10.1186/s40359-020-00397-2

Validation of the English version of the Mood Rhythm Instrument
Cited by: 6
Author(s): Melissa Alves Braga de Oliveira, Kristina Epifano, Salina Mathur, Felipe Gutiérrez Carvalho, Marina Scop, Alícia Carissimi, Ana Paula Francisco, Luciene L. S. Garay, Ana Adán, María Paz Loayza Hidalgo, Benício N. Frey
Software Mentions: 4
Published: over 6 years ago

10.3390/cells8121592

Dietary Immunostimulant CpG Modulates MicroRNA Biomarkers Associated with Immune Responses in Atlantic Salmon (Salmo salar)
Cited by: 22
Author(s): Xi Xue, Nardos Tesfaye Woldemariam, Albert Caballero‐Solares, Navaneethaiyer Umasuthan, Mark D. Fast, Richard G. Taylor, Matthew L. Rise, Rune Andreassen
Software Mentions: 4
Published: over 6 years ago

10.1016/j.stem.2020.07.019

Naive Pluripotent Stem Cells Exhibit Phenotypic Variability that Is Driven by Genetic Variation
Cited by: 36
Author(s): Daniel Ortmann, Stephanie Brown, Anne Czechanski, Selcan Aydin, Daniele Muraro, Yuanhua Huang, Rute Tomaz, Anna Osnato, Giovanni Canu, Brandon T Wesley, Daniel A. Skelly, Oliver Stegle, Tae-Young Choi, Gary A. Churchill, Christopher L. Baker, Peter J. Rugg‐Gunn, Steven C. Munger, Laura G. Reinholdt, Ludovic Vallier
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-020-78165-w

Diel-scale temporal dynamics in the abundance and composition of pollinators in the Arctic summer
Cited by: 10
Author(s): Leana Zoller, Joanne M. Bennett, Tiffany M. Knight
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-017-3566-0

Exploratory bioinformatics investigation reveals importance of “junk” DNA in early embryo development
Cited by: 51
Author(s): Steven Ge
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0187129

A cross-sectional study of the temporal evolution of electricity consumption of six commercial buildings
Cited by: 6
Author(s): Ethan Pickering, Mohammad A. Hossain, Jack P. Mousseau, Rachel A. Swanson, Roger H. French, Alexis R. Abramson
Software Mentions: 4
Published: almost 9 years ago

10.1017/cts.2020.556

Variable selection methods for identifying predictor interactions in data with repeatedly measured binary outcomes
Cited by: 0
Author(s): Bethany J. Wolf, Yunyun Jiang, Sylvia H. Wilson, Jim Oates
Software Mentions: 4
Published: over 5 years ago

10.3390/cells9071745

Ribosomal Protein uL11 as a Regulator of Metabolic Circuits Related to Aging and Cell Cycle
Cited by: 7
Author(s): Mateusz Mołoń, Eliza Molestak, Monika Kula-Maximenko, Przemysław Grela, Marek Tchórzewski
Software Mentions: 4
Published: about 6 years ago

10.1186/s40168-017-0344-9

Bottled aqua incognita: microbiota assembly and dissolved organic matter diversity in natural mineral waters
Cited by: 23
Author(s): Céline Lesaulnier, Craig W. Herbold, Claus Pelikan, David Berry, Cédric Gérard, Xavier Le Coz, Sophie Gagnot, Jutta Niggemann, Thorsten Dittmar, Gabriel Singer, Alexander Loy
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12918-018-0582-x

A powerful nonparametric method for detecting differentially co-expressed genes: distance correlation screening and edge-count test
Cited by: 6
Author(s): Qingyang Zhang
Software Mentions: 4
Published: about 8 years ago

10.1093/bioinformatics/btu274

Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation
Cited by: 64
Author(s): Tarmo Äijö, Vincent Butty, Zhi Chen, Verna Salo, Subhash Tripathi, Christopher B. Burge, Riitta Lahesmaa, Harri Lähdesmäki
Software Mentions: 4
Published: about 12 years ago

10.7717/peerj.11561

The m⁶A-related gene signature for predicting the prognosis of breast cancer
Cited by: 7
Author(s): Shanliang Zhong, Lin Zhenzhong, Huanwen Chen, Ling Mao, Jifeng Feng, Siying Zhou
Software Mentions: 4
Published: about 5 years ago

10.1186/s12859-020-3484-z

Short paired-end reads trump long single-end reads for expression analysis
Cited by: 13
Author(s): Adam H. Freedman, John Gaspar, Timothy B. Sackton
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-017-3840-1

Characterizing the reproductive transcriptomic correlates of acute dehydration in males in the desert-adapted rodent, Peromyscus eremicus
Cited by: 9
Author(s): Lauren Kordonowy, Matthew D. MacManes
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0164766

RNA-Seq Count Data Modelling by Grey Relational Analysis and Nonparametric Gaussian Process
Cited by: 1
Author(s): Thanh Nguyen, Asim Bhatti, Samuel Yang, Saeid Nahavandi
Software Mentions: 4
Published: almost 10 years ago

