Ecosyste.ms: Papers

10.1038/srep33555

The Tara Oceans voyage reveals global diversity and distribution patterns of marine planktonic ciliates
Cited by: 65
Author(s): Anna Gimmler, Ralf Korn, Colomban de Vargas, Stéphane Audic, Thorsten Stoeck
Software Mentions: 6
Published: about 8 years ago

10.3389/fbioe.2021.612893

Multiomics Data Collection, Visualization, and Utilization for Guiding Metabolic Engineering
Cited by: 4
Author(s): Somtirtha Roy, Tijana Radivojević, Mark Forrer, Jose Manuel Martí, Vamshi Jonnalagadda, Tyler W. H. Backman, William Morrell, Hector Plahar, Joonhoon Kim, Nathan J. Hillson, Héctor García Martín
Software Mentions: 6
Published: over 3 years ago

10.1038/srep43793

Hybrid sequencing and map finding (HySeMaFi): optional strategies for extensively deciphering gene splicing and expression in organisms without reference genome
Cited by: 24
Author(s): Guogui Ning, Cheng Xu, Ping Luo, Fan Liang, Zhen Wang, Guoliang Yu, Xin Li, Depeng Wang, Manzhu Bao
Software Mentions: 5
Published: over 7 years ago

10.1186/s12864-019-5838-3

Genome-wide profiling of the alternative splicing provides insights into development in Plutella xylostella
Cited by: 6
Author(s): Qian Zhao, Weimin Zhong, Weiyi He, Yiying Li, Yaqing Li, Tianpu Li, Liette Vasseur, Minsheng You
Software Mentions: 5
Published: over 5 years ago

10.3389/fpls.2020.01005

Similar Seed Composition Phenotypes Are Observed From CRISPR-Generated In-Frame and Knockout Alleles of a Soybean KASI Ortholog
Cited by: 8
Author(s): Kamaldeep S. Virdi, Madison Spencer, Adrian O. Stec, Yer Xiong, Ryan Merry, Gary J. Muehlbauer, Robert M. Stupar
Software Mentions: 5
Published: about 4 years ago

10.26508/lsa.202000709

Myeloid transformation by <i>MLL</i>-<i>ENL</i> depends strictly on C/EBP
Cited by: 4
Author(s): Radosław Wesołowski, Elisabeth Kowenz‐Leutz, Karin Zimmermann, Dorothea Dörr, Maria Hofstätter, Robert K. Slany, Alexander Mildner, Achim Leutz
Software Mentions: 5
Published: almost 4 years ago

10.2196/15918

Enabling Agile Clinical and Translational Data Warehousing: Platform Development and Evaluation
Cited by: 5
Author(s): Helmut Spengler, C. Lang, Tanmaya Mahapatra, Ingrid Gatz, Klaus A. Kuhn, Fabian Praßer
Software Mentions: 5
Published: about 4 years ago

10.1002/bimj.201800222

Multiple imputation for discrete data: Evaluation of the joint latent normal model
Cited by: 17
Author(s): Matteo Quartagno, James Carpenter
Software Mentions: 5
Published: over 5 years ago

10.1186/s12859-018-2288-x

HiCcompare: an R-package for joint normalization and comparison of HI-C datasets
Cited by: 94
Author(s): John C. Stansfield, Kellen Garrison Cresswell, Vladimir I. Vladimirov, Mikhail G. Dozmorov
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-020-66309-x

Comparative targeting analysis of KLF1, BCL11A, and HBG1/2 in CD34+ HSPCs by CRISPR/Cas9 for the induction of fetal hemoglobin
Cited by: 35
Author(s): Andrés Lamsfus‐Calle, Alberto Daniel‐Moreno, Justin S. Antony, Thomas Epting, Lukas Heumos, Praveen Baskaran, Jakob Admard, Nicolas Casadei, Ngadhnjim Latifi, Darina M. Siegmund, Michael Kormann, Rupert Handgretinger, Markus Mezger
Software Mentions: 4
Published: about 4 years ago

10.1093/gigascience/giaa035

Artifact-free whole-slide imaging with structured illumination microscopy and Bayesian image reconstruction
Cited by: 15
Author(s): Karl A. Johnson, Guy M. Hagen
Software Mentions: 4
Published: over 4 years ago

10.1186/s40425-018-0423-x

33rd Annual Meeting &amp; Pre-Conference Programs of the Society for Immunotherapy of Cancer (SITC 2018)
Cited by: 24
Author(s): Adi Diab, Scott S. Tykodi, Brendan D. Curti, Daniel Cho, M. K. Wong, Igor Puzanov, Karl D. Lewis, Michele Maio, Gregory A. Daniels, Alexander I. Spira, Mary Tagliaferri, Alison L. Hannah, Wendy Clemens, Michael J. Imperiale, Chantale Bernatchez, Cara L. Haymaker, Salah Eddine Bentebibel, Jonathan Zalevsky, Ute Hoch, Christie Fanton, Ahsan Rizwan, Sandra Aung, Fiore Cattaruzza, Ernesto Iaccucci, Dariusz Sawka, Mehmet Asım Bilen, Paul Lorigan, Giovanni Grignani, James Larkin, Sekwon Jang, Ewa Kalinka Warzocha, Mario Sznol, Mike Hurwitz
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12864-019-6163-6

