pypi: picard | Projects | Ecosyste.ms: Papers

10.1186/s13059-019-1819-8

SEPATH: benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines
Cited by: 12
Author(s): Abraham Gihawi, Ghanasyam Rallapalli, Rachel Hurst, Colin S. Cooper, Richard M. Leggett, Daniel Brewer
Software Mentions: 17
Published: about 5 years ago

10.1186/s13059-021-02349-4

PEPPRO: quality control and processing of nascent RNA profiling data
Cited by: 14
Author(s): Jason P. Smith, Arun B. Dutta, Kizhakke Mattada Sathyan, Michael J. Guertin, Nathan C. Sheffield
Software Mentions: 14
Published: over 3 years ago

10.1186/s13072-020-00343-x

BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracks
Cited by: 29
Author(s): Lőrinc Sándor Pongor, Jacob M. Gross, Roberto Vera Alvarez, Junko Murai, Sang‐Min Jang, Hongliang Zhang, Christophe E. Redon, Haiqing Fu, Shar-yin N. Huang, Bhushan Thakur, Adrian Baris, Leonardo Mariño‐Ramírez, David Landsman, Mirit I. Aladjem, Yves Pommier
Software Mentions: 13
Published: over 4 years ago

10.1099/mgen.0.000492

Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypes
Cited by: 13
Author(s): Chun Shen Lim, Vitina Sozzi, Margaret Littlejohn, Lilly Yuen, Nadia Warner, Brigid Betz‐Stablein, Fabio Luciani, Peter Revill, Chris M. Brown
Software Mentions: 13
Published: almost 4 years ago

10.1186/s12859-019-3251-1

BISR-RNAseq: an efficient and scalable RNAseq analysis workflow with interactive report generation
Cited by: 17
Author(s): Venkat Sundar Gadepalli, Hatice Gülçin Özer, Ayse Selen Yilmaz, Maciej Pietrzak, Amy Webb
Software Mentions: 13
Published: almost 5 years ago

10.1186/s13058-021-01451-6

Transcriptome and genome evolution during HER2-amplified breast neoplasia
Cited by: 3
Author(s): Peipei Lu, Joseph W. Foley, Chunfang Zhu, Katherine McNamara, Korsuk Sirinukunwattana, Sujay Vennam, Sushama Varma, Hamid Fehri, Arunima Srivastava, Shirley Zhu, Jens Rittscher, Parag Mallick, Christina Curtis, Robert B. West
Software Mentions: 11
Published: over 3 years ago

10.1128/mSystems.00316-20

Streamlined and Abundant Bacterioplankton Thrive in Functional Cohorts
Cited by: 8
Author(s): Rhiannon Mondav, Stefan Bertilsson, Moritz Buck, Silke Langenheder, Eva S. Lindström, Sarahi L. Garcia
Software Mentions: 11
Published: about 4 years ago

10.7554/eLife.51276

A genome-wide view of the de-differentiation of central nervous system endothelial cells in culture
Cited by: 39
Author(s): Mark F Sabbagh, Jeremy Nathans
Software Mentions: 11
Published: almost 5 years ago

10.3389/fgene.2020.580580

Global Analysis of Transcription Start Sites in the New Ovine Reference Genome (Oar rambouillet v1.0)
Cited by: 20
Author(s): Mazdak Salavati, Alex Caulton, Richard Clark, Iveta Gažová, Timothy P. L. Smith, Kim C. Worley, Noelle E. Cockett, Alan Archibald, Shannon Clarke, Brenda M. Murdoch, Emily L. Clark
Software Mentions: 11
Published: about 4 years ago

10.1016/j.devcel.2018.11.009

From Pioneer to Repressor: Bimodal foxd3 Activity Dynamically Remodels Neural Crest Regulatory Landscape In Vivo
Cited by: 90
Author(s): Martyna Lukoseviciute, Daria Gavriouchkina, Ruth M. Williams, Tatiana Hochgreb-Hägele, Upeka Senanayake, Vanessa Chong, Supat Thongjuea, Emmanouela Repapi, Adam J. Mead, Tatjana Sauka‐Spengler
Software Mentions: 11
Published: almost 6 years ago

10.7554/eLife.11613

Epigenomic landscapes of retinal rods and cones
Cited by: 107
Author(s): Alisa Mo, Chongyuan Luo, Fred P. Davis, Eran A. Mukamel, Gilbert L. Henry, Joseph R. Nery, Mark A. Urich, Serge Picard, Ryan Lister, Sean R. Eddy, M Beer, Joseph R. Ecker, Jeremy Nathans
Software Mentions: 11
Published: over 8 years ago

10.1186/s13059-021-02360-9

Role of epigenetics in unicellular to multicellular transition in Dictyostelium
Cited by: 8
Author(s): Simon Yuan Wang, Elizabeth A. Pollina, I‐Hao Wang, Lindsay K. Pino, Henry L. Bushnell, Ken Takashima, Colette Fritsche, George Sabin, Benjamin A. Garcia, Paul L. Greer, Eric Lieberman Greer
Software Mentions: 10
Published: over 3 years ago

10.1186/s12859-018-2296-x

Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines
Cited by: 47
Author(s): Neha Kulkarni, Luca Alessandrì, Riccardo Panero, Maddalena Arigoni, Martina Olivero, Giulio Ferrero, Francesca Cordero, Marco Beccuti, Raffaele Calogero
Software Mentions: 10
Published: about 6 years ago

