10.1038/s41598-019-55984-0

Patterns of diverse gene functions in genomic neighborhoods predict gene function and phenotype
Cited by: 16
Author(s): Matej Mihelčić, Tomislav Šmuc, Fran Supek
Software Mentions: 9
Published: over 6 years ago

10.1371/journal.pcbi.1006596

Whole genomes define concordance of matched primary, xenograft, and organoid models of pancreas cancer
Cited by: 43
Author(s): Deena M.A. Gendoo, Robert E. Denroche, Amy Zhang, Nikolina Radulovich, Gun Ho Jang, Mathieu Lemire, Sandra E. Fischer, Dianne Chadwick, Ilinca M. Lungu, Emin Ibrahimov, Pinjiang Cao, Lincoln Stein, Julie M. Wilson, John M.S. Bartlett, Ming‐Sound Tsao, Neesha C. Dhani, David W. Hedley, Steven Gallinger, Benjamin Haibe‐Kains
Software Mentions: 9
Published: over 7 years ago

10.1038/s41598-019-50565-7

Tradeoffs in hyphal traits determine mycelium architecture in saprobic fungi
Cited by: 14
Author(s): Anika Lehmann, Weiguo Zheng, Katharina Soutschek, Julien Roy, Andrey Yurkov, Matthias C. Rillig
Software Mentions: 9
Published: over 6 years ago

10.1371/journal.pone.0239919

The recurring impact of storm disturbance on black sea bass (Centropristis striata) movement behaviors in the Mid-Atlantic Bight
Cited by: 3
Author(s): Caroline J. Wiernicki, Michael H. P. O’Brien, Fan Zhang, Vyacheslav Lyubchich, Ming Li, David H. Secor
Software Mentions: 9
Published: over 5 years ago

10.1371/journal.ppat.1009577

Epigenomic regulation of human T-cell leukemia virus by chromatin-insulator CTCF
Cited by: 11
Author(s): Xiaogang Cheng, Ancy Joseph, Victor Castro, Alice Chen-Liaw, Zachary L. Skidmore, Takaharu Ueno, Jun–ichi Fujisawa, Daniel A. Rauch, Grant A. Challen, Michael P. Martinez, Patrick Green, Malachi Griffith, Jacqueline E. Payton, John Edwards, Lee Ratner
Software Mentions: 9
Published: about 5 years ago

10.3390/cancers13040722

Prognostic and Predictive Value of Integrated Qualitative and Quantitative Magnetic Resonance Imaging Analysis in Glioblastoma
Cited by: 19
Author(s): Maikel Verduin, Sergey Primakov, Inge Compter, Henry C. Woodruff, Sander M. J. van Kuijk, Bram Ramaekers, Maarten te Dorsthorst, Elles G. M. Revenich, Mark ter Laan, Sjoert Pegge, Frederick J. A. Meijer, Jan Beckervordersandforth, Ernst-Jan M. Speel, Benno Küsters, Wendy W.J. de Leng, Monique M. Anten, Martijn P. G. Broen, Linda Ackermans, Olaf Schijns, Onno P.M. Teernstra, Koos E. Hovinga, Marc Vooijs, Vivianne C. G. Tjan‐Heijnen, Daniëlle Eekers, Alida A. Postma, Ann Hoeben
Software Mentions: 9
Published: over 5 years ago

10.3390/cancers13122895

A Comparison of Hypofractionated and Twice-Daily Thoracic Irradiation in Limited-Stage Small-Cell Lung Cancer: An Overlap-Weighted Analysis
Cited by: 11
Author(s): Michael Yan, Samantha Sigurdson, Noah Greifer, Thomas Kennedy, Tzen S. Toh, Patricia Lindsay, Jessica Weiss, Katrina Hueniken, Celine Yeung, Vijithan Sugumar, Alexander Sun, Andrea Bezjak, B. C. John Cho, Srinivas Raman, Andrew Hope, Meredith Giuliani, Elizabeth A. Stuart, Timothy Owen, A. Ashworth, Andrew Robinson, Fábio Ynoe de Moraes, Geoffrey Liu, Benjamin H. Lok
Software Mentions: 9
Published: about 5 years ago

10.1371/journal.pone.0157423

Decline of a Rare Moth at Its Last Known English Site: Causes and Lessons for Conservation
Cited by: 2
Author(s): D. James Baker, Sinead Barrett, Colin M. Beale, Terry J. Crawford, Sam Ellis, Tallulah Gullett, Peter J. Mayhew, Mark Parsons, Penny Relf, Paul B. Robertson, J. L. Small, David Wainwright
Software Mentions: 9
Published: about 10 years ago

10.1155/2019/3717239

Primary Production in the Water Column as Major Structuring Element of the Biogeographical Distribution and Function of Archaea in Deep-Sea Sediments of the Central Pacific Ocean
Cited by: 9
Author(s): Franziska Wemheuer, Avril Jean Elisabeth von Hoyningen-Huene, Marion Pohlner, Julius Degenhardt, Bert Engelen, Rolf Daniel, Bernd Wemheuer
Software Mentions: 9
Published: over 7 years ago

