Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: kallisto

https://packages.ecosyste.ms/registries/pypi.org/packages/kallisto

The Kallisto software enables the efficient calculation of atomic features that can be used within a quantitative structure-activity relationship (QSAR) approach. Furthermore, several modelling helpers are implemented.
9 versions
Latest release: about 1 year ago
2 dependent packages
282 downloads last month

Papers Mentioning kallisto 307

10.1016/j.dib.2019.105025
RNA sequencing data of mouse 2-cell embryos treated with DMSO
Cited by: 0
Author(s): Min-Hee Kang, Seong-Yeob You, Kwonho Hong, Jin‐Hoi Kim
Software Mentions: 3
Published: almost 5 years ago
10.1186/s12885-019-5592-6
A TMEFF2-regulated cell cycle derived gene signature is prognostic of recurrence risk in prostate cancer
Cited by: 10
Author(s): Constantin Georgescu, Joshua M. Corbin, Sandra Thibivilliers, Zachary D. Webb, Yan Zhao, Jan Koster, Kar‐Ming Fung, Adam S. Asch, Jonathan D. Wren, Maria J. Ruiz-Echevarría
Software Mentions: 3
Published: over 5 years ago
10.1371/journal.pone.0232559
Transcriptome analysis indicates dominant effects on ribosome and mitochondrial function of a premature termination codon mutation in the zebrafish gene psen2
Cited by: 9
Author(s): Haowei Jiang, Stephen Pederson, Morgan Newman, Yang Dong, Karissa Barthelson, Michael Lardelli
Software Mentions: 3
Published: over 4 years ago
10.3390/ijms22137165
A Transcriptome-Wide Isoform Landscape of Melanocytic Nevi and Primary Melanomas Identifies Gene Isoforms Associated with Malignancy
Cited by: 7
Author(s): Siras Hakobyan, Henry Loeffler‐Wirth, Arsen Arakelyan, Hans Binder, Manfred Kunz
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pone.0175744
Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways
Cited by: 8
Author(s): Lynn Yi, Harold Pimentel, Lior Pachter
Software Mentions: 2
Published: over 7 years ago
10.3389/fmicb.2019.01514
Transcriptomic Analysis of Two Thioalkalivibrio Species Under Arsenite Stress Revealed a Potential Candidate Gene for an Alternative Arsenite Oxidation Pathway
Cited by: 8
Author(s): Anne Catherine Ahn, L. Cavalca, Monica Colombo, J. Merijn Schuurmans, Dimitry Y. Sorokin, Gerard Muyzer
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.pone.0244025
Coronavirus genomes carry the signatures of their habitats
Cited by: 21
Author(s): Yulong Wei, Jordan R. Silke, Parisa Aris, Xuhua Xia
Software Mentions: 2
Published: almost 4 years ago
10.3389/fpls.2017.00647
Large Differences in Gene Expression Responses to Drought and Heat Stress between Elite Barley Cultivar Scarlett and a Spanish Landrace
Cited by: 46
Author(s): Carlos Pérez Cantalapiedra, María Jesús García-Pereira, María Pilar Rivero Gracia, Ernesto Igartua, Ana M. Casas, Bruno Contreras‐Moreira
Software Mentions: 2
Published: over 7 years ago
10.1534/g3.119.400923
Sex Chromosome Evolution in Muscid Flies
Cited by: 12
Author(s): Richard P. Meisel, Pia U. Olafson, Kiran Adhikari, Felix D. Guerrero, Kranti Konganti, Joshua B. Benoit
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pntd.0009777
Characterization of the β-tubulin gene family in Ascaris lumbricoides and Ascaris suum and its implication for the molecular detection of benzimidazole resistance
Cited by: 10
Author(s): Sara Roose, Russell W. Avramenko, Stephen M. J. Pollo, James D. Wasmuth, Shaali Ame, Mio Ayana, Martha Betson, Piet Cools, Daniel Dana, Ben P. Jones, Zeleke Mekonnen, Arianna Morosetti, Abhinaya Venkatesan, Johnny Vlaminck, Matthew L. Workentine, Bruno Levecke, John S. Gilleard, Peter Geldhof
Software Mentions: 2
