10.1371/journal.pcbi.1007909

Perturbation biology links temporal protein changes to drug responses in a melanoma cell line
Cited by: 14
Author(s): Elin Nyman, Richard R. Stein, Xin Jing, Weiqing Wang, Benjamin Marks, Ioannis K. Zervantonakis, Anil Korkut, Nicholas Paul Gauthier, Chris Sander
Software Mentions: 4
Published: about 6 years ago

10.1111/2041-210X.12533

Shedding light on the ‘dark side’ of phylogenetic comparative methods
Cited by: 57
Author(s): Natalie Cooper, Gavin H. Thomas, Richard G. FitzJohn
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pgen.1008775

Transcriptomic stratification of late-onset Alzheimer's cases reveals novel genetic modifiers of disease pathology
Cited by: 26
Author(s): Nikhil Milind, Christoph Preuß, Annat Haber, Guruprasad Ananda, Shubhabrata Mukherjee, John Cai, Sarah Shapley, Benjamin A. Logsdon, Paul K. Crane, Gregory W. Carter
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0183679

Multidimensional pooled shRNA screens in human THP-1 cells identify candidate modulators of macrophage polarization
Cited by: 31
Author(s): Ewa Surdziel, Ieuan Clay, Florian Nigsch, Anke Thiemeyer, Cyril Allard, Gregory R. Hoffman, John S. Reece‐Hoyes, Tanushree Phadke, Romain Gambert, Caroline Gubser Keller, Marie-Gabrielle Ludwig, Birgit Baumgarten, Mathias Frederiksen, Dirk Schübeler, Klaus Seuwen, Tewis Bouwmeester, Barna D. Fodor
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pcbi.1000792

Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation (DIRAC)
Cited by: 74
Author(s): James A. Eddy, Leroy Hood, Nathan D. Price, Donald Geman
Software Mentions: 4
Published: about 16 years ago

10.1371/journal.pone.0149171

RNA-Seq Reveals the Angiogenesis Diversity between the Fetal and Adults Bone Mesenchyme Stem Cell
Cited by: 2
Author(s): Xin Zhao, Yingmin Han, Yu Liang, Chao Nie, Jian Wang
Software Mentions: 4
Published: over 10 years ago

10.3389/fimmu.2021.716075

Transcriptome Analysis of Peripheral Blood Mononuclear Cells Reveals Distinct Immune Response in Asymptomatic and Re-Detectable Positive COVID-19 Patients
Cited by: 10
Author(s): Jiaqi Zhang, Dan Lin, Kui Li, Xiangming Ding, Lin Li, Yuntao Liu, Dongdong Liu, Jing Lin, Xiangyun Teng, Yizhe Li, Ming Liu, Jian Shen, Xiaodan Wang, He Dan, Yawei Shi, Dawei Wang, Jianhua Xu
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.56554

Cytotoxic T cells swarm by homotypic chemokine signalling
Cited by: 32
Author(s): Jorge Luis Galeano Niño, Sophie V. Pageon, Szun S. Tay, Feyza Colakoglu, Daryan Kempe, Jack D. Hywood, Jessica K Mazalo, James Cremasco, Matt Govendir, Laura F. Dagley, Ku‐Lung Hsu, Simone Rizzetto, Jerzy Zieba, Gregory Rice, Victoria Prior, Geraldine M. O’Neill, Richard J. Williams, David R. Nisbet, Belinda Kramer, Andrew I. Webb, Fabio Luciani, Mark Read, Maté Biro
Software Mentions: 4
Published: almost 6 years ago

10.3389/fnins.2017.00112

Antidyskinetic Effects of MEK Inhibitor Are Associated with Multiple Neurochemical Alterations in the Striatum of Hemiparkinsonian Rats
Cited by: 21
Author(s): Guiqin Chen, Shuke Nie, Chao Han, Kai Ma, Xu Yan, Zhentao Zhang, Stella M. Papa, Xin Cao
Software Mentions: 4
Published: over 9 years ago

10.1186/s12890-018-0675-8

Latent class analysis to define radiological subgroups in pulmonary nontuberculous mycobacterial disease
Cited by: 12
Author(s): Steven Cowman, Joseph Jacob, S. Obaidee, Andres Floto, Robert Wilson, Charles Haworth, Michael R. Loebinger
Software Mentions: 4
Published: almost 8 years ago

10.1001/jamanetworkopen.2021.11329

Real-World Survival Outcomes Associated With First-Line Immunotherapy, Targeted Therapy, and Combination Therapy for Metastatic Clear Cell Renal Cell Carcinoma
Cited by: 15
Author(s): Nicholas H. Chakiryan, Da David Jiang, Kyle Gillis, Elizabeth Green, Ali Hajiran, Lee A. Hugar, Logan Zemp, Jingsong Zhang, Rohit Jain, Jad Chahoud, Philippe E. Spiess, Wade J. Sexton, Scott M. Gilbert, Brandon Manley
Software Mentions: 4
Published: about 5 years ago