PacBio single-molecule long-read sequencing shed new light on the complexity of the Carex breviculmis transcriptome
Cited by: 20
Author(s): Ke Teng, Wan Teng, Haifeng Wen, Yuesen Yue, Weier Guo, Juying Wu, Xing Fan
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12864-017-3691-9

Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human
Cited by: 106
Author(s): Richard Kuo, Elizabeth Tseng, Lél Eöry, Ian R. Paton, Alan Archibald, David W. Burt
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2288-12-184

Auxiliary variables in multiple imputation in regression with missing X: a warning against including too many in small sample research
Cited by: 113
Author(s): Jochen Hardt, Max Herke, Rainer Leonhart
Software Mentions: 4
Published: almost 12 years ago

10.1534/g3.116.032805

Assessing the Gene Content of the Megagenome: Sugar Pine (<i>Pinus lambertiana</i>)
Cited by: 45
Author(s): Daniel González-Ibeas, Pedro Manuel Martínez-García, Randi Famula, Annette Delfino-Mix, Kristian Stevens, Carol A. Loopstra, Charles H. Langley, David B. Neale, Jill L. Wegrzyn
Software Mentions: 4
Published: almost 8 years ago

10.1186/1759-4499-1-3

Head in the clouds: Re-imagining the experimental laboratory record for the web-based networked world
Cited by: 6
Author(s): Cameron Neylon
Software Mentions: 3
Published: over 15 years ago

10.1371/journal.pone.0257368

Who was buried with Nestor’s Cup? Macroscopic and microscopic analyses of the cremated remains from Tomb 168 (second half of the 8th century BCE, Pithekoussai, Ischia Island, Italy)
Cited by: 3
Author(s): Melania Gigante, Alessia Nava, Robert R. Paine, Ivana Fiore, Francesca Alhaique, Carmen Esposito, Alessandra Sperduti, Jacopo Bonetto, Teresa Cinquantaquattro, Bruno D’Agostino, Luca Bondioli
Software Mentions: 3
Published: almost 3 years ago

10.1534/g3.119.200997

Full-Length Transcriptome Sequencing and the Discovery of New Transcripts in the Unfertilized Eggs of Zebrafish (<i>Danio rerio</i>)
Cited by: 14
Author(s): Rumana Mehjabin, Lv Xiong, Rong Huang, Yang Cheng, Geng Chen, Libo He, Lanjie Liao, Zhu Zhang, Yaping Wang
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-020-58985-6

Facilitating gene editing in potato: a Single-Nucleotide Polymorphism (SNP) map of the Solanum tuberosum L. cv. Desiree genome
Cited by: 33
Author(s): François Sevestre, Maud Facon, Fabrice Wattebled, Nicolas Szydlowski
Software Mentions: 3
Published: over 4 years ago

10.1093/synbio/ysz016

Better research by efficient sharing: evaluation of free management platforms for synthetic biology designs
Cited by: 8
Author(s): Uriel Urquiza-García, Tomasz Zieliński, Andrew J. Millar
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-019-6000-y

Hybrid sequencing of the Gynostemma pentaphyllum transcriptome provides new insights into gypenoside biosynthesis
Cited by: 14
Author(s): Tongtong Liang, Li-Qiu Zou, Sijie Sun, Xue-Jun Kuang, Jianhe Wei, Lizhi Wang, Ying Liu, Chao Sun
Software Mentions: 3
Published: about 5 years ago

10.1101/2021.01.19.427194

BRD2 inhibition blocks SARS-CoV-2 infection by reducing transcription of the host cell receptor ACE2
Cited by: 7
Author(s): Ruilin Tian, Avi J. Samelson, Veronica V. Rezelj, Merissa Chen, Gokul N. Ramadoss, Xiaoyan Guo, Alice Mac Kain, Quang Tran, Shion A. Lim, Irene Lui, James K. Nuñez, Sarah J. Rockwood, Na Liu, Jared Carlson-Stevermer, Jennifer Oki, Travis J. Maures, Kevin Holden, Jonathan S. Weissman, James A. Wells, Bruce R. Conklin, Marco Vignuzzi, Martin Kampmann
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.69795

A zebrafish screen reveals Renin-angiotensin system inhibitors as neuroprotective via mitochondrial restoration in dopamine neurons
Cited by: 18
Author(s): Ghahyun J. Kim, Han Mo, Harrison Liu, Zhihao Wu, Steven Chen, Jiashun Zheng, Xiang Zhao, Daryl Nucum, James Shortland, Longping Peng, Mannuel Elepano, Benjamin C. Tang, Steven H. Olson, Nick A. Paras, Hao Li, Adam R. Renslo, Michelle R. Arkin, Bo Huang, Bingwei Lu, Marina Sirota, Su Guo
Software Mentions: 3
Published: almost 3 years ago

