pypi: bcbio-nextgen | Projects | Ecosyste.ms: Papers

10.1186/s12859-016-1241-0

systemPipeR: NGS workflow and report generation environment
Cited by: 148
Author(s): Tyler W. H. Backman, Thomas Girke
Software Mentions: 19
Published: about 8 years ago

CIPHER: a flexible and extensive workflow platform for integrative next-generation sequencing data analysis and genomic regulatory element prediction
Cited by: 24
Author(s): Carlos Guzmán, Iván D’Orso
Software Mentions: 10
Published: over 7 years ago

10.1186/s12859-018-2287-y

miRge 2.0 for comprehensive analysis of microRNA sequencing data
Cited by: 54
Author(s): Yin Lu, Alexander S. Baras, Marc K. Halushka
Software Mentions: 9
Published: over 6 years ago

10.1038/s41597-019-0095-5

Multi omics analysis of fibrotic kidneys in two mouse models
Cited by: 25
Author(s): Mira Pavkovic, Lorena Pantano, Cory V. Gerlach, Sergine Brutus, Sarah A. Boswell, Robert A. Everley, Jagesh V. Shah, Shannan Ho Sui, Vishal S. Vaidya
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0072614

DistMap: A Toolkit for Distributed Short Read Mapping on a Hadoop Cluster
Cited by: 46
Author(s): Ram Vinay Pandey, Christian Schlötterer
Software Mentions: 6
Published: about 11 years ago

10.1016/j.xpro.2020.100079

Using Chromatin Accessibility to Delineate Therapeutic Subtypes in Pancreatic Cancer Patient-Derived Cell Lines
Cited by: 4
Author(s): Holly Brunton, Ian Garner, Ulla-Maja Bailey, Rosanna Upstill-Goddard, Peter J. Bailey
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pone.0243807

Optimised generation of iPSC-derived macrophages and dendritic cells that are functionally and transcriptionally similar to their primary counterparts
Cited by: 17
Author(s): Susan J. Monkley, Jayendra Kumar Krishnaswamy, Melker Göransson, Maryam Clausen, Johan Meuller, Kristofer Thörn, Ryan Hicks, Stephen Delaney, Louise Stjernborg
Software Mentions: 6
Published: almost 4 years ago

10.1038/s41598-019-40786-1

Integrated analysis of relapsed B-cell precursor Acute Lymphoblastic Leukemia identifies subtype-specific cytokine and metabolic signatures
Cited by: 18
Author(s): M. Schroêder, Lorenz Bastian, Cornelia Eckert, Nicola Gökbuget, Alva Rani James, Jutta Ortiz Tanchez, Cornelia Schlee, Konstandina Isaakidis, Björn Häupl, Katharina Baum, Oscar Arturo Migueles Lozano, Khouloud Kouidri, Kuan‐Ting Pan, Henning Urlaub, Stefan Schwartz, Thomas Burmeister, Arend von Stackelberg, Dieter Hoelzer, Heike Pfeiffer, Michael A. Rieger, Stefanie Göllner, Thomas Oellerich, Martin Horstman, Martin Schrappe, Jana Wolf, Renate Kirschner-Schwabe, Monika Brüggemann, Carsten Müller‐Tidow, Hubert Serve, Martin Neumann, Claudia D. Baldus
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-014-0577-x

Churchill: an ultra-fast, deterministic, highly scalable and balanced parallelization strategy for the discovery of human genetic variation in clinical and population-scale genomics
Cited by: 109
Author(s): Benjamin J. Kelly, James Fitch, Yangqiu Patrick Hu, Donald J. Corsmeier, Huachun Zhong, Amy Wetzel, Russell D Nordquist, David L. Newsom, Peter White
Software Mentions: 5
Published: almost 10 years ago

10.1186/s13041-021-00835-1

Altered hippocampal transcriptome dynamics following sleep deprivation
Cited by: 14
Author(s): Marie E. Gaine, Ethan Bahl, Snehajyoti Chatterjee, Jacob J. Michaelson, Ted Abel, Lisa C. Lyons
Software Mentions: 5
Published: over 3 years ago

10.1530/ERC-19-0474

A xenograft and cell line model of SDH-deficient pheochromocytoma derived from Sdhb+/− rats
Cited by: 15
Author(s): James F. Powers, Brent Cochran, James D. Baleja, Hadley D. Sikes, Andrew Pattison, Xue Zhang, Inna Lomakin, Annette Shepard-Barry, Karel Pacák, Sun Jin Moon, Troy F. Langford, Kassi T. Stein, Richard W. Tothill, Ying-Bin Ouyang, Arthur S. Tischler
Software Mentions: 5
Published: over 4 years ago