10.3389/fgene.2018.00228

Network Rewiring in Cancer: Applications to Melanoma Cell Lines and the Cancer Genome Atlas Patients
Cited by: 6
Author(s): Kuan Fu Ding, Darren Finlay, Hongwei Yin, William P.D. Hendricks, Chris Sereduk, Jeffrey Kiefer, Aleksandar Sekulić, Patricia LoRusso, Kristiina Vuori, Jeffrey M. Trent, Nicholas J. Schork
Software Mentions: 4
Published: about 8 years ago

10.3390/ijerph16183435

A Multi-Center Competing Risks Model and Its Absolute Risk Calculation Approach
Cited by: 1
Author(s): Wang Jin-tao, Zhongshang Yuan, Yi Liu, Fuzhong Xue
Software Mentions: 4
Published: almost 7 years ago

10.1007/s00439-017-1808-5

Global skin colour prediction from DNA
Cited by: 96
Author(s): Susan Walsh, Lakshmi Chaitanya, Krystal Breslin, Charanya Muralidharan, Agnieszka Bronikowska, Ewelina Pośpiech, Júlia Koller, Leda Kovatsi, Andreas Wollstein, Wojciech Branicki, Fan Liu, Manfred Kayser
Software Mentions: 4
Published: over 9 years ago

10.1038/s41598-018-33671-w

Disentangling direct and indirect effects of water availability, vegetation, and topography on avian diversity
Cited by: 12
Author(s): Vladimír Remeš, Lenka Harmáčková
Software Mentions: 4
Published: almost 8 years ago

10.1002/advs.201903366

Transferrin Receptor 1 Regulates Thermogenic Capacity and Cell Fate in Brown/Beige Adipocytes
Cited by: 33
Author(s): Jin Li, Xiaohan Pan, Guihua Pan, Zijun Song, Yao He, Susu Zhang, Xueru Ye, Yang Xiang, Enjun Xie, Xinhui Wang, Xudong Mai, Xing Yin, Biyao Tang, Xuan Shu, Pengyu Chen, Xiaoshuang Dai, Ye Tian, Liheng Yao, Mulan Han, Guohuan Xu, Huijie Zhang, Jia Sun, Hong Chen, Fudi Wang, Junxia Min, Liwei Xie
Software Mentions: 4
Published: over 6 years ago

10.18632/aging.102034

A large-scale CRISPR screen and identification of essential genes in cellular senescence bypass
Cited by: 5
Author(s): Xuehui Li, Lei Wei, Qiongye Dong, Liyang Liu, Michael Q. Zhang, Zhen Xie, Xiaowo Wang
Software Mentions: 4
Published: about 7 years ago

10.1186/s12859-018-2508-4

CANDLE/Supervisor: a workflow framework for machine learning applied to cancer research
Cited by: 50
Author(s): Justin M. Wozniak, Rajeev Jain, Prasanna Balaprakash, Jonathan Ozik, Nicholson Collier, John Bauer, Fangfang Xia, Thomas Brettin, Rick Stevens, Jamaludin Mohd-Yusof, Cristina Garcia-Cardona, Brian Van Essen, Matthew Baughman
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-020-78392-1

Vital signs assessed in initial clinical encounters predict COVID-19 mortality in an NYC hospital system
Cited by: 37
Author(s): Elza Rechtman, Paul Curtin, Esmeralda Álvarez Navarro, Sharon Nirenberg, Megan Horton
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0072779

Biogeography of Deep-Sea Benthic Bacteria at Regional Scale (LTER HAUSGARTEN, Fram Strait, Arctic)
Cited by: 53
Author(s): Marianne Jacob, Thomas Soltwedel, Antje Boetius, Alban Ramette
Software Mentions: 4
Published: almost 13 years ago

10.1371/journal.pone.0130741

Characterisation of Brachycephalic Obstructive Airway Syndrome in French Bulldogs Using Whole-Body Barometric Plethysmography
Cited by: 61
Author(s): Nai‐Chieh Liu, David R. Sargan, Vicki Adams, Jane Ladlow
Software Mentions: 4
Published: about 11 years ago

10.1002/fsn3.1312

Functional approach and agro‐climatic information to improve the estimation of olive oil fatty acid content from near‐infrared data
Cited by: 5
Author(s): María Isabel Sánchez‐Rodríguez, Elena Sánchez‐López, Alberto Marinas, Francisco J. Urbano, José M. Caridad
Software Mentions: 4
Published: over 6 years ago

10.1111/acer.14259

Chronic Voluntary Ethanol Drinking in Cynomolgus Macaques Elicits Gene Expression Changes in Prefrontal Cortical Area 46
Cited by: 4
Author(s): Nicole A.R. Walter, Christina Zheng, Robert P. Searles, Shannon K. McWeeney, Kathleen A. Grant, Robert Hitzemann
Software Mentions: 4
Published: over 6 years ago

