pypi: tools | Projects | Ecosyste.ms: Papers

10.1371/journal.pcbi.1006361

scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data
Cited by: 92
Author(s): Tian Li, Shian Su, Xueyi Dong, Daniela Amann‐Zalcenstein, Christine Biben, Azadeh Seidi, Douglas J. Hilton, Shalin H. Naik, Matthew E. Ritchie
Software Mentions: 21
Published: over 6 years ago

10.1038/s42003-021-01941-5

CENP-A overexpression promotes distinct fates in human cells, depending on p53 status
Cited by: 23
Author(s): Daniel Jeffery, Alberto Gatto, Katrina Podsypanina, Charlène Renaud-Pageot, Rebeca Ponce Landete, Lorraine Bonneville, Marie Dumont, Daniele Fachinetti, Geneviève Almouzni
Software Mentions: 12
Published: over 3 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

10.1093/gigascience/giz146

Systematic processing of ribosomal RNA gene amplicon sequencing data
Cited by: 45
Author(s): Julien Tremblay, Étienne Yergeau
Software Mentions: 10
Published: almost 5 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

10.1038/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

10.1038/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

10.12688/f1000research.12974.1

Using bio.tools to generate and annotate workbench tool descriptions
Cited by: 8
Author(s): Kenzo-Hugo Hillion, Ivan Kuzmin, Anton Khodak, Helena Rasche, Michael R. Crusoe, Hedi Peterson, Jon C. Ison, Hervé Ménager
Software Mentions: 8
Published: almost 7 years ago

10.1038/srep40655

Epigenetic regulation of Plasmodium falciparum clonally variant gene expression during development in Anopheles gambiae
Cited by: 66
Author(s): Elena Gómez-Díaz, Rakiswendé Serge Yerbanga, Thierry Léfèvre, Anna Cohuet, M. Jordan Rowley, Jean-Bosco Ouédraogo, Victor G. Corcés
Software Mentions: 8
Published: almost 8 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

10.1186/s13059-021-02437-5

SCAPTURE: a deep learning-embedded pipeline that captures polyadenylation information from 3′ tag-based RNA-seq of single cells
Cited by: 11
Author(s): Guo-Wei Li, Nan Fang, Guo-Hua Yuan, Chu-Xiao Liu, Xindong Liu, Lingling Chen, Bin Tian, Li Yang
Software Mentions: 7
Published: over 3 years ago

10.1093/gigascience/giaa157

biotoolsSchema: a formalized schema for bioinformatics software description
Cited by: 7
Author(s): Jon C. Ison, Hans Ienasescu, Emil Karol Rydza, Piotr Jaroslaw Chmura, Kristoffer Rapacki, Alban Gaignard, Veit Schwämmle, Jacques van Helden, Matúš Kalaš, Hervé Ménager
Software Mentions: 7
Published: almost 4 years ago

10.7554/eLife.49658

Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification
Cited by: 278
Author(s): Matthew T Parker, Katarzyna Knop, Anna V. Sherwood, Nicholas J. Schurch, Katarzyna Mackinnon, Peter D Gould, Anthony Hall, Geoffrey J. Barton, Gordon G. Simpson
Software Mentions: 7
Published: almost 5 years ago

10.1038/s41598-019-44034-4

Transcript expression profiling in two contrasting cultivars and molecular cloning of a SKP-1 like gene, a component of SCF-ubiquitin proteasome system from mungbean Vigna radiate L.
Cited by: 8
Author(s): Nandita Bharadwaj, Sharmistha Barthakur, Akash Deep Biswas, Monoj Kumar Das, Manpreet Kour, Anand Ramteke, Nirmali Gogoi
Software Mentions: 6
Published: over 5 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

10.1371/journal.pcbi.1004274

Genome Modeling System: A Knowledge Management Platform for Genomics
Cited by: 77
Author(s): Malachi Griffith, Scott M. Smith, Avinash Ramu, Matthew B. Callaway, Anthony M. Brummett, Michael J. Kiwala, Adam Coffman, Allison Regier, Benjamin J. Oberkfell, Gabriel E. Sanderson, Thomas P. Mooney, Nathaniel G. Nutter, Edward A. Belter, Feiyu Du, R.L. Long, Travis E. Abbott, Ian T. Ferguson, David Morton, Mark M. Burnett, James V. Weible, Joshua B. Peck, Adam F. Dukes, Joshua F. McMichael, Justin T. Lolofie, Brian R. Derickson, Jasreet Hundal, Zachary L. Skidmore, Benjamin J. Ainscough, Nathan D. Dees, William Schierding, Cyriac Kandoth, Kyung H. Kim, Charles Lu, Christopher Harris, Nicole Maher, Christopher A. Maher, Vincent Magrini, Benjamin Abbott, Ken Chen, Eric M. Clark, Indraniel Das, Xian Fan, Amy E. Hawkins, Todd G. Hepler, Todd Wylie, Shawn Leonard, W.E. Schroeder, Xiaoqi Shi, Lynn K. Carmichael, Matthew R. Weil, Richard W. Wohlstadter, Gary Stiehr, Michael D. McLellan, Craig Pohl, Christopher A. Miller, Daniel C. Koboldt, Jason Walker, James M. Eldred, David E. Larson, David J. Dooling, Ding Li, Elaine R. Mardis, Richard K. Wilson
Software Mentions: 6
Published: over 9 years ago