Published: about 3 years ago
10.1093/g3journal/jkab113
Interacting impact of maternal inflammatory response and stress on the amygdala transcriptome of pigs
Cited by: 11
Author(s): Marissa R. Keever-Keigher, Pan Zhang, Courtni R. Bolt, Haley E Rymut, Adrienne M. Antonson, Megan P Corbett, Alexandra K Houser, Álvaro Gonzalez Hernández, Bruce R. Southey, Laurie A. Rund, Rodney W. Johnson, Sandra L. Rodriguez-Zas
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pgen.1008544
The derived allele of a novel intergenic variant at chromosome 11 associates with lower body mass index and a favorable metabolic phenotype in Greenlanders
Cited by: 4
Author(s): Mette K. Andersen, Emil Jørsboe, Line Skotte, Kristian Hanghøj, Camilla H. Sandholt, Ida Moltke, Niels Grarup, Timo Kern, Yuvaraj Mahendran, Bolette Søborg, Peter Bjerregaard, Christina Viskum Lytken Larsen, Inger Katrine Dahl-Petersen, Hemant K. Tiwari, Bjarke Feenstra, Anders Koch, Howard W. Wiener, Scarlett E. Hopkins, Oluf Pedersen, Mads Melbye, Bert B. Boyer, Marit Eika Jørgensen, Anders Albrechtsen, Torben Hansen
Software Mentions: 2
Published: almost 5 years ago
10.1371/journal.pgen.1008091
Expression estimation and eQTL mapping for HLA genes with a personalized pipeline
Cited by: 57
Author(s): Vitor R. C. Aguiar, Jônatas César, Olivier Delaneau, Emmanouil T. Dermitzakis, Diogo Meyer
Software Mentions: 2
Published: over 5 years ago
10.1111/gbb.12721
Combined change of behavioral traits for domestication and <scp>gene‐networks</scp> in mice selectively bred for active tameness
Cited by: 5
Author(s): Yuki Matsumoto, Hiromichi Nagayama, Hirofumi Nakaoka, Atsushi Toyoda, Tatsuhiko Goto, Tsuyoshi Koide
Software Mentions: 2
Published: almost 4 years ago
10.1186/s12864-020-07121-9
Genome-wide identification of ATP binding cassette (ABC) transporter and heavy metal associated (HMA) gene families in flax (Linum usitatissimum L.)
Cited by: 35
Author(s): Nadeem Khan, Frank M. You, Raju Datla, Sridhar Ravichandran, Bin Jia, Sylvie Cloutier
Software Mentions: 2
Published: about 4 years ago
10.1002/pld3.65
Transcriptome assembly and annotation of johnsongrass (<i>Sorghum halepense</i> ) rhizomes identify candidate rhizome-specific genes
Cited by: 8
Author(s): Nathan Ryder, Kevin M. Dorn, Mark Huitsing, Micah Adams, Jeff Ploegstra, Lee DeHaan, Steve Larson, Nathan L. Tintle
Software Mentions: 2
Published: over 6 years ago
10.1111/pbi.12697
An advanced reference genome of<i>Trifolium subterraneum</i>L. reveals genes related to agronomic performance
Cited by: 26
Author(s): Parwinder Kaur, Philipp E. Bayer, Zbyněk Milec, Jan Vrána, Yuxuan Yuan, R. Appels, David Edwards, Jacqueline Batley, Phillip Nichols, William Erskine, Jaroslav Doležel
Software Mentions: 2
Published: over 7 years ago
10.1111/pbi.12875
The pomegranate (<i>Punica granatum</i> L.) genome provides insights into fruit quality and ovule developmental biology
Cited by: 101
Author(s): Zhaohe Yuan, Yanming Fang, Taikui Zhang, Zhangjun Fei, Fengming Han, Cuiyu Liu, Min Liu, Wei Xiao, Wenjing Zhang, Shan Wu, Mengwei Zhang, Youhui Ju, Huili Xu, He Dai, Yujun Liu, Yanhui Chen, Lili Wang, Zhou Jian-qing, Dian Guan, Ming Yan, Yanhua Xia, Xianbin Huang, Dongyuan Liu, Hongmin Wei, Hongkun Zheng
Software Mentions: 2
Published: almost 7 years ago
10.7717/peerj.9614
Effects of early life stage exposure of largemouth bass to atrazine or a model estrogen (17α-ethinylestradiol)
Cited by: 9
Author(s): Jessica K. Leet, Catherine A. Richter, Robert S. Cornman, Jason P. Berninger, Ramji Kumar Bhandari, Diane Nicks, James L. Zajicek, Vicki S. Blazer, Donald E. Tillitt
Software Mentions: 2
