10.1186/s13073-020-0720-0

A reference profile-free deconvolution method to infer cancer cell-intrinsic subtypes and tumor-type-specific stromal profiles
Cited by: 30
Author(s): Li Wang, Robert Sebra, John P. Sfakianos, Kimaada Allette, Wenhui Wang, Seungyeul Yoo, Nina Bhardwaj, Eric E. Schadt, Xin Yao, Matthew D. Galsky, Jun Zhu
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-021-96149-2

Long noncoding RNA landscapes specific to benign and malignant thyroid neoplasms of distinct histological subtypes
Cited by: 2
Author(s): V. D. Yakushina, В. В. Стрельников, А. С. Танас, А. В. Лавров
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12874-017-0364-y

Simulation of complex data structures for planning of studies with focus on biomarker comparison
Cited by: 4
Author(s): Andreas Schulz, Daniela Zöller, Stefan Nickels, Manfred E. Beutel, Maria Blettner, Philipp S. Wild, Harald Binder
Software Mentions: 4
Published: about 9 years ago

10.1038/s41396-018-0237-3

Opposing effects of final population density and stress on Escherichia coli mutation rate
Cited by: 7
Author(s): Rok Krašovec, Huw Richards, Danna R. Gifford, Roman V. Belavkin, Alastair Channon, Elizabeth Aston, Andrew J. McBain, Christopher G. Knight
Software Mentions: 4
Published: almost 8 years ago

10.3389/fgene.2021.635794

Multi-Transcript Level Profiling Revealed Distinct mRNA, miRNA, and tRNA-Derived Fragment Bio-Signatures for Coping Behavior Linked Haplotypes in HPA Axis and Limbic System
Cited by: 3
Author(s): Kevin Gley, Frieder Hadlich, Nares Trakooljul, Fiete Haack, Eduard Muráni, Ulrike Gimsa, Klaus Wimmers, Siriluck Ponsuksili
Software Mentions: 4
Published: almost 5 years ago

10.15252/msb.20188664

Patient‐specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies
Cited by: 37
Author(s): Federica Eduati, Patricia Jaaks, Jessica Wappler, Thorsten Cramer, Christoph A. Merten, Mathew J. Garnett, Julio Sáez-Rodríguez
Software Mentions: 4
Published: over 6 years ago

10.1186/s13059-016-1062-5

CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types
Cited by: 17
Author(s): Brad Nelms, Levi Waldron, Luis Barrera, Andrew W. Weflen, Jeremy A. Goettel, Guoji Guo, Robert K. Montgomery, Marian R. Neutra, David T. Breault, Scott B. Snapper, Stuart H. Orkin, Martha L. Bulyk, Curtis Huttenhower, Wayne I. Lencer
Software Mentions: 4
Published: almost 10 years ago

10.1534/genetics.117.300077

RNA Interference (RNAi) Screening in<i>Drosophila</i>
Cited by: 86
Author(s): Florian Heigwer, Fillip Port, Michael Boutros
Software Mentions: 4
Published: over 8 years ago

10.7717/peerj.6107

Climatic niche shift and possible future spread of the invasive South African Orchid <i>Disa bracteata</i> in Australia and adjacent areas
Cited by: 7
Author(s): Kamil Konowalik, Marta Kolanowska
Software Mentions: 4
Published: over 7 years ago

10.1093/bioinformatics/bty125

AltHapAlignR: improved accuracy of RNA-seq analyses through the use of alternative haplotypes
Cited by: 28
Author(s): Wanseon Lee, Katharine Plant, Peter Humburg, Julian C. Knight
Software Mentions: 4
Published: over 8 years ago

10.1002/ece3.7623

Enhancing flowering plant functional richness improves wild bee diversity in vineyard inter‐rows in different floral kingdoms
Cited by: 6
Author(s): Sophie Kratschmer, Bärbel Pachinger, René Gaigher, James S. Pryke, J. van Schalkwyk, Michael J. Samways, Annalie Melin, Temitope Kehinde, Johann G. Zaller, Silvia Winter
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0230931

Motivation to access laparoscopic skills training: Results of a Canadian survey of obstetrics and gynecology residents
Cited by: 4
Author(s): Jocelyn Stairs, Bradley W. Bergey, Finlay Maguire, Stephanie Scott
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-020-6467-6

Diverse biological processes coordinate the transcriptional response to nutritional changes in a Drosophila melanogaster multiparent population
Cited by: 8
Author(s): Enoch Ng’oma, Patricka A. Williams-Simon, Aniqa Rahman, King Eg
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0179891

Estimating psychopathological networks: Be careful what you wish for
Cited by: 155
Author(s): Sacha Epskamp, Joost Kruis, Maarten Marsman
Software Mentions: 4
Published: about 9 years ago

10.1002/cam4.2969

Identification of hub methylated‐CpG sites and associated genes in oral squamous cell carcinoma
Cited by: 14
Author(s): Yuxin Dai, Qiao‐Li Lv, Tingting Qi, Jian Qu, Hongli Ni, Yongkang Liao, Peng Liu, Qiang Qu
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-018-34642-x

