kuang
Software Mentions: 2
Published: about 4 years ago

10.1038/s41392-021-00748-4

A novel missense variant in ACAA1 contributes to early-onset Alzheimer’s disease, impairs lysosomal function, and facilitates amyloid-β pathology and cognitive decline
Cited by: 17
Author(s): Rongcan Luo, Fan Yu, Jing Yang, Maosen Ye, Dengfeng Zhang, Kun Guo, Xiao Li, Rui Bi, Min Xu, Lu-Xiu Yang, Yu Liu, Xiaoqian Ran, Hong-Yan Jiang, Chen Zhang, Liwen Tan, Nengyin Sheng, Yong-Gang Yao
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pcbi.1006034

Integrative single-cell omics analyses reveal epigenetic heterogeneity in mouse embryonic stem cells
Cited by: 15
Author(s): Ye Luo, Jianlin He, Xiguang Xu, Miao‐Kun Sun, Xiaowei Wu, Xuemei Lu, Hehuang Xie
Software Mentions: 2
Published: over 6 years ago

10.1007/s11105-016-1000-4

Genome-Wide Discovery of DNA Polymorphisms in Mei (Prunus mume Sieb. et Zucc.), an Ornamental Woody Plant, with Contrasting Tree Architecture and their Functional Relevance for Weeping Trait
Cited by: 12
Author(s): Jie Zhang, Kai Zhao, Dan Hou, Junhuo Cai, Qixiang Zhang, Tangren Cheng, Huitang Pan, Weiru Yang
Software Mentions: 2
Published: over 8 years ago

10.7717/peerj.5507

Assessment of genomic changes in a CRISPR/Cas9 Phaeodactylum tricornutum mutant through whole genome resequencing
Cited by: 17
Author(s): Monia Teresa Russo, Riccardo Aiese Cigliano, Walter Sanseverino, Maria Immacolata Ferrante
Software Mentions: 2
Published: about 6 years ago

10.1186/s12859-015-0849-9

The diagnostic application of RNA sequencing in patients with thyroid cancer: an analysis of 851 variants and 133 fusions in 524 genes
Cited by: 31
Author(s): Moraima Pagan, Richard T. Kloos, Chu-Fang Lin, Kevin Travers, Hajime Matsuzaki, Edward Tom, Su Yeon Kim, Michael Y. Wong, Andrew C. Stewart, Jing Huang, P. Sean Walsh, R. J. Monroe, Giulia C. Kennedy
Software Mentions: 2
Published: almost 9 years ago

10.7717/peerj.1508

Reproducibility of SNV-calling in multiple sequencing runs from single tumors
Cited by: 3
Author(s): Dakota Z. Derryberry, Matthew C. Cowperthwaite, Claus O. Wilke
Software Mentions: 2
Published: almost 9 years ago

10.3390/v12040463

RNAseq Reveals the Contribution of Interferon Stimulated Genes to the Increased Host Defense and Decreased PPR Viral Replication in Cattle
Cited by: 8
Author(s): K.G. Tirumurugaan, Rahul Mohanchandra Pawar, G. Dhinakar Raj, A. Thangavelu, John A. Hammond, Satya Parida
Software Mentions: 2
Published: over 4 years ago

10.1186/1471-2164-15-491

Gonad transcriptome analysis of pearl oyster Pinctada margaritifera: identification of potential sex differentiation and sex determining genes
Cited by: 95
Author(s): Vaihiti Teaniniuraitemoana, Arnaud Huvet, Peva Levy, Christophe Klopp, Émeline Lhuillier, Nabila Gaertner‐Mazouni, Yannick Gueguen, Gilles Le Moullac
Software Mentions: 2
Published: over 10 years ago

10.3390/jof6040277

The Medical Triazole Voriconazole Can Select for Tandem Repeat Variations in Azole-Resistant Aspergillus Fumigatus Harboring TR34/L98H Via Asexual Reproduction
Cited by: 7
Author(s): Jianhua Zhang, Jan Zoll, Tobias Engel, Joost van den Heuvel, Paul E. Verweij, A.J.M. Debets
Software Mentions: 2
Published: about 4 years ago