10.1186/s13195-020-00598-2

Characterization of the chromatin accessibility in an Alzheimer’s disease (AD) mouse model
Cited by: 24
Author(s): Yaqi Wang, Xiaomin Zhang, Shan Qiao, Yuli Hou, Jing Liu, Yu Sun, Peichang Wang
Software Mentions: 4
Published: over 6 years ago

10.1016/j.ajhg.2016.05.030

BCL11A Haploinsufficiency Causes an Intellectual Disability Syndrome and Dysregulates Transcription
Cited by: 116
Author(s): Cristina Dias, Sara Busquets Estruch, Sarah A. Graham, Jeremy F. McRae, Stephen J. Sawiak, Jane A. Hurst, Shelagh Joss, Susan Holder, Jenny Morton, Claire Turner, Julien Thévenon, Kelly Mellul, Gabriela Sánchez-Andrade, Ximena Ibarra-Soria, Pelagia Derizioti, Rui F. Santos, Song-Choon Lee, Laurence Faivre, Tjitske Kleefstra, Pentao Liu, Mathew E. Hurles, Simon E. Fisher, Darren W. Logan
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pone.0168168

Vegetation Productivity in Natural vs. Cultivated Systems along Water Availability Gradients in the Dry Subtropics
Cited by: 4
Author(s): Germán Baldi, Marcos Texeira, Francisco Murray, Estéban G. Jobbágy
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0191822

Diagnostic performance of intravoxel incoherent motion diffusion-weighted imaging and dynamic contrast-enhanced MRI for assessment of anal fistula activity
Cited by: 7
Author(s): Philippe Lefrançois, Mathieu Zummo-Soucy, Damien Olivié, Jean-Sébastien Billiard, Guillaume Gilbert, Juliette Garel, E. Visée, Perrine Manchec, An Tang
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0133265

Can Static Habitat Protection Encompass Critical Areas for Highly Mobile Marine Top Predators? Insights from Coastal East Africa
Cited by: 30
Author(s): Sergi Pérez‐Jorge, Thalia Pereira, Chloe Corne, Zeno Wijtten, Mohamed Omar, Jillo Katello, Mark Kinyua, Daniel Oró, Maité Louzao
Software Mentions: 4
Published: about 11 years ago

10.1371/journal.pone.0258184

Modelling the impacts of climate change on thermal habitat suitability for shallow-water marine fish at a global scale
Cited by: 5
Author(s): Edward Lavender, Clive Fox, Michael T. Burrows
Software Mentions: 4
Published: almost 5 years ago

10.3390/ani9121063

Effect of Supplementing Hydrolysable Tannins to a Grower–Finisher Diet Containing Divergent PUFA Levels on Growth Performance, Boar Taint Levels in Back Fat and Intestinal Microbiota of Entire Males
Cited by: 24
Author(s): M. Tretola, Federica Maghin, Paolo Silacci, S. Ampuero, Giuseppe Bee
Software Mentions: 4
Published: over 6 years ago

10.3390/ani11061762

The Equine Faecal Microbiota of Healthy Horses and Ponies in The Netherlands: Impact of Host and Environmental Factors
Cited by: 17
Author(s): M. J. P. Theelen, Roosmarijn E C Luiken, Jaap A. Wagenaar, Marianne Sloet van Oldruitenborgh-Oosterbaan, John W. A. Rossen, Aldert Zomer
Software Mentions: 4
Published: about 5 years ago

10.1186/s42523-021-00076-6

Flexibility and resilience of great tit (Parus major) gut microbiomes to changing diets
Cited by: 23
Author(s): Kasun H. Bodawatta, Inga Freiberga, Kateřina Pužejová, Kateřina Sam, Michael Poulsen, Knud A. Jønsson
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2105-12-58

Taxon ordering in phylogenetic trees: a workbench test
Cited by: 4
Author(s): Francesco Cerutti, Luigi Bertolotti, Tony L. Goldberg, Mario Giacobini
Software Mentions: 4
Published: over 15 years ago

10.1371/journal.pone.0127292

Age Specific Survival Rates of Steller Sea Lions at Rookeries with Divergent Population Trends in the Russian Far East
Cited by: 17
Author(s): Alexey Altukhov, Russel D. Andrews, Donald G. Calkins, Thomas S. Gelatt, Eliezer Gurarie, Thomas R. Loughlin, Evgeny Mamaev, В. С. Никулин, Peter A. Permyakov, Sergey D. Ryazanov, Vladimir V. Vertyankin, Vladimir N. Burkanov
Software Mentions: 4
Published: about 11 years ago

10.1371/journal.pcbi.1006091

Divergent genome evolution caused by regional variation in DNA gain and loss between human and mouse
Cited by: 1
Author(s): R. Buckley, R. Daniel Kortschak, David L. Adelson
Software Mentions: 4
Published: over 8 years ago