10.15252/msb.20209698

<scp>CEN</scp> ‐tools: an integrative platform to identify the contexts of essential genes
Cited by: 9
Author(s): Sumana Sharma, Cansu Dinçer, Paula Weidemüller, Gavin J. Wright, Evangelia Petsalaki
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pgen.1007828

The Integrator complex regulates differential snRNA processing and fate of adult stem cells in the highly regenerative planarian Schmidtea mediterranea
Cited by: 13
Author(s): David Schmidt, Hanna Reuter, Katja Hüttner, Larissa Ruhe, Franziska Rabert, Florian Seebeck, Manuel Irimia, Jordi Solana, Kerstin Bartscherer
Software Mentions: 5
Published: almost 6 years ago

10.7554/eLife.38795

Enhanced ER proteostasis and temperature differentially impact the mutational tolerance of influenza hemagglutinin
Cited by: 20
Author(s): Angela M Phillips, Michael B. Doud, Luna O Gonzalez, Vincent Butty, Yu‐Shan Lin, Jesse D. Bloom, Matthew D. Shoulders
Software Mentions: 5
Published: about 6 years ago

10.1186/s12859-015-0590-4

Software for the analysis and visualization of deep mutational scanning data
Cited by: 101
Author(s): Jesse D. Bloom
Software Mentions: 5
Published: over 9 years ago

10.12688/f1000research.9357.2

Genomic variant annotation workflow for clinical applications
Cited by: 9
Author(s): Thomas Thurnherr, Franziska Singer, Daniel J. Stekhoven, Niko Beerenwinkel
Software Mentions: 5
Published: about 8 years ago

10.7554/eLife.37184

An alternative splicing switch in FLNB promotes the mesenchymal cell state in human breast cancer
Cited by: 68
Author(s): Ji Li, Peter S. Choi, Christine L. Chaffer, Katherine Labella, Justin Hwang, Andrew O. Giacomelli, Jong Wook Kim, Nina Ilić, John G. Doench, Seav Huong Ly, Chao Dai, Kimberly R. Hagel, Andrew L. Hong, Ole Gjoerup, Shom Goel, Jennifer Y Ge, David E. Root, Jean J. Zhao, Angela N. Brooks, Robert A. Weinberg, William C. Hahn
Software Mentions: 5
Published: over 6 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

10.1038/srep15782

Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut
Cited by: 213
Author(s): Christian Milani, Gabriele Andrea Lugli, Sabrina Duranti, Francesca Turroni, Leonardo Mancabelli, Chiara Ferrario, Marta Mangifesta, Arancha Hevia, Alice Viappiani, Matthias Scholz, Stefania Arioli, Borja Sánchez, Jonathan A. Lane, Doyle V. Ward, Rita M. Hickey, Diego Mora, Nicola Segata, Abelardo Margollés, Douwe van Sinderen, Marco Ventura
Software Mentions: 4
Published: about 9 years ago

10.7554/eLife.40292

Is it possible to reconstruct an accurate cell lineage using CRISPR recorders?
Cited by: 62
Author(s): Irepan Salvador-Martínez, Marco Grillo, Michalis Averof, Maximilian J. Telford
Software Mentions: 4
Published: almost 6 years ago

10.1002/ece3.3133

Transcriptomic differentiation underlying marine‐to‐freshwater transitions in the South American silversides Odontesthes argentinensis and O. bonariensis (Atheriniformes)
Cited by: 17
Author(s): Lily C. Hughes, Gustavo M. Somoza, Bryan Nguyen, James P. Bernot, Mariano González‐Castro, Juan Martín Díaz de Astarloa, Guillermo Ortı́
Software Mentions: 4
Published: over 7 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