10.3389/fonc.2019.01314

An Immune-Related Signature Predicts Survival in Patients With Lung Adenocarcinoma
Cited by: 94
Author(s): Minghui Zhang, Kaibin Zhu, Haihong Pu, Zhuozhong Wang, Hongli Zhao, Jinfeng Zhang, Yan Wang
Software Mentions: 8
Published: over 6 years ago

10.3389/fmicb.2018.01868

Exposure to Yeast Shapes the Intestinal Bacterial Community Assembly in Zebrafish Larvae
Cited by: 29
Author(s): Prabhugouda Siriyappagouder, Jorge Galindo-Villegas, Jep Lokesh, Victoriano Mulero, Jorge M. O. Fernandes, Viswanath Kiron
Software Mentions: 8
Published: almost 8 years ago

10.3389/fmicb.2021.728479

Cross-Sectional Study on the Gut Microbiome of Parkinson’s Disease Patients in Central China
Cited by: 11
Author(s): Liangwei Mao, Yu Zhang, Jing Tian, Ming Sang, Guimin Zhang, Yiming Zhou, Puqing Wang
Software Mentions: 8
Published: over 4 years ago

10.1186/s13059-020-02155-4

Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC
Cited by: 51
Author(s): Paul Saary, Alex L. Mitchell, Alex Bateman
Software Mentions: 8
Published: almost 6 years ago

10.3389/fonc.2020.568469

Aberrant RNA Splicing Events Driven by Mutations of RNA-Binding Proteins as Indicators for Skin Cutaneous Melanoma Prognosis
Cited by: 4
Author(s): Chao Mei, Pei-Yuan Song, Wei Zhang, Hong‐Hao Zhou, Xi Li, Zhao‐Qian Liu
Software Mentions: 8
Published: over 5 years ago

10.1186/s12889-021-10979-3

Associations of meeting 24-h movement guidelines with stress and self-rated health among adults: is meeting more guidelines associated with greater benefits?
Cited by: 16
Author(s): Kaja Kastelic, Željko Pedišić, Dean Lipovac, Nika Kastelic, Sitong Chen, Nejc Šarabon
Software Mentions: 8
Published: about 5 years ago

10.3389/fgene.2019.01143

Identification of a Tumor Microenvironment-Related Eight-Gene Signature for Predicting Prognosis in Lower-Grade Gliomas
Cited by: 24
Author(s): Jun Su, Wenyong Long, Qianquan Ma, Kai Xiao, Li Yang, Qian Xiao, Gang Peng, Jian Yuan, Qing Liu
Software Mentions: 8
Published: over 6 years ago

10.1111/1365-2656.13035

Movement reveals reproductive tactics in male elephants
Cited by: 22
Author(s): Lucy A. Taylor, Fritz Vollrath, Ben Lambert, Daniel Lunn, Iain Douglas‐Hamilton, George Wittemyer
Software Mentions: 8
Published: about 7 years ago

10.18632/oncotarget.24506

Systematic characterization of autophagy-related genes during the adipocyte differentiation using public-access data
Cited by: 13
Author(s): Mahmoud Ahmed, Huynh Quoc Nguyen, Jin Seok Hwang, Sahib Zada, Trang Huyen Lai, Sang Soo Kang, Deok Ryong Kim
Software Mentions: 8
Published: over 8 years ago

10.3390/cancers12010045

N-Terminal Truncated Myb with New Transcriptional Activity Produced Through Use of an Alternative MYB Promoter in Salivary Gland Adenoid Cystic Carcinoma
Cited by: 11
Author(s): Candace A. Frerich, Hailey N. Sedam, Huining Kang, Yoshitsugu Mitani, Adel K. El‐Naggar, Scott A. Ness
Software Mentions: 8
Published: over 6 years ago

10.34133/2020/3074916

RhizoVision Crown: An Integrated Hardware and Software Platform for Root Crown Phenotyping
Cited by: 65
Author(s): Anand Seethepalli, Haichao Guo, Xiuwei Liu, Marcus Griffiths, Hussien Almtarfi, Zenglu Li, Shuyu Liu, Alina Zare, Felix B. Fritschi, Elison B. Blancaflor, Xuefeng Ma, Larry M. York
Software Mentions: 8
Published: over 6 years ago

10.7717/peerj.8667

Element concentrations in pelagic<i>Sargassum</i>along the Mexican Caribbean coast in 2018-2019
Cited by: 78
Author(s): Rosa E. Rodríguez-Martínez, Priyadarsi D. Roy, Nuria Torrescano-Valle, Nancy Cabañillas-Terán, Silvia Carrillo‐Domínguez, Ligia Collado‐Vides, Marta García-Sánchez, Brigitta I. van Tussenbroek
Software Mentions: 8
Published: over 6 years ago