10.1007/s11306-017-1270-3

The dental calculus metabolome in modern and historic samples
Cited by: 43
Author(s): Irina M. Velsko, Katherine A. Overmyer, Camilla Speller, Lauren Klaus, Matthew J. Collins, Louise Loe, Laurent Frantz, Krithivasan Sankaranarayanan, Cecil M. Lewis, Juan Bautista Rodriguez Martinez, Eros Chaves, Joshua J. Coon, Greger Larson, Christina Warinner
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pone.0256657

Microbiota composition and mucosal immunity in patients with asymptomatic diverticulosis and controls
Cited by: 10
Author(s): Tessel Meike van Rossen, Rogier E. Ooijevaar, J. Kuyvenhoven, Anat Eck, Herman Bril, René Buijsman, Marja A. Boermeester, H. B. A. C. Stockmann, Niels de Korte, Andries E. Budding
Software Mentions: 4
Published: almost 5 years ago

10.7717/peerj.8873

Bioinformatics analyses of retinoblastoma reveal the retinoblastoma progression subtypes
Cited by: 6
Author(s): Manjing Cao, Sha Wang, Jing Zou, Wanpeng Wang
Software Mentions: 4
Published: about 6 years ago

10.7717/peerj.7135

Comprehensive analysis of an lncRNA-miRNA-mRNA competing endogenous RNA network in pulpitis
Cited by: 31
Author(s): Fangcao Lei, Han Zhang, Xiaoli Xie
Software Mentions: 4
Published: about 7 years ago

10.1186/1471-2164-14-S8-S1

Interdisciplinary dialogue for education, collaboration, and innovation: Intelligent Biology and Medicine in and beyond 2013
Cited by: 49
Author(s): Bing Zhang, Yufei Huang, Jason McDermott, Rebecca H Posey, Hua Xu, Zhongming Zhao
Software Mentions: 4
Published: over 13 years ago

10.1186/1471-2164-15-S6-S18

Comparative exomics of Phalariscultivars under salt stress
Cited by: 12
Author(s): Niina Haiminen, Manfred Klaas, Zeyu Zhou, Filippo Utro, Paul Cormican, Thomas Didion, Christian S. Jensen, Christopher E. Mason, Susanne Barth, Laxmi Parida
Software Mentions: 4
Published: almost 12 years ago

10.1111/tpj.14299

Hybrid sequencing reveals insight into heat sensing and signaling of bread wheat
Cited by: 46
Author(s): Xiaoming Wang, Siyuan Chen, Song Xue, Danni Liu, Peng Zhao, Yunze Lu, Yanbing Cheng, Zhenshan Liu, Xiaojun Nie, Weining Song, Qixin Sun, Shengbao Xu, Chuang Ma
Software Mentions: 4
Published: over 7 years ago

10.3389/fmicb.2021.605095

Improvement of Free Fatty Acid Secretory Productivity in Aspergillus oryzae by Comprehensive Analysis on Time-Series Gene Expression
Cited by: 4
Author(s): Pui Shan Wong, Koichi Tamano, Sachiyo Aburatani
Software Mentions: 4
Published: over 5 years ago

10.1186/s12874-019-0817-6

Statistical approaches to identify subgroups in meta-analysis of individual participant data: a simulation study
Cited by: 25
Author(s): Michail Belias, Maroeska M. Rovers, Johannes B. Reitsma, Thomas P A Debray, Joanna IntHout
Software Mentions: 4
Published: almost 7 years ago

10.18632/oncotarget.9370

Practical aspects of NGS-based pathways analysis for personalized cancer science and medicine
Cited by: 13
Author(s): Ekaterina Kotelnikova, Mikhail A. Pyatnitskiy, A. G. Paleeva, O. S. Kremenetskaya, D. V. Vinogradov
Software Mentions: 4
Published: about 10 years ago

10.3389/fmicb.2021.657471

Comparative Genomics and Environmental Distribution of Large dsDNA Viruses in the Family Asfarviridae
Cited by: 15
Author(s): Sangita Karki, Mohammad Moniruzzaman, Frank O. Aylward
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2121-14-43

In vitro three-dimensional modeling of fallopian tube secretory epithelial cells
Cited by: 39
Author(s): Kate Lawrenson, Maria Notaridou, Nathan Lee, E. Benjamin, Ian Jacobs, Christopher S. Jones, Simon A. Gayther
Software Mentions: 4
Published: almost 13 years ago

10.1016/j.celrep.2019.11.093

Dysregulation of RNA Splicing in Tauopathies
Cited by: 49
Author(s): Daniel J. Apicco, Cheng Zhang, Brandon F. Maziuk, Lulu Jiang, Heather Ballance, Samantha Boudeau, Choong Yong Ung, Hu Li, Benjamin Wolozin
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2021.703014

Distinct Endophytic Bacterial Communities Inhabiting Seagrass Seeds
Cited by: 14
Author(s): Flavia Tarquinio, Océane Attlan, Mathew A. Vanderklift, Oliver Berry, Andrew Bissett
Software Mentions: 4
Published: almost 5 years ago