10.1128/mSystems.00127-17

Genomic, Transcriptomic, and Phenotypic Analyses of Neisseria meningitidis Isolates from Disease Patients and Their Household Contacts
Cited by: 2
Author(s): Xiaoyun Ren, David Eccles, Gabrielle Greig, Jane Clapham, Nicole E. Wheeler, Stinus Lindgreen, Paul Geeleher, Joanna K. MacKichan
Software Mentions: 4
Published: almost 7 years ago

10.1128/mSphere.00160-20

An Extensive Meta-Metagenomic Search Identifies SARS-CoV-2-Homologous Sequences in Pangolin Lung Viromes
Cited by: 43
Author(s): Lamia Wahba, Nikhil Jain, Andrew Fire, Massa J. Shoura, Karen L. Artiles, Matthew J. McCoy, Dae‐Eun Jeong
Software Mentions: 4
Published: over 4 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

10.1186/s13059-021-02430-y

Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair
Cited by: 29
Author(s): Lingzhan Xue, Yu Gao, Meimei Wu, Tian Tian, Huitao Fan, Yongji Huang, Zhen Huang, Dapeng Li, Luohao Xu
Software Mentions: 4
Published: over 3 years ago

10.1002/ajpa.23763

The efficacy of whole human genome capture on ancient dental calculus and dentin
Cited by: 21
Author(s): Kirsten A. Ziesemer, Jazmín Ramos‐Madrigal, Allison E. Mann, Bernd W. Brandt, Krithivasan Sankaranarayanan, Andrew T. Ozga, Menno L. P. Hoogland, Courtney A. Hofman, Domingo C. Salazar‐García, Bruno Fröhlich, George R. Milner, Anne C. Stone, Mark Aldenderfer, Cecil M. Lewis, Corinne L. Hofman, Christina Warinner, Hannes Schroeder
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-021-96109-w

Inhibiting SARS-CoV-2 infection in vitro by suppressing its receptor, angiotensin-converting enzyme 2, via aryl-hydrocarbon receptor signal
Cited by: 17
Author(s): Keiji Tanimoto, Kiichi Hirota, Takahiro Fukazawa, Yoshiyuki Matsuo, Toshihito Nomura, Tanuza Nazmul, Nobuyuki Hirohashi, Hidemasa Bono, Takemasa Sakaguchi
Software Mentions: 3
Published: over 3 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

10.3389/fimmu.2021.629059

HLA RNA Sequencing With Unique Molecular Identifiers Reveals High Allele-Specific Variability in mRNA Expression
Cited by: 15
Author(s): Tiira Johansson, Dawit A. Yohannes, Satu Koskela, Jukka Partanen, Päivi Saavalainen
Software Mentions: 3
Published: over 3 years ago

10.1186/s13059-021-02441-9

ExOrthist: a tool to infer exon orthologies at any evolutionary distance
Cited by: 7
Author(s): Yamile Márquez, Federica Mantica, Luca Cozzuto, Demián Burguera, Toni Hermoso Pulido, Julia Ponomarenko, Scott William Roy, Manuel Irimia
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2164-14-99

Nuclear Factor I genomic binding associates with chromatin boundaries
Cited by: 25
Author(s): Milos Pjanic, Christoph D. Schmid, Armelle Gaussin, Giovanna Ambrosini, Jozef Adamčík, Petar Pjanić, Genta Plasari, Jan Kerschgens, Giovani Dietler, Philipp Bücher, Nicolas Mermod
Software Mentions: 3
Published: almost 12 years ago

10.1186/s13059-019-1631-5

Genomic introgression through interspecific hybridization counteracts genetic bottleneck during soybean domestication
Cited by: 37
Author(s): Xutong Wang, Liyang Chen, Jianxin Ma
Software Mentions: 3
Published: almost 6 years ago

10.1534/g3.112.004127

Natural Variation in the Yeast Glucose-Signaling Network Reveals a New Role for the Mig3p Transcription Factor
Cited by: 19
Author(s): Jeffrey A. Lewis, Audrey P. Gasch
Software Mentions: 3
Published: almost 12 years ago

10.1186/1471-2105-13-S17-S26

Phylogenetic reconstruction in the Order Nymphaeales: ITS2 secondary structure analysis and in silico testing of maturase k (matK) as a potential marker for DNA bar coding
Cited by: 15
Author(s): Devendra Kumar Biswal, Manish Debnath, Sunil Kumar, Pramod Tandon
Software Mentions: 3
Published: almost 12 years ago

10.1242/bio.042754

Defining the dynamic chromatin landscape of mouse nephron progenitors
Cited by: 17
Author(s): Sylvia Hilliard, Renming Song, Hongbing Liu, Chao‐Hui Chen, Yuwen Li, Melody Baddoo, Erik Flemington, Alanna Wanek, Jay K. Kolls, Zubaida Saifudeen, Samir S. El‐Dahr
Software Mentions: 3
Published: almost 6 years ago