Machine Learning Reveals Protein Signatures in CSF and Plasma Fluids of Clinical Value for ALS
Cited by: 27
Author(s): Michael S. Bereman, Joshua Beri, Jeffrey R. Enders, Tara Nash
Software Mentions: 4
Published: over 7 years ago

10.1186/1752-0509-8-55

TGF-β stimulation in human and murine cells reveals commonly affected biological processes and pathways at transcription level
Cited by: 29
Author(s): Khalid Abnaof, Nikhil Mallela, Gudrun Walenda, Steffen K. Meurer, Kristin Seré, Qiong Lin, Boudewijn J. J. Smeets, Kurt Hoffmann, Wolfgang Wagner, Martin Zenke, Ralf Weiskirchen, Holger Fröhlich
Software Mentions: 4
Published: over 12 years ago

10.1186/s13071-021-04597-6

Gene co-expression network analysis of Trypanosoma brucei in tsetse fly vector
Cited by: 5
Author(s): Kennedy W. Mwangi, Rosaline W. Macharia, Joel L. Bargul
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2018.03075

Pregnancy Epigenetic Signature in T Helper 17 and T Regulatory Cells in Multiple Sclerosis
Cited by: 22
Author(s): Andrea Iannello, Simona Rolla, Alessandro Maglione, Giulio Ferrero, Valentina Bardina, Ilenia Inaudi, Stefania De Mercanti, Francesco Novelli, Lucrezia D'Antuono, Simona Cardaropoli, Tullia Todros, Maria Vittoria Turrini, Cinzia Cordioli, Giorgia Puorro, Angela Marsili, Roberta Lanzillo, Vincenzo Brescia Morra, Francesca Cordero, Michele De Bortoli, Luca Durelli, Andrea Visconti, Santina Cutrupi, Marinella Clerico
Software Mentions: 4
Published: over 7 years ago

10.1186/s13040-015-0052-6

DNA microarray integromics analysis platform
Cited by: 11
Author(s): Tomasz Waller, Tomasz Gubała, Krzysztof Sarapata, Monika Piwowar, Wiktor Jurkowski
Software Mentions: 4
Published: about 11 years ago

10.3389/fimmu.2021.638571

Different Disease Endotypes in Phenotypically Similar Vasculitides Affecting Small-to-Medium Sized Blood Vessels
Cited by: 7
Author(s): Erin E. Gill, Maren L. Smith, Kristen M Gibson, Kimberly Morishita, Ahwon Lee, Reza Falsafi, Jinko Graham, Dirk Foell, Susanne M. Benseler, Colin J. Ross, Raashid Luqmani, David A. Cabral, Robert E. W. Hancock, Kelly L. Brown, PedVas Initiative Investigators
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2018.01829

Human Bone Marrow-Resident Natural Killer Cells Have a Unique Transcriptional Profile and Resemble Resident Memory CD8+ T Cells
Cited by: 28
Author(s): Janine Melsen, Gertjan Lugthart, Carly Vervat, Szymon M. Kiełbasa, Sander A.J. van der Zeeuw, Henk P.J. Buermans, Monique M. van Ostaijen-ten Dam, Arjan C. Lankester, Marco W. Schilham
Software Mentions: 4
Published: almost 8 years ago

10.1038/s41598-021-92455-x

Genome-wide association analyses identify genotype-by-environment interactions of growth traits in Simmental cattle
Cited by: 14
Author(s): Camila Urbano Braz, Troy N. Rowan, Robert D. Schnabel, Jared E. Decker
Software Mentions: 4
Published: about 5 years ago

10.18632/aging.101691

SNCA overexpression disturbs hippocampal gene expression trajectories in midlife
Cited by: 6
Author(s): Thomas Hentrich, Zinah Wassouf, Olaf Rieß, Julia M. Schulze‐Hentrich
Software Mentions: 4
Published: over 7 years ago

10.3390/v13040593

Probing into the Effects of Grapevine Leafroll-Associated Viruses on the Physiology, Fruit Quality and Gene Expression of Grapes
Cited by: 23
Author(s): Yashu Song, Robert Hanner, Bin Meng
Software Mentions: 4
Published: over 5 years ago

10.3389/fpls.2020.574982

Metabolic, Enzymatic Activity, and Transcriptomic Analysis Reveals the Mechanism Underlying the Lack of Characteristic Floral Scent in Apricot Mei Varieties
Cited by: 6
Author(s): Fei Bao, Tengxun Zhang, Anqi Ding, Aiqin Ding, Weiru Yang, Jia Wang, Tangren Cheng, Qixiang Zhang
Software Mentions: 4
Published: almost 6 years ago

10.1017/gmh.2020.5

Suicide on Facebook-the tales of unnoticed departure in Bangladesh
Cited by: 9
Author(s): Tanjir Rashid Soron, Sheikh Mohammed Shariful Islam
Software Mentions: 4
Published: over 6 years ago