10.1089/crispr.2020.0022

Deconvolution of Complex DNA Repair (DECODR): Establishing a Novel Deconvolution Algorithm for Comprehensive Analysis of CRISPR-Edited Sanger Sequencing Data
Cited by: 39
Author(s): Kevin Bloh, Rohan Kanchana, Pawel Bialk, Kelly Banas, Zugui Zhang, Byung-Chun Yoo, Eric B. Kmiec
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2021.656137

Single-Molecule Real-Time and Illumina-Based RNA Sequencing Data Identified Vernalization-Responsive Candidate Genes in Faba Bean (Vicia faba L.)
Cited by: 3
Author(s): Xuesong Yuan, Qiong Wang, Bin Yan, Jiong Zhang, Chenchen Xue, Jingbin Chen, Yun Lin, Xiaoyan Zhang, Wenbiao Shen, Xin Chen
Software Mentions: 3
Published: about 3 years ago

10.3390/genes12020283

Estimating Copy-Number Proportions: The Comeback of Sanger Sequencing
Cited by: 7
Author(s): Eyal Seroussi
Software Mentions: 2
Published: over 3 years ago

10.3390/s19051114

Intelligent and Dynamic Ransomware Spread Detection and Mitigation in Integrated Clinical Environments
Cited by: 47
Author(s): Lorenzo Fernández Maimó, Alberto Huertas Celdrán, Ángel Luis Perales Gómez, Félix J. García Clemente, James Weimer, Insup Lee
Software Mentions: 2
Published: over 5 years ago

10.1007/978-3-030-53291-8_31

Manthan: A Data-Driven Approach for Boolean Function Synthesis
Cited by: 25
Author(s): Priyanka Golia, Subhajit Roy, Kuldeep S. Meel
Software Mentions: 2
Published: over 4 years ago

10.3390/ijms20235864

microRNAs Regulating Human and Mouse Naïve Pluripotency
Cited by: 9
Author(s): Yuliang Wang, Abdiasis M. Hussein, Logeshwaran Somasundaram, Rithika Sankar, Damien Detraux, Julie Mathieu, Hannele Ruohola‐Baker
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0237018

Creation of novel alleles of fragrance gene OsBADH2 in rice through CRISPR/Cas9 mediated gene editing
Cited by: 64
Author(s): Shanthinie Ashokkumar, Deepa Jaganathan, V. Ramanathan, Hifzur Rahman, Rakshana Palaniswamy, Rohit Kambale, M. Raveendran
Software Mentions: 2
Published: about 4 years ago

10.3390/ijms22010396

First Report of CRISPR/Cas9 Mediated DNA-Free Editing of 4CL and RVE7 Genes in Chickpea Protoplasts
Cited by: 75
Author(s): Sapna Badhan, Andrew S. Ball, Nitin Mantri
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0197585

Eye position affects flight altitude in visual approach to landing independent of level of expertise of pilot
Cited by: 8
Author(s): David M. Jacobs, Antoine H.P. Morice, Cyril Camachon, Gilles Montagne
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-016-2596-3

A streamlined tethered chromosome conformation capture protocol
Cited by: 17
Author(s): Idan Gabdank, Sreejith Ramakrishnan, Anne M. Villeneuve, Andrew Fire
Software Mentions: 2
Published: over 8 years ago

10.1534/g3.120.401110

Proxies of CRISPR/Cas9 Activity To Aid in the Identification of Mutagenized Arabidopsis Plants
Cited by: 9
Author(s): Renyu Li, Charles Vavrik, Cristian H. Danna
Software Mentions: 2
Published: over 4 years ago

10.1186/1471-2164-13-35

IntegromeDB: an integrated system and biological search engine
Cited by: 10
Author(s): Michael Baitaluk, Sergey Kozhenkov, Yulia Dubinina, Julia Ponomarenko
Software Mentions: 2
Published: over 12 years ago

10.1186/s12864-019-6036-z

Comparative transcriptome and coexpression network analysis of carpel quantitative variation in Paeonia rockii
Cited by: 16
Author(s): Na Liu, Fangyun Cheng, Yuan Zhong, Xin Guo
Software Mentions: 2
Published: about 5 years ago

10.3390/ijms22031217

Gene Editing Correction of a Urea Cycle Defect in Organoid Stem Cell Derived Hepatocyte-like Cells
Cited by: 14
Author(s): Mihaela Zabulica, Tomas Jakobsson, Francesco Ravaioli, Massoud Vosough, Roberto Gramignoli, Ewa Ellis, Olav Rooyackers, Stephen C. Strom
Software Mentions: 2
Published: over 3 years ago

10.1089/crispr.2019.0026

Expanding the CRISPR Toolbox with ErCas12a in Zebrafish and Human Cells
Cited by: 31
Author(s): Wesley A. Wierson, Brandon W. Simone, Zachary WareJoncas, Carla M. Mann, Jordan M. Welker, Bibekananda Kar, Michael J. Emch, Iddo Friedberg, William A.C. Gendron, Michael A. Barry, Karl J. Clark, Drena Dobbs, Maura McGrail, Stephen C. Ekker, Jeffrey J. Essner
Software Mentions: 2
Published: almost 5 years ago