10.1111/tgis.12657

CityJSON in QGIS: Development of an open‐source plugin
Cited by: 13
Author(s): Stelios Vitalis, Ken Arroyo Ohori, J.E. Stoter
Software Mentions: 4
Published: about 6 years ago

10.1007/s10461-020-02965-4

Combination HIV Prevention Strategies Among Montreal Gay, Bisexual, and Other Men Who Have Sex with Men in the PrEP Era: A Latent Class Analysis
Cited by: 16
Author(s): Carla M. Doyle, Mathieu Maheu‐Giroux, Gilles Lambert, Sharmistha Mishra, Herak Apelian, Marc Messier-Peet, Joanne Otis, Daniel Grace, Trevor A. Hart, David Moore, Nathan J. Lachowsky, Joseph Cox
Software Mentions: 4
Published: about 6 years ago

10.1534/genetics.119.302757

Historical Introgressions from a Wild Relative of Modern Cassava Improved Important Traits and May Be Under Balancing Selection
Cited by: 26
Author(s): Marnin D. Wolfe, Guillaume Bauchet, A. M. C. Chan, Roberto Lozano, Punna Ramu, Chiedozie Egesi, Robert Kawuki, Peter Kulakow, Ismail Rabbi, Jean‐Luc Jannink
Software Mentions: 4
Published: over 6 years ago

10.1186/s12889-019-7384-y

Global comparison of cancer outcomes: standardization and correlation with healthcare expenditures
Cited by: 10
Author(s): Hyun‐Seok Choi, Ka-On Lam, Herbert Pang, Steven K. C. Tsang, Roger K.C. Ngan, Anne W.M. Lee
Software Mentions: 4
Published: about 7 years ago

10.1186/s12859-018-2081-x

Control procedures and estimators of the false discovery rate and their application in low-dimensional settings: an empirical investigation
Cited by: 18
Author(s): Regina Brinster, Anna Köttgen, Bamidele O. Tayo, Martin Schumacher, Peggy Sekula
Software Mentions: 4
Published: over 8 years ago

10.26508/lsa.201900303

Rate of brain aging and <i>APOE ε4</i> are synergistic risk factors for Alzheimer’s disease
Cited by: 10
Author(s): Christin Glorioso, Andreas R. Pfenning, Sam S Lee, David A. Bennett, Etienne Sibille, M Kellis, Leonard Guarente
Software Mentions: 4
Published: about 7 years ago

10.1186/1755-8794-8-S2-S13

SeedsGraph: an efficient assembler for next-generation sequencing data
Cited by: 2
Author(s): Chuyu Wang, Maozu Guo, Xiaoyan Liu, Yang Liu, Quan Zou
Software Mentions: 4
Published: about 11 years ago

10.1007/s00253-019-09904-x

Effect of ethanol supplementation on the transcriptional landscape of bionanocellulose producer Komagataeibacter xylinus E25
Cited by: 30
Author(s): Małgorzata Ryngajłło, Paulina Jacek, Izabela Cielecka, Halina Kalinowska, Stanisław Bielecki
Software Mentions: 4
Published: about 7 years ago

10.3390/microorganisms9010030

New Insights into the Ecology and Physiology of Methanomassiliicoccales from Terrestrial and Aquatic Environments
Cited by: 17
Author(s): Marc Cozannet, Guillaume Borrel, Erwan G. Roussel, Yann Moalic, Maxime Allioux, Sanvoisin Amandine, Laurent Toffin, Karine Alain
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0253989

Evaluating extraction methods to study canine urine microbiota
Cited by: 7
Author(s): Ryan Mrofchak, Christopher Madden, Morgan V. Evans, Vanessa L. Hale
Software Mentions: 4
Published: about 5 years ago

10.1186/s12859-019-2623-x

MNEMONIC: MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations
Cited by: 2
Author(s): Aleksandra Perz, Cory B. Giles, Chase A. Brown, Hunter Porter, Xiavan Roopnarinesingh, Jonathan D. Wren
Software Mentions: 4
Published: over 7 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

10.1186/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

10.3389/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

10.1037/met0000337

Power contours: Optimising sample size and precision in experimental psychology and human neuroscience.
Cited by: 96
Author(s): Daniel H. Baker, Greta Vilidaitė, Freya Lygo, Anika Smith, Tessa R. Flack, André Gouws, Timothy J. Andrews
Software Mentions: 4
Published: about 5 years ago

10.1186/s12898-016-0104-x

A century of morphological variation in Cyprinidae fishes
Cited by: 19
Author(s): Stephen J. Jacquemin, Mark Pyron
Software Mentions: 4
Published: almost 10 years ago