10.7554/eLife.59073

Re-expression of SMARCA4/BRG1 in small cell carcinoma of ovary, hypercalcemic type (SCCOHT) promotes an epithelial-like gene signature through an AP-1-dependent mechanism
Cited by: 15
Author(s): Krystal A. Orlando, Amber K Douglas, Aierken Abudu, Yemin Wang, Basile Tessier‐Cloutier, Weiping Su, Alec Peters, Larry S. Sherman, Regan P. Moore, Vinh Nguyen, Gian Luca Negri, Shane Colborne, Gregg B. Morin, Friedrich Kommoss, Jessica D. Lang, William P.D. Hendricks, Elizabeth A. Raupach, Patrick Pirrotte, David G. Huntsman, Jeffrey M. Trent, Joel S. Parker, Jesse R. Raab, Bernard E. Weissman
Software Mentions: 9
Published: almost 4 years ago

10.1099/mgen.0.000511

Transmission, adaptation and geographical spread of the Pseudomonas aeruginosa Liverpool epidemic strain
Cited by: 12
Author(s): Matthew P. Moore, Iain L. Lamont, David Williams, Steve Paterson, Iréna Kukavica-Ibrulj, Nicholas P. Tucker, D. Kenna, Jane F. Turton, Julie Jeukens, Luca Freschi, Bryan A. Wee, Nicholas J. Loman, Stephen Holden, Susan Manzoor, Peter M. Hawkey, Kevin W Southern, Martin Walshaw, Roger C. Levesque, Joanne L. Fothergill, Craig Winstanley
Software Mentions: 9
Published: over 3 years ago

10.1038/s41598-020-60336-4

Linagliptin and telmisartan induced effects on renal and urinary exosomal miRNA expression in rats with 5/6 nephrectomy
Cited by: 18
Author(s): Denis Delić, Franziska Wiech, Richard Urquhart, Ogsen Gabrielyan, Kathrin Rieber, Marcel Rolser, Oleg Tsuprykov, Ahmed A. Hasan, Bernhard K. Krämer, Patrick Baum, A Köhler, Florian Gantner, Mark Michael, Berthold Hocher, Thomas Klein
Software Mentions: 9
Published: over 4 years ago

10.3389/fgene.2020.00817

Changes in H3K27ac at Gene Regulatory Regions in Porcine Alveolar Macrophages Following LPS or PolyIC Exposure
Cited by: 17
Author(s): Júber Herrera-Uribe, Haibo Li, Kristen A Byrne, Zahra F Bond, Crystal L. Loving, Christopher K. Tuggle
Software Mentions: 9
Published: over 4 years ago

10.1016/j.celrep.2020.108546

RTEL1 Regulates G4/R-Loops to Avert Replication-Transcription Collisions
Cited by: 33
Author(s): Panagiotis Kotsantis, Sandra Segura-Bayona, Pol Margalef, Paulina Marzec, Phil Ruis, Graeme Hewitt, Roberto Bellelli, Harshil Patel, Robert Goldstone, Anna R. Poetsch, Simon J. Boulton
Software Mentions: 9
Published: almost 4 years ago

10.1111/mec.15648

Genomic signatures of convergent adaptation to Alpine environments in three Brassicaceae species
Cited by: 11
Author(s): Christian Rellstab, Stefan Zoller, Christian Sailer, Andrew Tedder, Félix Gugerli, Kentaro Shimizu, Rolf Holderegger, Alex Widmer, Martin C. Fischer
Software Mentions: 9
Published: about 4 years ago

10.1371/journal.pgen.1008658

Parallelism in eco-morphology and gene expression despite variable evolutionary and genomic backgrounds in a Holarctic fish
Cited by: 63
Author(s): Arne Jacobs, Madeleine Carruthers, Andrey A. Yurchenko, Н. В. Гордеева, S. S. Alekseyev, Oliver E. Hooker, Jong S. Leong, David R. Minkley, Eric B. Rondeau, Ben F. Koop, Colin E. Adams, Kathryn R. Elmer
Software Mentions: 8
Published: over 4 years ago

10.3389/fgene.2018.00123

Inferring Variation in Copy Number Using High Throughput Sequencing Data in R
Cited by: 15
Author(s): Brian J. Knaus, Niklaus J. Grünwald
Software Mentions: 8
Published: over 6 years ago

10.1038/s41380-020-0844-z

Developmental excitation-inhibition imbalance underlying psychoses revealed by single-cell analyses of discordant twins-derived cerebral organoids
Cited by: 66
Author(s): Tomoyo Sawada, Thomas E. Chater, Yohei Sasagawa, Mika Yoshimura, Noriko Fujimori-Tonou, Kaori Tanaka, Kynon J.M. Benjamin, Apuã C.M. Paquola, Jennifer A. Erwin, Yukiko Goda, Itoshi Nikaido, Takeshi Kato
Software Mentions: 8
Published: over 4 years ago

10.3389/fimmu.2021.617592

Phenotypic and Epigenetic Adaptations of Cord Blood CD4+ T Cells to Maternal Obesity
Cited by: 11
Author(s): Suhas Sureshchandra, Norma Mendoza, Allen Jankeel, Randall M. Wilson, Nicole Marshall, Ilhem Messaoudi
Software Mentions: 8
Published: over 3 years ago

10.1038/s41598-019-40503-y

Sequential conditioning-stimulation reveals distinct gene- and stimulus-specific effects of Type I and II IFN on human macrophage functions
Cited by: 23
Author(s): Quen J. Cheng, Faraz Behzadi, Supriya Sen, Sho Ohta, Roberto Spreafico, Rosane M. B. Teles, Robert L. Modlin, Alexander Hoffmann
Software Mentions: 8
Published: over 5 years ago