10.1002/2211-5463.13242

A methylation‐driven gene panel predicts survival in patients with colon cancer
Cited by: 6
Author(s): Yawen Peng, Jing Zhao, Fang‐Fang Yin, Gaowa Sharen, Qiyan Wu, Qi Chen, Xiaoxuan Sun, Juan Yang, Huan Wang, Dong Zhang
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2021.658988

Rock-Hosted Subsurface Biofilms: Mineral Selectivity Drives Hotspots for Intraterrestrial Life
Cited by: 15
Author(s): Caitlin P. Casar, Brittany R. Kruger, M. R. Osburn
Software Mentions: 4
Published: over 5 years ago

10.1007/s00330-019-06167-y

Application of a deep learning algorithm for detection and visualization of hip fractures on plain pelvic radiographs
Cited by: 164
Author(s): Chi‐Tung Cheng, Tsung-Ying Ho, Tao-Yi Lee, Ching-Fang Chang, Ching-Cheng Chou, Chih-Chi Chen, I‐Fang Chung, Chien‐Hung Liao
Software Mentions: 4
Published: over 7 years ago

10.7150/jca.56506

Identification of Hub Genes and Small Molecule Drugs Associated with Acquired Resistance to Gefitinib in Non-Small Cell Lung Cancer
Cited by: 8
Author(s): Guangda Li, You-Zhi Ma, Mingwei Yu, Xiaoxiao Li, Xinjie Chen, Yu Tang Gao, Pei-Yu Cheng, Gan‐Lin Zhang, Xiaomin Wang
Software Mentions: 4
Published: over 5 years ago

10.3389/fnins.2021.616760

Tracking Eye Movements During Sleep in Mice
Cited by: 11
Author(s): Qingshu Meng, Xinrong Tan, Chengyong Jiang, Yanyu Xiong, Biao Yan, Jiayi Zhang
Software Mentions: 4
Published: over 5 years ago

10.1016/j.celrep.2020.03.053

Whole-Genome and RNA Sequencing Reveal Variation and Transcriptomic Coordination in the Developing Human Prefrontal Cortex
Cited by: 82
Author(s): Donna M. Werling, Sirisha Pochareddy, Jinmyung Choi, Joon Yong An, Brooke Sheppard, Minshi Peng, Zhen Li, Claudia Dastmalchi, Gabriel Santpere, André M. M. Sousa, Andrew T.N. Tebbenkamp, Navjot Kaur, Forrest O. Gulden, Michael S. Breen, Lindsay Liang, Michael C. Gilson, Xuefang Zhao, Shan Dong, Lambertus Klei, A. Ercüment Çiçek, Joseph D. Buxbaum, Homa Adle‐Biassette, Jean Léon Thomas, Kimberly A. Aldinger, Diana R. O’Day, Ian A. Glass, Noah Zaitlen, Michael E. Talkowski, Kathryn Roeder, Matthew W. State, Bernie Devlin, Stephan J. Sanders, Nenad Šestan
Software Mentions: 4
Published: over 6 years ago

10.1186/s40537-021-00492-0

Text Data Augmentation for Deep Learning
Cited by: 667
Author(s): Connor Shorten, Taghi M. Khoshgoftaar, Borko Furht
Software Mentions: 4
Published: about 5 years ago

10.1186/s12935-021-01792-4

Identification of a prognostic and therapeutic immune signature associated with hepatocellular carcinoma
Cited by: 42
Author(s): Yanan Peng, Chang Liu, Mengting Li, Wenjie Li, Mengna Zhang, Xiang Jiang, Ying Chang, Lan Liu, Wei Fan, Qiu Zhao
Software Mentions: 4
Published: over 5 years ago

10.1016/j.celrep.2021.109105

Efficient generation of isogenic primary human myeloid cells using CRISPR-Cas9 ribonucleoproteins
Cited by: 24
Author(s): Joseph Hiatt, Devin A. Cavero, Michael McGregor, Weihao Zheng, Jonathan M. Budzik, Theodore L. Roth, Kelsey M. Haas, David Wu, Ujjwal Rathore, Anke Meyer-Franke, Mohamed S. Bouzidi, Eric Shifrut, Youjin Lee, Vigneshwari Easwar Kumar, Eric V. Dang, David E. Gordon, Jason A. Wojcechowskyj, Judd F. Hultquist, Krystal A. Fontaine, Satish K. Pillai, Jeffery S. Cox, Joel D. Ernst, Nevan J. Krogan, Alexander Marson
Software Mentions: 4
Published: over 5 years ago

10.1016/j.celrep.2021.108758

SOX17 integrates HOXA and arterial programs in hemogenic endothelium to drive definitive lympho-myeloid hematopoiesis
Cited by: 23
Author(s): Ho Sun Jung, Gene I. Uenishi, Mi Ae Park, Peng Liu, Kran Suknuntha, Matthew Raymond, Yoon Jung Choi, James A. Thomson, Irene M. Ong, Igor I. Slukvin
Software Mentions: 4
Published: over 5 years ago