10.3390/ijms20071686

Distinct Dopamine D2 Receptor Antagonists Differentially Impact D2 Receptor Oligomerization
Cited by: 24
Author(s): Elise Wouters, Adrián Ricarte Marín, James A. R. Dalton, Jesús Giraldo
Software Mentions: 2
Published: over 5 years ago

10.3390/plants9091218

Transcriptome-Wide Analysis of Nitrogen-Regulated Genes in Tea Plant (Camellia sinensis L. O. Kuntze) and Characterization of Amino Acid Transporter CsCAT9.1
Cited by: 10
Author(s): Xinwan Zhang, Hongling Liu, Elizabeth A. H. Pilon‐Smits, Wei Huang, Pu Wang, Mingle Wang, Fei Guo, Yu Wang, Ruiyuan Li, Hua Zhao, Dejiang Ni
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12874-016-0157-8

Comparison of non-parametric methods for ungrouping coarsely aggregated data
Cited by: 5
Author(s): Silvia Rizzi, Mikael Thinggaard, Gerda Engholm, N. E. Christensen, Tom Børge Johannesen, James W. Vaupel, Rune Lindahl-Jacobsen
Software Mentions: 2
Published: over 8 years ago

10.1038/s41421-021-00286-x

The Cardamine enshiensis genome reveals whole genome duplication and insight into selenium hyperaccumulation and tolerance
Cited by: 11
Author(s): Chuying Huang, Hongqin Ying, Xibiao Yang, Yuan Gao, Tuo Li, Bo Wu, Mindong Ren, Zixiong Zhang, Jun Ding, Jianhua Gao, Dan Wen, Xingzhi Ye, Ling Liu, Huan Wang, Guogen Sun, Yi Zou, Nansheng Chen, Li Wang
Software Mentions: 2
Published: about 3 years ago

10.3390/cells10051020

In Vitro Evaluation of CD276-CAR NK-92 Functionality, Migration and Invasion Potential in the Presence of Immune Inhibitory Factors of the Tumor Microenvironment
Cited by: 12
Author(s): Stefan Grote, Guillermo Ureña-Bailén, Kenneth Chun-Ho Chan, Caroline Baden, Markus Mezger, Rupert Handgretinger, Sabine Schleicher
Software Mentions: 2
Published: over 3 years ago

10.3390/ijms20184426

Hybrid Sequencing of Full-Length cDNA Transcripts of the Medicinal Plant Scutellaria baicalensis
Cited by: 5
Author(s): Ting Gao, Zhichao Xu, Xiaojun Song, Kai Huang, Ying Liu, Jianhe Wei, Xinghua Zhu, Haoran Ren, Chao Sun
Software Mentions: 2
Published: about 5 years ago

10.1186/s13578-021-00618-0

A ribonucleoprotein transfection strategy for CRISPR/Cas9‐mediated gene editing and single cell cloning in rainbow trout cells
Cited by: 5
Author(s): Marina Zoppo, Nicole Okoniewski, Stanislav Pantelyushin, Johannes vom Berg, Kristin Schirmer
Software Mentions: 2
Published: over 3 years ago

10.12688/wellcomeopenres.15447.2

A CRISPR/Cas9 genome editing pipeline in the EndoC-βH1 cell line to study genes implicated in beta cell function
Cited by: 13
Author(s): Antje Grotz, Fernando Abaitua, Elena Navarro-Guerrero, Benoît Hastoy, Daniel Ebner, Anna L. Gloyn
Software Mentions: 2
Published: over 4 years ago

10.3389/fpls.2017.01205

Transcriptome Profiling Using Single-Molecule Direct RNA Sequencing Approach for In-depth Understanding of Genes in Secondary Metabolism Pathways of Camellia sinensis
Cited by: 70
Author(s): Qingshan Xu, Junyan Zhu, Sheng Zhao, Yan Hou, Fangdong Li, Yuling Tai, Xiaochun Wan, Chaoling Wei
Software Mentions: 1
Published: about 7 years ago

10.1136/flgastro-2019-101177

Development and implementation of a commissioned pathway for the identification and stratification of liver disease in the community
Cited by: 41
Author(s): John M. Chalmers, Emilie Wilkes, Rebecca Harris, Lucy Kent, Sonali Kinra, Guruprasad P. Aithal, Mary Holmes, Jeanette Johnson, Joanne R Morling, Indra Neil Guha
Software Mentions: 1
Published: about 5 years ago

10.3390/genes11060628

Rapid Evaluation of CRISPR Guides and Donors for Engineering Mice
Cited by: 7
Author(s): Elena McBeath, Jan Parker-Thornburg, Yuka Fujii, Neeraj K. Aryal, Chad Smith, Marie‐Claude Hofmann, Jun Abe, Keigi Fujiwara
Software Mentions: 1
Published: over 4 years ago