10.1016/j.celrep.2019.10.018

Aryl Hydrocarbon Receptor Contributes to the Transcriptional Program of IL-10-Producing Regulatory B Cells
Cited by: 91
Author(s): Christopher Piper, Elizabeth C. Rosser, Kristīne Oļeiņika, Kiran Nistala, Thomas Krausgruber, André F. Rendeiro, Aggelos Banos, Ignat Drozdov, Matteo Villa, Scott Thomson, Georgina Xanthou, Christoph Bock, Brigitta Stockinger, Claudia Mauri
Software Mentions: 8
Published: about 5 years ago

10.1186/s12915-019-0726-5

Multi-species annotation of transcriptome and chromatin structure in domesticated animals
Cited by: 80
Author(s): Sylvain Foissac, Sarah Djebali, Kylie Munyard, Nathalie Vialaneix, Andrea Rau, Kévin Muret, Diane Esquerré, Matthias Zytnicki, Thomas Derrien, Philippe Bardou, Fany Blanc, Cédric Cabau, Elisa Crisci, Sophie Dhorne–Pollet, Françoise Drouet, Thomas Faraut, Ignacio González, Adeline Goubil, Sonia Lacroix‐Lamandé, Fabrice Laurent, Sylvain Marthey, Maria Marti-Marimon, Raphaëlle Momal-Leisenring, Florence Mompart, Pascale Quéré, David Robelin, Magali San Cristobal, Gwenola Tosser‐Klopp, Silvia Vincent‐Naulleau, Stéphane Fabre, Marie-Hélène Pinard van der Laan, Christophe Klopp, Michèle Tixier‐Boichard, Hervé Acloque, Sandrine Lagarrigue, Elisabetta Giuffra
Software Mentions: 8
Published: almost 5 years ago

10.1186/s13059-020-02038-8

Personalized and graph genomes reveal missing signal in epigenomic data
Cited by: 25
Author(s): Cristian Groza, Tony Kwan, Nicole Soranzo, Tomi Pastinen, Guillaume Bourque
Software Mentions: 8
Published: over 4 years ago

10.1038/s41598-017-14366-0

Erythropoietin Signaling Regulates Key Epigenetic and Transcription Networks in Fetal Neural Progenitor Cells
Cited by: 10
Author(s): Christina Sollinger, Jacquelyn Lillis, Jeffrey Malik, Michael Getman, Christoph Pröschel, Laurie A. Steiner
Software Mentions: 7
Published: about 7 years ago

10.15252/emmm.202012525

<scp>LSD</scp> 1 inhibition induces differentiation and cell death in Merkel cell carcinoma
Cited by: 36
Author(s): Lukas Leiendecker, Pauline S. Jung, Izabela Krecioch, Tobias Neumann, Alexander Schleiffer, Karl Mechtler, Thomas Wiesner, Anna C. Obenauf
Software Mentions: 7
Published: about 4 years ago

10.1186/s12859-018-2353-5

XenofilteR: computational deconvolution of mouse and human reads in tumor xenograft sequence data
Cited by: 81
Author(s): Roelof J.C. Kluin, Kristel Kemper, Thomas Kuilman, Julian R. de Ruiter, Vivek Iyer, Josep V. Forment, Paulien Cornelissen-Steijger, Iris de Rink, Petra ter Brugge, Ji‐Ying Song, Sjoerd Klarenbeek, Ultan McDermott, Jos Jonkers, Arno Velds, David J. Adams, Daniel S. Peeper, Oscar Krijgsman
Software Mentions: 7
Published: about 6 years ago

10.1111/mec.13891

Genomic epidemiology of Cryptococcus yeasts identifies adaptation to environmental niches underpinning infection across an African <scp>HIV</scp>/<scp>AIDS</scp> cohort
Cited by: 51
Author(s): Mathieu Vanhove, Mathew A. Beale, Johanna Rhodes, Duncan Chanda, Shabir Lakhi, Geoffrey Kwenda, Síle F. Molloy, Natasha Karunaharan, Neil Stone, Thomas S. Harrison, Tihana Bicanic, Matthew C. Fisher
Software Mentions: 7
Published: about 8 years ago

10.1186/s12920-020-0695-0

Specific chromatin landscapes and transcription factors couple breast cancer subtype with metastatic relapse to lung or brain
Cited by: 20
Author(s): Wesley L. Cai, Celeste B. Greer, Jocelyn F. Chen, Anna Arnal-Estapé, Jian Cao, Qin Yan, Don X. Nguyen
Software Mentions: 7
Published: over 4 years ago

10.1016/j.cell.2021.01.002

Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition
Cited by: 412
Author(s): Kevin Litchfield, James L. Reading, Clare Puttick, Krupa Thakkar, Chris Abbosh, Robert Bentham, Thomas B.K. Watkins, Rachel Rosenthal, Dhruva Biswas, Andrew Rowan, Emilia L. Lim, Maise Al Bakir, Virginia Turati, José Afonso Guerra-Assunção, Lucía Conde, Andrew J.S. Furness, Sunil Kumar Saini, Sine Reker Hadrup, Javier Herrero, Se‐Hoon Lee, Peter Van Loo, Tariq Enver, James Larkin, Matthew D. Hellmann, Samra Turajlic, Sergio A. Quezada, Nicholas McGranahan, Charles Swanton
Software Mentions: 7
Published: almost 4 years ago

10.1093/gbe/evx067

Genomic Differentiation and Demographic Histories of Atlantic and Indo-Pacific Yellowfin Tuna (Thunnus albacares) Populations
Cited by: 37
Author(s): Julia Maria Isis Barth, Malte Damerau, Michael Matschiner, Sissel Jentoft, Reinhold Hanel
Software Mentions: 6
Published: over 7 years ago