10.1007/s00018-021-03822-w

Immune cells lacking Y chromosome show dysregulation of autosomal gene expression
Cited by: 43
Author(s): Jan P. Dumanski, Jonatan Halvardson, Hanna Davies, Edyta Rychlicka-Buniowska, Jonas Mattisson, Behrooz Torabi Moghadam, Noémi Nagy, Kazimierz Węglarczyk, Karolina Bukowska-Straková, Marcus Danielsson, Paweł Olszewski, Arkadiusz Piotrowski, Erin Oerton, Aleksandra Ambicka, Marcin Przewoźnik, Łukasz Bełch, Tomasz Grodzicki, Piotr Chłosta, Stefan Imreh, Vilmantas Giedraitis, Lena Kilander, Jessica Nordlund, Adam Ameur, Ulf Gyllensten, Åsa Johansson, Alicja Józkowicz, Maciej Siedlar, Alicja Klich-Rączka, Janusz Jaszczyński, Stefan Enroth, Jarosław Baran, Martin Ingelsson, John Perry, Janusz Ryś, Lars A. Forsberg
Software Mentions: 4
Published: over 5 years ago

10.1186/s12955-021-01736-6

Validation of the Portuguese version of Amsterdam Preoperative Anxiety and Information Scale (APAIS)
Cited by: 6
Author(s): Sandra Maurício, Isabel Rebêlo, Catarina Madeira, Filipa Resende, Susana Esteves
Software Mentions: 4
Published: over 5 years ago

10.1002/ece3.2961

Longevity is associated with relative brain size in birds
Cited by: 46
Author(s): Piotr Minias, Patrycja Podlaszczuk
Software Mentions: 4
Published: over 9 years ago

10.3390/cancers13030527

Radiosensitizing Pancreatic Cancer with PARP Inhibitor and Gemcitabine: An In Vivo and a Whole-Transcriptome Analysis after Proton or Photon Irradiation
Cited by: 7
Author(s): Waisse Waissi, Anaïs Nicol, Matthieu Jung, M. Rousseau, D. Jarnet, Georges Noël, Hélène Burckel
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1007773

Dysregulated biodynamics in metabolic attractor systems precede the emergence of amyotrophic lateral sclerosis
Cited by: 9
Author(s): Paul Curtin, Christine Austin, Austen Curtin, Chris Gennings, Claudia Figueroa‐Romero, Kristen A. Mikhail, Tatiana M. Botero, Stephen A. Goutman, Eva L. Feldman, Manish Arora
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0224644

Transcriptomic profiling of PBDE-exposed HepaRG cells unveils critical lncRNA- PCG pairs involved in intermediary metabolism
Cited by: 5
Author(s): Angela Zhang, Cindy Yanfei Li, Edward J. Kelly, Lianne Sheppard, Julia Yue Cui
Software Mentions: 4
Published: over 6 years ago

10.1186/s12859-020-3450-9

Data-based RNA-seq simulations by binomial thinning
Cited by: 19
Author(s): David Gerard
Software Mentions: 4
Published: about 6 years ago

10.1128/mBio.01157-20

Previremic Identification of Ebola or Marburg Virus Infection Using Integrated Host-Transcriptome and Viral Genome Detection
Cited by: 2
Author(s): Emily Speranza, Ignacio Caballero, Anna N. Honko, Joshua C. Johnson, J. Kyle Bohannon, Lisa Evans DeWald, Dawn M. Gerhardt, Jennifer Sword, Lisa E. Hensley, Richard S. Bennett, John H. Connor
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-020-72818-6

Detection of genomic alterations in breast cancer with circulating tumour DNA sequencing
Cited by: 6
Author(s): Dimitrios Kleftogiannis, David Ho, Jun Xian Liew, Polly Poon, Anna Gan, Raymond Ng, Benita Kiat‐Tee Tan, Kiang Hiong Tay, Swee Ho Lim, Gek San Tan, Chih Chuan Shih, Tony Kiat-Hon Lim, Ann Siew‐Gek Lee, Iain Beehuat Tan, Yoon Sim Yap, Sarah Ng
Software Mentions: 4
Published: almost 6 years ago

10.1186/1471-2164-9-110

Search for the genes involved in oocyte maturation and early embryo development in the hen
Cited by: 47
Author(s): Sébastien Elis, Florence Batellier, Isabelle Couty, Sandrine Balzergue, Marie‐Laure Martin‐Magniette, Philippe Monget, Élisabeth Blesbois, Marina Govoroun
Software Mentions: 4
Published: over 18 years ago

10.1371/journal.pone.0189955

A genome-wide study to identify genes responsible for oviduct development in chickens
Cited by: 9
Author(s): Manman Shen, Liang Qu, Meng Ma, Taocun Dou, Jian Lü, Jun Guo, Yuping Hu, Xingguo Wang, Yongfeng Li, Kehua Wang, Ning Yang
Software Mentions: 4
Published: over 8 years ago