10.1186/s12859-019-3219-1

uap: reproducible and robust HTS data analysis
Cited by: 12
Author(s): Christoph Kämpf, Michael Specht, Alexander Scholz, Sven-Holger Puppel, Gero Doose, Kristin Reiche, Jana Schor, Jörg Hackermüller
Software Mentions: 5
Published: almost 5 years ago

10.3389/fnmol.2019.00236

Sex-Dependent Changes in miRNA Expression in the Bed Nucleus of the Stria Terminalis Following Stress
Cited by: 16
Author(s): Maria Mavrikaki, Lorena Pantano, David N. Potter, Maximilian Rogers-Grazado, Eleni Anastasiadou, Frank J. Slack, Sami S. Amr, Kerry J. Ressler, Nikolaos P. Daskalakis, Elena H. Chartoff
Software Mentions: 5
Published: about 5 years ago

10.1186/s12864-020-07218-1

Targeted mutagenesis of ∆5 and ∆6 fatty acyl desaturases induce dysregulation of lipid metabolism in Atlantic salmon (Salmo salar)
Cited by: 6
Author(s): Yang Jin, Alex K. Datsomor, Rolf Erik Olsen, Jon Olav Vik, Jacob Torgersen, Rolf B. Edvardsen, Anna Wargelius, Per Winge, Fabian Grammes
Software Mentions: 4
Published: about 4 years ago

10.1186/s12859-015-0795-6

TOGGLE: toolbox for generic NGS analyses
Cited by: 20
Author(s): Cécile Monat, Christine Tranchant‐Dubreuil, Ayité Kougbeadjo, Cédric Farcy, Enrique Ortega-Abboud, Souhila Amanzougarene, Sébastien Ravel, Mawussé Agbessi, Julie Orjuela, Marilyne Summo, François Sabot
Software Mentions: 4
Published: about 9 years ago

10.1038/s41598-018-25022-6

DNAp: A Pipeline for DNA-seq Data Analysis
Cited by: 13
Author(s): Jason Causey, Cody Ashby, Karl Walker, Zhiping Paul Wang, Mary Qu Yang, Yuanfang Guan, Jason H. Moore, Xiuzhen Huang
Software Mentions: 4
Published: over 6 years ago

10.18632/oncotarget.26322

Differential gene expression in human tissue resident regulatory T cells from lung, colon, and blood
Cited by: 13
Author(s): Magdalena Niedzielska, Elisabeth Israelsson, B. Angermann, Ben S. Sidders, Maryam Clausen, Matthew C. Catley, Rajneesh Malhotra, Céline Dumont
Software Mentions: 4
Published: about 6 years ago

10.1038/s12276-021-00559-1

Practical prediction model of the clinical response to programmed death-ligand 1 inhibitors in advanced gastric cancer
Cited by: 9
Author(s): Myung‐Giun Noh, Young‐In Yoon, Gihyeon Kim, Hyun Kim, Eulgi Lee, Yeongmin Kim, Chang-Ho Park, Kyung‐Hwa Lee, Hansoo Park
Software Mentions: 4
Published: almost 4 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

10.1186/s40168-019-0650-5

Species-specific enhancement of enterohemorrhagic E. coli pathogenesis mediated by microbiome metabolites
Cited by: 93
Author(s): Alessio Tovaglieri, Alexandra Sontheimer-Phelps, Annelies Geirnaert, Rachelle Prantil‐Baun, Diogo M. Camacho, David B. Chou, Hossein Baharvand, Tomás de Wouters, Magdalena Kasendra, Michael Super, Mark Cartwright, Camilla A. Richmond, David T. Breault, Christophe Lacroix, Donald E. Ingber
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-94292-4

Prevalence of cancer susceptibility variants in patients with multiple Lynch syndrome related cancers
Cited by: 7
Author(s): Yoon Young Choi, Su‐Jin Shin, Jae Eun Lee, Lisa Madlensky, Seung Tae Lee, Ji Soo Park, Jeong-Hyeon Jo, Hyun Ki Kim, Daniela Nachmanson, Xiaojun Xu, Sung Hoon Noh, Jae‐Ho Cheong, Olivier Harismendy
Software Mentions: 4
Published: over 3 years ago

10.1038/srep14283

SeqMule: automated pipeline for analysis of human exome/genome sequencing data
Cited by: 56
Author(s): Yunfei Guo, Xiaolei Ding, Yufeng Shen, Gholson J. Lyon, Kai Wang
Software Mentions: 3
Published: about 9 years ago

10.1186/s12859-017-1747-0

Investigating reproducibility and tracking provenance – A genomic workflow case study
Cited by: 56
Author(s): Sehrish Kanwal, Farah Zaib Khan, Andrew Lonie, Richard O. Sinnott
Software Mentions: 3
Published: over 7 years ago