10.7554/eLife.45672

Tumor suppressor SMARCB1 suppresses super-enhancers to govern hESC lineage determination
Cited by: 27
Author(s): Lee Langer, James M. Ward, Trevor Archer
Software Mentions: 6
Published: over 5 years ago

10.1111/mec.13914

Genome biogeography reveals the intraspecific spread of adaptive mutations for a complex trait
Cited by: 44
Author(s): Jill K. Olofsson, Matheus E Bianconi, Guillaume Besnard, Luke T. Dunning, Marjorie R. Lundgren, Hélène Holota, Maria S. Vorontsova, Oriane Hidalgo, Ilia J. Leitch, Patrik Nosil, Colin P. Osborne, Pascal‐Antoine Christin
Software Mentions: 6
Published: almost 8 years ago

10.1186/s12864-018-5066-2

A comparative analysis of library prep approaches for sequencing low input translatome samples
Cited by: 52
Author(s): Yang Song, Béatrice Milon, Sandra Ott, Xüna Zhao, Lisa Sadzewicz, Amol C. Shetty, Erich T. Boger, Luke J. Tallon, Robert J. Morell, Anup Mahurkar, Ronna Hertzano
Software Mentions: 6
Published: about 6 years ago

10.1038/s42003-018-0219-z

RELACS nuclei barcoding enables high-throughput ChIP-seq
Cited by: 27
Author(s): Laura Arrigoni, Hoor Al-Hasani, Fidel Ramírez, Ilaria Panzeri, Devon P. Ryan, Diana Santacruz, Nadia Kress, J. Andrew Pospisilik, Ulrike Bönisch, Thomas Manke
Software Mentions: 6
Published: almost 6 years ago

10.7554/eLife.59388

Gene regulation gravitates toward either addition or multiplication when combining the effects of two signals
Cited by: 10
Author(s): Eric M. Sanford, Benjamin Emert, Allison Coté, Arjun Raj
Software Mentions: 6
Published: almost 4 years ago

10.1534/g3.117.300489

DrosophilaLarval Brain Neoplasms Present Tumour-Type Dependent Genome Instability
Cited by: 4
Author(s): Fabrizio Rossi, Camille Stephan‐Otto Attolini, José Luis Mosquera, Cayetano González
Software Mentions: 6
Published: over 6 years ago

10.1080/20013078.2020.1785746

Influence of species and processing parameters on recovery and content of brain tissue‐derived extracellular vesicles
Cited by: 62
Author(s): Yiyao Huang, Lesley Cheng, Andrey Turchinovich, Vasiliki Mahairaki, Juan C. Troncoso, Olga Pletniková, Norman J. Haughey, Laura J. Vella, Andrew F. Hill, Lei Zheng, Kenneth W. Witwer
Software Mentions: 6
Published: over 4 years ago

10.1038/s41598-020-75998-3

Transcriptomic profiling of feline teeth highlights the role of matrix metalloproteinase 9 (MMP9) in tooth resorption
Cited by: 8
Author(s): S. Lee, Stephen J. Bush, Susan Thorne, Nicola Mawson, Colin Farquharson, Guraa Bergkvist
Software Mentions: 6
Published: about 4 years ago

10.1016/j.celrep.2019.06.039

Acute Iron Deprivation Reprograms Human Macrophage Metabolism and Reduces Inflammation In Vivo
Cited by: 67
Author(s): Marie Pereira, Tai‐Di Chen, Norzawani Buang, Antoni Olona, Jeong‐Hun Ko, Maria Prendecki, Ana S.H. Costa, Efterpi Nikitopoulou, Laura Tronci, Charles D. Pusey, H. Terence Cook, Stephen P. McAdoo, Christian Frezza, Jacques Behmoaras
Software Mentions: 6
Published: over 5 years ago

10.1038/sdata.2016.25

Extensive sequencing of seven human genomes to characterize benchmark reference materials
Cited by: 535
Author(s): Justin M. Zook, David Catoe, Jennifer McDaniel, Lindsay K. Vang, Noah Spies, Arend Sidow, Ziming Weng, Yuling Liu, Christopher E. Mason, Noah Alexander, Elizabeth Hénaff, Alexa B. R. McIntyre, Dhruva Chandramohan, Feng Chen, Erich B. Jaeger, Ali Moshrefi, Khoa Pham, William Stedman, Tiffany Y. Liang, Michael Saghbini, Željko Džakula, Alex Hastie, Han Cao, Gintaras Deikus, Eric E. Schadt, Robert Sebra, Ali Kashif Bashir, Rebecca Truty, Christopher Chang, Natali Gulbahce, Keyan Zhao, Srinka Ghosh, Fiona Hyland, Yutao Fu, Mark Chaisson, Chunlin Xiao, Jonathan Trow, Stephen T. Sherry, Alexander Wait Zaranek, Madeleine Ball, Jason Bobe, Preston W. Estep, George M. Church, Patrick Marks, Sofia Kyriazopoulou-Panagiotopoulou, Grace Zheng, Michael Schnall-Levin, Heather Ordonez, Patrice A Mudivarti, Kristina Giorda, Ying Sheng, Karoline Bjarnesdatter Rypdal, Marc Salit
Software Mentions: 6
Published: over 8 years ago

10.1111/acel.12890

Cell‐free DNA as a biomarker of aging
Cited by: 68
Author(s): Yee Voan Teo, Miriam Capri, Cristina Morsiani, G Pizza, Ana Maria Caetano Faria, Claudio Franceschi, Nicola Neretti
Software Mentions: 6
Published: almost 6 years ago