10.3389/fpsyg.2020.00198

Conceptual Metaphors for Designing Smart Environments: Device, Robot, and Friend
Cited by: 11
Author(s): Jingoog Kim, Mary Lou Maher
Software Mentions: 4
Published: over 6 years ago

10.3389/fpsyt.2019.00593

Can an Emoji a Day Keep the Doctor Away? An Explorative Mixed-Methods Feasibility Study to Develop a Self-Help App for Youth With Mental Health Problems
Cited by: 16
Author(s): Levi van Dam, Sianne Rietstra, Eva Van der Drift, Geert Jan Stams, Rob van der Mei, Maria Mahfoud, Arne Popma, Eric Schlossberg, Alex Pentland, Todd G. Reid
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0233277

Linguistic signaling, emojis, and skin tone in trust games
Cited by: 8
Author(s): J. Jobu Babin
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-021-86406-9

Extreme philopatry and genetic diversification at unprecedented scales in a seabird
Cited by: 6
Author(s): D. K. Danckwerts, Laurence Humeau, Patrick Pinet, Christopher D. McQuaid, Matthieu Le Corre
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0230813

Metabolic reprograming of LPS-stimulated human lung macrophages involves tryptophan metabolism and the aspartate-arginosuccinate shunt
Cited by: 14
Author(s): Fanta Fall, Elodie Lamy, Marion Brollo, Emmanuel Naline, Natacha Lenuzza, Etienne Thévenot, Philippe Devillier, Stanislas Grassin-Delyle
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-017-03222-w

Changes in novel haematological parameters following thermal injury: A prospective observational cohort study
Cited by: 15
Author(s): Robert J. Dinsdale, Amarpreet Devi, Peter Hampson, Christopher M. Wearn, Amy Bamford, Jon Hazeldine, Jonathan Bishop, Sumiya Ahmed, Chris Watson, Janet M. Lord, Naiem Moiemen, Paul Harrison
Software Mentions: 4
Published: about 9 years ago

10.1038/s41438-021-00531-0

Whole-genome resequencing of Osmanthus fragrans provides insights into flower color evolution
Cited by: 28
Author(s): Chen Hong-guo, Xiangling Zeng, Jie Yang, Xuan Cai, Yumin Shi, Rencheng Zheng, Zhenqi Wang, Junyi Liu, Xiao Su Yi, Siwei Xiao, Qiang Fu, Jingjing Zou, Caiyun Wang
Software Mentions: 4
Published: over 5 years ago

10.3390/ijerph18042194

The Impact of Individual Mobility on Long-Term Exposure to Ambient PM2.5: Assessing Effect Modification by Travel Patterns and Spatial Variability of PM2.5
Cited by: 12
Author(s): Eun-Hye Yoo, Qiang Pu, Youngseob Eum, Xiangyu Jiang
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-84774-w

Culture and differentiation of rabbit intestinal organoids and organoid-derived cell monolayers
Cited by: 8
Author(s): Egi Kardia, Michael Frese, Elena Smertina, Tanja Strive, Xi‐Lei Zeng, Mary K. Estes, Robyn N. Hall
Software Mentions: 4
Published: over 5 years ago

10.1038/s41438-021-00471-9

The genome of Magnolia biondii Pamp. provides insights into the evolution of Magnoliales and biosynthesis of terpenoids
Cited by: 27
Author(s): Shanshan Dong, Min Liu, Yang Liu, Fei Chen, Ting Yang, Lu Chen, Xingtan Zhang, Xing Guo, Dongming Fang, Linzhou Li, Tian Deng, Zhen Yao, Xiaoan Lang, Yiqing Gong, Ernest Wu, Yaling Wang, Yamei Shen, Xun Gong, Huan Liu, Shouzhou Zhang
Software Mentions: 4
Published: over 5 years ago

10.1186/s12917-020-02373-9

Transcriptome profiling of porcine testis tissue reveals genes related to sperm hyperactive motility
Cited by: 5
Author(s): Maren van Son, Nina Hårdnes Tremoen, Ann Helen Gaustad, Dag Inge Våge, Teklu Tewoldebrhan Zeremichael, Frøydis Deinboll Myromslien, Eli Grindflek
Software Mentions: 4
Published: about 6 years ago

10.1093/gigascience/giab037

The genome of the venomous snail <i>Lautoconus ventricosus</i> sheds light on the origin of conotoxin diversity
Cited by: 21
Author(s): José Ramón Pardos-Blas, Iker Irisarri, Samuel Abalde, Carlos M.L. Afonso, Manuel Jiménez‐Tenorio, Rafael Zardoya
Software Mentions: 4
Published: over 5 years ago

10.1111/acel.12928

Increased intron retention is a post‐transcriptional signature associated with progressive aging and Alzheimer’s disease
Cited by: 65
Author(s): Swarnaseetha Adusumalli, Zhen‐Kai Ngian, Wei‐Qi Lin, Touati Benoukraf, Chin‐Tong Ong
Software Mentions: 4
Published: over 7 years ago