10.1186/s12936-019-3038-x

Changing plasma cytokine, chemokine and growth factor profiles upon differing malaria transmission intensities
Cited by: 6
Author(s): Ruth Aguilar, Joseph J. Campo, Silvia Chicuecue, Pau Cisteró, Alba Català, Leopoldina Luís, Itziar Ubillos, Beatriz Galatas, Pedro Aíde, Caterina Guinovart, Gemma Moncunill, Carlota Dobaño
Software Mentions: 4
Published: over 6 years ago

10.1098/rsos.201717

Fertility and mortality impacts of thermal stress from experimental heatwaves on different life stages and their recovery in a model insect
Cited by: 43
Author(s): Kris Sales, Ramakrishnan Vasudeva, Matthew J. G. Gage
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2021.654657

Discovery and Verification of an Immune-Related Gene Pairs Signature for Predicting Prognosis in Head and Neck Squamous Cell Carcinoma
Cited by: 0
Author(s): Jiarong He, Xinqi Fang, Mingming Han
Software Mentions: 4
Published: about 5 years ago

10.3389/fpls.2020.555071

Inheritance of Rootstock Effects in Avocado (Persea americana Mill.) cv. Hass
Cited by: 19
Author(s): Paula H. Reyes-Herrera, Laura Muñoz-Baena, Valeria Velásquez-Zapata, Laura Patiño, Oscar A. Delgado-Paz, Cipriano A. Díaz-Diez, Alejandro A. Navas-Arboleda, Andrés J. Cortés
Software Mentions: 4
Published: over 5 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

10.1371/journal.pone.0014782

Genome-Wide Footprints of Pig Domestication and Selection Revealed through Massive Parallel Sequencing of Pooled DNA
Cited by: 122
Author(s): Andreia J. Amaral, Luca Ferretti, Hendrik‐Jan Megens, R.P.M.A. Crooijmans, Haisheng Nie, Sebastián E. Ramos-Onsins, Miguel Pérez‐Enciso, Lawrence B. Schook, Martien A. M. Groenen
Software Mentions: 4
Published: over 15 years ago

10.1371/journal.pbio.3000128

Genetic redundancy fuels polygenic adaptation in Drosophila
Cited by: 198
Author(s): Neda Barghi, Raymond Tobler, Viola Nolte, Ana Marija Jakšić, François Mallard, Kerstin Otte, Marlies Dolezal, Thomas Taus, Robert Kofler, Christian Schlötterer
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0250338

Die-off of plant pathogenic bacteria in tile drainage and anoxic water from a managed aquifer recharge site
Cited by: 5
Author(s): Carina Eisfeld, J.M. van der Wolf, Boris M. van Breukelen, Gertjan Medema, J. Velstra, Jack Schijven
Software Mentions: 4
Published: over 5 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/s12859-017-1586-z

MOST: most-similar ligand based approach to target prediction
Cited by: 25
Author(s): Tao Huang, Hong Mi, Chengyuan Lin, Ling Zhao, Linda L. D. Zhong, Fengbin Liu, Ge Zhang, Aiping Lu, Zhaoxiang Bian
Software Mentions: 4
Published: over 9 years ago

10.3390/microorganisms9020357

Soil Bacterial Diversity Is Positively Correlated with Decomposition Rates during Early Phases of Maize Litter Decomposition
Cited by: 18
Author(s): Akane Chiba, Yoshitaka Uchida, Susanne Kublik, Gisle Vestergaard, Franz Buegger, Michael Schloter, Stefanie Schulz
Software Mentions: 4
Published: over 5 years ago

10.1186/s12915-019-0626-8

Transcriptome, proteome and draft genome of Euglena gracilis
Cited by: 88
Author(s): ThankGod Echezona Ebenezer, Martin Zoltner, Alana Burrell, Anna Nenarokova, Anna M. G. Novák Vanclová, Binod Prasad, Petr Soukal, Carlos Santana-Molina, Ellis C. O’Neill, Nerissa N. Nankissoor, Nithya Vadakedath, Viktor Daiker, Samson O. Obado, Sara Silva Pereira, Andrew P. Jackson, Damien P. Devos, Julius Lukeš, Michael Lebert, Sue Vaughan, Vladimı́r Hampl, Mark Carrington, Michael L. Ginger, Joel B. Dacks, Steven L. Kelly, Mark C. Field
Software Mentions: 4
Published: over 7 years ago

10.1186/s12915-021-01104-2

A novel plant-fungal association reveals fundamental sRNA and gene expression reprogramming at the onset of symbiosis
Cited by: 7
Author(s): Ena Šečić, Silvia Zanini, Daniel Wibberg, Lukas Jelonek, Tobias Busche, Jörn Kalinowski, Sabrine Nasfi, Jennifer Thielmann, Jafargholi Imani, Jens Steinbrenner, Karl‐Heinz Kogel
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12915-020-00779-3