10.1016/j.celrep.2015.11.024

Differential DNA Methylation Analysis without a Reference Genome
Cited by: 35
Author(s): Johanna Klughammer, Paul Datlinger, Dieter Printz, Nathan C. Sheffield, Matthias Farlik, Johanna Hadler, Gerhard Fritsch, Christoph Bock
Software Mentions: 6
Published: almost 9 years ago

10.1093/femsyr/foaa044

Pseudohyphal differentiation in Komagataella phaffii: investigating the FLO gene family
Cited by: 3
Author(s): Sonakshi De, Corinna Rebnegger, Josef W. Moser, Nadine E Tatto, Alexandra B. Graf, Diethard Mattanovich, Brigitte Gasser
Software Mentions: 6
Published: over 4 years ago

10.1155/2018/8989252

Uncontrolled Diabetes Mellitus Has No Major Influence on the Platelet Transcriptome
Cited by: 6
Author(s): Thomas Nührenberg, Marco Cederqvist, Fédérico Marini, Christian Stratz, Björn Grüning, Dietmar Trenk, Harald Binder, Ralf Gilsbach, Franz–Josef Neumann, Lutz Hein
Software Mentions: 6
Published: about 6 years ago

10.1186/s13059-021-02348-5

Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana
Cited by: 65
Author(s): Pierre Baduel, Basile Leduque, Amandine Ignace, Isabelle Gy, José Pedro Gil, Olivier Loudet, Vincent Colot, Leandro Quadrana
Software Mentions: 5
Published: over 3 years ago

10.1111/mec.15539

No evidence for accumulation of deleterious mutations and fitness degradation in clonal fish hybrids: Abandoning sex without regrets
Cited by: 16
Author(s): Ján Kočí, Jan Röslein, Jan Pačes, Jan Kotusz, Karel Halačka, Ján Koščo, Jakub Fedorčák, Nataliia Iakovenko, Karel Janko
Software Mentions: 5
Published: over 4 years ago

10.18632/oncotarget.26929

Deregulated expression of NKL homeobox genes in T-cell lymphomas
Cited by: 10
Author(s): Stefan Nagel, Claudia Pommerenke, Roderick A.F. MacLeod, Corinna Meyer, Maren Kaufmann, Silke Fähnrich, Hans Drexler
Software Mentions: 5
Published: over 5 years ago

10.1186/1471-2164-15-141

Transcriptome sequencing of Atlantic salmon (Salmo salar L.) notochord prior to development of the vertebrae provides clues to regulation of positional fate, chordoblast lineage and mineralisation
Cited by: 40
Author(s): Wang Shou, Tomasz Furmanek, Harald Kryvi, Christel Krossøy, Geir K. Totland, Sindre Grotmol, Anna Wargelius
Software Mentions: 5
Published: almost 11 years ago

10.1002/ece3.5260

Ultraconserved element (UCE) probe set design: Base genome and initial design parameters critical for optimization
Cited by: 17
Author(s): Grey T. Gustafson, Alana Alexander, John S. Sproul, James M. Pflug, David R. Maddison, Andrew Edward Z. Short
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-021-02417-9

Elevated retrotransposon activity and genomic instability in primed pluripotent stem cells
Cited by: 10
Author(s): Haifeng Fu, Weiyu Zhang, Niannian Li, Jiao Yang, Xiaoying Ye, Chenglei Tian, Xinyi Lu, Lin Liu
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.62850

Individual differences in honey bee behavior enabled by plasticity in brain gene regulatory networks
Cited by: 24
Author(s): Beryl M. Jones, Vikyath D. Rao, Tim Gernat, Tobias Jagla, Amy Cash Ahmed, Rubin Be, Troy J. Comi, Shounak Bhogale, Syed Sameed Husain, Charles Blatti, Martin Middendorf, Saurabh Sinha, Sriram Chandrasekaran, Gene E. Robinson
Software Mentions: 5
Published: almost 4 years ago

10.1002/advs.202001402

TRADES: Targeted RNA Demethylation by SunTag System
Cited by: 25
Author(s): Jing Mo, Zonggui Chen, Shanshan Qin, Shu Li, Chuangang Liu, Lu Zhang, Ruoxi Ran, Ying Kong, Fang Wang, Song-Mei Liu, Yu Zhou, Xiaolian Zhang, Xiaocheng Weng, Xiang Zhou
Software Mentions: 5
Published: over 4 years ago

10.1093/gigascience/giy132

Comprehensive evaluation of RNA-seq analysis pipelines in diploid and polyploid species
Cited by: 21
Author(s): Miriam Payá‐Milans, James W. Olmstead, Gerardo H. Nunez, Timothy A. Rinehart, Margaret Staton
Software Mentions: 5
Published: about 6 years ago

10.1186/s13059-019-1878-x

Evaluation of commonly used analysis strategies for epigenome- and transcriptome-wide association studies through replication of large-scale population studies
Cited by: 24
Author(s): Jeroen van Rooij, Pooja R. Mandaviya, Annique Claringbould, Janine F. Felix, Jenny van Dongen, Rick Jansen, Lude Franke, Peter A.C. ’t Hoen, B.T. Heijmans, Joyce B. J. van Meurs
Software Mentions: 5
Published: about 5 years ago