10.1098/rspb.2021.1456

Immune challenges increase network centrality in a queenless ant
Cited by: 8
Author(s): Giacomo Alciatore, Line V. Ugelvig, Erik T. Frank, Jérémie Bidaux, A. Gal, Thomas Schmitt, Daniel J. C. Kronauer, Yuko Ulrich
Software Mentions: 4
Published: almost 5 years ago

10.5194/aab-62-113-2019

Identification of potential genomic regions and candidate genes for egg albumen quality by a genome-wide association study
Cited by: 9
Author(s): Liang Qu, Manman Shen, Jun Guo, Xingguo Wang, Taocun Dou, Yuping Hu, Yongfeng Li, Meng Ma, Kehua Wang, Honglin Liu
Software Mentions: 4
Published: over 7 years ago

10.1186/s13059-018-1591-1

NmeCas9 is an intrinsically high-fidelity genome-editing platform
Cited by: 93
Author(s): Nadia Amrani, Xin D. Gao, Pengpeng Liu, Alireza Edraki, Aamir Mir, Raed Ibraheim, Ankit Gupta, Kyoyu Sasaki, Tong Wu, Paul D. Donohoue, Alexander Settle, Alexandra M. Lied, Kyle McGovern, Christopher R. Fuller, P. Simmons Cameron, Thomas G. Fazzio, Lihua Julie Zhu, Scot A. Wolfe, Erik J. Sontheimer
Software Mentions: 4
Published: over 7 years ago

10.1186/s12885-018-4757-z

Association of tamoxifen resistance and lipid reprogramming in breast cancer
Cited by: 98
Author(s): Susanne Hultsch, Matti Kankainen, Lassi Paavolainen, Ruusu-Maaria Kovanen, Elina Ikonen, Sara Kangaspeska, Vilja Pietiäinen, Olli Kallioniemi
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0256048

Comparison of enteric methane yield and diversity of ruminal methanogens in cattle and buffaloes fed on the same diet
Cited by: 14
Author(s): P. K. Malik, Shraddha Trivedi, A. Mohapatra, Atul P. Kolte, Veerasamy Sejian, Raghavendra Bhatta, Husna Abdul Rahman
Software Mentions: 4
Published: almost 5 years ago

10.1093/bib/bbv037

Building a virtual ligand screening pipeline using free software: a survey
Cited by: 68
Author(s): Enrico Glaab
Software Mentions: 4
Published: about 11 years ago

10.1371/journal.pone.0226057

Estrogen receptor β exerts tumor suppressive effects in prostate cancer through repression of androgen receptor activity
Cited by: 16
Author(s): Surendra Chaurasiya, Scott Widmann, Cindy Botero, Chin-Yo Lin, Jan‐Åke Gustafsson, Anders Ström
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-018-4526-z

Global study of holistic morphological effectors in the budding yeast Saccharomyces cerevisiae
Cited by: 19
Author(s): Godai Suzuki, Yang Wang, Kosuke Kubo, Eri Hirata, Shinsuke Ohnuki, Yoshikazu Ohya
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-020-73515-0

Preliminary insights into the impact of primary radiochemotherapy on the salivary microbiome in head and neck squamous cell carcinoma
Cited by: 15
Author(s): Christina Kumpitsch, Christine Moissl-Eichinger, Jakob Pock, Dietmar Thurnher, Axel Wolf
Software Mentions: 4
Published: almost 6 years ago

10.1002/evl3.230

Antagonistic pleiotropy and the evolution of extraordinary lifespans in eusocial organisms
Cited by: 3
Author(s): Jan J. Kreider, Ido Pen, Boris H. Kramer
Software Mentions: 4
Published: about 5 years ago

10.1186/1471-2164-11-294

Consistent annotation of gene expression arrays
Cited by: 28
Author(s): Benoît Ballester, Nathan Johnson, G Proctor, Paul Flicek
Software Mentions: 4
Published: about 16 years ago

10.1186/s41927-019-0078-3

Abstracts of scientific contributions to GCOM 2019
Cited by: 0
Author(s):
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0184566

Atopic asthmatic immune phenotypes associated with airway microbiota and airway obstruction
Cited by: 23
Author(s): Benjamin A. Turturice, Halvor S. McGee, Brian G. Oliver, Melissa Baraket, Brian Nguyen, Christian Ascoli, Ravi Ranjan, Asha Rani, David L. Perkins, Patricia W. Finn
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pone.0072200

A Network Extension of Species Occupancy Models in a Patchy Environment Applied to the Yosemite Toad (Anaxyrus canorus)
Cited by: 15
Author(s): Eric L. Berlow, Roland A. Knapp, Steven M. Ostoja, Richard J. Williams, Heather C. McKenny, John R. Matchett, Qinghua Guo, Gary M. Fellers, Patrick M. Kleeman, Matthew L. Brooks, Lucas Joppa
Software Mentions: 4
Published: almost 13 years ago