10.3390/genes11091029

PEG-Delivered CRISPR-Cas9 Ribonucleoproteins System for Gene-Editing Screening of Maize Protoplasts
Cited by: 30
Author(s): Rodrigo Ribeiro Arnt Sant’Ana, Clarissa Alves Caprestano, Rubens Onofre Nodari, Sarah Zanon Agapito-Tenfen
Software Mentions: 1
Published: about 4 years ago

10.1186/gb-2014-15-4-r61

Effectively identifying regulatory hotspots while capturing expression heterogeneity in gene expression studies
Cited by: 30
Author(s): Jong Wha J. Joo, Jae Hoon Sul, Buhm Han, Chun Yuan, Eleazar Eskin
Software Mentions: 1
Published: over 10 years ago

10.1186/1467-4866-8-11

Physicochemical conditions and timing of rodingite formation: evidence from rodingite-hosted fluid inclusions in the JM Asbestos mine, Asbestos, Québec
Cited by: 29
Author(s): C. W. B. Normand, Anthony E. Williams‐Jones
Software Mentions: 1
Published: almost 17 years ago

10.1120/jacmp.v17i5.6091

Characteristics of quantitative perfusion parameters on dynamic contrast-enhanced MRI in mammographically occult breast cancer
Cited by: 10
Author(s): Jung Kyu Ryu, Sun Jung Rhee, Jeong Yoon Song, Soo Hyun Cho, Geon‐Ho Jahng
Software Mentions: 1
Published: about 8 years ago

10.1186/1754-1611-7-2

2ab assembly: a methodology for automatable, high-throughput assembly of standard biological parts
Cited by: 10
Author(s): Mariana Leguía, Jennifer A N Brophy, Douglas Densmore, Angel Asante, Janet S. Anderson
Software Mentions: 1
Published: over 11 years ago

10.1021/acs.jctc.1c00081

Comparison of Many-Particle Representations for Selected Configuration Interaction: II. Numerical Benchmark Calculations
Cited by: 16
Author(s): Vijay Gopal Chilkuri, Frank Neese
Software Mentions: 1
Published: over 3 years ago

10.1016/j.reprotox.2021.06.006

The potential of mechanistic information organised within the AOP framework to increase regulatory uptake of the developmental neurotoxicity (DNT) in vitro battery of assays
Cited by: 17
Author(s): Magdalini Sachana, Catherine Willett, Kathrin Herrmann, Anna Bal‐Price
Software Mentions: 1
Published: about 3 years ago

10.1038/s41598-017-15952-y

Statistically strong label-free quantitative identification of native fluorophores in a biological sample
Cited by: 28
Author(s): Saabah B. Mahbub, Martin Plöschner, Martin E. Gosnell, Ayad G. Anwer, Ewa M. Goldys
Software Mentions: 1
Published: almost 7 years ago

10.3390/s120607648

A Communication Model to Integrate the Request-Response and the Publish-Subscribe Paradigms into Ubiquitous Systems
Cited by: 36
Author(s): Carlos Rodríguez-Domínguez, Kawtar Benghazi, Manuel Noguera, José Luis García Garrido, María Luisa Rodríguez, Tomás Ruiz-López
Software Mentions: 1
Published: over 12 years ago

10.3390/s17061333

On Line Service Composition in the Integrated Clinical Environment for eHealth and Medical Systems
Cited by: 6
Author(s): Marisol García-Valls, Imad Eddine Touahria
Software Mentions: 1
Published: over 7 years ago

10.1016/j.stemcr.2019.09.008

Hippocampal CA1 Somatostatin Interneurons Originate in the Embryonic MGE/POA
Cited by: 14
Author(s): Zeinab Asgarian, Lorenza Magno, Niki Ktena, Kenneth D. Harris, Nicoletta Kessaris
Software Mentions: 1
Published: almost 5 years ago

10.1186/s13063-018-3169-3

Gabapentin as add-on to morphine for severe neuropathic or mixed pain in children from age 3 months to 18 years - evaluation of the safety, pharmacokinetics, and efficacy of a new gabapentin liquid formulation: study protocol for a randomized controlled trial
Cited by: 6
Author(s): Tom G. de Leeuw, Laura Mangiarini, Rebecca Lundin, Florentia Kaguelidou, Tjitske van der Zanden, Oscar Della Pasqua, Dick Tibboel, Adriana Ceci, Saskia N. de Wildt
Software Mentions: 1
Published: over 5 years ago

10.1186/1475-9276-13-3

Inequalities in out-of-pocket payments for health care services among elderly Germans – results of a population-based cross-sectional study
Cited by: 31
Author(s): Jens‐Oliver Bock, Herbert Matschinger, Hermann Brenner, Beate Wild, Walter E. Haefeli, Renate Quinzler, Kai Uwe Saum, Dirk Heider, Hans Helmut König
Software Mentions: 1
Published: over 10 years ago