10.1038/s42003-020-01382-6

Adaptation by copy number variation increases insecticide resistance in the fall armyworm
Cited by: 40
Author(s): Sylvie Gimenez, Heba Abdelgaffar, Gaëlle Le Goff, Frédérique Hilliou, Carlos A. Blanco, Sabine Hänniger, Anthony Bretaudeau, Fabrice Legeai, Nicolas Nègre, Juan Luís Jurat-Fuentes, Emmanuelle d’Alençon, Kiwoong Nam
Software Mentions: 5
Published: about 4 years ago

10.3389/fimmu.2021.627036

Single Cell RNA-Seq and Machine Learning Reveal Novel Subpopulations in Low-Grade Inflammatory Monocytes With Unique Regulatory Circuits
Cited by: 8
Author(s): Jiyoung Lee, Shuo Geng, Song Li, Liwu Li
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12864-020-07111-x

Genome-wide patterns of differentiation within and among U.S. commercial honey bee stocks
Cited by: 19
Author(s): Perot Saelao, Michael Simone-Finstrom, Arián Avalos, Lelania Bilodeau, Robert G. Danka, Lilia de Guzman, Frank D. L. Rinkevich, Philip Tokarz
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pgen.1008420

Physiological and genomic evidence that selection on the transcription factor Epas1 has altered cardiovascular function in high-altitude deer mice
Cited by: 50
Author(s): Rena M. Schweizer, Jonathan P. Velotta, Catherine M. Ivy, Matthew R. Jones, Sarah M. Muir, Gideon S. Bradburd, Jay F. Storz, Graham R. Scott, Zachary A. Cheviron
Software Mentions: 5
Published: about 5 years ago

10.3389/fgene.2020.505441

SCCNV: A Software Tool for Identifying Copy Number Variation From Single-Cell Whole-Genome Sequencing
Cited by: 5
Author(s): Xiao Dong, Lei Zhang, Xiaoxiao Hao, Tao Wang, Jan Vijg
Software Mentions: 5
Published: about 4 years ago

10.1186/s40064-016-2743-y

Identification of differentially expressed genes implicated in peel color (red and green) of Dimocarpus confinis
Cited by: 9
Author(s): Jun Fan, Xiuping Chen, Wen-shun Hu, Shaoquan Zheng
Software Mentions: 5
Published: over 8 years ago

10.1016/j.celrep.2021.108735

Specification and epigenomic resetting of the pig germline exhibit conservation with the human lineage
Cited by: 38
Author(s): Qifan Zhu, Fei Sang, Sarah Withey, Walfred W.C. Tang, Sabine Dietmann, Doris Klisch, Priscila Ramos‐Ibeas, Haixin Zhang, Cristina E. Requena, Petra Hájková, Matt Loose, M. Azim Surani, Ramiro Alberio
Software Mentions: 5
Published: almost 4 years ago

10.1186/1755-8794-6-S2-S6

BioBin: a bioinformatics tool for automating the binning of rare variants using publicly available biological knowledge
Cited by: 33
Author(s): Carrie Moore, John R. Wallace, Alex T. Frase, Sarah A. Pendergrass, Marylyn D. Ritchie
Software Mentions: 5
Published: over 11 years ago

10.1038/sdata.2018.142

A multi-omic atlas of the human frontal cortex for aging and Alzheimer’s disease research
Cited by: 306
Author(s): Philip L. De Jager, Yiyi Ma, Cristin McCabe, Jishu Xu, Badri N. Vardarajan, Daniel Felsky, Hans‐Ulrich Klein, Charles C. White, Mette A. Peters, Ben Lodgson, Parham Nejad, Ao Tang, Lara M. Mangravite, Lei Yu, Chris Gaiteri, Sara Mostafavi, Julie A. Schneider, David A. Bennett
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0241861

Lipopolysaccharide triggers different transcriptional signatures in taurine and indicine cattle macrophages: Reactive oxygen species and potential outcomes to the development of immune response to infections
Cited by: 5
Author(s): Raquel Morais de Paiva Daibert, Carlos Alberto Oliveira de Biagi, Felipe de Oliveira Vieira, Marcos Vinícius Gualberto Barbosa da Silva, Eugênio D. Hottz, Mariana Brandi Mendonça Pinheiro, Daniele Ribeiro de Lima Reis Faza, Hyago Passe Pereira, Marta Fonseca Martins, Humberto M. Brandão, M. A. Machado, Wanessa A. Carvalho
Software Mentions: 5
Published: about 4 years ago

10.1186/s13059-020-02188-9

Convergent network effects along the axis of gene expression during prostate cancer progression
Cited by: 14
Author(s): Konstantina Charmpi, Tiannan Guo, Qing Zhong, Ulrich Wagner, Rui Sun, Nora C. Toussaint, Christine Fritz, Chunhui Yuan, Hao Chen, Niels J. Rupp, Ailsa J. Christiansen, Dorothea Rutishauser, Jan H. Rüschoff, Christian Daniel Fankhauser, Karim Saba, Cédric Poyet, Thomas Hermanns, Kathrin Oehl, Ariane L. Moore, Christian Beisel, Laurence Calzone, Loredana Martignetti, Qiushi Zhang, Yi Zhu, María Rodríguez Martínez, Matteo Manica, Michael C. Haffner, Ruedi Aebersold, Peter J. Wild, Andreas Beyer
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12284-019-0322-x

Signatures of differential selection in chloroplast genome between japonica and indica
Cited by: 17
Author(s): Lin Cheng, Jungrye Nam, Sang-Ho Chu, Rungnapa Phitaktansakul, Myeong-Hyeon Min, Cheng Yuan, Ji-Min Yoo, Jee-Su Kang, Kyu‐Won Kim, Yong‐Jin Park
Software Mentions: 5
Published: over 5 years ago