10.1111/acel.13195

Growth differentiation factor 15 protects against the aging‐mediated systemic inflammatory response in humans and mice
Cited by: 59
Author(s): Ji Sun Moon, Ludger Goeminne, Jung Tae Kim, Jing Tian, Seok Hwan Kim, Ha Thi Nga, Sun Hyung Kang, Baeki E. Kang, Jin Seok Byun, Young‐Sun Lee, Jae‐Han Jeon, Minho Shong, Johan Auwerx, Dongryeol Ryu, Hyon‐Seung Yi
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-020-58942-3

Amplicon sequencing analysis of arbuscular mycorrhizal fungal communities colonizing maize roots in different cover cropping and tillage systems
Cited by: 25
Author(s): Masao Higo, Yuya Tatewaki, Karen Iida, Kana Yokota, Katsunori Isobe
Software Mentions: 4
Published: over 6 years ago

10.1093/gigascience/giz136

Trochodendron aralioides, the first chromosome-level draft genome in Trochodendrales and a valuable resource for basal eudicot research
Cited by: 20
Author(s): Joeri S. Strijk, Damien Daniel Hinsinger, Fengping Zhang, Kaihua Cao
Software Mentions: 4
Published: almost 7 years ago

10.1093/gigascience/giz112

Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima)
Cited by: 49
Author(s): Yu Xing, Yang Liu, Qing Zhang, Xinghua Nie, Yamin Sun, Zhiyong Zhang, Huchen Li, Kefeng Fang, Guangpeng Wang, Hongwen Huang, Ton Bisseling, Qingqin Cao, Ling Qin
Software Mentions: 4
Published: almost 7 years ago

10.1111/acel.13012

The conserved histone chaperone LIN‐53 is required for normal lifespan and maintenance of muscle integrity in <i>Caenorhabditis elegans</i>
Cited by: 11
Author(s): Stefanie Müthel, Bora Uyar, Ming He, Anne Krause, Burcu Vitrinel, Selman Bulut, Djordje Vasiljevic, Iris Marchal, Stefan Kempa, Altuna Akalin, Baris Tursun
Software Mentions: 4
Published: almost 7 years ago

10.3389/fnmol.2018.00363

Assessing Transcriptome Quality in Patch-Seq Datasets
Cited by: 33
Author(s): Shreejoy J. Tripathy, Lilah Toker, Claire Bomkamp, B. Ogan Mancarci, Manuel Belmadani, Paul Pavlidis
Software Mentions: 4
Published: almost 8 years ago

10.3389/fnmol.2021.699562

Spatial RNA Sequencing Identifies Robust Markers of Vulnerable and Resistant Human Midbrain Dopamine Neurons and Their Expression in Parkinson’s Disease
Cited by: 20
Author(s): Julio Águila, Shu Cheng, Nigel Kee, Mengshu Cao, Menghan Wang, Qiaolin Deng, Eva Hedlund
Software Mentions: 4
Published: about 5 years ago

10.1186/s42523-021-00098-0

The microbiota of healthy dogs demonstrates individualized responses to synbiotic supplementation in a randomized controlled trial
Cited by: 6
Author(s): Jirayu Tanprasertsuk, Aashish R. Jha, Justin Shmalberg, Roshonda B. Jones, Lee M. Perry, Heather Maughan, Ryan W. Honaker
Software Mentions: 4
Published: about 5 years ago

10.3390/ani11041002

Differentially Expressed Gene Patterns in Ascarid-Infected Chickens of Higher- or Lower-Performing Genotypes
Cited by: 0
Author(s): Isabel Kilic, Manuel Stehr, Mark Hennies, C. C. Metges, Sören Franzenburg, Clemens Falker‐Gieske, Jens Tetens, Gürbüz Daş
Software Mentions: 4
Published: over 5 years ago

10.1101/2021.06.06.446826

Evolution of enhanced innate immune evasion by the SARS-CoV-2 B.1.1.7 UK variant
Cited by: 84
Author(s): Lucy Thorne, Mehdi Bouhaddou, Ann-Kathrin Reuschl, Lorena Zuliani-Alvarez, Benjamin J. Polacco, Adrian Pelin, Jyoti Batra, Matt Whelan, Manisha R. Ummadi, Ajda Roic, Jane Turner, Kirsten Obernier, Hannes Braberg, Margaret Soucheray, Alicia Richards, Kuei‐Ho Chen, Bhavya Harjai, Danish Memon, Myra Hosmillo, Joseph Hiatt, Aminu S. Jahun, Ian Goodfellow, Mahdad Noursadeghi, Jacqueline M. Fabius, Kevan M. Shokat, Natalia Jura, Kliment A. Verba, Pedro Beltrão, Danielle L. Swaney, Adolfo Garcı́a-Sastre, Clare Jolly, Greg J. Towers, Nevan J. Krogan
Software Mentions: 4
Published: about 5 years ago