10.1128/mBio.01871-18

Structural and Nonstructural Genes Contribute to the Genetic Diversity of RNA Viruses
Cited by: 27
Author(s): Natalie D. Collins, Andrew S. Beck, Steven G. Widen, Thomas G. Wood, Stephen Higgs, Alan D.T. Barrett
Software Mentions: 3
Published: about 6 years ago

10.1002/ece3.5322

Disadvantages and benefits of evolved unicellularity versus multicellularity in budding yeast
Cited by: 23
Author(s): Jennie J. Kuzdzal‐Fick, Lin Chen, Gábor Balázsi
Software Mentions: 3
Published: over 5 years ago

10.1186/s12859-018-2593-4

An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping
Cited by: 44
Author(s): Qiangwei Zhou, Jing-Quan Lim, Wing-Kin Sung, Guoliang Li
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-017-15795-7

Intelligence is associated with the modular structure of intrinsic brain networks
Cited by: 95
Author(s): Kirsten Hilger, Matthias Ekman, Christian J. Fiebach, Ulrike Basten
Software Mentions: 3
Published: about 7 years ago

10.7717/peerj.8275

Algorithms for efficiently collapsing reads with Unique Molecular Identifiers
Cited by: 9
Author(s): Daniel Liu
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12859-021-04294-2

HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences
Cited by: 22
Author(s): Phuoc Truong Nguyen, Ilya Plyusnin, Tarja Sironen, Olli Vapalahti, Ravi Kant, Teemu Smura
Software Mentions: 3
Published: over 3 years ago

10.1038/srep45012

Stressor exposure has prolonged effects on colonic microbial community structure in Citrobacter rodentium-challenged mice
Cited by: 29
Author(s): Jeffrey D. Galley, Amy R. Mackos, Vanessa A. Varaljay, Michael T. Bailey
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.48284

Sustained expression of HeyL is critical for the proliferation of muscle stem cells in overloaded muscle
Cited by: 37
Author(s): Sumiaki Fukuda, Akihiro Kaneshige, Takayuki Kaji, Yu Taro Noguchi, Yusei Takemoto, Lidan Zhang, Kazutake Tsujikawa, Hiroki Kokubo, Akiyoshi Uezumi, Kazuhira Maehara, Akihito Harada, Yasuyuki Ohkawa, So Ichiro Fukada
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0055895

A Microarray Platform-Independent Classification Tool for Cell of Origin Class Allows Comparative Analysis of Gene Expression in Diffuse Large B-cell Lymphoma
Cited by: 61
Author(s): Matthew A. Care, Sharon Barrans, Lisa Worrillow, Andrew Jack, David R. Westhead, Reuben Tooze
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0113800

ViVar: A Comprehensive Platform for the Analysis and Visualization of Structural Genomic Variation
Cited by: 44
Author(s): Tom Sante, Sarah Vergult, Pieter-Jan Volders, Wigard P. Kloosterman, Geert Trooskens, Katleen De Preter, Annelies Dheedene, Franki Speleman, Tim De Meyer, Björn Menten
Software Mentions: 3
Published: almost 10 years ago

10.1016/j.dib.2019.105001

Dataset for transcriptome analysis of abscisic acid degrading bacterium Novosphingobium sp. P6W
Cited by: 1
Author(s): Natalia Gogoleva, Tatiana A. Konnova, Timur T. Ismailov, Alexander S. Balkin, Andrey A. Belimov, Alexander A. Kamnev
Software Mentions: 3
Published: almost 5 years ago

10.1016/j.dib.2020.105297

Transcriptomic data of Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S treated with novobiocin
Cited by: 4
Author(s): Natalia Gogoleva, Tatiana A. Konnova, Alexander S. Balkin, А. О. Плотников, Alexander A. Kamnev
Software Mentions: 3
Published: over 4 years ago

10.7150/ijms.50916

Somatic Mutation Profiling of Papillary Thyroid Carcinomas by Whole-exome Sequencing and Its Relationship with Clinical Characteristics
Cited by: 3
Author(s): Tingyue Qi, Xin Rong, Qingling Feng, Hongyan Sun, Haiyan Cao, Yan Yang, Hao Feng, Linhai Zhu, Lei Wang, Qiu Du
Software Mentions: 2
Published: almost 4 years ago