Mapping DNA interaction landscapes in psoriasis susceptibility loci highlights KLF4 as a target gene in 9q31
Cited by: 15
Author(s): Helen Ray-Jones, Kate Duffus, Amanda McGovern, Paul Martin, Chenfu Shi, Jenny Hankinson, Oliver Gough, Annie Yarwood, Andrew P. Morris, Antony Adamson, Craig Taylor, Julia Ding, Vasanthi Priyadarshini Gaddi, Yao Fu, Patrick M. Gaffney, Gisela Orozco, Richard B Warren, Steve Eyre
Software Mentions: 4
Published: over 6 years ago

10.1186/s12915-017-0352-z

The landscape of sex-differential transcriptome and its consequent selection in human adults
Cited by: 180
Author(s): Moran Gershoni, Shmuel Pietrokovski
Software Mentions: 4
Published: over 9 years ago

10.1186/s12870-020-02706-8

Molecular insights into the compatible and incompatible interactions between sugar beet and the beet cyst nematode
Cited by: 19
Author(s): Razieh Ghaemi, Ebrahim Pourjam, Naser Safaie, Bruno Verstraeten, S B Mahmoudi, Rahim Mehrabi, Tim De Meyer, Tina Kyndt
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12913-018-3345-x

A hospital-wide evaluation of delirium prevalence and outcomes in acute care patients - a cohort study
Cited by: 108
Author(s): Maria Schubert, Roger Schürch, Soenke Böettger, David Garcia Nuñez, Urs Schwarz, Dominique Béttex, Josef Jenewein, Jasmina Bogdanović, Marina Lynne Staehli, Rebecca Spirig, Alain Rudiger
Software Mentions: 4
Published: about 8 years ago

10.1186/1752-0509-5-1

Metabolomic correlation-network modules in Arabidopsis based on a graph-clustering approach
Cited by: 118
Author(s): Atsushi Fukushima, Miyako Kusano, Henning Redestig, Masanori Arita, Kazuki Saito
Software Mentions: 4
Published: over 15 years ago

10.1186/s12885-021-08218-4

MACE-Seq-based coding RNA and TrueQuant-based small RNA profile in breast cancer: tumor-suppressive miRNA-1275 identified as a novel marker
Cited by: 5
Author(s): Sevan Omer Majed, Suhad Asad Mustafa
Software Mentions: 4
Published: over 5 years ago

10.1007/s00442-019-04576-w

Seasonal variation in exploitative competition between honeybees and bumblebees
Cited by: 26
Author(s): Veronica R. Wignall, Isabella Campbell Harry, Natasha L. Davies, Stephen D. Kenny, Jack K. McMinn, Francis L. W. Ratnieks
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-016-2888-7

Comparison of pre-processing methods for multiplex bead-based immunoassays
Cited by: 13
Author(s): Tanja K. Rausch, Arne Schillert, Andreas Ziegler, Angelika Lüking, Hans‐Dieter Zucht, Peter Schulz‐Knappe
Software Mentions: 4
Published: about 10 years ago

10.1186/s12885-020-07513-w

Ovarian cancer cells direct monocyte differentiation through a non-canonical pathway
Cited by: 5
Author(s): Kaitlin C. Fogg, Andrew Miller, Ying Liu, Will Flanigan, Alyssa Walker, Amy O'Shea, Christina Kendziorski, Pamela K. Kreeger
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pgen.1008518

Sex biased expression and co-expression networks in development, using the hymenopteran Nasonia vitripennis
Cited by: 10
Author(s): Alfredo Rago, John H. Werren, John K. Colbourne
Software Mentions: 4
Published: over 6 years ago

10.1186/gb-2014-15-1-r7

RIP-seq analysis of eukaryotic Sm proteins identifies three major categories of Sm-containing ribonucleoproteins
Cited by: 32
Author(s): Zhipeng Lu, Xiaojun Guan, Casey A. Schmidt, A. Gregory Matera
Software Mentions: 4
Published: over 12 years ago

10.1016/j.cell.2018.03.043

Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal
Cited by: 436
Author(s): Samra Turajlic, Hang Xu, Kevin Litchfield, Andrew Rowan, Stuart Horswell, Tim Chambers, Tim O’Brien, José I. López, Thomas B.K. Watkins, David Nicol, Mark Stares, Ben Challacombe, Steve Hazell, Ashish Chandra, Thomas J. Mitchell, Lewis Au, Claudia Eichler-Jonsson, Faiz Jabbar, Aspasia Soultati, Simon Chowdhury, Sarah Rudman, Joanna Lynch, A. Fernando, Gordon Stamp, Emma Nye, Aengus Stewart, Xing Wei, Jonathan C. Smith, Mickael Escudero, Adam Huffman, Nik Matthews, Greg Elgar, Ben Phillimore, Marta Costa, Sharmin Begum, Sophia Ward, Max Salm, Stefan Boeing, Rosalie Fisher, Lavinia Spain, Carolina Navas, Eva Grönroos, Sebastijan Hobor, Sarkhara Sharma, Ismaeel Aurangzeb, Sharanpreet Lall, Alexander Polson, Mary Varia, Catherine Horsfield, Nicos Fotiadis, Lisa Pickering, Roland F. Schwarz, Bruno Silva, Javier Herrero, Nick M. Luscombe, Mariam Jamal‐Hanjani, Rachel Rosenthal, Nicolai J. Birkbak, Gareth A. Wilson, Orsolya Pipek, Dezső Ribli, Marcin Krzystanek, István Csabai, Zoltan Szállási, Martin Gore, Nicholas McGranahan, Peter Van Loo, Peter J. Campbell, James Larkin, Charles Swanton
Software Mentions: 4
Published: over 8 years ago