10.1186/s12859-018-2440-7

Comparing the performance of selected variant callers using synthetic data and genome segmentation
Cited by: 35
Author(s): Xiaopeng Bian, Bin Zhu, Mingyi Wang, Ying Hu, Qingrong Chen, Cu Nguyen, Belynda Hicks, Daoud Meerzaman
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-020-07224-3

Red panda: a novel method for detecting variants in single-cell RNA sequencing
Cited by: 0
Author(s): Adam Cornish, Shrabasti Roychoudhury, Krishna Sarma, Suravi Pramanik, Kishor K. Bhakat, Andrew T. Dudley, Nitish K. Mishra, Chittibabu Guda
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0248886

Detection of new drivers of frequent B-cell lymphoid neoplasms using an integrated analysis of whole genomes
Cited by: 11
Author(s): Adrián Mosquera Orgueira, Roi Ferreiro Ferro, José Ángel Díaz Arias, Cristina Santos, Beatriz Antelo Rodríguez, Laura Bao Pérez, Natalia Alonso Vence, Ággeles Bendaña López, Ayelén Melisa Blanco, Paula Melero Valentín, And Res Peleteiro Raindo, Marcos Pérez López, Manuel Mateo Pérez Encinas, Marta Sonia González Pérez, Marianela Rodríguez, José Luis Bello López
Software Mentions: 3
Published: over 3 years ago

10.3390/cancers13061340

Detection of Rare Germline Variants in the Genomes of Patients with B-Cell Neoplasms
Cited by: 9
Author(s): Adrián Mosquera Orgueira, Marcos Pérez López, Andrés Peleteiro Raíndo, José Ángel Díaz Arias, Beatriz Antelo Rodríguez, Laura Bao Pérez, Natalia Alonso Vence, Ángeles Bendaña López, Ayelén Melisa Blanco, Paula Melero Valentín, Roi Ferreiro Ferro, Cristina Santos, Marianela Rodríguez, Marta Sonia González Pérez, Manuel Pérez‐Encinas, José Luis Bello López
Software Mentions: 3
Published: over 3 years ago

10.12688/f1000research.18142.2

Visualization of the small RNA transcriptome using seqclusterViz
Cited by: 6
Author(s): Lorena Pantano, Francisco Pantano, Eulàlia Martı́, Shannan Ho Sui
Software Mentions: 3
Published: over 5 years ago

10.3389/fonc.2019.01525

Involvement of Glutathione Depletion in Selective Cytotoxicity of Oridonin to p53-Mutant Esophageal Squamous Carcinoma Cells
Cited by: 19
Author(s): Yinchao Li, Nana Li, Jianxiang Shi, Tanzeel Ahmed, Hong‐Min Liu, Guo Liang Jiang, Wenxue Tang, Yongjun Guo, Qi Zhang
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13075-018-1702-0

Cytokine production by activated plasmacytoid dendritic cells and natural killer cells is suppressed by an IRAK4 inhibitor
Cited by: 38
Author(s): Karin Hjorton, Niklas Hagberg, Elisabeth Israelsson, Lisa Jinton, Olof Berggren, Johanna K. Sandling, Kristofer Thörn, John Mo, Maija‐Leena Eloranta, Lars Rönnblom
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-018-21727-w

Bronchial extracellular matrix from COPD patients induces altered gene expression in repopulated primary human bronchial epithelial cells
Cited by: 32
Author(s): Ulf Hedström, Oskar Hällgren, Lisa Öberg, Amy DeMicco, Outi Vaarala, Gunilla Westergren‐Thorsson, Xin Zhou
Software Mentions: 3
Published: over 6 years ago

10.3389/fnagi.2018.00155

Associations of MAP2K3 Gene Variants With Superior Memory in SuperAgers
Cited by: 19
Author(s): Matthew J. Huentelman, Ignazio S. Piras, Ashley L. Siniard, Matthew De Both, Ryan Richholt, Chris Balak, Pouya Jamshidi, Eileen H. Bigio, Sandra Weıntraub, Emmaleigh Loyer, Marek-Marsel Mesulam, Changiz Geula, Emily Rogalskı
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0132868

elPrep: High-Performance Preparation of Sequence Alignment/Map Files for Variant Calling
Cited by: 23
Author(s): Charlotte Herzeel, Pascal Costanza, Dries Decap, Jan Fostier, Joke Reumers
Software Mentions: 2
Published: over 9 years ago

10.1007/s00109-019-01792-y

Prospect and challenge of detecting dynamic gene copy number increases in stem cells by whole genome sequencing
Cited by: 2
Author(s): Ulrike Fischer, Christina Backes, Tobias Fehlmann, Valentina Galata, Andreas Keller, Eckart Meese
Software Mentions: 2
Published: over 5 years ago