10.1093/gigascience/gix109

Genome sequence of the small brown planthopper, Laodelphax striatellus
Cited by: 90
Author(s): Jiachen Zhu, Feng Jiang, Xianhui Wang, Pengcheng Yang, Yan-Yuan Bao, Wan Zhao, Wei Wang, Hong Liang, Qianshuo Wang, Na Cui, Jing Li, Xiaofang Chen, Luo Li, Jianping Yu, Le Kang, Feng Cui
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0179581

Bioinformatic training needs at a health sciences campus
Cited by: 8
Author(s): Jeffrey C. Oliver
Software Mentions: 4
Published: about 9 years ago

10.1186/s12935-018-0681-1

Identification of RPL5 and RPL10 as novel diagnostic biomarkers of Atypical teratoid/rhabdoid tumors
Cited by: 6
Author(s): Yanming Ren, Chuanmin Tao, Xiliang Wang, Yan Ju
Software Mentions: 4
Published: over 7 years ago

10.1007/s00702-021-02359-3

Covariation of psychobiological stress regulation with valence and quantity of social interactions in everyday life: disentangling intra- and interindividual sources of variation
Cited by: 5
Author(s): Martin Stoffel, Elvira Abbruzzese, Stefanie Rahn, Ulrike Bossmann, Markus Moessner, Beate Ditzen
Software Mentions: 4
Published: about 5 years ago

10.1016/j.gpb.2019.01.006

Global Analysis of Gene Expression Profiles Provides Novel Insights into the Development and Evolution of the Large Crustacean Eriocheir sinensis
Cited by: 3
Author(s): Jun Wang, Xiaowen Chen, Funan He, Xian‐Rong Song, Shu Huang, Wucheng Yue, Yipei Chen, Zhixi Su
Software Mentions: 4
Published: about 6 years ago

10.1186/s13059-021-02333-y

Genomic insights into the origin, domestication and genetic basis of agronomic traits of castor bean
Cited by: 28
Author(s): Wei Xu, Di Wu, Tianquan Yang, Chao Sun, Zaiqing Wang, Bing Han, Shibo Wu, Anmin Yu, Mark A. Chapman, Sammy Muraguri, Qing Tan, Wenbo Wang, Zhigui Bao, Aizhong Liu, Li D
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1009734

Recovery from heat shock requires the microRNA pathway in Caenorhabditis elegans
Cited by: 10
Author(s): Delaney C Pagliuso, Devavrat M Bodas, Amy E. Pasquinelli
Software Mentions: 4
Published: almost 5 years ago

10.3390/ani10010002

Atmospheric Ammonia Affects Myofiber Development and Lipid Metabolism in Growing Pig Muscle
Cited by: 10
Author(s): Shouwei Tang, Jingjing Xie, Sheng Zhang, Weida Wu, Bao Yi, Hongfu Zhang
Software Mentions: 4
Published: over 6 years ago

10.1186/s12862-018-1288-9

Evolutionary diversity and novelty of DNA repair genes in asexual Bdelloid rotifers
Cited by: 16
Author(s): Bette Hecox-Lea, David B. Mark Welch
Software Mentions: 4
Published: over 7 years ago

10.3390/healthcare8040558

Impact of the COVID-19 Pandemic on Manual Therapy Service Utilization within the Australian Private Healthcare Setting
Cited by: 17
Author(s): Reidar P. Lystad, Benjamin T. Brown, M. V. Swain, Roger Engel
Software Mentions: 4
Published: over 5 years ago

10.1093/gigascience/giy118

Extensive evaluation of the generalized relevance network approach to inferring gene regulatory networks
Cited by: 5
Author(s): Vladimir Kuzmanovski, Ljupčo Todorovski, Sašo Džeroski
Software Mentions: 4
Published: almost 8 years ago

10.1038/s41598-021-95000-y

Rodent host population dynamics drive zoonotic Lyme Borreliosis and Orthohantavirus infections in humans in Northern Europe
Cited by: 3
Author(s): Mahdi Aminikhah, Jukka T. Forsman, Esa Koskela, Tapio Mappes, Jussi Sane, Jukka Ollgren, Sami M. Kivelä, Eva R. Kallio
Software Mentions: 4
Published: almost 5 years ago

10.1186/s40168-018-0404-9

Commensal microbiota modulate gene expression in the skin
Cited by: 126
Author(s): Jacquelyn S. Meisel, Georgia Sfyroera, Casey Bartow‐McKenney, Ciara Gimblet, Julia Bugayev, Joseph Horwinski, Brian Kim, Jonathan R. Brestoff, Amanda S. Tyldsley, Qi Zheng, Brendan P. Hodkinson, David Artis, Elizabeth A. Grice
Software Mentions: 4
Published: over 8 years ago

10.1038/srep29434

Tumour sampling method can significantly influence gene expression profiles derived from neoadjuvant window studies
Cited by: 13
Author(s): Dominic Pearce, Laura Arthur, Arran Turnbull, Lorna Renshaw, Victoria Sabine, Jeremy Thomas, John M.S. Bartlett, J. Michael Dixon, Andrew H. Sims
Software Mentions: 4
Published: about 10 years ago