10.3390/ijerph15102144

Neighborhood Violence Impacts Disease Control and Surveillance: Case Study of Cali, Colombia from 2014 to 2016
Cited by: 6
Author(s): Amy R. Krystosik, Andrew Curtis, A. Desirée LaBeaud, Diana Dávalos, Robinson Pacheco, Paola Buritica, Álvaro Álvarez, Madhav P. Bhatta, Jorge Humberto Rojas Palacios, Mark A. James
Software Mentions: 4
Published: almost 8 years ago

10.1098/rsif.2019.0080

Improved forecasts of influenza-associated hospitalization rates with Google Search Trends
Cited by: 14
Author(s): Sasikiran Kandula, Sen Pei, Jeffrey Shaman
Software Mentions: 4
Published: about 7 years ago

10.1186/s12864-016-3130-3

Differential gene expression in Varroa jacobsoni mites following a host shift to European honey bees (Apis mellifera)
Cited by: 15
Author(s): Gladys K. Andino, Michael Gribskov, Denis L. Anderson, Jay D. Evans, Greg J. Hunt
Software Mentions: 4
Published: over 9 years ago

10.3390/ijms22094864

Characterization of Extracellular Vesicle Cargo in Sjögren’s Syndrome through a SWATH-MS Proteomics Approach
Cited by: 11
Author(s): Francesco Finamore, Antonella Cecchettini, Elisa Ceccherini, Giovanni Signore, Francesco Ferro, Silvia Rocchiccioli, Chiara Baldini
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0238124

Elderly patients with cancer admitted to intensive care unit: A multicenter study in a middle-income country
Cited by: 0
Author(s): Antônio Paulo Nassar, Mariane da Silva Trevisani, Bárbara Beltrame Bettim, Fernando G. Zampieri, José Albani Carvalho, Amílton Silva, Flávio Geraldo Rezende Freitas, José Roberto Aparecido dos Santos Pinto, Edson Romano, Sílvia Regina Ramos, Guilherme Brenande Alves Faria, Ulysses V. Andrade e Silva, Robson Correa Santos, Edmundo de Oliveira Tommasi, Ana Paula Pierre de Moraes, Bruno Azevedo da Cruz, Fernando A. Bozza, Pedro Caruso, Jorge I. Salluh, Márcio Soares
Software Mentions: 4
Published: almost 6 years ago

10.3390/cancers12123786

Stroma Transcriptomic and Proteomic Profile of Prostate Cancer Metastasis Xenograft Models Reveals Prognostic Value of Stroma Signatures
Cited by: 9
Author(s): Sofia Karkampouna, Maria Rosaria De Filippo, Charlotte K.Y. Ng, Irena Klima, Eugenio Zoni, Martin Spahn, Frank Stein, Per Haberkant, George N. Thalmann, Marianna Kruithof-de Julio
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-020-06899-y

The wheat pathogen Zymoseptoria tritici senses and responds to different wavelengths of light
Cited by: 7
Author(s): Cassandra B. McCorison, Stephen B. Goodwin
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-016-2801-4

RNA-Seq analysis of Gtf2ird1 knockout epidermal tissue provides potential insights into molecular mechanisms underpinning Williams-Beuren syndrome
Cited by: 8
Author(s): Susan M. Corley, Cesar P Canales, Paulina Carmona-Mora, Veronica Mendoza-Reinosa, Annemiek Beverdam, Edna C. Hardeman, Marc R. Wilkins, Steve Palmer
Software Mentions: 4
Published: about 10 years ago

10.3389/fonc.2021.683282

Development of Nomograms for Predicting Lymph Node Metastasis and Distant Metastasis in Newly Diagnosed T1-2 Non-Small Cell Lung Cancer: A Population-Based Analysis
Cited by: 7
Author(s): Yihong Qi, Shuangshuang Wu, Linghui Tao, Yunfu Shi, Wenjuan Yang, Lina Zhou, Bo Zhang, Jing Li
Software Mentions: 4
Published: almost 5 years ago

10.1186/1471-2164-11-74

Automated design of genomic Southern blot probes
Cited by: 6
Author(s): Mike D. R. Croning, David Fricker, Noboru H. Komiyama, Seth G. N. Grant
Software Mentions: 4
Published: over 16 years ago