10.1016/j.dib.2019.104022

Data on somatic mutations obtained by whole exome sequencing of FFPE tissue samples from Russian patients with prostate cancer
Cited by: 0
Author(s): Anastasia S. Nikitina, Е. И. Шарова, S. A. Danilenko, Oksana V. Selezneva, Liubov O. Skorodumova, Aleksandra V Kanygina, Konstantin Babalyan, A.O. Vasiliev, А. В. Говоров, E. A. Prilepskaya, Dmitry Pushkar, Elena S. Kostryukova, Edward V. Generozov
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-59243-5

Novel Mutation Hotspots within Non-Coding Regulatory Regions of the Chronic Lymphocytic Leukemia Genome
Cited by: 4
Author(s): Adrián Mosquera Orgueira, Beatriz Antelo, José Ángel Díaz Arias, Nicolas Varela, Natalia Alonso Vence, Marta Sonia González Pérez, José Luis Bello López
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-021-99347-0

Enhancing adoptive CD8 T cell therapy by systemic delivery of tumor associated antigens
Cited by: 5
Author(s): Ditte Jæhger, Mie Linder Hübbe, Martin Kisha Kræmer, Gael Clergeaud, André Vidas Olsen, Camilla Stavnsbjerg, Mette N. Wiinholt, Andreas Kjær, Jonas Rosager Henriksen, Anders Elias Hansen, Thomas Lars Andresen
Software Mentions: 1
Published: about 3 years ago

10.1093/jncics/pkab028

Preexisting Somatic Mutations of Estrogen Receptor Alpha (<i>ESR1</i>) in Early-Stage Primary Breast Cancer
Cited by: 15
Author(s): Malin Dahlgren, Anthony George, Christian Brueffer, Sergii Gladchuk, Yilun Chen, Johan Vallon‐Christersson, Cecilia Hegardt, Jari Häkkinen, Lisa Rydén, Martin Malmberg, Christer Larsson, Sofia K. Gruvberger-Saal, Anna Ehinger, Niklas Loman, Åke Borg, Lao H. Saal
Software Mentions: 1
Published: over 3 years ago

10.1186/s13073-015-0191-x

Cpipe: a shared variant detection pipeline designed for diagnostic settings
Cited by: 75
Author(s): Simon Sadedin, Harriet Dashnow, Paul James, Melanie Bahlo, Denis C. Bauer, Andrew Lonie, Sebastian Lunke, Ivan Macciocca, Jason P. Ross, Kirby Siemering, Zornitza Stark, Susan White, Graham R. Taylor, Clara Gaff, Alicia Oshlack, Natalie Thorne
Software Mentions: 1
Published: over 9 years ago

10.3389/fgene.2021.643546

High Genetic Heterogeneity in Chinese Patients With Waardenburg Syndrome Revealed by Next-Generation Sequencing
Cited by: 5
Author(s): Sen Zhang, Hongen Xu, Yongan Tian, Danhua Liu, Xinyue Hou, Beiping Zeng, Bei Chen, Huanfei Liu, Ruijun Li, Xiaohua Li, Bin Zuo, Ryan W. Tang, Wenxue Tang
Software Mentions: 1
Published: over 3 years ago

10.3390/genes12040484

Novel GRHL2 Gene Variant Associated with Hearing Loss: A Case Report and Review of the Literature
Cited by: 2
Author(s): Katarina Trebušak Podkrajšek, Tine Tesovnik, Nina Božanić Urbančič, Saba Battelino
Software Mentions: 1
Published: over 3 years ago

10.1038/srep20768

Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry
Cited by: 47
Author(s): Pavel Flegontov, Piya Changmai, Anastassiya Zidkova, Maria D. Logacheva, N. Ezgi Altınışık, Olga Flegontova, Mikhail S. Gelfand, Evgeny S. Gerasimov, Ekaterina E. Khrameeva, Olga P. Konovalova, Tatyana V. Neretina, Yuri Nikolsky, George Starostin, Vita Stepanova, Igor V. Travinsky, Martin Tříska, Petr Tříska, Tatiana V. Tatarinova
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12907-015-0004-6

A reliable method for the detection of BRCA1 and BRCA2 mutations in fixed tumour tissue utilising multiplex PCR-based targeted next generation sequencing
Cited by: 47
Author(s): Gillian Ellison, Shuwen Huang, T. Hedley Carr, Andrew Wallace, Miika J. Ahdesmäki, Sanjeev S. Bhaskar, John Mills
Software Mentions: 1
Published: over 9 years ago

Projects: pypi: bcbio-nextgen

Papers Mentioning bcbio-nextgen 43