10.1186/s13059-016-1145-3

Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species
Cited by: 539
Author(s): Thomas C. Mathers, Yazhou Chen, Gemy Kaithakottil, Fabrice Legeai, Sam T. Mugford, Patrice Bâa-Puyoulet, Anthony Bretaudeau, Bernardo Clavijo, Stefano Colella, Olivier Collin, Tamás Dalmay, Thomas Derrien, Honglin Feng, Toni Gabaldón, Anna Jordan, Irene Julca, Graeme J. Kettles, Krissana Kowitwanich, Dominique Lavenier, Paolo Lenzi, Sara López-Gomollón, Damian Loska, Daniel Mapleson, Florian Maumus, Simon Moxon, Daniel D. Price, Akiko Sugio, Manuella van Munster, Marilyne Uzest, Darren Waite, Georg Jander, Denis Tagu, Alex C. C. Wilson, Cock van Oosterhout, David Swarbreck, Saskia A. Hogenhout
Software Mentions: 4
Published: over 9 years ago

10.2196/18839

Computer-Controlled Virtual Humans in Patient-Facing Systems: Systematic Review and Meta-Analysis
Cited by: 29
Author(s): Debaleena Chattopadhyay, Tengteng Ma, Hasti Sharifi, Pamela Martyn‐Nemeth
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0173320

Dynamic time warping assessment of high-resolution melt curves provides a robust metric for fungal identification
Cited by: 22
Author(s): Sha Lu, Гордана Мирчевска, Sayali S. Phatak, Dongmei Li, Janos Luka, Richard Calderone, William A. Fonzi
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0240171

Tracing gestation and lactation in free ranging gray whales using the stable isotopic composition of epidermis layers
Cited by: 7
Author(s): Michelle Gelippi, Brian N. Popp, Marco F. W. Gauger, Javier Caraveo-Patiño
Software Mentions: 4
Published: almost 6 years ago

10.3389/fphar.2019.00747

Bioinformatic Study of Transcriptome Changes in the Mice Lumbar Spinal Cord After the 30-Day Spaceflight and Subsequent 7-Day Readaptation on Earth: New Insights Into Molecular Mechanisms of the Hypogravity Motor Syndrome
Cited by: 8
Author(s): M. S. Kuznetsov, Artur Nicolaevich Lisukov, Albert A. Rizvanov, O. V. Tyapkina, Oleg Gusev, P. N. Rezvyakov, I. B. Kozlovskaya, E. E. Nikolskiy, Р. Р. Исламов
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.ppat.1009697

Listeria monocytogenes infection rewires host metabolism with regulatory input from type I interferons
Cited by: 3
Author(s): Duygu Demiröz, Ekaterini Platanitis, Marsha Bryant, Philipp Fischer, Michaela Prchal-Murphy, Alexander Lercher, Caroline Lassnig, Manuela Baccarini, Mathias Müller, Andréas Bergthaler, Veronika Sexl, Marlies Dolezal, Thomas Decker
Software Mentions: 4
Published: about 5 years ago

10.3390/e23070882

Assessment and Prediction of Water Resources Vulnerability Based on a NRS-RF Model: A Case Study of the Song-Liao River Basin, China
Cited by: 4
Author(s): Weizhong Chen, Yan Chen, Yazhong Feng
Software Mentions: 4
Published: about 5 years ago

10.1002/ece3.7501

Interactive effects of body mass changes and species‐specific morphology on flight behavior of chick‐rearing Antarctic fulmarine petrels under diurnal wind patterns
Cited by: 5
Author(s): Nina Dehnhard, Andrew Klekociuk, Louise Emmerson
Software Mentions: 4
Published: over 5 years ago

10.1007/s00360-020-01322-0

Phenotypic flexibility in heat production and heat loss in response to thermal and hydric acclimation in the zebra finch, a small arid-zone passerine
Cited by: 10
Author(s): Michał S. Wojciechowski, Anna Kowalczewska, Roger Colominas‐Ciuró, Małgorzata Jefimow
Software Mentions: 4
Published: almost 6 years ago

10.3390/jcm10132797

Predictors for Perioperative Blood Transfusion in Patients Undergoing Open Cystectomy and Urinary Diversion and Development of a Nomogram: An Observational Cohort Study
Cited by: 4
Author(s): Dominique Engel, Christian M. Beilstein, Pascal Jerney, Marc A. Furrer, Fiona C. Burkhard, Lukas M. Löffel, Patrick Y. Wuethrich
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-020-6524-1

Transcriptome sequencing and whole genome expression profiling of hexaploid sweetpotato under salt stress
Cited by: 17
Author(s): Mohamed Hamed Arisha, Hesham Aboelnasr, Muhammad Qadir Ahmad, Yaju Liu, Wei Tang, Runfei Gao, Hui Yan, Meng Kou, Xin Wang, Yungang Zhang, Qiang Li
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-019-50046-x