10.1007/s13365-020-00931-3

Transcriptional signatures of Zika virus infection in astrocytes
Cited by: 3
Author(s): Blake Schouest, Tiffany A. Peterson, Dawn Szeltner, Elizabeth A. Scheef, Melody Baddoo, Nathan Ungerleider, Erik K. Flemington, Andrew G. MacLean, Nicholas J. Maness
Software Mentions: 8
Published: over 5 years ago

10.3390/ijms21010293

Docker4Circ: A Framework for the Reproducible Characterization of circRNAs from RNA-Seq Data
Cited by: 8
Author(s): Giulio Ferrero, Nicola Licheri, Lucia Coscujuela Tarrero, Carlo De Intinis, Valentina Miano, Raffaele Calogero, Francesca Cordero, Michele De Bortoli, Marco Beccuti
Software Mentions: 8
Published: over 6 years ago

10.1371/journal.pone.0185528

tsiR: An R package for time-series Susceptible-Infected-Recovered models of epidemics
Cited by: 38
Author(s): Alexander D. Becker, Bryan T. Grenfell
Software Mentions: 8
Published: over 8 years ago

10.7717/peerj.6362

Empirical analysis and modeling of Argos Doppler location errors in Romania
Cited by: 4
Author(s): Laurenţiu Rozyłowicz, Florian Bodescu, Cristiana Maria Ciocănea, Athanasios Alexandru Gavrilidis, Steluţa Manolache, Mihaela Matache, Iulia V. Miu, Ionut C Moale, Andreea Niţă, Viorel D. Popescu
Software Mentions: 8
Published: over 7 years ago

10.12688/wellcomeopenres.14847.1

Using machine learning to guide targeted and locally-tailored empiric antibiotic prescribing in a children's hospital in Cambodia
Cited by: 45
Author(s): Mathupanee Oonsivilai, Yin Mo, Nantasit Luangasanatip, Yoel Lubell, Thyl Miliya, Pisey Tan, Lorn Loeuk, Paul Turner, Ben S. Cooper
Software Mentions: 8
Published: over 7 years ago

10.1007/s12282-020-01191-z

Immune-related gene data-based molecular subtyping related to the prognosis of breast cancer patients
Cited by: 1
Author(s): Guoyu Mu, Hong Ji, Hui He, Hongjiang Wang
Software Mentions: 8
Published: over 5 years ago

10.1042/BSR20203676

Identification of pivotal genes associated with the prognosis of gastric carcinoma through integrated analysis
Cited by: 7
Author(s): Zhenchao Ma, Jingyu Xu, Lixin Ru, Weihua Zhu
Software Mentions: 8
Published: about 5 years ago

10.1155/2020/5843874

Identification of Biomarkers to Construct a Competing Endogenous RNA Network and Establishment of a Genomic-Clinicopathologic Nomogram to Predict Survival for Children with Rhabdoid Tumors of the Kidney
Cited by: 1
Author(s): Xiaoqing Wang, Xiangyu Wu, Tianyou Li, Meng Cui, Lichao Zhu, Gang Wang, Feng Guo
Software Mentions: 8
Published: almost 6 years ago

10.1186/s12859-019-3105-x

MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis
Cited by: 190
Author(s): Valerio Licursi, Federica Conte, Giulia Fiscon, Paola Paci
Software Mentions: 8
Published: over 6 years ago

10.18632/aging.202515

Cell differentiation trajectory predicts patient potential immunotherapy response and prognosis in gastric cancer
Cited by: 18
Author(s): Renshen Xiang, Yuping Rong, Yuhang Ge, Wei Song, Jun Ren, Tao Fu
Software Mentions: 8
Published: over 5 years ago

10.1002/ece3.6390

Can ancestry and morphology be used as surrogates for species niche relationships?
Cited by: 5
Author(s): Friedrich W. Keppeler, Kirk O. Winemiller
Software Mentions: 8
Published: about 6 years ago

10.1186/s12936-018-2627-4

Diagnostic performance of salivary urea nitrogen dipstick to detect and monitor acute kidney disease in patients with malaria
Cited by: 11
Author(s): Viviane Calice‐Silva, Euclides Nenga Manuel Sacomboio, Jochen G. Raimann, Rhys Evans, Cruz S. Sebastião, Adelino Tchilanda Tchivango, Peter Kotanko, Nathan W. Levin, Roberto Pecoits‐Filho
Software Mentions: 8
Published: over 7 years ago

10.1371/journal.pcbi.1007814

Genome-wide prediction of topoisomerase IIβ binding by architectural factors and chromatin accessibility
Cited by: 4
Author(s): Pedro Manuel Martínez-García, Miguel García-Torres, Federico Divina, José Terrón-Bautista, Irene Delgado‐Sainz, Felipe Cortés‐Ledesma
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pone.0203346

Feasibility of developing reliable gene expression modules from FFPE derived RNA profiled on Affymetrix arrays
Cited by: 3
Author(s): Vinu José, Debora Fumagalli, Françoise Rothé, Samira Majjaj, Sherene Loi, Stefan Michiels, Christos Sotiriou
Software Mentions: 8
Published: almost 8 years ago