10.18632/oncotarget.15611

OSR1 is a novel epigenetic silenced tumor suppressor regulating invasion and proliferation in renal cell carcinoma
Cited by: 23
Author(s): Yixiang Zhang, Yeqing Yuan, Peidong Liang, Xiaojing Guo, Ying Ying, Xing-sheng Shu, Michael Gao, Yingduan Cheng
Software Mentions: 2
Published: over 7 years ago

10.3389/fgene.2020.00616

Whole Genome Low-Coverage Sequencing Concurrently Detecting Copy Number Variations and Their Underlying Complex Chromosomal Rearrangements by Systematic Breakpoint Mapping in Intellectual Deficiency/Developmental Delay Patients
Cited by: 5
Author(s): Bing Xiao, Xiantao Ye, Lili Wang, Yanjie Fan, Xuefan Gu, Xing Ji, Yu Sun, Yongguo Yu
Software Mentions: 2
Published: over 4 years ago

10.1038/s42003-020-0812-9

Genetic and phenotypic landscape of the mitochondrial genome in the Japanese population
Cited by: 18
Author(s): Kenichi Yamamoto, Saori Sakaue, Koichi Matsuda, Yoshinori Murakami, Yoichiro Kamatani, Keiichi Ozono, Yukihide Momozawa, Yukinori Okada
Software Mentions: 2
Published: over 4 years ago

10.1111/1751-7915.13555

Myriocin‐induced adaptive laboratory evolution of an industrial strain of Saccharomyces cerevisiae reveals its potential to remodel lipid composition and heat tolerance
Cited by: 13
Author(s): Francisca Randez‐Gil, José A. Prieto, Alejandro Rodríguez‐Puchades, Josefina Casas, Vicente Sentandreu, Francisco Estruch
Software Mentions: 2
Published: over 4 years ago

10.1016/j.csbj.2017.01.002

Deep Assessment of Genomic Diversity in Cassava for Herbicide Tolerance and Starch Biosynthesis
Cited by: 14
Author(s): Jorge Duitama, Lina Kafuri, Daniel Tello, Ana Marı́a Leiva, Bernhard J. Hofinger, Sneha Datta, Zaida Lentini, Ericson Aranzales, Bradley J. Till, Hernán Ceballos
Software Mentions: 2
Published: almost 8 years ago

10.1186/s41199-019-0045-0

Genomic and human papillomavirus profiling of an oral cancer cohort identifies TP53 as a predictor of overall survival
Cited by: 14
Author(s): Neil Mundi, Stephenie D. Prokopec, Farhad Ghasemi, Andrew Warner, Krupal Patel, Danielle MacNeil, Christopher J. Howlett, William Stecho, Paul Plantinga, Nicole Pinto, Kara M. Ruicci, Mohammed I. Khan, Myung Woul Han, John Yoo, Kevin Fung, Axel Sahovaler, David A. Palma, Eric Winquist, Joe S. Mymryk, John W. Barrett, Paul C. Boutros, Anthony C. Nichols
Software Mentions: 2
Published: almost 5 years ago

10.3389/fnmol.2017.00067

Transcriptome Analysis Reveals Altered Expression of Memory and Neurotransmission Associated Genes in the REM Sleep Deprived Rat Brain
Cited by: 19
Author(s): Santosh C. Narwade, Birendra Nath Mallick, Deepti D. Deobagkar
Software Mentions: 2
Published: over 7 years ago

10.1186/gm434

Tumor-associated copy number changes in the circulation of patients with prostate cancer identified through whole-genome sequencing
Cited by: 297
Author(s): Ellen Heitzer, Peter Ulz, Jelena Belic, S. Gutschi, Franz Quehenberger, Katja Fischereder, Theresa Benezeder, Martina Auer, Carina Pischler, Sebastian Mannweiler, Martin Pichler, Florian Eisner, Martin Haeusler, Sabine Riethdorf, Klaus Pantel, Hellmut Samonigg, Gerald Höefler, Herbert Augustin, Jochen B. Geigl, Michael R. Speicher
Software Mentions: 2
Published: almost 12 years ago