Autoregulation assessment by direct visualisation of pial arterial blood flow in the piglet brain
Cited by: 13
Author(s): Samuel Patrick Klein, Veerle De Sloovere, Geert Meyfroidt, Bart Depreitere
Software Mentions: 4
Published: almost 7 years ago

10.1111/1462-2920.15554

Comparative genomics reveals a core gene toolbox for lifestyle transitions in Hypocreales fungi
Cited by: 7
Author(s): Baojun Wu, Murray P. Cox
Software Mentions: 4
Published: about 5 years ago

10.1007/s12079-020-00575-2

Spermatozoa induce transcriptomic alterations in bovine oviductal epithelial cells prior to initial contact
Cited by: 7
Author(s): Qurat Ul Ain Reshi, Janeli Viil, James Ord, Freddy Lättekivi, Kasun Godakumara, Mohammad Mehedi Hasan, Monika Nõmm, Kersti Jääger, Agne Velthut-Meikas, Ülle Jaakma, Andres Salumets, Alireza Fazeli
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12931-018-0932-7

Inflammatory pathways are upregulated in the nasal epithelium in patients with idiopathic pulmonary fibrosis
Cited by: 13
Author(s): Marc A. Sala, Yalbi I. Balderas-Martínez, Ivette Buendía-Roldán, Hiam Abdala‐Valencia, Ki-Won Nam, Manu Jain, Sangeeta Bhorade, Ankit Bharat, Paul A. Reyfman, Karen M. Ridge, Annie Pardo, Jacob I. Sznajder, G. R. Scott Budinger, Alexander V. Misharin, Moisés Selman
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-019-6204-1

Transcriptome profiling of ‘Kyoho’ grape at different stages of berry development following 5-azaC treatment
Cited by: 7
Author(s): Da‐Long Guo, Qiong Li, Xiao-Ru Ji, Zhenguang Wang, Yi‐He Yu
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-019-48283-1

De novo transcriptome assembly for four species of crustose coralline algae and analysis of unique orthologous genes
Cited by: 9
Author(s): Tessa M. Page, Carmel McDougall, Guillermo Díaz-Pulido
Software Mentions: 4
Published: almost 7 years ago

10.7554/eLife.02626

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways
Cited by: 80
Author(s): Benoît Ballester, Alejandra Medina-Rivera, Dominic Schmidt, Mar Gonzàlez-Porta, Matthew Carlucci, Marc E. Rothenberg, Kyle Chessman, Aline Faure, Alister P. W. Funnell, Ângela Gonçalves, Claudia Kutter, Margus Lukk, Suraj Menon, William McLaren, Klara Stefflova, Stephen Watt, Matthew T. Weirauch, Merlin Crossley, John C. Marioni, Duncan T. Odom, Paul Flicek, Michael D. Wilson
Software Mentions: 4
Published: almost 12 years ago

10.3390/cancers12020470

Transcriptome Analysis Identifies ALCAM Overexpression as a Prognosis Biomarker in Laryngeal Squamous Cell Carcinoma
Cited by: 10
Author(s): Pedro Nicolau-Neto, Paulo Thiago de Souza-Santos, Mariana Severo Ramundo, Priscila Valverde, Ivanir Martins, Izabella Costa Santos, Fernando Luiz Dias, Tatiana de Almeida Simão, Luís Felipe Ribeiro Pinto
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0233543

A transcriptome-based approach to identify functional modules within and across primary human immune cells
Cited by: 10
Author(s): Saraï Mola, Sylvain Foisy, Gabrielle Boucher, François Major, Claudine Beauchamp, Mohamad Karaky, Philippe Goyette, Sylvie Lesage, John D. Rioux
Software Mentions: 4
Published: about 6 years ago

10.1186/s13024-021-00462-3

A proteomic network approach resolves stage-specific molecular phenotypes in chronic traumatic encephalopathy
Cited by: 4
Author(s): Laura Gutierrez-Quiceno, Eric B. Dammer, Ashlyn G. Johnson, James Webster, Rhythm Shah, Duc M. Duong, Luming Yin, Nicholas T. Seyfried, Victor E. Alvarez, Thor D. Stein, Ann C. McKee, Chadwick M. Hales
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-019-48665-5

Near-future ocean acidification does not alter the lipid content and fatty acid composition of adult Antarctic krill
Cited by: 11
Author(s): Jessica A. Ericson, Nicole Hellessey, So Kawaguchi, Peter D. Nichols, Stephen Nicol, Nils Hoem, Patti Virtue
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12864-015-1767-y

Experimental validation of methods for differential gene expression analysis and sample pooling in RNA-seq
Cited by: 132
Author(s): Anto P. Rajkumar, Per Qvist, Ross Lazarus, Francesco Lescai, Jia Ju, Mette Nyegaard, Ole Mors, Anders D. Børglum, Qibin Li, Jane H. Christensen
Software Mentions: 4
Published: about 11 years ago