10.1186/s12874-020-00986-0

Experts’ perceptions on the use of visual analytics for complex mental healthcare planning: an exploratory study
Cited by: 3
Author(s): Erin Walsh, Younjin Chung, Nicolas Cherbuin, Luis Salvador‐Carulla
Software Mentions: 8
Published: about 6 years ago

10.1093/molbev/msaa057

Genome Architecture Facilitates Phenotypic Plasticity in the Honeybee (Apis mellifera)
Cited by: 30
Author(s): Elizabeth J. Duncan, Megan Leask, Peter K. Dearden
Software Mentions: 8
Published: about 6 years ago

10.1186/s13148-020-00996-1

Integrated analysis reveals the alterations that LMNA interacts with euchromatin in LMNA mutation-associated dilated cardiomyopathy
Cited by: 9
Author(s): Xiaolin Zhang, Xiuli Shao, Ruijia Zhang, Rongli Zhu, Rui Feng
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pone.0248889

Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanisms
Cited by: 10
Author(s): Jozsef Karman, Jing Wang, Corneliu Bodea, Sherry Cao, Marc C. Levesque
Software Mentions: 8
Published: over 5 years ago

10.1186/s13321-018-0270-2

PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions
Cited by: 86
Author(s): Jie Dong, Zhi‐Jiang Yao, Lin Zhang, Feijun Luo, Qinlu Lin, Aiping Lu, Alex F. Chen, Dong‐Sheng Cao
Software Mentions: 8
Published: over 8 years ago

10.1186/s12864-019-5926-4

lncDIFF: a novel quasi-likelihood method for differential expression analysis of non-coding RNA
Cited by: 6
Author(s): Qian Li, Xiaoqing Yu, Ritu Chaudhary, Robbert J.C. Slebos, Christine H. Chung, Xuefeng Wang
Software Mentions: 8
Published: almost 7 years ago

10.1186/s12859-016-1051-4

gtrellis: an R/Bioconductor package for making genome-level Trellis graphics
Cited by: 17
Author(s): Zuguang Gu, Roland Eils, Matthias Schlesner
Software Mentions: 8
Published: about 10 years ago

10.1111/1755-0998.13280

The genome of <i>Draba nivalis</i> shows signatures of adaptation to the extreme environmental stresses of the Arctic
Cited by: 13
Author(s): Michael Nowak, Siri Birkeland, Terezie Mandáková, Rimjhim Roy Choudhury, Xi Guo, Lovisa Gustafsson, Abel Gizaw, Audun Schrøder-Nielsen, Marco Fracassetti, Anne K. Brysting, Loren H. Rieseberg, Tanja Slotte, Christian Parisod, Martin A. Lysak, Christian Brochmann
Software Mentions: 8
Published: over 5 years ago

10.3389/fgene.2019.00182

Detection of Differentially Expressed Cleavage Site Intervals Within 3′ Untranslated Regions Using CSI-UTR Reveals Regulated Interaction Motifs
Cited by: 9
Author(s): Benjamin J. Harrison, Juw Won Park, Cynthia Gomes, Jeffrey C. Petruska, Matthew R. Sapio, Michael J. Iadarola, Julia H. Chariker, Eric C. Rouchka
Software Mentions: 8
Published: over 7 years ago

10.1093/cz/zoab026

Hormonal modulation of reproduction and fertility signaling in polistine wasps
Cited by: 8
Author(s): Cíntia Akemi Oi, Rafael Carvalho da Silva, I. D. R. Stevens, Helena Mendes Ferreira, Fábio Santos do Nascimento, Tom Wenseleers
Software Mentions: 8
Published: over 5 years ago

10.3389/fpls.2020.601975

Flower Diversification Across “Pollinator Climates”: Sensory Aspects of Corolla Color Evolution in the Florally Diverse South American Genus Jaborosa (Solanaceae)
Cited by: 9
Author(s): Marcela Moré, Ana C. Ibañez, María Eugenia Drewniak, Andrea A. Cocucci, Robert A. Raguso
Software Mentions: 8
Published: over 5 years ago

10.3389/fpls.2021.647375

Molecular Evolution and Organization of Ribosomal DNA in the Hawkweed Tribe Hieraciinae (Cichorieae, Asteraceae)
Cited by: 11
Author(s): Judith Fehrer, Renata Slavíková, Ladislava Paštová, Jiřina Josefiová, Patrik Mráz, Jindřich Chrtek, Yann Bertrand
Software Mentions: 8
Published: over 5 years ago

10.7717/peerj.1360

Getting the most out of RNA-seq data analysis
Cited by: 22
Author(s): Tsung Fei Khang, Ching Yee Lau
Software Mentions: 8
Published: over 10 years ago

10.1038/s41598-019-56713-3

Individual and seasonal variation in contact rate, connectivity and centrality in red fox (Vulpes vulpes) social groups
Cited by: 11
Author(s): Jo Dorning, Stephen Harris
Software Mentions: 8
Published: over 6 years ago

