Ecosyste.ms: Papers

10.3390/biom11010040

From Prevention to Disease Perturbations: A Multi-Omic Assessment of Exercise and Myocardial Infarctions
Cited by: 6
Author(s): Melanie T. Odenkirk, Kelly G. Stratton, Lisa Bramer, Bobbie‐Jo Webb‐Robertson, Kent Bloodsworth, Matthew E. Monroe, Kristin Burnum-Johnson, Erin Baker
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0146447

Transcriptome Analysis of Honeybee (Apis Mellifera) Haploid and Diploid Embryos Reveals Early Zygotic Transcription during Cleavage
Cited by: 30
Author(s): Camilla Valente Pires, Flávia Cristina de Paula Freitas, Alexandre S. Cristino, Peter K. Dearden, Zilá Luz Paulino Simões
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0033933

Identification of Early Zygotic Genes in the Yellow Fever Mosquito Aedes aegypti and Discovery of a Motif Involved in Early Zygotic Genome Activation
Cited by: 46
Author(s): James K. Biedler, Wanqi Hu, Hongseok Tae, Zhijian Tu
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pone.0053085

The Transcriptional and Gene Regulatory Network of Lactococcus lactis MG1363 during Growth in Milk
Cited by: 23
Author(s): Anne de Jong, Morten Ejby, Oscar P. Kuipers, Mogens Kilstrup, Jan Kok
Software Mentions: 3
Published: over 11 years ago

10.1038/s41598-020-76599-w

Integrating single-cell RNA-seq and imaging with SCOPE-seq2
Cited by: 15
Author(s): Zhouzerui Liu, Jinzhou Yuan, Anna Lasorella, Antonio Iavarone, Jeffrey N. Bruce, Peter Canoll, Peter A. Sims
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0020924

The Reconstruction of Condition-Specific Transcriptional Modules Provides New Insights in the Evolution of Yeast AP-1 Proteins
Cited by: 17
Author(s): Christel Goudot, Catherine Etchebest, Frédéric Devaux, Gaëlle Lelandais
Software Mentions: 3
Published: over 13 years ago

10.3389/fpls.2014.00652

Genome wide transcriptome analysis reveals ABA mediated response in Arabidopsis during gold (AuCl−4) treatment
Cited by: 34
Author(s): Devesh Shukla, Sneha Krishnamurthy, Shivendra V. Sahi
Software Mentions: 3
Published: almost 10 years ago

10.1186/1471-2164-14-216

CAMTA 1 regulates drought responses in Arabidopsis thaliana
Cited by: 136
Author(s): Neha Pandey, Alok Ranjan, Poonam Pant, Rajiv Kumar Tripathi, Farha Ateek, Haushilla P Pandey, Uday V Patre, Samir V. Sawant
Software Mentions: 2
Published: over 11 years ago

10.1155/2014/232419

Spontaneous Ad Hoc Mobile Cloud Computing Network
Cited by: 23
Author(s): Raquel Lacuesta, Jaime Lloret, Sandra Sendra, Lourdes Peñalver
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0059851

Computational Discovery of Transcriptional Regulatory Modules in Fungal Ribosome Biogenesis Genes Reveals Novel Sequence and Function Patterns
Cited by: 0
Author(s): Viktor Martyanov, Robert Gross
Software Mentions: 2
Published: over 11 years ago

10.1534/g3.116.035402

Alternative Oxidase Transcription Factors AOD2 and AOD5 of<i>Neurospora crassa</i>Control the Expression of Genes Involved in Energy Production and Metabolism
Cited by: 6
Author(s): Zhigang Qi, Kristina M. Smith, Erin L. Bredeweg, Natasa Bosnjak, Michael Freitag, Frank E. Nargang
Software Mentions: 2
Published: over 7 years ago

10.3390/s18092994

Urban Planning and Smart City Decision Management Empowered by Real-Time Data Processing Using Big Data Analytics
Cited by: 78
Author(s): Bhagya Nathali Silva, Murad Khan, Changsu Jung, Jihun Seo, Muhammad Diyan, Jing Han, Yongtak Yoon, Kijun Han
Software Mentions: 2
Published: about 6 years ago

10.1038/s42003-020-1044-8

Single-cell sequencing of genomic DNA resolves sub-clonal heterogeneity in a melanoma cell line
Cited by: 31
Author(s): Enrique I. Velazquez-Villarreal, Shamoni Maheshwari, Jon M. Sorenson, Ian T. Fiddes, Vijay Kumar, Yifeng Yin, Michelle G. Webb, Claudia Catalanotti, M. Grigorova, Paul A.W. Edwards, John D. Carpten, David W. Craig
Software Mentions: 2
Published: over 4 years ago