10.1371/journal.pone.0058294

Sequencing and Comparative Analysis of the Straw Mushroom (Volvariella volvacea) Genome
Cited by: 128
Author(s): Dapeng Bao, Ming Gong, Huajun Zheng, Mingjie Chen, Liang Zhang, Hong Wang, Jianping Jiang, Lin Wu, Yaping Zhu, Gang Zhu, Yan Zhou, Chuanhua Li, Shengyue Wang, Yan Zhao, Guoping Zhao, Qian Tan
Software Mentions: 4
Published: over 13 years ago

10.1186/s13071-018-3139-3

Come rain or come shine: environmental effects on the infective stages of Sparicotyle chrysophrii, a key pathogen in Mediterranean aquaculture
Cited by: 16
Author(s): Mar Villar-Torres, Francisco E. Montero, Juan Antonio Raga, Aigües Repullés-Albelda
Software Mentions: 4
Published: almost 8 years ago

10.7717/peerj.3216

Analysis of genomic variation in lung adenocarcinoma patients revealed the critical role of PI3K complex
Cited by: 9
Author(s): Zhao min Deng, Lizhu Lin, Wen Qiu, Yong qun Zhang, Hong Zhong, Ping Liao, Wu Yun
Software Mentions: 4
Published: about 9 years ago

10.1038/s41598-019-42692-y

Risks of hydroclimatic regime shifts across the western United States
Cited by: 2
Author(s): Subhrendu Gangopadhyay, Gregory J. McCabe, Gregory T. Pederson, Jessica Martin, Jeremy S. Littell
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2288-12-163

Fitting parametric random effects models in very large data sets with application to VHA national data
Cited by: 15
Author(s): Mulugeta Gebregziabher, Leonard E. Egede, Gregory E. Gilbert, Kelly J. Hunt, Paul J. Nietert, Patrick D. Mauldin
Software Mentions: 4
Published: almost 14 years ago

10.3390/genes12050702

Identification and Functional Annotation of Genes Related to Bone Stability in Laying Hens Using Random Forests
Cited by: 3
Author(s): Simon Jansen, Ulrich Baulain, Christin Habig, Faisal Ramzan, Jens Schauer, Armin O. Schmitt, Armin M. Scholz, Ahmad Sharifi, Annett Weigend, Steffen Weigend
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-019-6397-3

Host plant adaptation in the polyphagous whitefly, Trialeurodes vaporariorum, is associated with transcriptional plasticity and altered sensitivity to insecticides
Cited by: 25
Author(s): Adam Pym, Kumar Saurabh Singh, A. Nordgren, T.G. Emyr Davies, Christoph Zimmer, Jan Eliáš, Russell Slater, Chris Bass
Software Mentions: 4
Published: over 6 years ago

10.3390/genes12020227

Phenotypic Response to Light Versus Shade Associated with DNA Methylation Changes in Snapdragon Plants (Antirrhinum majus)
Cited by: 4
Author(s): Pierick Mouginot, Nelia Luviano Aparicio, Delphine Gourcilleau, Mathieu Latutrie, Sara Marin, Jean‐Louis Hemptinne, Christoph Grunau, Benoît Pujol
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-021-07558-6

The draft genome of the specialist flea beetle Altica viridicyanea (Coleoptera: Chrysomelidae)
Cited by: 5
Author(s): Huai‐Jun Xue, Yiwei Niu, Kari A. Segraves, Rui Nie, Ya Jing Hao, Li Li Zhang, Xin Cheng, Xuewen Zhang, Wen Zhu Li, Run Sheng Chen, Xing Yang
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-018-27314-3

Sample tracking in microbiome community profiling assays using synthetic 16S rRNA gene spike-in controls
Cited by: 16
Author(s): Dieter M. Tourlousse, Akiko Ohashi, Yuji Sekiguchi
Software Mentions: 4
Published: about 8 years ago

10.1186/s12983-021-00391-3

Polymorphism of winter phenotype in Siberian hamster: consecutive litters do not differ in photoresponsiveness but prolonged acclimation to long photoperiod inhibits winter molt
Cited by: 4
Author(s): Anna S. Przybylska-Piech, Michał S. Wojciechowski, Małgorzata Jefimow
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-018-26498-y

Possible Obesogenic Effects of Bisphenols Accumulation in the Human Brain
Cited by: 39
Author(s): Pantelis Charisiadis, Xanthi Andrianou, Thomas P. van der Meer, Wilfred F. A. den Dunnen, D.F. Swaab, Bruce H. R. Wolffenbuttel, Konstantinos C. Makris, Jana V. van Vliet-Ostaptchouk
Software Mentions: 4
Published: about 8 years ago

10.1186/s12864-021-07902-w

Increased abundance of secreted hydrolytic enzymes and secondary metabolite gene clusters define the genomes of latent plant pathogens in the Botryosphaeriaceae
Cited by: 16
Author(s): Jan Hendrik Nagel, Michael J. Wingfield, Bernard Slippers
Software Mentions: 4
Published: almost 5 years ago