10.1371/journal.pmed.1002223

Master Regulators of Oncogenic KRAS Response in Pancreatic Cancer: An Integrative Network Biology Analysis
Cited by: 38
Author(s): Shivan Sivakumar, Inês de Santiago, L Chlon, Florian Markowetz
Software Mentions: 8
Published: over 9 years ago

10.12688/f1000research.13196.2

Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR
Cited by: 42
Author(s): Yunshun Chen, Bhupinder Pal, Jane E. Visvader, Gordon K. Smyth
Software Mentions: 8
Published: over 7 years ago

10.1371/journal.pone.0230262

So far, so good… Similar fitness consequences and overall energetic costs for short and long-distance migrants in a seabird
Cited by: 10
Author(s): David Pelletier, Yannick Seyer, Stefan Garthe, Salomé Bonnefoi, Richard A. Phillips, Magella Guillemette
Software Mentions: 8
Published: over 6 years ago

10.1186/1471-2164-14-S5-S9

Detection and classification of peaks in 5' cap RNA sequencing data
Cited by: 4
Author(s): Dario Strbenac, Nicola J. Armstrong, Jean Yee Hwa Yang
Software Mentions: 8
Published: over 12 years ago

10.3389/fneur.2019.00331

Googling Boundaries for Operating Mobile Stroke Unit for Stroke Codes
Cited by: 7
Author(s): Thanh G. Phan, Richard Beare, Mark Parsons, Henry Zhao, Stephen M. Davis, Geoffrey A. Donnan, Velandai Srikanth, Henry Ma
Software Mentions: 8
Published: about 7 years ago

10.3390/jcm9051251

Dysregulations of MicroRNA and Gene Expression in Chronic Venous Disease
Cited by: 12
Author(s): Daniel Zalewski, Karol P Ruszel, Andrzej Stępniewski, Dariusz Gałkowski, Jacek Bogucki, Łukasz Komsta, Przemysław Kołodziej, Paulina Chmiel, Tomasz Zubilewicz, Marcin Feldo, Janusz Kocki, Anna Bogucka‐Kocka
Software Mentions: 8
Published: about 6 years ago

10.1002/ece3.6172

Habitat transitions alter the adaptive landscape and shape phenotypic evolution in needlefishes (Belonidae)
Cited by: 10
Author(s): Matthew A. Kolmann, Michael D. Burns, Justin Y. K. Ng, Nathan R. Lovejoy, Devin D. Bloom
Software Mentions: 8
Published: over 6 years ago

10.7554/eLife.52690

Sphingosine 1-phosphate-regulated transcriptomes in heterogenous arterial and lymphatic endothelium of the aorta
Cited by: 28
Author(s): Eric Engelbrecht, Michel V. Levesque, Liqun He, Michael Vanlandewijck, Anja Nitzsche, Hira Niazi, Andrew Kuo, Sasha A Singh, Masamichi Aikawa, Kristina M. Holton, Richard L. Proia, Mari Kono, William T. Pu, Eric Camerer, Christer Betsholtz, Timothy Hla
Software Mentions: 8
Published: over 6 years ago

10.1371/journal.pone.0069624

Transcriptomic Analysis of Insulin-Sensitive Tissues from Anti-Diabetic Drug Treated ZDF Rats, a T2DM Animal Model
Cited by: 4
Author(s): Yo Na Kim, Sangok Kim, Il Yong Kim, Jae Hoon Shin, Sooyoung Cho, Sun Shin Yi, Wankyu Kim, Kyung Sub Kim, Sanghyuk Lee, Je Kyung Seong
Software Mentions: 8
Published: almost 13 years ago

10.1002/ece3.2641

Convergent evolution in social swallows (Aves: Hirundinidae)
Cited by: 12
Author(s): Allison E. Johnson, Jonathan S. Mitchell, Mary Bomberger Brown
Software Mentions: 8
Published: over 9 years ago

10.3390/cells9030786

Systematic Identification of Housekeeping Genes Possibly Used as References in Caenorhabditis elegans by Large-Scale Data Integration
Cited by: 13
Author(s): Jingxin Tao, Youjin Hao, Xudong Li, Huachun Yin, Xiner Nie, Jie Zhang, Bo-Ying Xu, Chen Qiao, Bo Li
Software Mentions: 8
Published: over 6 years ago

10.1093/database/baz098

Progress in the study of genome size evolution in Asteraceae: analysis of the last update
Cited by: 14
Author(s): Daniel Vitales, P. Fernández, Teresa Garnatje, Sònia Garcia
Software Mentions: 8
Published: over 7 years ago

10.1534/g3.119.400373

isqg: A Binary Framework for<i>in Silico</i>Quantitative Genetics
Cited by: 1
Author(s): Fernando H. Toledo, Paulino Pérez‐Rodríguez, J. Crossa, Juan Burgueño
Software Mentions: 8
Published: almost 7 years ago