10.1016/j.jalz.2015.07.490

The pattern of amyloid accumulation in the brains of adults with Down syndrome
Cited by: 132
Author(s): Tiina Annus, Liam R. Wilson, Young T. Hong, Julio Acosta‐Cabronero, Tim D. Fryer, Arturo Cárdenas-Blanco, Robert V. Smith, István Boros, Jonathan P. Coles, Franklin I. Aigbirhio, David Menon, Shahid Zaman, Peter J. Nestor, Anthony Holland
Software Mentions: 2
Published: about 9 years ago

10.1186/s12859-019-3280-9

Gencore: an efficient tool to generate consensus reads for error suppressing and duplicate removing of NGS data
Cited by: 37
Author(s): Shifu Chen, Yanqing Zhou, Yaru Chen, Tanxiao Huang, Wenting Liao, Yun Xu, Zhicheng Li, Jia Gu
Software Mentions: 2
Published: almost 5 years ago

10.1186/1471-2105-8-334

EDISA: extracting biclusters from multiple time-series of gene expression profiles
Cited by: 51
Author(s): Jochen Supper, Martin Strauch, Dierk Wanke, Klaus Harter, Andreas Zell
Software Mentions: 2
Published: about 17 years ago

10.1186/1471-2164-11-168

Transcriptome survey of the anhydrobiotic tardigrade Milnesium tardigradum in comparison with Hypsibius dujardini and Richtersius coronifer
Cited by: 47
Author(s): Brahim Mali, Markus A. Grohme, Frank Förster, Thomas Dandekar, Martina Schnölzer, Dirk Reuter, Weronika Wełnicz, Ralph O. Schill, Marcus Frohme
Software Mentions: 2
Published: almost 15 years ago

10.1186/s12870-020-02694-9

Integration analysis of PacBio SMRT- and Illumina RNA-seq reveals candidate genes and pathway involved in selenium metabolism in hyperaccumulator Cardamine violifolia
Cited by: 23
Author(s): Shen Rao, Yu Tian, Xin Cong, Feng Xu, Xiaozhuo Lai, Weiwei Zhang, Yongling Liao, Shuiyuan Cheng
Software Mentions: 2
Published: about 4 years ago

10.1186/1756-0500-2-214

SNP_tools: A compact tool package for analysis and conversion of genotype data for MS-Excel
Cited by: 59
Author(s): Bowang Chen, Stefan Wilkening, M. Drechsel, Kari Hemminki
Software Mentions: 2
Published: almost 16 years ago

10.1093/bib/bbz075

Community curation of bioinformatics software and data resources
Cited by: 13
Author(s): Jon C. Ison, Hervé Ménager, Bryan Brancotte, Erik Jaaniso, Ahto Salumets, Tomáš Raček, Anna‐Lena Lamprecht, Magnus Palmblad, Matúš Kalaš, Piotr Jaroslaw Chmura, John M. Hancock, Veit Schwämmle, Hans Ienasescu
Software Mentions: 2
Published: about 5 years ago

10.1002/mgg3.576

Exome sequencing in families with chronic central serous chorioretinopathy
Cited by: 13
Author(s): Rosa L. Schellevis, Elon H. C. van Dijk, Myrte B. Breukink, Jan E.E. Keunen, Gijs Santen, Carel B. Hoyng, Eiko K. de Jong, Camiel J F Boon, Anneke I. den Hollander
Software Mentions: 2
Published: almost 6 years ago

10.1002/mgg3.575

Analysis of the Prader–Willi syndrome imprinting center using droplet digital PCR and next‐generation whole‐exome sequencing
Cited by: 15
Author(s): Samantha N. Hartin, Waheeda A. Hossain, David Francis, David E. Godler, Sangjucta Barkataki, Merlin G. Butler
Software Mentions: 2
Published: almost 6 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

10.1371/journal.pone.0252786

DNAH11 compound heterozygous variants cause heterotaxy and congenital heart disease
Cited by: 5
Author(s): Xia Hong, Xiangjun Huang, Sheng Deng, Hongbo Xu, Yan Yang, Xin Liu, Lamei Yuan, Hao Deng
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0152574

Genomic Characterization and Comparison of Multi-Regional and Pooled Tumor Biopsy Specimens
Cited by: 13
Author(s): Je‐Gun Joung, Joon Seol Bae, Sang Cheol Kim, Hyunchul Jung, Woong-Yang Park, Sang‐Yong Song
Software Mentions: 2
Published: over 8 years ago