10.1093/bib/bbab069

Converting single nucleotide variants between genome builds: from cautionary tale to solution
Cited by: 9
Author(s): Cathal Ormond, Niamh Ryan, Aiden Corvin, Elizabeth A. Heron
Software Mentions: 2
Published: over 3 years ago

10.15252/embj.201592862

Mitochondria are required for pro‐ageing features of the senescent phenotype
Cited by: 482
Author(s): Clara Correia‐Melo, Francisco D.M. Marques, Rosaleen J. Anderson, Graeme Hewitt, Rachael N. Hewitt, John Cole, Bernadette Carroll, Soichi Miwa, Jodie Birch, Alina Merz, Michael D. Rushton, Michelle Charles, Diana Jurk, Stephen W.G. Tait, Rafal Czapiewski, Laura C. Greaves, Glyn Nelson, Mohammad Bohlooly‐Y, Sergio Rodríguez‐Cuenca, Antonio Vidal‐Puig, Derek A. Mann, Gabriele Saretzki, Giovanni Quarato, Douglas R. Green, Peter D. Adams, Thomas von Zglinicki, Viktor I. Korolchuk, João F. Passos
Software Mentions: 2
Published: almost 9 years ago

10.7554/eLife.22474

Distinct modes of SMAD2 chromatin binding and remodeling shape the transcriptional response to NODAL/Activin signaling
Cited by: 40
Author(s): Davide Martino Coda, Tessa Gaarenstroom, Philip East, Harshil Patel, Daniel S. J. Miller, Anna Lobley, Nik Matthews, Aengus Stewart, Caroline S. Hill
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0183081

Whole exome sequencing as a diagnostic tool for patients with ciliopathy-like phenotypes
Cited by: 8
Author(s): Sheila Castro-Sánchez, María Álvarez-Satta, M.A. Tohamy, Sergi Beltrán, Sophia Derdak, Diana Valverde
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0120585

Genetic Heterogeneity of Induced Pluripotent Stem Cells: Results from 24 Clones Derived from a Single C57BL/6 Mouse
Cited by: 11
Author(s): Li Cheng, Jeffery M. Klco, Nichole Helton, Daniel R. George, Jacqueline Mudd, Christopher A. Miller, Charles Lu, Robert S. Fulton, Michelle O’Laughlin, Catrina C. Fronick, Richard K. Wilson, Timothy J. Ley
Software Mentions: 2
Published: over 9 years ago

10.1186/s13072-019-0272-y

Profiling of chromatin accessibility and identification of general cis-regulatory mechanisms that control two ocular lens differentiation pathways
Cited by: 32
Author(s): Yilin Zhao, Deyou Zheng, Aleš Cvekl
Software Mentions: 2
Published: over 5 years ago

10.1002/brb3.2069

The role of interindividual licking received and dopamine genotype on later‐life licking provisioning in female rat offspring
Cited by: 5
Author(s): Samantha C Lauby, David G. Ashbrook, Hannan R. Malik, Diptendu Chatterjee, Pauline Pan, Alison S. Fleming, Patrick O. McGowan
Software Mentions: 2
Published: almost 4 years ago

10.1186/s42523-021-00082-8

A diet-specific microbiota drives Salmonella Typhimurium to adapt its in vivo response to plant-derived substrates
Cited by: 5
Author(s): Nicoletta Prax, Stefanie Wagner, Jakob Schardt, Klaus Neuhaus, Thomas Clavel, Thilo M. Fuchs
Software Mentions: 2
Published: over 3 years ago

10.1038/s41437-019-0260-9

Conservation genomic analysis reveals ancient introgression and declining levels of genetic diversity in Madagascar’s hibernating dwarf lemurs
Cited by: 14
Author(s): Rachel C. Williams, Marina B. Blanco, Jelmer W. Poelstra, Kelsie E Hunnicutt, Aaron A. Comeault, Anne D. Yoder
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pntd.0007184

Application of a targeted-enrichment methodology for full-genome sequencing of Dengue 1-4, Chikungunya and Zika viruses directly from patient samples
Cited by: 10
Author(s): Uma S. Kamaraj, Jun Tan, Ong Xin Mei, Louise Pan, Tanu Chawla, Anna Uehara, Lin‐Fa Wang, Eng Eong Ooi, Duane J. Gubler, Hasitha Tissera, Lee Ching Ng, Annelies Wilder‐Smith, Paola Flórez de Sessions, Timothy Barkham, Danielle E. Anderson, October M. Sessions
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0212645