Published: about 4 years ago
10.7717/peerj.4227
FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data
Cited by: 62
Author(s): Saima Sultana Tithi, Frank O. Aylward, Roderick V. Jensen, Liqing Zhang
Software Mentions: 2
Published: almost 7 years ago
10.3390/v10120672
Communities of Phytoplankton Viruses across the Transition Zone of the St. Lawrence Estuary
Cited by: 5
Author(s): Myriam Labbé, Frédéric Raymond, Alice V. Lévesque, Mary Thaler, Vani Mohit, Martyne Audet, Jacques Corbeil, Alexander I. Culley
Software Mentions: 2
Published: almost 6 years ago
10.1186/s13059-021-02392-1
Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis
Cited by: 27
Author(s): Zhiqiang Chen, Yanjun Zan, Pascal Milesi, Linghua Zhou, Jun Chen, Lili Li, Binbin Cui, Shihui Niu, Johan Westin, Bo Karlsson, Maria Rosario García‐Gil, Martin Lascoux, Harry X. Wu
Software Mentions: 2
Published: over 3 years ago
10.7554/eLife.53174
NHR-8 and P-glycoproteins uncouple xenobiotic resistance from longevity in chemosensory C. elegans mutants
Cited by: 4
Author(s): Gabriel A Guerrero, Maxime Derisbourg, Felix A.M.C. Mayr, Laura E Wester, Marco Giorda, J Eike Dinort, Matías D. Hartman, Klara Schilling, María José Alonso-De Gennaro, Rong Lu, Bérénice A. Benayoun, Martin S. Denzel
Software Mentions: 2
Published: about 3 years ago
10.1016/j.gpb.2019.02.002
Brain Banks Spur New Frontiers in Neuropsychiatric Research and Strategies for Analysis and Validation
Cited by: 11
Author(s): Le Wang, Yan Xia, Yu Chen, Rujia Dai, Wenying Qiu, Qingtuan Meng, Liz Kuney, Chao Chen
Software Mentions: 2
Published: over 5 years ago
10.3390/ijms20061344
Specificity of the Metallothionein-1 Response by Cadmium-Exposed Normal Human Urothelial Cells
Cited by: 18
Author(s): Rhiannon V. McNeill, Andrew S. Mason, Mark E. Hodson, James W.F. Catto, Jennifer Southgate
Software Mentions: 2
Published: over 5 years ago
10.1186/s13100-020-0204-1
Characterising a human endogenous retrovirus(HERV)-derived tumour-associated antigen: enriched RNA-Seq analysis of HERV-K(HML-2) in mantle cell lymphoma cell lines
Cited by: 10
Author(s): Witold Tatkiewicz, James Dickie, Franchesca Bedford, Alexander Jones, Mark Atkin, Michele Kiernan, Emmanuel A. Maze, Bora Agit, Garry Farnham, Alexander Kanapin, Robert Belshaw
Software Mentions: 2
Published: almost 5 years ago
10.1098/rspb.2019.0830
Of eyes and embryos: subfunctionalization of the<i>CRX</i>homeobox gene in mammalian evolution
Cited by: 6
Author(s): Amy H. Royall, Stephen Frankenberg, Andrew J Pask, Peter W.H. Holland
Software Mentions: 2
Published: over 5 years ago
10.3390/ijms21020474
A Biostimulant Obtained from the Seaweed Ascophyllum nodosum Protects Arabidopsis thaliana from Severe Oxidative Stress
Cited by: 37
Author(s): Mohammad Amin Omidbakhshfard, Neerakkal Sujeeth, Saurabh Gupta, Nooshin Omranian, Kieran J. Guinan, Yariv Brotman, Zoran Nikoloski, Alisdair R. Fernie, Bernd Mueller‐Roeber, Tsanko Gechev
Software Mentions: 2
Published: almost 5 years ago
10.21203/rs.3.rs-784784/v1
Upper airway gene expression reveals a more robust innate and adaptive immune response to SARS-CoV-2 in children compared with older adults
Cited by: 2
Author(s): Eran Mick, Alexandra Tsitsiklis, Natasha Spottiswoode, Saharai Caldera, Paula Hayakawa Serpa, Angela M. Detweiler, Norma Neff, Angela Oliveira Pisco, Lucy M Li, Hanna Retallack, Kalani Ratnasiri, Kayla Williamson, Victoria Soesanto, Eric A F Simões, Amy Kistler, Brandie D. Wagner, Joseph L. DeRisi, Lilliam Ambroggio, Peter M. Mourani, Charles Langelier
Software Mentions: 2
Published: about 3 years ago
10.1038/s41597-019-0094-6