10.12688/f1000research.52569.1

Bioimage analysis workflows: community resources to navigate through a complex ecosystem
Cited by: 8
Author(s): Perrine Paul‐Gilloteaux, Sébastien Tosi, Jean-Karim Hèriché, Alban Gaignard, Hervé Ménager, Raphaël Marée, Volker Baecker, Anna H. Klemm, Matúš Kalaš, Chong Zhang, Kota Miura, Julien Colombelli
Software Mentions: 2
Published: over 3 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.2020.00229

Morpho-Physiological and Genomic Evaluation of Juglans Species Reveals Regional Maladaptation to Cold Stress
Cited by: 4
Author(s): Aziz Ebrahimi, Shaneka S. Lawson, James R. McKenna, Douglass F. Jacobs
Software Mentions: 2
Published: over 4 years ago

10.1186/s13059-016-0897-0

GATA3-dependent cellular reprogramming requires activation-domain dependent recruitment of a chromatin remodeler
Cited by: 115
Author(s): Motoki Takaku, Sara A. Grimm, Takashi Shimbo, Lalith Perera, Roberta Menafra, Hendrik G. Stunnenberg, Trevor Archer, Shuichi Machida, Hitoshi Kurumizaka, Paul A. Wade
Software Mentions: 2
Published: over 8 years ago

10.1016/j.gpb.2018.07.008

Multi-omics Analysis of Primary Cell Culture Models Reveals Genetic and Epigenetic Basis of Intratumoral Phenotypic Diversity
Cited by: 10
Author(s): Sixue Liu, Zuyu Yang, Guanghao Li, Chunyan Li, Ye Luo, Qiang Gong, Xin Wu, Tao Li, Zhiqian Zhang, Baocai Xing, Xiaolan Xu, Xuemei Lu
Software Mentions: 2
Published: almost 5 years ago

10.1172/jci.insight.148920

HIV infection drives interferon signaling within intestinal SARS-CoV-2 target cells
Cited by: 6
Author(s): Rabiah Fardoos, Osaretin E. Asowata, Nicholas Herbert, Sarah K. Nyquist, Yenzekile Zungu, Abhijeet Singh, Abigail Ngoepe, Ian Mbano, Ntombifuthi Mthabela, Dirhona Ramjit, Farina Karim, Warren Kuhn, Fusi G. Madela, Vukani T. Manzini, Frank Anderson, Bonnie Berger, Tune H. Pers, Alex K. Shalek, Alasdair Leslie, Henrik N. Kløverpris
Software Mentions: 2
Published: over 3 years ago

10.1093/jxb/eru337

Small RNAs as important regulators for the hybrid vigour of super-hybrid rice
Cited by: 30
Author(s): Lei Zhang, Yonggang Peng, Xiaoli Wei, Yan Dai, Dawei Yuan, Yufei Lu, Yangyang Pan, Zhen Zhu
Software Mentions: 2
Published: over 10 years ago

10.1002/prot.26018

<scp>PDB‐tools</scp> web: A user‐friendly interface for the manipulation of <scp>PDB</scp> files
Cited by: 12
Author(s): Brian Jiménez‐García, João M.C. Teixeira, Mikaël Trellet, João P. G. L. M. Rodrigues, Alexandre M. J. J. Bonvin
Software Mentions: 2
Published: about 4 years ago

10.1038/srep35819

Transstadial Transmission and Long-term Association of Crimean-Congo Hemorrhagic Fever Virus in Ticks Shapes Genome Plasticity
Cited by: 28
Author(s): Han Xia, Andrew S. Beck, Ayşen Gargılı, Naomi L. Forrester, Alan D.T. Barrett, Dennis A. Bente
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-019-39873-0

Age-related gene and miRNA expression changes in airways of healthy individuals
Cited by: 29
Author(s): Jennie Ong, Roy R Woldhuis, Ilse M. Boudewijn, Anke van den Berg, Joost Kluiver, Klaas Kok, Martijn Terpstra, Victor Guryev, Maaike de Vries, Cornelis J Vermeulen, Wim Timens, C. A. Brandsma
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-64515-1

Transcriptional profiling of murine macrophages stimulated with cartilage fragments revealed a strategy for treatment of progressive osteoarthritis
Cited by: 11
Author(s): Masanari Hamasaki, Mohamad Alaa Terkawi, Tomohiro Onodera, Yuan Tian, Taku Ebata, Gen Matsumae, Hend Alhasan, Daisuke Takahashi, Norimasa Iwasaki
Software Mentions: 2
Published: over 4 years ago

10.1128/mBio.01977-16

Bacteria Getting into Shape: Genetic Determinants of E. coli Morphology
Cited by: 24
Author(s): Shawn French, Jean-Philippe Côté, Jonathan Stokes, Ray Truant, Eric D. Brown
Software Mentions: 2
Published: over 7 years ago