10.1111/febs.15292

Fibroblast‐specific genome‐scale modelling predicts an imbalance in amino acid metabolism in Refsum disease
Cited by: 4
Author(s): Agnieszka B. Wegrzyn, Katharina Herzog, Albert Gerding, Marcel Kwiatkowski, Justina C. Wolters, Amalia M. Dolga, A. E. M. van Lint, Ronald J. A. Wanders, Hans R. Waterham, Barbara M. Bakker
Software Mentions: 5
Published: over 4 years ago

10.15252/msb.202010138

Natural variants suppress mutations in hundreds of essential genes
Cited by: 10
Author(s): Leopold Parts, Amandine Batté, Maykel Lopes, Michael Wai-Keong Yuen, Meredith Laver, Bryan-Joseph San Luis, Jia-Xing Yue, Carles Pons, Elise Eray, Patrick Aloy, Gianni Liti, Jolanda van Leeuwen
Software Mentions: 5
Published: over 3 years ago

10.3390/biology10060503

Discovering Cellular Mitochondrial Heteroplasmy Heterogeneity with Single Cell RNA and ATAC Sequencing
Cited by: 6
Author(s): Aidan S. Marshall, Nick Jones
Software Mentions: 5
Published: over 3 years ago

10.1093/gigascience/giy049

Population genomic data reveal genes related to important traits of quail
Cited by: 23
Author(s): Yan Wu, Yaolei Zhang, Zhuocheng Hou, Guangyi Fan, Jinsong Pi, Shuai Sun, Chen Jiang, Huaqiao Liu, Xiao Du, Jie Shen, Gang Hu, Wenbin Chen, Angelo Pan, Yin PingPing, Xiaoli Chen, Yuejin Pu, Zhonghu He, Zhen-Hua Liang, Jianbo Jian, Hao Zhang, Bin Wu, Jing Sun, Jianwei Chen, Hu Tao, Ting Yang, Hong‐Wei Xiao, Huan Yang, Chuanwei Zheng, Mingzhou Bai, Xiaodong Fang, David W. Burt, Wen Wang, Qingyi Li, Xun Xu, Chengfeng Li, Huanming Yang, Jian Wang, Ning Yang, Xin Liu, Junzheng Du
Software Mentions: 4
Published: over 6 years ago

10.1002/cam4.2581

Clinical candidate and genistein analogue AXP107‐11 has chemoenhancing functions in pancreatic adenocarcinoma through G protein‐coupled estrogen receptor signaling
Cited by: 11
Author(s): Fahmi Mesmar, Bingbing Dai, Ahmed Atef Ibrahim, Linnea Hases, Mohammed Hakim Jafferali, Jithesh J. Augustine, Sebastian DiLorenzo, Ya’an Kang, Yang Zhao, Jing Wang, Michael Kim, Chin Yo Lin, Anders Berkenstam, Jason B. Fleming, Cecilia Williams
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.67577

Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation in Drosophila
Cited by: 57
Author(s): Heather E. Machado, Alan O. Bergland, Ryan W. Taylor, Susanne Tilk, Emily L. Behrman, Kelly A. Dyer, Daniel K. Fabian, Thomas Flatt, Josefa González, Talia L. Karasov, Bernard Kim, Iryna Kozeretska, Brian P. Lazzaro, Thomas J. S. Merritt, John E. Pool, Katherine R. O’Brien, Subhash Rajpurohit, Paula R. Roy, Stephen W. Schaeffer, Svitlana Serga, Paul S. Schmidt, Dmitri A. Petrov
Software Mentions: 4
Published: over 3 years ago

10.1186/s13059-020-02257-z

Evolutionary conservation and divergence of the human brain transcriptome
Cited by: 22
Author(s): William G Pembroke, Christopher Hartl, Daniel H. Geschwind
Software Mentions: 4
Published: almost 4 years ago

10.1093/g3journal/jkab190

Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes
Cited by: 3
Author(s): Jaclyn M. Noshay, Zhikai Liang, Peng Zhou, Peter A. Crisp, Alexandre P. Marand, Candice N. Hirsch, Robert J. Schmitz, Nathan M. Springer
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0166862

Drosophila DDX3/Belle Exerts Its Function Outside of the Wnt/Wingless Signaling Pathway
Cited by: 1
Author(s): Fabian H. Jenny, Konrad Basler
Software Mentions: 4
Published: almost 8 years ago

10.1038/s42003-020-01214-7

Genome sequence of segmented filamentous bacteria present in the human intestine
Cited by: 20
Author(s): Hans Jonsson, Luisa W. Hugerth, John Sundh, E. Lundin, Anders F. Andersson
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0214677

PAN-INTACT enables direct isolation of lineage-specific nuclei from fibrous tissues
Cited by: 8
Author(s): Samadrita Bhattacharyya, Adwait Amod Sathe, Minoti Bhakta, Chao Xing, Nikhil V. Munshi
Software Mentions: 4
Published: over 5 years ago

10.1128/mBio.00617-20

EspFu-Mediated Actin Assembly Enhances Enteropathogenic Escherichia coli Adherence and Activates Host Cell Inflammatory Signaling Pathways
Cited by: 12
Author(s): Fernando Henrique Martins, Ashwani Kumar, Cecília M. Abe, Enéas Carvalho, Milton Yutaka Nishiyama-Jr, Chao Xing, Vanessa Sperandio, Waldir P. Elias
Software Mentions: 4
Published: over 4 years ago

