pypi: caller | Projects | Ecosyste.ms: Papers

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

10.1371/journal.pone.0054835

Base-Calling Algorithm with Vocabulary (BCV) Method for Analyzing Population Sequencing Chromatograms
Cited by: 10
Author(s): Yuri S. Fantin, Alexey D. Neverov, Alexander V. Favorov, Maria V. Alvarez-Figueroa, Svetlana I. Braslavskaya, М. А. Гордукова, И. В. Карандашова, Konstantin V. Kuleshov, Anna I. Myznikova, M. S. Polishchuk, Denis A. Reshetov, Yana A. Voiciehovskaya, А. Миронов, Vladimir Chulanov
Software Mentions: 6
Published: almost 12 years ago

10.1016/j.ccell.2017.03.007

TIAM1 Antagonizes TAZ/YAP Both in the Destruction Complex in the Cytoplasm and in the Nucleus to Inhibit Invasion of Intestinal Epithelial Cells
Cited by: 69
Author(s): Zoi Diamantopoulou, Gavin R M White, Muhammad Zaki Hidayatullah Fadlullah, Marcel Dreger, Karen Pickering, Joe Maltas, Garry Ashton, Ruth MacLeod, George S. Baillie, Valérie Kouskoff, Georges Lacaud, Graeme I. Murray, Owen J. Sansom, Adam Hurlstone, Angeliki Malliri
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.pgen.1008799

BRM-SWI/SNF chromatin remodeling complex enables functional telomeres by promoting co-expression of TRF2 and TRF1
Cited by: 9
Author(s): Shu Wu, Yuanlong Ge, Xiaocui Li, Yiding Yang, Huan Zhou, Kaixuan Lin, Zepeng Zhang, Yong Zhao
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pcbi.1006731

Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes
Cited by: 19
Author(s): Ivar Grytten, Knut Dagestad Rand, Alexander J. Nederbragt, Geir Storvik, Ingrid K. Glad, Geir Kjetil Sandve
Software Mentions: 5
Published: almost 6 years ago

10.1128/mSystems.00208-20

Combined RNAseq and ChIPseq Analyses of the BvgA Virulence Regulator of Bordetella pertussis
Cited by: 7
Author(s): Loïc Coutte, Rudy Antoine, Stéphanie Slupek, Luis Solans, Julien Derop, Amélie Bonnefond, David Hot, Camille Locht
Software Mentions: 3
Published: over 4 years ago

10.1186/s12859-015-0458-7

ViVaMBC: estimating viral sequence variation in complex populations from illumina deep-sequencing data using model-based clustering
Cited by: 12
Author(s): Bie Verbist, Lieven Clement, Joke Reumers, Kim Thys, A. Vapirev, Willem Talloen, Yves Wetzels, Joris Meys, Jeroen Aerssens, Luc Bijnens, Olivier Thas
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12864-018-4508-1

CoVaCS: a consensus variant calling system
Cited by: 22
Author(s): Matteo Chiara, Silvia Gioiosa, Giovanni Chillemi, Mattia D’Antonio, Tiziano Flati, Ernesto Picardi, Federico Zambelli, David S. Horner, Graziano Pesole, Tiziana Castrignanò
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-018-4749-z

Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs
Cited by: 11
Author(s): Matthew T. Oetjens, Axel Martin, Krishna R. Veeramah, Jeffrey M. Kidd
Software Mentions: 3
Published: over 6 years ago

10.1007/s10549-018-4798-7

FFPE breast tumour blocks provide reliable sources of both germline and malignant DNA for investigation of genetic determinants of individual tumour responses to treatment
Cited by: 6
Author(s): Anna Wilkins, Ritika Chauhan, Alistair G. Rust, Alex Pearson, Frances Daley, Floriana Manodoro, Kerry Fenwick, Judith Bliss, John Yarnold, Navita Somaiah
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-61514-0

Proximity-dependent biotin labelling reveals CP190 as an EcR/Usp molecular partner
Cited by: 17
Author(s): M. Yu. Mazina, Rustam H. Ziganshin, Mikhail D. Magnitov, Anton Golovnin, Nadezhda E. Vorobyeva
Software Mentions: 3
Published: over 4 years ago

10.1186/s13148-016-0274-6

Global DNA methylation profiling reveals new insights into epigenetically deregulated protein coding and long noncoding RNAs in CLL
Cited by: 40
Author(s): Santhilal Subhash, Per‐Ola Andersson, Subazini Thankaswamy Kosalai, Chandrasekhar Kanduri, Meena Kanduri
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0143199

Reliably Detecting Clinically Important Variants Requires Both Combined Variant Calls and Optimized Filtering Strategies
Cited by: 39
Author(s): Matthew A. Field, Vicky Cho, Thomas D. Andrews, Christopher C. Goodnow
Software Mentions: 2
Published: about 9 years ago

10.1038/srep19006

Knock-down of ZBED6 in insulin-producing cells promotes N-cadherin junctions between beta-cells and neural crest stem cells in vitro
Cited by: 5
Author(s): Xuan Wang, Bin Xie, Qingxu Yu, Ola Wallerman, Svitlana Vasylovska, Leif Andersson, Elena N. Kozlova, Nils Welsh
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pcbi.1003494

Universal Count Correction for High-Throughput Sequencing
Cited by: 17
Author(s): Tatsunori Hashimoto, Matthew D. Edwards, David K. Gifford
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2105-8-92

Discarding duplicate ditags in LongSAGE analysis may introduce significant error
Cited by: 9
Author(s): Jeppe Emmersen, A Heidenblut, Annabeth Laursen Høgh, Stephan A. Hahn, Karen G. Welinder, Kåre Lehmann Nielsen
Software Mentions: 1
Published: over 17 years ago