10.1371/journal.pgen.1004604

Foxf Genes Integrate Tbx5 and Hedgehog Pathways in the Second Heart Field for Cardiac Septation
Cited by: 77
Author(s): Andrew D. Hoffmann, Xinan Yang, Ozanna Burnicka-Turek, Joshua D. Bosman, Xiaomeng Ren, Jeffrey D. Steimle, Steven A. Vokes, Andrew P. McMahon, Vladimir V. Kalinichenko, Ivan P. Moskowitz
Software Mentions: 4
Published: almost 12 years ago

10.1186/s12864-021-07889-4

Experimental Babesia rossi infection induces hemolytic, metabolic, and viral response pathways in the canine host
Cited by: 6
Author(s): Rachel Smith, Amelia Goddard, Arun K. Boddapati, Steven Brooks, Johan P. Schoeman, Justin Lack, Andrew L. Leisewitz, Hans Ackerman
Software Mentions: 4
Published: almost 5 years ago

10.7554/eLife.41023

Potential herd protection against Plasmodium falciparum infections conferred by mass antimalarial drug administrations
Cited by: 14
Author(s): Daniel M. Parker, Sai Thein Than Tun, Lisa J. White, Ladda Kajeechiwa, May Myo Thwin, Jordi Landier, Victor Chaumeau, Vincent Corbel, Arjen M. Dondorp, Lorenz von Seidlein, Nicholas J. White, Richard J. Maude, François Nosten
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0242158

Calcium salts of long-chain fatty acids from linseed oil decrease methane production by altering the rumen microbiome in vitro
Cited by: 7
Author(s): Yoshibumi Sato, Keiko Tominaga, Hirotatsu Aoki, Masayuki Murayama, Kazato Oishi, Hiroyuki Hirooka, Takashi Yoshida, Hajime Kumagai
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms221910891

A Survey of Autoencoder Algorithms to Pave the Diagnosis of Rare Diseases
Cited by: 6
Author(s): David Pratella, Samira Ait-El-Mkadem Saadi, Sylvie Bannwarth, Véronique Paquis‐Fluckinger, Silvia Bottini
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12918-016-0344-6

A method for automated pathogenic content estimation with application to rheumatoid arthritis
Cited by: 9
Author(s): Xiaoyuan Zhou, Christine Nardini
Software Mentions: 4
Published: over 9 years ago

10.1186/s12870-015-0661-8

A bulk segregant transcriptome analysis reveals metabolic and cellular processes associated with Orange allelic variation and fruit β-carotene accumulation in melon fruit
Cited by: 51
Author(s): Noam Chayut, Hui Yuan, Shachar Ohali, Ayala Meir, Yelena Yeselson, Vitaly Portnoy, Yi Zheng, Zhangjun Fei, Efraim Lewinsohn, Nurit Katzir, Arthur A. Schaffer, Shimon Gepstein, Joseph Burger, L i Li, Yaakov Tadmor
Software Mentions: 4
Published: over 10 years ago

10.1016/j.mex.2019.01.009

RppH can faithfully replace TAP to allow cloning of 5′-triphosphate carrying small RNAs
Cited by: 18
Author(s): Miguel Vasconcelos Almeida, António Miguel de Jesus Domingues, Hanna Lukas, María Méndez-Lago, René F. Ketting
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0256471

Radiology- and gene-based risk stratification in small renal cell carcinoma: A preliminary study
Cited by: 0
Author(s): Takao Sugiyama, Yasuhiro Ushijima, Yuki Motomura, Katsumi Sakamoto, Masakazu Hirakawa, Akihiro Nishie, Koshi Mimori, Yasuo Yamashita, Takashi Tsutsumi, Kousei Ishigami
Software Mentions: 4
Published: almost 5 years ago

10.1016/j.pain.2013.05.021

HDAC inhibitors attenuate the development of hypersensitivity in models of neuropathic pain
Cited by: 127
Author(s): Franziska Denk, Wenlong Huang, Ben S. Sidders, Angela Bithell, Megan Crow, John Grist, Simone Sharma, Daniel Ziemek, Andrew S.C. Rice, Noel J. Buckley, Stephen B. McMahon
Software Mentions: 4
Published: almost 13 years ago

10.1371/journal.pone.0249424

miRGTF-net: Integrative miRNA-gene-TF network analysis reveals key drivers of breast cancer recurrence
Cited by: 15
Author(s): Stepan Nersisyan, A. V. Galatenko, Vladimir Galatenko, M. Yu. Shkurnikov, Alexander G. Tonevitsky
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2021.633396

The Sputum Microbiome in Pulmonary Tuberculosis and Its Association With Disease Manifestations: A Cross-Sectional Study
Cited by: 8
Author(s): Monica R. Ticlla, Jerry Hella, Hellen Hiza, Mohamed Sasamalo, Francis Mhimbira, Liliana K. Rutaihwa, Sara Droz, Sarah Schaller, Klaus Reither, Markus Hilty, Iñaki Comas, Christian Beisel, Christoph D. Schmid, Lukas Fenner, Sébastien Gagneux
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0208054