10.1155/2020/7156408

Retinal Mosaicking with Vascular Bifurcations Detected on Vessel Mask by a Convolutional Network
Cited by: 6
Author(s): Xiuxia Feng, Guang-Wei Cai, Xiaofang Gou, Zhaoqiang Yun, Wenhui Wang, Wei Yang
Software Mentions: 1
Published: over 4 years ago

10.3390/ijerph120910391

Estimation of Chlorophyll-a Concentration and the Trophic State of the Barra Bonita Hydroelectric Reservoir Using OLI/Landsat-8 Images
Cited by: 125
Author(s): Fernanda Watanabe, Enner Alcântara, Thanan Rodrigues, Nilton Nobuhiro Imai, Cláudio Clemente Faria Barbosa, Luiz Rotta
Software Mentions: 1
Published: about 9 years ago

10.7554/eLife.51662

Herpesviral lytic gene functions render the viral genome susceptible to novel editing by CRISPR/Cas9
Cited by: 29
Author(s): Hyung Suk Oh, Werner M. Neuhausser, Pierce Eggan, Magdalena Angelova, Rory Kirchner, Kevin Eggan, David M. Knipe
Software Mentions: 1
Published: almost 5 years ago

10.3390/ijms21031024

Expanding the CRISPR Toolbox in P. patens Using SpCas9-NG Variant and Application for Gene and Base Editing in Solanaceae Crops
Cited by: 35
Author(s): Florian Veillet, Laura Perrot, Anouchka Guyon‐Debast, Marie-Paule Kermarrec, Laura Chauvin, Jean-Éric Chauvin, Jean‐Luc Gallois, Marianne Mazier, Fabien Nogué
Software Mentions: 1
Published: over 4 years ago

10.3390/ijms22041878

CRISPR/Cas9-Mediated Generation of Pathogen-Resistant Tomato against Tomato Yellow Leaf Curl Virus and Powdery Mildew
Cited by: 51
Author(s): Dibyajyoti Pramanik, Rahul Mahadev Shelake, Jiyeon Park, Mi Jung Kim, Indeok Hwang, Young-Hoon Park, Jae‐Yean Kim
Software Mentions: 1
Published: over 3 years ago

10.3390/ijms22126427

Conserved Opposite Functions in Plant Resistance to Biotrophic and Necrotrophic Pathogens of the Immune Regulator SRFR1
Cited by: 5
Author(s): Geon Hui Son, Ji‐Yun Moon, Rahul Mahadev Shelake, Uyen Thi Vuong, Robert A. Ingle, Walter Gassmann, Jae‐Yean Kim, Sang Hee Kim
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2105-11-425

TF-finder: A software package for identifying transcription factors involved in biological processes using microarray data and existing knowledge base
Cited by: 13
Author(s): Xiaoqi Cui, Tong Wang, Huann-Sheng Chen, Victor Busov, Hairong Wei
Software Mentions: 1
Published: about 14 years ago

10.1186/s12859-020-03832-8

Identification and utilization of copy number information for correcting Hi-C contact map of cancer cell lines
Cited by: 3
Author(s): Ahmed Ibrahim Samir Khalil, Siti Rawaidah Binte Mohammad Muzaki, Anupam Chattopadhyay, Amartya Sanyal
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12859-018-2464-z

Reconstructing high-resolution chromosome three-dimensional structures by Hi-C complex networks
Cited by: 15
Author(s): Tong Liu, Zheng Wang
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12896-020-00626-x

Efficient CRISPR/Cas9 genome editing in a salmonid fish cell line using a lentivirus delivery system
Cited by: 28
Author(s): Remi L. Gratacap, Tim Regan, Carola E. Dehler, Samuel Martín, Pierre Boudinot, Bertrand Collet, Ross D. Houston
Software Mentions: 1
Published: about 4 years ago

10.1186/s12885-021-07957-8

FOXD1 regulates cell division in clear cell renal cell carcinoma
Cited by: 9
Author(s): Kyle H. Bond, Jennifer L. Fetting, Christine W. Lary, Ivette F. Emery, Leif Oxburgh
Software Mentions: 1
Published: over 3 years ago

10.1186/s12875-020-01329-0

Management of chlamydia and gonorrhoea infections diagnosed in primary care using a centralised nurse-led telephone-based service: mixed methods evaluation
Cited by: 1
Author(s): Jeremy Horwood, Emer Brangan, Petra Manley, Patrick J Horner, Peter Muir, Paul North, John Macleod
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12864-019-5963-z

Insertion/deletion-activated frame-shift fluorescence protein is a sensitive reporter for genomic DNA editing
Cited by: 5
Author(s): Akhilesh Kumar, Michael D. Birnbaum, Balaji T. Moorthy, Jayanti Singh, Anna Palovcak, Dhruti Patel, Fangliang Zhang
Software Mentions: 1
Published: about 5 years ago

10.1186/s12916-018-1051-5

Is telephone health coaching a useful population health strategy for supporting older people with multimorbidity? An evaluation of reach, effectiveness and cost-effectiveness using a ‘trial within a cohort’
Cited by: 26
Author(s): Maria Panagioti, David Reeves, Rachel Meacock, Beth Parkinson, Karina Lovell, Mark Hann, Kelly Howells, Amy Blakemore, Lisa Riste, Peter Coventry, Tom Blakeman, Mark Sidaway, Peter Bower
Software Mentions: 1
Published: over 6 years ago