10.3389/fpls.2019.00382

The Potential of Liming to Improve Drought Tolerance of Norway Spruce [Picea abies (L.) Karst.]
Cited by: 6
Author(s): M. Köhler, Jörg Kunz, Johannes Herrmann, Peter Hartmann, Lelde Jansone, Heike Puhlmann, Klaus von Wilpert, Jürgen Bauhus
Software Mentions: 8
Published: about 7 years ago

10.1371/journal.pone.0228782

Learning about the Ellsberg Paradox reduces, but does not abolish, ambiguity aversion
Cited by: 6
Author(s): Ruonan Jia, Ellen E. Furlong, Sean Gao, Laurie R. Santos, Ifat Levy
Software Mentions: 8
Published: over 6 years ago

10.3390/v12111240

TBEV Subtyping in Terms of Genetic Distance
Cited by: 19
Author(s): Andrei A. Deviatkin, Galina G. Karganova, Yulia A. Vakulenko
Software Mentions: 8
Published: over 5 years ago

10.1186/s13059-020-02072-6

HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis
Cited by: 7
Author(s): Guy Karlebach, Peter J. Hansen, Diogo Veiga, Robin Steinhaus, Daniel Daniš, Sheng Li, Olga Anczuków, Peter N. Robinson
Software Mentions: 8
Published: almost 6 years ago

10.3389/fpls.2018.00108

Optimization of an RNA-Seq Differential Gene Expression Analysis Depending on Biological Replicate Number and Library Size
Cited by: 61
Author(s): Sophie Lamarre, Pierre Frasse, Mohamed Zouine, Delphine Labourdette, Elise Sainderichin, Guojian Hu, Véronique Le Berre-Anton, Mondher Bouzayen, Élie Maza
Software Mentions: 8
Published: over 8 years ago

10.3389/fgene.2018.00588

DREAMSeq: An Improved Method for Analyzing Differentially Expressed Genes in RNA-seq Data
Cited by: 10
Author(s): Zhihua Gao, Zhiyuan Zhao, Wenqiang Tang
Software Mentions: 8
Published: over 7 years ago

10.1371/journal.pcbi.1004956

Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis
Cited by: 38
Author(s): Rebeca Campos-Sánchez, Marzia A. Cremona, Alessia Pini, Francesca Chiaromonte, Kateryna D. Makova
Software Mentions: 8
Published: about 10 years ago

10.1371/journal.pone.0031630

Optimizing a Massive Parallel Sequencing Workflow for Quantitative miRNA Expression Analysis
Cited by: 33
Author(s): Francesca Cordero, Marco Beccuti, Maddalena Arigoni, Susanna Donatelli, Raffaele Calogero
Software Mentions: 8
Published: over 14 years ago

10.1186/s13148-020-00889-3

The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability
Cited by: 6
Author(s): Holly Russell, Katarzyna Kedzierska, Daniel D. Buchanan, Russell J. Thomas, Emma Tham, Miriam Mints, Anne Keränen, Graham G. Giles, Melissa C. Southey, Roger L. Milne, Ian Tomlinson, David N. Church, Amanda B. Spurdle, Tracy A. O’Mara, Annabelle Lewis
Software Mentions: 8
Published: almost 6 years ago

10.3389/fcimb.2018.00326

In Search of Biomarkers for Pathogenesis and Control of Leishmaniasis by Global Analyses of Leishmania-Infected Macrophages
Cited by: 16
Author(s): Patrícia Sampaio Tavares Veras, Pablo Ivan Pereira Ramos, Juliana Perrone Bezerra de Menezes
Software Mentions: 8
Published: almost 8 years ago

10.3390/jcm10010111

Evaluating the Effect of Topical Atropine Use for Myopia Control on Intraocular Pressure by Using Machine Learning
Cited by: 19
Author(s): Tzu-En Wu, Hsin‐An Chen, Mao-Jhen Jhou, Yen-Ning Chen, Ting-Jen Chang, Chi-Jie Lu
Software Mentions: 8
Published: over 5 years ago

10.7554/eLife.38519

Insulin mutations impair beta-cell development in a patient-derived iPSC model of neonatal diabetes
Cited by: 106
Author(s): Diego Balboa, Jonna Saarimäki-Vire, Daniel Borshagovski, Mantas Survila, Päivi Lindholm, Emilia Galli, Solja Eurola, Jarkko Ustinov, Heli Grym, Hanna Huopio, Juha Partanen, Kirmo Wartiovaara, Timo Otonkoski
Software Mentions: 8
Published: over 7 years ago

10.3389/fcell.2021.677697

Single-Cell RNA-Sequencing Portraying Functional Diversity and Clinical Implications of IFI6 in Ovarian Cancer
Cited by: 7
Author(s): Hongyu Zhao, Zhefeng Li, Yan Gao, Jie Li, Xiaoting Zhao, Wentao Yue
Software Mentions: 8
Published: almost 5 years ago