Agnostic detection of genomic alterations by holistic DNA structural interrogation
Cited by: 1
Author(s): Ryan K. Shultzaberger, Rachel E. Abrams, Challise J. Sullivan, Anthony Schmitt, T. W. Thompson, John Dresios
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0148818

Meta-Analysis of Tumor Stem-Like Breast Cancer Cells Using Gene Set and Network Analysis
Cited by: 14
Author(s): Wonjun Lee, Sang Cheol Kim, Jong Ho Yoon, Sang Jun Yoon, Jong-Tae Lim, You Sun Kim, Sung Won Kwon, Jeong Hill Park
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0255915

Reciprocal interplay between asporin and decorin: Implications in gastric cancer prognosis
Cited by: 6
Author(s): Dipjit Basak, Zarqua Jamal, Arnab Ghosh, Pronoy Kanti Mondal, Priyanka Dey Talukdar, Semanti Ghosh, Biswadeep Ghosh Roy, Ranajoy Ghosh, Ajay Halder, Abhijit Chowdhury, Gopal Krishna Dhali, Brajadulal Chattopadhyay, Makhan Saha, Abhimanyu Basu, Sukanta Roy, Chitranjan Mukherjee, Nidhan K. Biswas, Urmi Chatterji, Shalini Datta
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12874-016-0277-1

Clinical prediction in defined populations: a simulation study investigating when and how to aggregate existing models
Cited by: 21
Author(s): Glen P. Martin, Mamas A. Mamas, Niels Peek, Iain Buchan, Matthew Sperrin
Software Mentions: 4
Published: over 9 years ago

10.1038/s41598-020-58711-2

Nucleus accumbens pathways control cell-specific gene expression in the medial prefrontal cortex
Cited by: 5
Author(s): Takatoshi Hikida, Shuhei Yao, Tom Macpherson, Ayumi Fukakusa, Maki Morita, Haruhide Kimura, Keisuke Hirai, Tatsuya Ando, Hiroyoshi Toyoshiba, Akira Sawa
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-021-82731-1

Mating system evolution and genetic structure of diploid sexual populations of Cyrtomium falcatum in Japan
Cited by: 0
Author(s): Ryōsuke Imai, Yoshiaki Tsuda, Atsushi Ebihara, Sadamu Matsumoto, Ayumi Tezuka, Atsushi J. Nagano, Ryo Ootsuki, Yasuyuki Watano
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-016-2403-1

RNA sequencing-based analysis of the spleen transcriptome following infectious bronchitis virus infection of chickens selected for different mannose-binding lectin serum concentrations
Cited by: 20
Author(s): Edin Hamzić, Rikke Brødsgaard Kjærup, Núria Mach, Guilietta Minozzi, Francesco Strozzi, V. Gualdi, J. L. Williams, Jun Chen, Eva Wattrang, Bart Buitenhuis, Helle R. Juul‐Madsen, Tina Sørensen Dalgaard
Software Mentions: 4
Published: over 10 years ago

10.3390/ijms21165847

Deep Learning Modeling of Androgen Receptor Responses to Prostate Cancer Therapies
Cited by: 11
Author(s): Oliver Snow, Nada Lallous, Martin Ester, Artem Cherkasov
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12913-021-06492-3

Prediction of hospital bed capacity during the COVID− 19 pandemic
Cited by: 27
Author(s): Mieke Deschepper, Kristof Eeckloo, Simon Malfait, Dominique Benoît, Steven Callens, Stijn Vansteelandt
Software Mentions: 4
Published: about 5 years ago

10.1097/MD.0000000000010153

Comorbid risks of psychological disorders and gastroesophageal reflux disorder using the national health insurance service—National Sample Cohort
Cited by: 11
Author(s): Ye-Seul Lee, Bo‐Hyoung Jang, Seong‐Gyu Ko, Younbyoung Chae
Software Mentions: 4
Published: over 8 years ago

10.7717/peerj.1592

The role of geography and host abundance in the distribution of parasitoids of an alien pest
Cited by: 7
Author(s): Petra Nováková, Jaroslav Holuša, Jakub Horák
Software Mentions: 4
Published: over 10 years ago

10.3390/cancers13051126

Transformed Canine and Murine Mesenchymal Stem Cells as a Model for Sarcoma with Complex Genomics
Cited by: 5
Author(s): Natasja Franceschini, Bas Verbruggen, Marianna A. Tryfonidou, Alwine B. Kruisselbrink, Hans J. Baelde, Karin E. de Visser, Károly Szuhai, Anne‐Marie Cleton‐Jansen, Judith V.M.G. Bovée
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-77520-1

Time-course profiling of bovine alphaherpesvirus 1.1 transcriptome using multiplatform sequencing
Cited by: 8
Author(s): Norbert Moldován, Gábor Torma, Gábor Gulyás, Ákos Hornyák, Zoltán Zádori, Victoria A Jefferson, Zsolt Csabai, Miklós Boldogkői, Dóra Tombácz, Florencia Meyer, Zsolt Boldogköi
Software Mentions: 4
Published: over 5 years ago