10.1186/1472-6947-12-3

Use of name recognition software, census data and multiple imputation to predict missing data on ethnicity: application to cancer registry records
Cited by: 29
Author(s): Ronan Ryan, Sally Vernon, Gavin P. Lawrence, Sue Wilson
Software Mentions: 1
Published: over 12 years ago

10.1186/s12870-018-1273-x

The Antarctic sea ice alga Chlamydomonas sp. ICE-L provides insights into adaptive patterns of chloroplast evolution
Cited by: 16
Author(s): Zhenhua Zhang, Meiling An, Jun Miao, Zhiqiang Gu, Chang Liu, Bojian Zhong
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-244X-13-171

Preventing the onset of major depression based on the level and profile of risk of primary care attendees: protocol of a cluster randomised trial (the predictD-CCRT study)
Cited by: 20
Author(s): Juan Ángel Bellón, Sonia Conejo-Cerón, Patrícia Moreno-Peral, Michael King, Irwin Nazareth, Carlos Martín-Pérez, Carmen Fernández-Alonso, María Isabel Ballesta-Rodríguez, Anna Fernández, José María Aiarzagüena, Carmen Montón-Franco, Inmaculada Ibáñez-Casas, Emiliano Rodríguez‐Sánchez, Antonina Rodríguez-Bayón, Antoni Serrano‐Blanco, María Cruz Sánchez Gómez, Pilar Lafuente, María del Mar Muñoz-García, Pilar Mínguez-Gonzalo, Luz Araujo, Diego Palao, Maite Espinosa, Fernando Zubiaga, Desirée Navas-Campaña, Juan Manuel Mendive, José Manuel Aranda-Regules, Alberto Rodríguez-Morejón, Luis Salvador‐Carulla, Juan de Dios Luna
Software Mentions: 1
Published: about 11 years ago

10.1186/1752-0509-4-74

Co-expression module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progression
Cited by: 113
Author(s): Zhiao Shi, Catherine K Derow, Bing Zhang
Software Mentions: 1
Published: over 14 years ago

10.26508/lsa.202000940

Evaluating CRISPR-based prime editing for cancer modeling and CFTR repair in organoids
Cited by: 55
Author(s): Maarten H. Geurts, Eyleen de Poel, Cayetano Pleguezuelos-Manzano, Rurika Oka, Léo Carrillo, Amanda Andersson-Rolf, Matteo Boretto, Jesse E. Brunsveld, Ruben van Boxtel, Jeffrey M. Beekman, Hans Clevers
Software Mentions: 1
Published: about 3 years ago

10.1186/s12936-016-1173-1

Analysis of ex vivo drug response data of Plasmodium clinical isolates: the pros and cons of different computer programs and online platforms
Cited by: 12
Author(s): Grennady Wirjanata, Irene Handayuni, Sophie Zaloumis, Ferryanto Chalfein, Pak Prayoga, Enny Kenangalem, Jeanne Rini Poespoprodjo, Rintis Noviyanti, Julie A. Simpson, Ric N. Price, Jutta Marfurt
Software Mentions: 1
Published: over 8 years ago

10.1007/s10126-020-09995-y

Efficient Genome Editing in Multiple Salmonid Cell Lines Using Ribonucleoprotein Complexes
Cited by: 13
Author(s): Remi L. Gratacap, Ye Jin, Marina Mantsopoulou, Ross D. Houston
Software Mentions: 1
Published: almost 4 years ago

10.3390/molecules18010997

Supercritical Carbon Dioxide Extraction of Seed Oil from Winter Melon (Benincasa hispida) and Its Antioxidant Activity and Fatty Acid Composition
Cited by: 43
Author(s): Mandana Bimakr, Russly Abdul Rahman, Farah Saleena Taip, Noranizan Mohd Adzahan, Zaidul Islam Sarker, Ali Ganjloo
Software Mentions: 1
Published: over 11 years ago

10.12688/wellcomeopenres.15225.3

What factors indicate prognosis for adults with depression in primary care? A protocol for meta-analyses of individual patient data using the Dep-GP database
Cited by: 9
Author(s): Joshua E J Buckman, Rob Saunders, Zachary D. Cohen, Katherine Clarke, Gareth Ambler, Robert J. DeRubeis, Simon Gilbody, Steven D. Hollon, Tony Kendrick, Ed Watkins, Ian R. White, Glyn Lewis, Stephen Pilling
Software Mentions: 1
Published: over 4 years ago

10.1186/s13071-020-04384-9

Diminished adherence of Biomphalaria glabrata embryonic cell line to sporocysts of Schistosoma mansoni following programmed knockout of the allograft inflammatory factor
Cited by: 7
Author(s): Fernanda Sales Coelho, Rutchanee Rodpai, André Miller, Shannon E. Karinshak, Victoria H. Mann, Omar dos Santos Carvalho, Roberta Lima Caldeira, Marina Moraes Mourão, Paul J. Brindley, Wannaporn Ittiprasert
Software Mentions: 1
Published: almost 4 years ago