10.1186/s12893-020-01033-x

Prognostic factors in patients who underwent surgery for common peroneal nerve injury: a nest case–control study
Cited by: 2
Author(s): Zhenhui Liu, Maimaiaili Yushan, Yanshi Liu, Aihemaitijiang Yusufu
Software Mentions: 4
Published: over 5 years ago

10.1097/MD.0000000000021087

Moxibustion for the side effects of surgical therapy and chemotherapy in patients with gastric cancer
Cited by: 5
Author(s): Shuqing Liu, Jianrong Chen, Yanping Wang, Xu Zhou, Weifeng Zhu
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0252533

Large scale meta-analysis of preclinical toxicity data for target characterisation and hypotheses generation
Cited by: 2
Author(s): Jordi Muñoz‐Muriedas
Software Mentions: 4
Published: about 5 years ago

10.3390/cells10051163

Anthracyclins Increase PUFAs: Potential Implications in ER Stress and Cell Death
Cited by: 9
Author(s): David Balgoma, Fredrik Kullenberg, Carlemi Calitz, Maria Kopsida, Femke Heindryckx, Hans Lennernäs, Mikael Hedeland
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2021.736573

Development and Validation of a Clinical Prognostic Nomogram for Esophageal Adenocarcinoma Patients
Cited by: 11
Author(s): Chengchen Shao, Yue Yu, Qi-fan Li, Xiaolong Liu, Haiyan Song, Yi Shen, Jun Yi
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12864-019-6018-1

Transcriptome profile of Corynebacterium pseudotuberculosis in response to iron limitation
Cited by: 19
Author(s): Izabela Coimbra Ibraim, Mariana Teixeira Dornelles Parise, Doglas Parise, Michelle Zibetti Tadra Sfeir, Thiago Luiz de Paula Castro, Alice R. Wattam, Preetam Ghosh, Debmalya Barh, Emannuel Maltempi Souza, Aristóteles Goés-Neto, Anne Cybelle Pinto Gomide, Vasco Azevedo
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-021-83922-6

Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences
Cited by: 47
Author(s): Anna Paola Carrieri, Niina Haiminen, Sean Maudsley-Barton, Laura‐Jayne Gardiner, Barry Murphy, Andrew E. Mayes, Sarah Paterson, Sally Grimshaw, Martyn Winn, Cameron Shand, Panagiotis E. Hadjidoukas, Will Rowe, Stacy S. Hawkins, Ashley MacGuire-Flanagan, Jane Tazzioli, John Kenny, Laxmi Parida, Michael Hoptroff, Edward O. Pyzer‐Knapp
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-019-6147-6

The role of nitric oxide during embryonic wound healing
Cited by: 16
Author(s): Pavel Abaffy, Silvie Tománková, Ravindra Naraine, Mikael Kubista, Radek Šindelka
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12864-020-06871-w

Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria
Cited by: 29
Author(s): Alice Feurtey, Cécile Lorrain, Daniel Croll, Christoph Eschenbrenner, Michael Freitag, Michael Habig, Janine Haueisen, Mareike Möller, Klaas Schotanus, Eva H. Stukenbrock
Software Mentions: 4
Published: almost 6 years ago

10.1186/s40709-020-00118-1

Genome wide meta-analysis of cDNA datasets reveals new target gene signatures of colorectal cancer based on systems biology approach
Cited by: 11
Author(s): Umair Ilyas, Shahiq uz Zaman, Reem Altaf, Humaira Nadeem, Syed Aun Muhammad
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pgen.1008830

Zebrafish rbm8a and magoh mutants reveal EJC developmental functions and new 3′UTR intron-containing NMD targets
Cited by: 18
Author(s): Pooja Gangras, Thomas L. Gallagher, Michael A. Parthun, Zhongxia Yi, Robert D. Patton, Kiel T. Tietz, Natalie C. Deans, Ralf Bundschuh, Sharon L. Amacher, Guramrit Singh
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-017-4362-6

Comparative ribosome profiling uncovers a dominant role for translational control in Toxoplasma gondii
Cited by: 20
Author(s): Musa A. Hassan, Juan J. Vasquez, Guo-Liang Chew, Markus Meissner, T. Nicolai Siegel
Software Mentions: 4
Published: over 8 years ago

10.3389/fneur.2020.00370

Dopamine Buffering Capacity Imaging: A Pharmacodynamic fMRI Method for Staging Parkinson Disease
Cited by: 5
Author(s): Kevin J. Black, Haley Acevedo, Jonathan M. Koller
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-65638-1

Genomic analyses of early responses to radiation in glioblastoma reveal new alterations at transcription, splicing, and translation levels
Cited by: 11
Author(s): Saket Choudhary, Suzanne Perea Burns, Hoda Mirsafian, Wenzheng Li, Dat T. Vo, Mu Qiao, Xiufen Lei, Andrew D. Smith, Luiz O. F. Penalva
Software Mentions: 4
Published: about 6 years ago