10.1016/j.stem.2019.05.013

Engineering Genetic Predisposition in Human Neuroepithelial Stem Cells Recapitulates Medulloblastoma Tumorigenesis
Cited by: 53
Author(s): Miller Huang, Jignesh Tailor, Qiqi Zhen, Aaron H. Gillmor, Matthew Miller, Holger Weishaupt, Justin Chen, Tina Zheng, Emily K. Nash, Lauren McHenry, Zhenyi An, Fubaiyang Ye, Yasuhiro Takashima, James Clarke, Harold Ayetey, Florence M.G. Cavalli, Betty Luu, Branden S. Moriarity, Shirin Ilkhanizadeh, Lukas Chávez, Chunying Yu, Kathreena M. Kurian, Thierry Magnaldo, Nicolas Sévenet, Philipp Koch, Steven M. Pollard, Peter B. Dirks, M Snyder, David A. Largaespada, Yoon Jae Cho, Joanna J. Phillips, Fredrik J. Swartling, A. Sorana Morrissy, Marcel Kool, Stefan M. Pfister, Michael D. Taylor, Austin Smith, William A. Weiss
Software Mentions: 4
Published: almost 7 years ago

10.1038/s42003-021-02059-4

Three-dimensional tissue-engineered human skeletal muscle model of Pompe disease
Cited by: 13
Author(s): Jason Wang, Chris J. Zhou, Alastair Khodabukus, Sabrina Tran, Sang-oh Han, Aaron L. Carlson, Lauran Madden, Priya S. Kishnani, Dwight D. Koeberl
Software Mentions: 4
Published: over 5 years ago

10.1186/s13072-015-0040-6

RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships
Cited by: 127
Author(s): Julie Nadel, Rodoniki Athanasiadou, Christophe Lemetre, N. Ari Wijetunga, Pilib Ó Broin, Hanae Sato, Zhengdong Zhang, Jeffrey A. Jeddeloh, Cristina Montagna, Aaron Golden, Cathal Seoighe, John M. Greally
Software Mentions: 4
Published: over 10 years ago

10.3389/fcvm.2018.00186

Spatial Principles of Chromatin Architecture Associated With Organ-Specific Gene Regulation
Cited by: 15
Author(s): Douglas J. Chapski, Manuel Rosa‐Garrido, Haiyang Nan, Frank Alber, Thomas M. Vondriska
Software Mentions: 4
Published: over 7 years ago

10.3389/fcimb.2021.678482

Deleterious Effects of SARS-CoV-2 Infection on Human Pancreatic Cells
Cited by: 38
Author(s): Syairah Hanan Shaharuddin, Victoria Wang, Reginaldo da Silva Santos, Andrew Gross, Yizhou Wang, Harneet Jawanda, Yi Zhang, Wohaib Hasan, Gustavo García, Vaithilingaraja Arumugaswami, Dhruv Sareen
Software Mentions: 4
Published: about 5 years ago

10.1186/s12898-019-0271-7

Adaptation of wild boar (Sus scrofa) activity in a human-dominated landscape
Cited by: 52
Author(s): Franz Johann, Markus Handschuh, Peter Linderoth, Carsten F. Dormann, Janosch Arnold
Software Mentions: 4
Published: over 6 years ago

10.1038/srep11353

Reassortment and distinct evolutionary dynamics of Rift Valley Fever virus genomic segments
Cited by: 17
Author(s): Caio Castro Freire, Atila Iamarino, Peinda O. Ly Soumaré, Ousmane Faye, Amadou Alpha Sall, Paolo M. A. Zanotto
Software Mentions: 4
Published: about 11 years ago

10.1371/journal.pgen.1006636

TFAP2 paralogs regulate melanocyte differentiation in parallel with MITF
Cited by: 69
Author(s): Hannah Seberg, Eric Van Otterloo, Stacie K. Loftus, Huan Liu, Greg Bonde, Ramakrishna Sompallae, Derek Gildea, Juan Francisco de Paz Santana, J. Robert Manak, William J. Pavan, Trevor Williams, Robert A. Cornell
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pgen.1007890

Genes encoding SATB2-interacting proteins in adult cerebral cortex contribute to human cognitive ability
Cited by: 15
Author(s): Isabella Cera, Laura Whitton, Gary Donohoe, Derek W. Morris, Georg Dechant, Galina Apostolova
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pntd.0002636

Molecular Evolution of Zika Virus during Its Emergence in the 20th Century
Cited by: 642
Author(s): Oumar Faye, Caio Castro Freire, Atila Iamarino, Juliana Velasco Castro de Oliveira, Mawlouth Diallo, Paolo Marinho de Andrade Zanotto, Amadou Alpha Sall
Software Mentions: 4
Published: over 12 years ago

10.1111/acel.12479

Characterization of the direct targets of <scp>FOXO</scp> transcription factors throughout evolution
Cited by: 158
Author(s): Ashley E. Webb, Anshul Kundaje, Anne Brunet
Software Mentions: 4
Published: over 10 years ago