10.1363/4303011

Is Parenting Associated with Teenagers’ Early Sexual Risk-Taking, Autonomy And Relationship with Sexual Partners?
Cited by: 97
Author(s): Alison Parkes, Marion Henderson, Daniel Wight, Catherine Nixon
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pbio.1002310

SBOL Visual: A Graphical Language for Genetic Designs
Cited by: 72
Author(s): Jacqueline Quinn, Robert Sidney Cox, Aaron Adler, Jacob Beal, Swapnil Bhatia, Yizhi Cai, Joanna Chen, Kevin Clancy, Michal Galdzicki, Nathan J. Hillson, Nicolas Le Novère, Akshay J. Maheshwari, James Alastair McLaughlin, Chris J. Myers, P Umesh, Matthew Pocock, César Rodríguez, Larisa Soldatova, Guy-Bart Stan, Neil Swainston, Anil Wipat, Herbert M. Sauro
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pcbi.1005537

An independent component analysis confounding factor correction framework for identifying broad impact expression quantitative trait loci
Cited by: 12
Author(s): Jin Hyun Ju, Sushila Shenoy, Ronald G. Crystal, Jason G. Mezey
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0126627

Valuing Blue Carbon: Carbon Sequestration Benefits Provided by the Marine Protected Areas in Colombia
Cited by: 38
Author(s): Tatiana G. Zarate-Barrera, Jorge Higinio Maldonado
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0211598

Comparison of efficiency and specificity of CRISPR-associated (Cas) nucleases in plants: An expanded toolkit for precision genome engineering
Cited by: 32
Author(s): Oleg Raitskin, Christian Schudoma, Anthony P. West, Nicola J. Patron
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0253245

CRISPR/Cas9-mediated mutagenesis of sweet basil candidate susceptibility gene ObDMR6 enhances downy mildew resistance
Cited by: 28
Author(s): Jeremieh Abram R. Hasley, Natasha Navet, Mingxing Tian
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0228910

An improved strategy for CRISPR/Cas9 gene knockout and subsequent wildtype and mutant gene rescue
Cited by: 16
Author(s): Jiankang Jin, Yan Xu, Longfei Huo, Lang Ma, Ailing W. Scott, Melissa Pool Pizzi, Yuan Li, Ying Wang, Xiaodan Yao, Shumei Song, Jaffer A. Ajani
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0224857

CRISPR/Cas9 gene editing in the West Nile Virus vector, Culex quinquefasciatus Say
Cited by: 20
Author(s): Michelle A. E. Anderson, Jessica Mavica, Lewis Shackleford, Ilona Flis, Sophia Fochler, Subhash Basu, Luke Alphey
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0202673

Simultaneous multislice acquisition with multi-contrast segmented EPI for separation of signal contributions in dynamic contrast-enhanced imaging
Cited by: 5
Author(s): Klaus Eickel, David A. Porter, Anika Söhner, Marc Maaß, Lutz Lüdemann, Matthias Günther
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0218653

High throughput, efficacious gene editing &amp; genome surveillance in Chinese hamster ovary cells
Cited by: 9
Author(s): Steven Huhn, Yang Ou, Amit Kumar, R. Liu, Ziyun Du
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0049764

Image Corruption Detection in Diffusion Tensor Imaging for Post-Processing and Real-Time Monitoring
Cited by: 31
Author(s): Yue Li, Steven M. Shea, Christine H. Lorenz, Hangyi Jiang, Ming-Dah Chou, Susumu Mori
Software Mentions: 1
Published: almost 11 years ago

10.3390/cancers13123024

The CRISPR/Cas9 Minipig—A Transgenic Minipig to Produce Specific Mutations in Designated Tissues
Cited by: 11
Author(s): Martin F. Berthelsen, Maria Riedel, Huiqiang Cai, Søren Helbo Skaarup, Aage Kristian Olsen Alstrup, Frederik Dagnæs‐Hansen, Yonglun Luo, Uffe Birk Jensen, Henrik Hager, Ying Liu, Henrik Callesen, Mikkel Holm Vendelbo, Jannik E. Jakobsen, Martin K. Thomsen
Software Mentions: 1
Published: over 3 years ago

10.3390/cancers13153783

Therapeutic Potential of EWSR1–FLI1 Inactivation by CRISPR/Cas9 in Ewing Sarcoma
Cited by: 13
Author(s): Saint T. Cervera, Carlos Rodríguez-Martín, Enrique Fernández-Tabanera, Raquel M. Melero-Fernández de Mera, Matías Morin, Sergio Fernández-Peñalver, Maria Iranzo-Martínez, Jorge Amhih-Cardenas, Laura García-García, Laura González-González, Miguel A. Moreno-Pelayo, Javier Alonso
Software Mentions: 1
Published: about 3 years ago