Bald thigh syndrome in sighthounds—Revisiting the cause of a well-known disease
Cited by: 5
Author(s): Magdalena A. T. Brunner, Silvia Rüfenacht, Anina Bauer, Susanne Erpel, Natasha Buchs, Sophie Braga-Lagache, Manfred Heller, Tosso Leeb, Vidhya Jagannathan, Dominique J Wiener, Monika Maria Welle
Software Mentions: 2
Published: over 5 years ago

10.15252/emmm.202114365

Oxidized LDL‐dependent pathway as new pathogenic trigger in arrhythmogenic cardiomyopathy
Cited by: 14
Author(s): Elena Sommariva, Ilaria Stadiotti, Michela Casella, Valentina Catto, Antonio Dello Russo, Corrado Carbucicchio, Lorenzo Arnaboldi, S. De Metrio, Giuseppina Milano, Alessandro Scopece, Manuel Casaburo, Daniele Andreini, Saima Mushtaq, Edoardo Conte, Mattia Chiesa, Walter Birchmeier, Elisa Cogliati, Adolfo Paolin, Eva König, Viviana Meraviglia, Monica De Musso, Chiara Volani, Giada Cattelan, Werner Rauhe, Linda Turnu, Benedetta Porro, Matteo Pedrazzini, Marina Camera, Alberto Corsini, Claudio Tondo, Alessandra Rossini, Giulio Pompilio
Software Mentions: 1
Published: over 3 years ago

10.1186/s12859-016-1451-5

Variational inference for rare variant detection in deep, heterogeneous next-generation sequencing data
Cited by: 3
Author(s): Fan Zhang, Patrick Flaherty
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0170940

Comparing Ancient DNA Preservation in Petrous Bone and Tooth Cementum
Cited by: 129
Author(s): Henrik Hansen, Peter B. Damgaard, Ashot Margaryan, Jesper Stenderup, Niels Lynnerup, Eske Willerslev, Morten E. Allentoft
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12859-016-1097-3

Evaluating the necessity of PCR duplicate removal from next-generation sequencing data and a comparison of approaches
Cited by: 101
Author(s): Mark T. W. Ebbert, Mark E. Wadsworth, Lyndsay A. Staley, Kaitlyn L. Hoyt, Brandon D. Pickett, Justin Miller, John Duce, John Kauwe, Perry G. Ridge
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0060482

Massively Parallel Sequencing Reveals the Complex Structure of an Irradiated Human Chromosome on a Mouse Background in the Tc1 Model of Down Syndrome
Cited by: 92
Author(s): Susan Gribble, Frances K. Wiseman, Stephen Clayton, Elena Prigmore, Elizabeth Langley, Fengtang Yang, Sean Maguire, Beiyuan Fu, Diana Rajan, Olivia Sheppard, Carol Scott, Heidi Hauser, Philip J. Stephens, Lucy Stebbings, Bee Ling Ng, Tomas Fitzgerald, Michael A. Quail, Ruby Banerjee, Kai Rothkamm, Victor L. J. Tybulewicz, Elizabeth Fisher, Nigel P. Carter
Software Mentions: 1
Published: over 11 years ago

10.1002/2211-5463.12366

Two nonsense somatic mutations in MEN1 identified in sporadic insulinomas
Cited by: 2
Author(s): Qi Cheng, Jiayue Duan, Qingfeng Shi, Mingguang Wang, Changqing Yan
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0207747

Mutation of a serine near the catalytic site of the choline acetyltransferase a gene almost completely abolishes motility of the zebrafish embryo
Cited by: 6
Author(s): Swarnima Joshi, Sanamjeet Virdi, Christelle Etard, Robert Geisler, Uwe Strähle
Software Mentions: 1
Published: about 6 years ago