10.7717/peerj.2843

A gene expression study of dorso-ventrally restricted pigment pattern in adult fins of<i>Neolamprologus meeli</i>, an African cichlid species
Cited by: 26
Author(s): Ehsan Pashay Ahi, Kristina M. Sefc
Software Mentions: 2
Published: over 7 years ago

10.1186/2041-9139-5-40

Transcriptional dynamics of a conserved gene expression network associated with craniofacial divergence in Arctic charr
Cited by: 37
Author(s): Ehsan Pashay Ahi, Kalina H. Kapralova, Arnar Pálsson, Valerie H. Maier, Jóhannes Guðbrandsson, Sigurður S. Snorrason, Zophonı́as O. Jónsson, Sigríður Rut Franzdóttir
Software Mentions: 2
Published: almost 10 years ago

10.12688/f1000research.9093.1

Cluster analysis of Plasmodium RNA-seq time-course data identifies stage-specific co-regulated biological processes and regulatory elements
Cited by: 1
Author(s): Efejiro Ashano, Itunuoluwa Isewon, Jelili Oyelade, Ezekiel Adebiyi
Software Mentions: 2
Published: about 8 years ago

10.1186/1471-2164-12-82

RNA-seq analyses of blood-induced changes in gene expression in the mosquito vector species, Aedes aegypti
Cited by: 124
Author(s): Mariangela Bonizzoni, William A. Dunn, Corey L. Campbell, Ken E. Olson, Michelle Dimon, Osvaldo Marinotti, Anthony A. James
Software Mentions: 2
Published: over 13 years ago

10.7554/eLife.00473

Accurate timekeeping is controlled by a cycling activator in Arabidopsis
Cited by: 160
Author(s): Polly Yingshan Hsu, Upendra Kumar Devisetty, Stacey L. Harmer
Software Mentions: 2
Published: over 11 years ago

10.1038/srep14392

Expression profile of a Caenorhabditis elegans model of adult neuronal ceroid lipofuscinosis reveals down regulation of ubiquitin E3 ligase components
Cited by: 7
Author(s): Hannah V. McCue, Xi Chen, Jeff W. Barclay, Alan Morgan, Robert D. Burgoyne
Software Mentions: 2
Published: about 9 years ago

10.1186/1471-2105-8-102

SAMPI: Protein Identification with Mass Spectra Alignments
Cited by: 6
Author(s): Hans‐Michael Kaltenbach, Andreas Wilke, Sebastian Böcker
Software Mentions: 2
Published: over 17 years ago

10.1186/s13024-015-0046-3

Ethosuximide ameliorates neurodegenerative disease phenotypes by modulating DAF-16/FOXO target gene expression
Cited by: 26
Author(s): Xi Chen, Hannah V. McCue, Shi Quan Wong, Sudhanva S. Kashyap, Brian C. Kraemer, Jeff W. Barclay, Robert D. Burgoyne, Alan Morgan
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.ppat.1002485

The bZIP Transcription Factor Rca1p Is a Central Regulator of a Novel CO2 Sensing Pathway in Yeast
Cited by: 44
Author(s): Fabien Cottier, Martine Raymond, Oliver Kurzai, M. Bolstad, Worraanong Leewattanapasuk, Claudia Jiménez-López, Michael Lorenz, Dominique Sanglard, Libuše Váchová, Norman Pavelka, Zdena Palková, Fritz A. Mühlschlegel
Software Mentions: 1
Published: over 12 years ago

10.1038/srep17998

The Cerato-Platanin protein Epl-1 from Trichoderma harzianum is involved in mycoparasitism, plant resistance induction and self cell wall protection
Cited by: 72
Author(s): Eriston Vieira Gomes, Mariana do Nascimento Costa, Renato Graciano de Paula, Rafael Ricci de Azevedo, Francilene Lopes da Silva, Eliane Ferreira Noronha, Cirano José Ulhôa, Valdirene Neves Monteiro, Rosa E. Cardoza, Santiago Gutiérrez, Roberto Nascimento Silva
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-018-32602-z