10.1038/s41598-020-69160-2

Individual-based population genomics reveal different drivers of adaptation in sympatric fish
Cited by: 10
Author(s): Héctor Torrado, Carlos Carreras, Núria Raventós, Enrique Macpherson, Marta Pascual
Software Mentions: 8
Published: almost 6 years ago

10.1016/j.stem.2020.03.005

GATA3 Mediates a Fast, Irreversible Commitment to BMP4-Driven Differentiation in Human Embryonic Stem Cells
Cited by: 42
Author(s): Alexandra Gunne-Braden, Adrienne E. Sullivan, Borzo Gharibi, Rahuman S. Malik Sheriff, Alok Kumar Maity, Yi Fang Wang, A. Edwards, Ming Jiang, Michael Howell, Robert Goldstone, Roy Wollman, Philip East, Silvia Santos
Software Mentions: 8
Published: about 6 years ago

10.1186/s12864-018-4772-0

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics
Cited by: 1,344
Author(s): Kelly Street, Davide Risso, Russell B. Fletcher, Diya Das, John Ngai, Nir Yosef, Elizabeth Purdom, Sandrine Dudoit
Software Mentions: 8
Published: about 8 years ago

10.1186/s12967-021-02981-5

N6-Methyladenosine RNA modification in cerebrospinal fluid as a novel potential diagnostic biomarker for progressive multiple sclerosis
Cited by: 14
Author(s): Fei Ye, Tianzhu Wang, Xiaoxin Wu, Jie Liang, Jiaoxing Li, Wenli Sheng
Software Mentions: 8
Published: almost 5 years ago

10.1111/2041-210X.12490

hext , a software supporting tree‐based screens for hybrid taxa in multilocus data sets, and an evaluation of the homoplasy excess test
Cited by: 4
Author(s): Kevin Schneider, Stephan Koblmüller, Kristina M. Sefc
Software Mentions: 8
Published: over 10 years ago

10.1371/journal.pone.0051609

Comparative Transcriptome Profiling of the Early Response to Magnaporthe oryzae in Durable Resistant vs Susceptible Rice (Oryza sativa L.) Genotypes
Cited by: 129
Author(s): Paolo Bagnaresi, Chiara Biselli, Luigi Orrù, Simona Urso, Laura Crispino, Pamela Abbruscato, Pietro Piffanelli, Elisabetta Lupotto, Luigi Cattivelli, Giampiero Valè
Software Mentions: 8
Published: over 13 years ago

10.1186/s12864-017-3746-y

GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases
Cited by: 29
Author(s): Lihua Julie Zhu, Michael C. Lawrence, Ankit Gupta, Hervé Pagès, Alper Küçükural, Manuel Garber, Scot A. Wolfe
Software Mentions: 8
Published: about 9 years ago

10.1186/s12864-020-6653-6

Novel approach in whole genome mining and transcriptome analysis reveal conserved RiPPs in Trichoderma spp
Cited by: 14
Author(s): Gabriel A. Vignolle, Robert L. Mach, Astrid R. Mach-Aigner, Christian Derntl
Software Mentions: 8
Published: about 6 years ago

10.1371/journal.pone.0133581

Spatial Scales of Genetic Structure in Free-Standing and Strangler Figs (Ficus, Moraceae) Inhabiting Neotropical Forests
Cited by: 12
Author(s): Katrin Heer, Elisabeth K. V. Kalko, Larissa Albrecht, Roosevelt García‐Villacorta, Felix C. Staeps, Edward Allen Herre, Christopher W. Dick
Software Mentions: 8
Published: almost 11 years ago

10.1186/s13059-019-1855-4

Common DNA sequence variation influences 3-dimensional conformation of the human genome
Cited by: 66
Author(s): David U. Gorkin, Yunjiang Qiu, Ming Hu, Kipper Fletez-Brant, Tristin Liu, Anthony Schmitt, Amina Noor, Joshua Chiou, Kyle J. Gaulton, Jonathan Sebat, Yun Li, Kasper D. Hansen, Bing Ren
Software Mentions: 8
Published: over 6 years ago

10.3390/ijms22158285

Maize DNA Methylation in Response to Drought Stress Is Involved in Target Gene Expression and Alternative Splicing
Cited by: 14
Author(s): Qi Wang, Jie Xu, Xuemei Pu, Haozhe Lv, Yanjun Liu, Huihui Ma, Fengkai Wu, Qingjun Wang, Xin Feng, Tianhong Liu, Qinghua Tang, Yanli Lu
Software Mentions: 8
Published: almost 5 years ago

10.3389/fmicb.2019.02872

Soil Bacterial and Fungal Communities Exhibit Distinct Long-Term Responses to Disturbance in Temperate Forests
Cited by: 33
Author(s): Ernest D. Osburn, Steven G. McBride, Frank O. Aylward, Brian D. Badgley, Brian D. Strahm, Jennifer D. Knoepp, John E. Barrett
Software Mentions: 8
Published: over 6 years ago