10.3389/fpls.2021.654604

The Rlm13 Gene, a New Player of Brassica napus–Leptosphaeria maculans Interaction Maps on Chromosome C03 in Canola
Cited by: 14
Author(s): Harsh Raman, Rosy Raman, Yu Qiu, Yuanyuan Zhang, Jacqueline Batley, Liu S
Software Mentions: 1
Published: over 3 years ago

10.1186/s13073-019-0633-y

Interchromosomal template-switching as a novel molecular mechanism for imprinting perturbations associated with Temple syndrome
Cited by: 16
Author(s): Claudia M.B. Carvalho, Zeynep Coban‐Akdemir, Hadia Hijazi, Bo Yuan, Matthew Pendleton, Eoghan Harrington, John Beaulaurier, Sissel Juul, Daniel J. Turner, Rupa S. Kanchi, Shalini N. Jhangiani, Donna M. Muzny, Richard A. Gibbs, Paweł Stankiewicz, John W. Belmont, Chad A. Shaw, Sau Wai Cheung, Neil A. Hanchard, V. Reid Sutton, Patricia I. Bader, James R. Lupski
Software Mentions: 1
Published: over 5 years ago

10.1093/gigascience/giy160

Divergent evolution in the genomes of closely-related lacertids, Lacerta viridis and L. bilineata and implications for speciation
Cited by: 6
Author(s): Sree Rohit Raj Kolora, Anne Weigert, Amin Zarif Saffari, Stephanie Kehr, Maria Beatriz Walter Costa, Cathrin Spröer, Henrike Indrischek, Manjusha Chintalapati, Konrad Lohse, Gero Doose, Jörg Overmann, Boyke Bunk, Christoph Bleidorn, Annegret Grimm‐Seyfarth, Klaus Henle, Katja Nowick, Rui Faria, Peter F. Stadler, Martin Schlegel
Software Mentions: 1
Published: almost 6 years ago

10.1073/pnas.1908239116

Genetic ablation of purine salvage in Cryptosporidium parvum reveals nucleotide uptake from the host cell
Cited by: 40
Author(s): Mattie C. Pawlowic, Mastanbabu Somepalli, Adam Sateriale, Gillian T. Herbert, Alexis R Gibson, Gregory D. Cuny, Lizbeth Hedstrom, Boris Striepen
Software Mentions: 1
Published: about 5 years ago

10.1038/srep34083

Evidence for Direct Control of Virulence and Defense Gene Circuits by the Pseudomonas aeruginosa Quorum Sensing Regulator, MvfR
Cited by: 91
Author(s): Damien Maura, Ronen Hazan, Tomoe Kitao, Alicia E. Ballok, Laurence G. Rahme
Software Mentions: 1
Published: about 8 years ago

10.1186/s12859-016-1189-0

Analysis of amplicon-based NGS data from neurological disease gene panels: a new method for allele drop-out management
Cited by: 10
Author(s): Susanna Zucca, Margherita Villaraggia, Stella Gagliardi, Gaetano S. Grieco, Marialuisa Valente, Cristina Cereda, Paolo Magni
Software Mentions: 1
Published: about 8 years ago

10.4056/sigs.2255041

High quality draft genome sequence of Segniliparus rugosus CDC 945T= (ATCC BAA-974T)
Cited by: 6
Author(s): Ashlee M. Earl, Christopher A. Desjardins, Michael G. FitzGerald, Harindra Arachchi, Qiandong Zeng, Teena Mehta, Allison Griggs, Bruce W. Birren, Nadege C. Toney, Janice Carr, James E. Posey, W. Ray Butler
Software Mentions: 1
Published: almost 13 years ago

10.3390/v13020245

Characterization of Hepatitis B Virus Integrations Identified in Hepatocellular Carcinoma Genomes
Cited by: 6
Author(s): Pranav Mathkar, X Chen, Arvis Sulovari, Dawei Li
Software Mentions: 1
Published: almost 4 years ago

10.1128/MRA.00078-21

Updated Genome Sequence for the Probiotic Bacterium Bifidobacterium animalis subsp. lactis BB-12
Cited by: 2
Author(s): Kristian Jensen, Kosai Al-Nakeeb, Anna Koza, Ahmad A. Zeidan
Software Mentions: 1
Published: over 3 years ago

10.1186/1755-8794-6-48

Hi-Plex for high-throughput mutation screening: application to the breast cancer susceptibility gene PALB2
Cited by: 13
Author(s): Tú Nguyen-Dumont, Zhi L. Teo, Bernard J. Pope, Fleur Hammet, Maryam Mahmoodi, Helen Tsimiklis, Nelly Sabbaghian, Marc Tischkowitz, William D. Foulkes, Graham G. Giles, John L. Hopper, Melissa C. Southey, Daniel J. Park
Software Mentions: 1
Published: about 11 years ago

10.1186/s12864-016-2859-z

Genome of Rhizobium leucaenae strains CFN 299T and CPAO 29.8: searching for genes related to a successful symbiotic performance under stressful conditions
Cited by: 12
Author(s): Ernesto Ormeño‐Orrillo, Douglas Fabiano Gomes, Pablo del Cerro, Ana Tereza Ribeiro de Vasconcelos, Carlos Canchaya, Luiz Gonzaga Paula de Almeida, Fábio Martins Mercante, Francisco Javier Ollero, Manuel Megı́as, Mariángela Hungria
Software Mentions: 1
Published: over 8 years ago

Ecosyste.ms: Papers

Projects: pypi: caller

Papers Mentioning caller 27