10.3389/fimmu.2020.00445

Perirenal Adipose Tissue Displays an Age-Dependent Inflammatory Signature Associated With Early Graft Dysfunction of Marginal Kidney Transplants
Cited by: 6
Author(s): Romain Boissier, Pauline François, B. Gondran Tellier, Meunier Maité, Luc Lyonnet, Stéphanie Simoncini, Jéremy Magalon, Tristan Legris, Alexis Laurent, Laurent Guy, Françoise Dignat-George, G. Karsenty, Stéphane Burtey, É. Lechevallier, Florence Sabatier, Pascale Paul
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-021-87635-8

H3K4me2 ChIP-Seq reveals the epigenetic landscape during mushroom formation and novel developmental regulators of Schizophyllum commune
Cited by: 9
Author(s): Peter Jan Vonk, Robin A. Ohm
Software Mentions: 4
Published: over 3 years ago

10.3390/cells9112452

Photochemotherapy Induces Interferon Type III Expression via STING Pathway
Cited by: 0
Author(s): Edyta Biskup, Brian D. Larsen, Leonor Rib, Lasse Folkersen, Omid Niazi, Maria R. Kamstrup, Claus Storgaard Sørensen
Software Mentions: 4
Published: about 4 years ago

10.1186/s12920-021-00916-z

Identification of super enhancer-associated key genes for prognosis of germinal center B-cell type diffuse large B-cell lymphoma by integrated analysis
Cited by: 6
Author(s): Xi Li, Yan Duan, Yuxia Hao
Software Mentions: 4
Published: over 3 years ago

10.1186/s12920-020-00820-y

Mutational profiling of micro-dissected pre-malignant lesions from archived specimens
Cited by: 4
Author(s): Daniela Nachmanson, J. S. Steward, Huazhen Yao, Adam Officer, Eliza Jeong, Thomas J. O’Keefe, Farnaz Hasteh, Kristen Jepsen, Gillian L. Hirst, Laura J. Esserman, Alexander D. Borowsky, Olivier Harismendy
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pgen.1007376

Colorectal cancer mutational profiles correlate with defined microbial communities in the tumor microenvironment
Cited by: 59
Author(s): Michael B. Burns, Emmanuel Montassier, Juan E. Abrahante, Sambhawa Priya, David Niccum, Alexander Khoruts, Timothy K. Starr, Dan Knights, Ran Blekhman
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-021-07627-w

Draft genome of a biparental beetle species, Lethrus apterus
Cited by: 0
Author(s): Nikolett Nagy, R. Rácz, Oliver Rimington, Szilárd Póliska, Pablo Orozco‐terWengel, Michael William Bruford, Zoltán Barta
Software Mentions: 4
Published: over 3 years ago

10.1186/s12859-016-1276-2

dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data
Cited by: 87
Author(s): Sergi Sayols, Denise Scherzinger, H. Klein
Software Mentions: 4
Published: about 8 years ago

10.3389/fcell.2018.00164

The Transcriptome of Human Endometrial Mesenchymal Stem Cells Under TGFβR Inhibition Reveals Improved Potential for Cell-Based Therapies
Cited by: 31
Author(s): Shanti Gurung, Sarah Williams, James A. Deane, Jerome A. Werkmeister, Caroline E. Gargett
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12920-015-0130-0

TumorTracer: a method to identify the tissue of origin from the somatic mutations of a tumor specimen
Cited by: 42
Author(s): Andrea Marion Marquard, Nicolai J. Birkbak, Cecilia Engel Thomas, Francesco Favero, Marcin Krzystanek, Céline Lefèbvre, Charles Ferté, Mariam Jamal‐Hanjani, Gareth A. Wilson, Seema Shafi, Charles Swanton, Fabrice André, Zoltán Szállási, Aron C. Eklund
Software Mentions: 4
Published: about 9 years ago

10.1111/eva.12944

Seascape genomics as a new tool to empower coral reef conservation strategies: An example on north‐western Pacific Acropora digitifera
Cited by: 26
Author(s): Oliver Selmoni, Estelle Rochat, Gaël Lecellier, Véronique Berteaux‐Lecellier, Stéphane Joost
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-018-26416-2

An improved assembly and annotation of the melon (Cucumis melo L.) reference genome
Cited by: 62
Author(s): Valentino Ruggieri, Konstantinos G. Alexiou, Jordi Morata, Jason Argyris, Marta Pujol, Ryoichi Yano, Satoko Nonaka, Hiroshi Ezura, David Latrasse, Adnane Boualem, Moussa Benhamed, Abdelhafid Bendahmane, Riccardo Aiese Cigliano, Walter Sanseverino, Pere Puigdomènech, Josep M. Casacuberta, Jordi García-Más
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.49748

Genetically diverse uropathogenic Escherichia coli adopt a common transcriptional program in patients with UTIs
Cited by: 41
Author(s): Anna Sintsova, Arwen E Frick-Cheng, Sara N. Smith, Ali Pirani, Sargurunathan Subashchandrabose, Evan S. Snitkin, Harry L. T. Mobley
Software Mentions: 4
Published: about 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

10.1111/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

10.1186/1471-2105-15-281

BESST - Efficient scaffolding of large fragmented assemblies
Cited by: 136
Author(s): Kristoffer Sahlin, Francesco Vezzi, Björn Nystedt, Joakim Lundeberg, Lars Arvestad
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-018-4751-5

Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast
Cited by: 33
Author(s): Cene Gostinčar, Jason E. Stajich, Jerneja Zupančič, Polona Zalar, Nina Gunde‐Cimerman
Software Mentions: 3
Published: over 6 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

Projects: pypi: picard

Papers Mentioning picard 243