10.1186/s12864-020-07123-7

Illuminating the dark side of the human transcriptome with long read transcript sequencing
Cited by: 76
Author(s): Richard Kuo, Yuanyuan Cheng, Runxuan Zhang, John W. Brown, Jacqueline Smith, Alan Archibald, David W. Burt
Software Mentions: 8
Published: over 5 years ago

10.1186/s12859-018-2069-6

A gene profiling deconvolution approach to estimating immune cell composition from complex tissues
Cited by: 12
Author(s): Shu Hwa Chen, Wen Yu Kuo, Sheng Su, Wei Chun Chung, Jen Ming Ho, Henry Horng Shing Lu, Chung Yen Lin
Software Mentions: 8
Published: about 8 years ago

10.1186/s13059-020-01998-1

Wheat chromatin architecture is organized in genome territories and transcription factories
Cited by: 89
Author(s): Lorenzo Concia, Alaguraj Veluchamy, Juan S. Ramirez-Prado, Azahara Martin-Ramirez, Ying Huang, Magali Perez, Séverine Domenichini, Natalia Y. Rodriguez Granados, Soon-Kap Kim, Thomas Blein, Susan Duncan, Clement Pichot, Deborah Manza‐Mianza, Caroline Juéry, Etienne Paux, Graham Moore, Heribert Hirt, Catherine Bergounioux, Martín Crespi, Magdy M. Mahfouz, Abdelhafid Bendahmane, Chang Liu, Anthony Hall, Cécile Raynaud, David Latrasse, Moussa Benhamed
Software Mentions: 8
Published: about 6 years ago

10.1002/ece3.6941

A priori estimation of sequencing effort in complex microbial metatranscriptomes
Cited by: 2
Author(s): Toni Monleón-Getino, Jorge Frias-Lopez
Software Mentions: 8
Published: over 5 years ago

10.1002/ece3.5033

Evidence for contemporary and historical gene flow between guppy populations in different watersheds, with a test for associations with adaptive traits
Cited by: 18
Author(s): Léa Blondel, Lyndsey Baillie, Jessica Quinton, Jahson Berhane Alemu, Ian G. Paterson, Andrew P. Hendry, Paul Bentzen
Software Mentions: 8
Published: about 7 years ago

10.3389/fgene.2020.573515

SETDB1 Overexpression Sets an Intertumoral Transcriptomic Divergence in Non-small Cell Lung Carcinoma
Cited by: 8
Author(s): Yong‐Kook Kang, Byungkuk Min
Software Mentions: 8
Published: over 5 years ago

10.1038/s41598-021-86529-z

Impact of land cover and landfills on the breeding effect and nest occupancy of the white stork in Poland
Cited by: 12
Author(s): Joanna T. Białas, Łukasz Dylewski, Andrzej Dylik, Tomasz Janiszewski, Ireneusz Kaługa, Tomek Królak, Robert Kruszyk, Krzysztof Pawlukojć, Zuzanna Pestka, M. Polakowski, Adam Zbyryt, Marcin Tobółka
Software Mentions: 8
Published: about 5 years ago

10.1038/srep35903

Genome-wide methylation analysis identified sexually dimorphic methylated regions in hybrid tilapia
Cited by: 59
Author(s): Zi Yi Wan, Jun Xia, Grace Lin, Le Wang, Valerie Chun Ling Lin, Gen Hua Yue
Software Mentions: 8
Published: over 9 years ago

10.1186/1471-2164-13-556

Proteome remodelling during development from blood to insect-form Trypanosoma brucei quantified by SILAC and mass spectrometry
Cited by: 117
Author(s): Kapila Gunasekera, Daniel Wüthrich, Sophie Braga-Lagache, Manfred Heller, Torsten Ochsenreiter
Software Mentions: 8
Published: over 13 years ago

10.1038/s41598-021-97221-7

An interaction regression model for crop yield prediction
Cited by: 25
Author(s): Javad Ansarifar, Lizhi Wang, Sotirios Archontoulis
Software Mentions: 8
Published: almost 5 years ago

10.1371/journal.pcbi.1008488

On the NF-Y regulome as in ENCODE (2019)
Cited by: 4
Author(s): Mirko Ronzio, Andrea Bernardini, Giulio Pavesi, Roberto Mantovani, Diletta Dolfini
Software Mentions: 8
Published: over 5 years ago

10.1111/eva.13273

Planned missing data designs and methods: Options for strengthening inference, increasing research efficiency and improving animal welfare in ecological and evolutionary research
Cited by: 7
Author(s): Daniel W. A. Noble, Shinichi Nakagawa
Software Mentions: 8
Published: almost 5 years ago

10.1016/j.molcel.2020.06.002

Nascent Transcript Folding Plays a Major Role in Determining RNA Polymerase Elongation Rates
Cited by: 41
Author(s): Tomasz W. Turowski, Elisabeth Petfalski, Benjamin D. Goddard, Sarah L. French, Aleksandra Helwak, David Tollervey
Software Mentions: 8
Published: almost 6 years ago