10.3390/ijms20215515

Comparative Transcriptome Analysis Reveals the Cause for Accumulation of Reactive Oxygen Species During Pollen Abortion in Cytoplasmic Male-Sterile Kenaf Line 722HA
Cited by: 11
Author(s): Bujin Zhou, Liu Yiding, Zhenxia Chen, Dongmei Li, Yining Wang, Jie Zheng, Xiaofang Liao, And Ruiyang Zhou
Software Mentions: 2
Published: about 5 years ago

10.1523/JNEUROSCI.0189-20.2020

α-Synuclein Induces Progressive Changes in Brain Microstructure and Sensory-Evoked Brain Function That Precedes Locomotor Decline
Cited by: 10
Author(s): Winston T. Chu, Jesse C. DeSimone, Cara J. Riffe, Han Liu, Paramita Chakrabarty, Benoit I. Giasson, Vinata Vedam‐Mai, David E. Vaillancourt
Software Mentions: 2
Published: over 4 years ago

10.1186/s13048-019-0494-4

Next-generation sequencing-based genomic profiling analysis reveals novel mutations for clinical diagnosis in Chinese primary epithelial ovarian cancer patients
Cited by: 26
Author(s): Lei Zhang, Min Luo, Hongjiang Yang, Shaoyan Zhu, Xianliang Cheng, Qing Chen
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12863-015-0175-2

Transcriptome analysis between invasive Pomacea canaliculata and indigenous Cipangopaludina cahayensis reveals genomic divergence and diagnostic microsatellite/SSR markers
Cited by: 15
Author(s): Xuemei Mu, Guangyuan Hou, Hongmei Song, Peng Xu, Dehai Luo, Donghong Gu, Meng Xu, Jingjing Luo, Jiaen Zhang, Yinchan Hu
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2156-9-78

Genomic complexity of the variable region-containing chitin-binding proteins in amphioxus
Cited by: 35
Author(s): Larry J. Dishaw, Mathias Mueller, Natasha R. Gwatney, John P. Cannon, Robert N. Haire, Ronda T. Litman, Chris T. Amemiya, Toshitaka Ota, Lee Rowen, Gustavo Glusman, Gary W. Litman
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2105-10-S6-S17

Deciphering the connectivity structure of biological networks using MixNet
Cited by: 43
Author(s): Franck Picard, Vincent Miele, Jean‐Jacques Daudin, Ludovic Cottret, Stéphane Robin
Software Mentions: 1
Published: over 15 years ago

10.1038/s41597-021-00885-z

Database of Wannier tight-binding Hamiltonians using high-throughput density functional theory
Cited by: 19
Author(s): Kevin F. Garrity, Kamal Choudhary
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0159437

Identification of SNP and SSR Markers in Finger Millet Using Next Generation Sequencing Technologies
Cited by: 55
Author(s): Davis Gimode, Damaris Achieng Odeny, Etienne P. de Villiers, Solomon Wanyonyi, Mathews M. Dida, Emmarold E. Mneney, Alice Muchugi, Jesse Machuka, Santie M. de Villiers
Software Mentions: 1
Published: over 8 years ago

10.1007/s13280-015-0744-7

Changing ideas in forestry: A comparison of concepts in Swedish and American forestry journals during the early twentieth and twenty-first centuries
Cited by: 15
Author(s): Erland Mårald, Nancy Langston, Anna Sténs, Jon Moen
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0053750

Identification and Characterization of New Molecular Partners for the Protein Arginine Methyltransferase 6 (PRMT6)
Cited by: 8
Author(s): Alessandra Lo Sardo, Sandro Altamura, Silvia Pegoraro, E Maurizio, Riccardo Sgarra, Guidalberto Manfioletti
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0226039

De novo transcriptome analysis and identification of genes associated with immunity, detoxification and energy metabolism from the fat body of the tephritid gall fly, Procecidochares utilis
Cited by: 5
Author(s): Lifang Li, Xi Gao, Mingxian Lan, Yuan Yuan, Zhixin Guo, Peng Tang, Mengyue Li, Xianbin Liao, Jia‐Ying Zhu, Li ZhengYue, Min Ye, Guoxing Wu
Software Mentions: 1
Published: almost 5 years ago

10.1111/pin.13054

Evaluation of clinical formalin‐fixed paraffin‐embedded tissue quality for targeted‐bisulfite sequencing
Cited by: 5
Author(s): Hideki Ohmomo, Shohei Komaki, Kanako Ono, Yoichi Sutoh, Tsuyoshi Hachiya, Eri Arai, Hiroyuki Fujimoto, Teruhiko Yoshida, Yae Kanai, Makoto Sasaki, Atsushi Shimizu
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-017-16676-9