Sun-induced fluorescence and gross primary productivity during a heat wave
Cited by: 81
Author(s): Georg Wohlfahrt, Katharina Gerdel, Mirco Migliavacca, Eyal Rotenberg, Fyodor Tatarinov, Jonathan Müller, Albin Hammerle, Tommaso Julitta, Felix M. Spielmann, Dan Yakir
Software Mentions: 1
Published: about 6 years ago

10.3390/s16040480

Investigation of Atmospheric Effects on Retrieval of Sun-Induced Fluorescence Using Hyperspectral Imagery
Cited by: 8
Author(s): Zhuoya Ni, Zhigang Liu, Zhao Liang Li, Françoise Nerry, Hongyuan Huo, Rui Sun, Peiqi Yang, Weiwei Zhang
Software Mentions: 1
Published: over 8 years ago

10.3390/s17051131

Modeling the Footprint and Equivalent Radiance Transfer Path Length for Tower-Based Hemispherical Observations of Chlorophyll Fluorescence
Cited by: 20
Author(s): Xinjie Liu, Liangyun Liu, Jian Hu, Shanshan Du
Software Mentions: 1
Published: over 7 years ago

10.3390/s19133000

Estimation of Chlorophyll Fluorescence at Different Scales: A Review
Cited by: 31
Author(s): Zhuoya Ni, Qifeng Lu, Hongyuan Huo, Huili Zhang
Software Mentions: 1
Published: over 5 years ago

10.3390/s20030815

The Solar-Induced Chlorophyll Fluorescence Imaging Spectrometer (SIFIS) Onboard the First Terrestrial Ecosystem Carbon Inventory Satellite (TECIS-1): Specifications and Prospects
Cited by: 10
Author(s): Shanshan Du, Liangyun Liu, Xinjie Liu, Xinwei Zhang, Xianlian Gao, Weigang Wang
Software Mentions: 1
Published: over 4 years ago

10.3390/s21103482

Optimizing the Empirical Parameters of the Data-Driven Algorithm for SIF Retrieval for SIFIS Onboard TECIS-1 Satellite
Cited by: 3
Author(s): Chu Zou, Shanshan Du, Xinjie Liu, Liangyun Liu, Yuyang Wang, Zhen Li
Software Mentions: 1
Published: over 3 years ago

10.3390/s21144886

Retrieving Sun-Induced Chlorophyll Fluorescence from Hyperspectral Data with TanSat Satellite
Cited by: 3
Author(s): Shilei Li, Maofang Gao, Zhao-Liang Li
Software Mentions: 1
Published: about 3 years ago

10.1155/2012/320648

The Association between Hypertension and Dementia in the Elderly
Cited by: 44
Author(s): Michiya Igase, Katsuhiko Kohara, Tetsuro Miki
Software Mentions: 1
Published: almost 13 years ago

10.7554/eLife.18981

Transcriptional rewiring over evolutionary timescales changes quantitative and qualitative properties of gene expression
Cited by: 47
Author(s): Chiraj K. Dalal, Ignacio A. Zuleta, Kaitlin Mitchell, David R. Andes, Hana El-Samad, Alexander D. Johnson
Software Mentions: 1
Published: about 8 years ago

10.7554/eLife.14679

Long-range population dynamics of anatomically defined neocortical networks
Cited by: 96
Author(s): Jerry L. Chen, Fabian F. Voigt, Mitra Javadzadeh, Roland Krueppel, Fritjof Helmchen
Software Mentions: 1
Published: over 8 years ago

10.1186/ar2550

Therapeutic efficacy of intra-articular adrenomedullin injection in antigen-induced arthritis in rabbits
Cited by: 19
Author(s): Toshiyuki Okura, Kousuke Marutsuka, Hirofumi Hamada, Tomohisa Sekimoto, Tsuyoshi Fukushima, Yujiro Asada, Kazuo Kïtamura, Etsuo Chosa
Software Mentions: 1
Published: almost 17 years ago

10.1186/s11689-016-9158-5

Neural correlates of reward processing in adults with 22q11 deletion syndrome
Cited by: 13
Author(s): Esther D.A. van Duin, Liesbet Goossens, Dennis Hernaus, Fabiana da Silva Alves, Nicole Schmitz, Koen Schruers, Thérèse van Amelsvoort
Software Mentions: 1
Published: about 8 years ago

10.1186/ar1980

Inhibitory effect of ribbon-type NF-κB decoy oligodeoxynucleotides on osteoclast induction and activity in vitro and in vivo
Cited by: 19
Author(s): Yasuo Kunugiza, Tadanori Tomita, Naruya Tomita, Ryuichi Morishita, Hideki Yoshikawa
Software Mentions: 1
Published: almost 19 years ago