10.3389/fcvm.2017.00011

Validation and Utilization of a Clinical Next-Generation Sequencing Panel for Selected Cardiovascular Disorders
Cited by: 8
Author(s): Patrícia B. S. Celestino-Soper, Hongyu Gao, Ty C. Lynnes, Hai Lin, Yunlong Liu, Katherine G. Spoonamore, Peng‐Sheng Chen, Matteo Vatta
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0072362

Divergent Evolutionary and Expression Patterns between Lineage Specific New Duplicate Genes and Their Parental Paralogs in Arabidopsis thaliana
Cited by: 19
Author(s): Jun Wang, Nicholas C. Marowsky, Chuanzhu Fan
Software Mentions: 1
Published: about 11 years ago

10.3389/fgene.2021.684905

Diaphyseal and Metaphyseal Modeling Defects—Clinical Findings and Identification of WRAP53 Deficiency in Craniometadiaphyseal Dysplasia
Cited by: 0
Author(s): Yun Hao, Xiaolin Wang, Jun Xiao, Chunlei Jiao, Xinyao Meng, Jiachao Guo, Jingfan Shao, Jiexiong Feng, Jinpeng He
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pgen.1003929

Recurrent Tissue-Specific mtDNA Mutations Are Common in Humans
Cited by: 128
Author(s): David C. Samuels, Chun Li, Bingshan Li, Zhuo Song, Eric S. Torstenson, Hayley B. Clay, Antonis Rokas, Tricia A. Thornton‐Wells, Jason H. Moore, Tia M. Hughes, Robert D. Hoffman, Jonathan L. Haines, Deborah G. Murdock, Douglas P. Mortlock, Scott M. Williams
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pgen.1008383

Temperature preference can bias parental genome retention during hybrid evolution
Cited by: 29
Author(s): Caiti Smukowski Heil, Christopher R. L. Large, Kira Patterson, Angela Shang-Mei Hickey, Yeh Cc, Maitreya J. Dunham
Software Mentions: 1
Published: about 5 years ago

10.3390/antibiotics10080992

Role of dipA and pilD in Francisella tularensis Susceptibility to Resazurin
Cited by: 1
Author(s): Kendall Souder, Emma Beatty, Siena McGovern, Michael Whaby, Emily Young, Jacob Pancake, Daron Marshall Weekley, Justin Rice, Donald A. Primerano, James Denvir, Joseph Horzempa, Deanna Schmitt
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2021.714732

Composition and Seasonality of Membrane Transporters in Marine Picoplankton
Cited by: 0
Author(s): Åke Hagström, Ulla Li Zweifel, John Sundh, Christofer M. G. Osbeck, Carina Bunse, Johanna Sjöstedt, Bärbel Müller‐Karulis, Jarone Pinhassi
Software Mentions: 1
Published: about 3 years ago

10.3389/fmicb.2020.582590

Physiology of Highly Radioresistant Escherichia coli After Experimental Evolution for 100 Cycles of Selection
Cited by: 6
Author(s): Steven T. Bruckbauer, Joel Martin, Benjamin B. Minkoff, Mike T. Veling, Illissa Lancaster, Jessica Liu, Joseph D. Trimarco, Brian Bushnell, Anna Lipzen, Elizabeth A. Wood, Michael R. Sussman, Christa Pennacchio, Michael M. Cox
Software Mentions: 1
Published: about 4 years ago

10.3389/fped.2021.651621

A Novel Homozygous VPS13B Splice-Site Mutation Causing the Skipping of Exon 38 in a Chinese Family With Cohen Syndrome
Cited by: 3
Author(s): Liangshan Li, Xiangmao Bu, Yuhua Ji, Ping Tan, Shiguo Liu
Software Mentions: 1
Published: over 3 years ago

10.3389/fped.2020.600446

Molecular Diagnosis of Panel-Based Next-Generation Sequencing Approach and Clinical Symptoms in Patients With Glycogen Storage Disease: A Single Center Retrospective Study
Cited by: 2
Author(s): Ying Shen, Zhihua Zhong, Yang Zheng, Jin Yu, Qian Lin, Bixia Zheng, Wei-xia Cheng, Zhifeng Liu
Software Mentions: 1
Published: almost 4 years ago

Projects: pypi: picard

Papers Mentioning picard 243