ATP1A3 mutations can cause progressive auditory neuropathy: a new gene of auditory synaptopathy
Cited by: 46
Author(s): Kyu Hee Han, Doo Yi Oh, Seungmin Lee, Chung Lee, Jin Hee Han, Min Young Kim, Hye Rim Park, Moo Kyun Park, Nayoung K.D. Kim, Jaekwang Lee, Eunyoung Yi, Jong Min Kim, Jeong Whun Kim, Jong Hee Chae, Seung Ha Oh, Woong-Yang Park, Byung Yoon Choi
Software Mentions: 1
Published: almost 7 years ago

10.3390/ijms10031121

Folding of Trp-cage Mini Protein Using Temperature and Biasing Potential Replica—Exchange Molecular Dynamics Simulations
Cited by: 18
Author(s): Srinivasaraghavan Kannan, Martin Zacharias
Software Mentions: 1
Published: over 15 years ago

10.3390/v13081445

Live Bird Markets in Nigeria: A Potential Reservoir for H9N2 Avian Influenza Viruses
Cited by: 8
Author(s): Lanre Sulaiman, Ismaila Shittu, Alice Fusaro, Bitrus Inuwa, Bianca Zecchin, Dorcas A. Gado, Alessia Schivo, Alice Bianco, Agnes Tinuke Laleye, Federica Gobbo, Columba Vakuru, Tony M. Joannis, Isabella Monne, Clement Meseko
Software Mentions: 1
Published: over 3 years ago

10.1002/mgg3.1321

Co‐occurrence of neurofibromatosis type 1 and optic nerve gliomas with autosomal dominant polycystic kidney disease type 2
Cited by: 4
Author(s): R Peces, Rocío Mena, Yolanda Martín, C Hernández, Carlos Peces, Dolores Tellerı́a, Emilio Cuesta, Rafael Selgas, Pablo Lapunzina, Julián Nevado
Software Mentions: 1
Published: over 4 years ago

10.3390/molecules24010027

Direct Experimental Evidence of Biomimetic Surfaces with Chemical Modifications Interfering with Adhesive Protein Adsorption
Cited by: 12
Author(s): Hui Yang, Wei Zhang, Ting Chen, Shizhe Huang, Baogang Quan, Min Wang, Junjie Li, Changzhi Gu, Jinben Wang
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12967-020-02614-3

Dysregulated PDGFR alpha expression and novel somatic mutations in colorectal cancer: association to RAS wild type status and tumor size
Cited by: 5
Author(s): N. Ben Jemii, H. Guettiti Tounsi-Kettiti, H. Yaïche, Najla Mezghanni, Amira Jaballah Gabteni, Emna Fehri, Chayma Ben Fayala, Sonia Abdelhak, Samir Boubaker
Software Mentions: 1
Published: about 4 years ago

10.1093/molbev/msw249

Genome-wide Analysis in Brazilians Reveals Highly Differentiated Native American Genome Regions
Cited by: 13
Author(s): Josyf C. Mychaleckyj, Alexandre Havt, Uma Nayak, Relana C. Pinkerton, Emily Farber, Patrick Concannon, Aldo A. M. Lima, Richard L. Guerrant
Software Mentions: 1
Published: almost 8 years ago

10.3390/ijms21103600

Zygotic Vsx1 Plays a Key Role in Defining V2a Interneuron Sub-Lineage by Directly Repressing tal1 Transcription in Zebrafish
Cited by: 3
Author(s): Qi Zhang, Haomang Xu, Wei Zhao, Jianbo Zheng, Lei Sun, Chen Luo
Software Mentions: 1
Published: over 4 years ago

10.1128/mBio.01021-17

Genome-Wide Mutation Rate Response to pH Change in the Coral Reef Pathogen Vibrio shilonii AK1
Cited by: 20
Author(s): Chloe Strauss, Hongan Long, Caitlyn E. Patterson, Ronald Te, Michael Lynch
Software Mentions: 1
Published: about 7 years ago

10.3390/ma12172691

Robocasting of SiO2-Based Bioactive Glass Scaffolds with Porosity Gradient for Bone Regeneration and Potential Load-Bearing Applications
Cited by: 34
Author(s): Jacopo Barberi, Francesco Baino, Elisa Fiume, Gissur Örlygsson, Amy Nommeots‐Nomm, Jonathan Massera, Enrica Verné
Software Mentions: 1
Published: over 5 years ago

Projects: pypi: tools

Papers Mentioning tools 118