10.1186/s12859-015-0540-1

OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction
Cited by: 13
Author(s): Yaojun Wang, Fei Yang, Pei-Ming Wu, Dongbo Bu, Shiwei Sun
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2105-8-249

A novel ensemble learning method for de novo computational identification of DNA binding sites
Cited by: 46
Author(s): Arijit Chakravarty, Jonathan M. Carlson, Radhika S. Khetani, Robert Gross
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2105-13-S3-S3

Algorithms for optimizing cross-overs in DNA shuffling
Cited by: 7
Author(s): Lu He, Alan M. Friedman, Chris Bailey‐Kellogg
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2105-12-346

ProbPS: A new model for peak selection based on quantifying the dependence of the existence of derivative peaks on primary ion intensity
Cited by: 3
Author(s): Shenghui Zhang, Yaojun Wang, Dongbo Bu, Hong Zhang, Shiwei Sun
Software Mentions: 1
Published: about 13 years ago

10.1186/s12877-019-1277-x

Theory and Design of the Community for successful ageing (ComSA) program in Singapore: connecting BioPsychoSocial health and quality of life experiences of older adults
Cited by: 6
Author(s): Su Aw, Gerald Choon‐Huat Koh, Chuen Seng Tan, Mee Lian Wong, Hubertus J. M. Vrijhoef, Susana Concordo Harding, Mary Ann B. Geronimo, Zoe Hildon
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12916-020-01766-9

External validation of prognostic models predicting pre-eclampsia: individual participant data meta-analysis
Cited by: 11
Author(s): Kym I E Snell, John Allotey, Melanie Smuk, Richard Hooper, Calvin M. L. Chan, Asif Ahmed, Lucy C Chappell, Peter von Dadelszen, Marcus Green, Louise C. Kenny, Asma Khalil, Khalid S. Khan, Ben W. Mol, Jenny Myers, Lucilla Poston, B. Thilaganathan, Annetine Staff, Gordon C. S. Smith, Wessel Ganzevoort, Hannele Laivuori, Anthony O. Odibo, J. Arenas Ramírez, John Kingdom, G. Daskalakis, Diane Farrar, Ahmet Baschat, Paul Seed, Federico Prefumo, Fabrício da Silva Costa, Henk Groen, François Audibert, Jacques Massé, Ragnhild Bergene Skråstad, Kjell Å. Salvesen, Camilla Haavaldsen, Chie Nagata, Alice Rumbold, Seppo Heinonen, Lisa Askie, Luc Smits, Christina Anne Vinter, Per Magnus, Eero Kajantie, Pia Villa, Anne Karen Jenum, Louise Bjørkholt Andersen, Jane E. Norman, Akihide Ohkuchi, Anne Eskild, Sohinee Bhattacharya, Fionnuala M. McAuliffe, Alberto Galindo, Ignacio Herraı̀z, Lionel Carbillon, Kerstin Klipstein‐Grobusch, SeonAe Yeo, Joyce L. Browne, Karel G.M. Moons, Richard D Riley, Shakila Thangaratinam
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12888-020-02569-1

Assessing vulnerability to risk of suicide and self-harm in prisoners: a Rasch analysis of the suicide concerns for offenders in the prison environment (SCOPE-2)
Cited by: 3
Author(s): Amanda Perry, Mike Horton
Software Mentions: 1
Published: over 4 years ago

10.3390/molecules23081904

Permeability of Ciprofloxacin-Loaded Polymeric Micelles Including Ginsenoside as P-glycoprotein Inhibitor through a Caco-2 Cells Monolayer as an Intestinal Absorption Model
Cited by: 18
Author(s): Behzad Sharif Makhmalzadeh, Golbarg Esfahani, Anayatollah Salimi
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pgen.1002770

Genome-Wide Location Analysis Reveals Distinct Transcriptional Circuitry by Paralogous Regulators Foxa1 and Foxa2
Cited by: 45
Author(s): Irina M. Bochkis, Jonathan Schug, Diana Z. Ye, Svitlana Kurinna, Sabrina A. Stratton, Michelle C. Barton, Klaus H. Kaestner
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0006390

Bat Eyes Have Ultraviolet-Sensitive Cone Photoreceptors
Cited by: 88
Author(s): Brigitte Müller, Martin Glösmann, Leo Peichl, Gabriel Knop, Cornelia Hagemann, Josef Ammermüller
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0179460

An R-CaMP1.07 reporter mouse for cell-type-specific expression of a sensitive red fluorescent calcium indicator
Cited by: 45
Author(s): Philipp Bethge, Stefano Carta, Dayra A. Lorenzo, Ladan Egolf, Despoina Goniotaki, Linda Madisen, Fabian F. Voigt, Jerry L. Chen, Bernard L. Schneider, Masamichi Ohkura, Junichi Nakai, Hongkui Zeng, Adriano Aguzzi, Fritjof Helmchen
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0048176

In Vitro Site Selection of a Consensus Binding Site for the Drosophila melanogaster Tbx20 Homolog Midline
Cited by: 7
Author(s): Nima Najand, Jae-Ryeon Ryu, William J. Brook
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0104072

Extensive Transcription Analysis of the Hyposoter didymator Ichnovirus Genome in Permissive and Non-Permissive Lepidopteran Host Species
Cited by: 24
Author(s): Tristan Dorémus, Clément François, Gábor Gyapay, Véronique Jouan, Patrícia Milano, Éric Wajnberg, Isabelle Darboux, Fernando L. Cônsoli, Anne Nathalie Volkoff
Software Mentions: 1
Published: about 10 years ago

10.1080/10717544.2018.1451934

Transcriptional control of the MUC16 promoter facilitates follicle-stimulating hormone peptide-conjugated shRNA nanoparticle-mediated inhibition of ovarian carcinoma <i>in vivo</i>
Cited by: 9
Author(s): Mingxing Zhang, Shanshan Hong, Qingqing Cai, Meng Zhang, Jun Chen, Xiaoyan Zhang, Congjian Xu
Software Mentions: 1
Published: almost 7 years ago

10.3389/fmicb.2015.00184

A new high-performance heterologous fungal expression system based on regulatory elements from the Aspergillus terreus terrein gene cluster
Cited by: 65
Author(s): Markus Gressler, Peter Hortschansky, Elena Geib, Matthias Brock
Software Mentions: 1
Published: over 9 years ago

10.3389/fonc.2017.00231

Bridge-Induced Translocation between NUP145 and TOP2 Yeast Genes Models the Genetic Fusion between the Human Orthologs Associated With Acute Myeloid Leukemia
Cited by: 3
Author(s): Valentina Tosato, Nicole West, Jan Zrimec, Dmitri Nikitin, Giannino Del Sal, Roberto B. M. Marano, Michael Breitenbach, Carlo V. Bruschi
Software Mentions: 1
Published: about 7 years ago

10.3389/frobt.2021.735566

A Digital Twin Approach for Contextual Assistance for Surgeons During Surgical Robotics Training
Cited by: 7
Author(s): Katharina Hagmann, Anja Hellings-Kuß, Julian Klodmann, Rebecca Richter, Freek Stulp, Daniel Leidner
Software Mentions: 1
Published: about 3 years ago

10.1186/s13012-019-0959-2

Sustainment, Sustainability, and Spread Study (SSaSSy): protocol for a study of factors that contribute to the sustainment, sustainability, and spread of practice changes introduced through an evidence-based quality-improvement intervention in Canadian nursing homes
Cited by: 19
Author(s): Whitney Berta, Adrian Wagg, Lisa Cranley, Malcolm Doupe, Liane Ginsburg, Matthias Hoben, Lauren MacEachern, Stephanie Chamberlain, Fiona Clement, Adam Easterbrook, Janice Keefe, Jennifer Knopp-Sihota, Tim Rappon, C. Reid, Yuting Song, Carole A. Estabrooks
Software Mentions: 1
Published: almost 5 years ago

10.1001/jamanetworkopen.2019.2597

Application of a Neural Network Whole Transcriptome–Based Pan-Cancer Method for Diagnosis of Primary and Metastatic Cancers
Cited by: 52
Author(s): Jasleen K. Grewal, Basile Tessier‐Cloutier, Steven J.M. Jones, Sitanshu Gakkhar, Yussanne Ma, Richard A. Moore, Andrew J. Mungall, Yongjun Zhao, Michael D. Taylor, Karen A. Gelmon, Howard John Lim, Daniel J. Renouf, Janessa Laskin, Marco A. Marra, Stephen Yip, Steven J.M. Jones
Software Mentions: 1
Published: over 5 years ago