Long non-coding and coding RNA profiling using strand-specific RNA-seq in human hypertrophic cardiomyopathy
Cited by: 44
Author(s): Xuanyu Liu, Yi Ma, Kunlun Yin, Wenke Li, Wen Chen, Yujing Zhang, Changsheng Zhu, Tianjiao Li, Bianmei Han, Xuewen Li, Shuiyun Wang, Zhou Zhou
Software Mentions: 2
Published: over 5 years ago
10.1099/mgen.0.000148
Coupling next-generation sequencing to dominant positive screens for finding antibiotic cellular targets and resistance mechanisms in Escherichia coli
Cited by: 6
Author(s): Hélène Gingras, Bédis Dridi, Philippe Leprohon, Marc Ouellette
Software Mentions: 2
Published: almost 7 years ago
10.1038/srep39259
A cloud-based workflow to quantify transcript-expression levels in public cancer compendia
Cited by: 67
Author(s): PJ Tatlow, Stephen R. Piccolo
Software Mentions: 2
Published: almost 8 years ago
10.1186/s12859-016-1357-2
The Lair: a resource for exploratory analysis of published RNA-Seq data
Cited by: 14
Author(s): Harold Pimentel, Pascal Sturmfels, Nicolas Bray, Páll Melsted, Lior Pachter
Software Mentions: 2
Published: almost 8 years ago
10.1038/s41598-018-20536-5
Novel global effector mining from the transcriptome of early life stages of the soybean cyst nematode Heterodera glycines
Cited by: 27
Author(s): Michael Gardner, Andi Dhroso, Nia Johnson, Eric Davis, Thomas J. Baum, Dmitry Korkin, Melissa G. Mitchum
Software Mentions: 2
Published: almost 7 years ago
10.1186/s13075-017-1312-2
Pregnancy-induced gene expression changes in vivo among women with rheumatoid arthritis: a pilot study
Cited by: 8
Author(s): Dana E. Goin, Mette Kiel Smed, Lior Pachter, Elizabeth Purdom, J. Lee Nelson, Hanne Wacher Kjærgaard, Jørn Olsen, Merete Lund Hetland, Vibeke Zoffmann, Bent Ottesen, Damini Jawaheer
Software Mentions: 2
Published: over 7 years ago
10.1038/s41598-018-30873-0
Physiological characterization of the emergence from diapause: A transcriptomics approach
Cited by: 36
Author(s): Vittoria Roncalli, Stephanie A. Sommer, Matthew Cieslak, Cheryl Clarke, Russell R. Hopcroft, Petra H. Lenz
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-019-49889-1
Comparative evaluation of RNA-Seq library preparation methods for strand-specificity and low input
Cited by: 20
Author(s): Dimitra Sarantopoulou, Soon Yew Tang, Emanuela Ricciotti, Nicholas F. Lahens, Damien Lekkas, Jonathan Schug, Xiaofeng Guo, Georgios K. Paschos, Garret A. FitzGerald, Allan I. Pack, Gregory R. Grant
Software Mentions: 2
Published: about 5 years ago
10.1038/s41598-019-55573-1
Computational discovery of hidden breaks in 28S ribosomal RNAs across eukaryotes and consequences for RNA Integrity Numbers
Cited by: 25
Author(s): Paschalis Natsidis, Philipp H. Schiffer, Irepan Salvador-Martínez, Maximilian J. Telford
Software Mentions: 2
Published: almost 5 years ago
10.1186/s12934-020-01326-z
Assessment of the ptxD gene as a growth and selective marker in Trichoderma atroviride using Pccg6, a novel constitutive promoter
Cited by: 6
Author(s): Nohemí Carreras-Villaseñor, José Guillermo Rico-Ruiz, Ricardo A. Chávez Montes, Lenin Yong-Villalobos, José Fabricio López-Hernández, Pedro Martı́nez-Hernández, Luis Herrera‐Estrella, Damar López‐Arredondo
Software Mentions: 2
Published: over 4 years ago
10.1038/s41598-020-64311-x
Phenotypic and functional characterization of corneal endothelial cells during in vitro expansion
Cited by: 34
Author(s): Ricardo F. Frausto, Vinay Swamy, Gary S L Peh, Payton Boere, E. Maryam Hanser, Dang Huu Chung, Benjamin L. George, Marco Morselli, Liyo Kao, Rustam Azimov, Jessica Wu, Matteo Pellegrini, Ira Kurtz, Jodhbir S. Mehta, Anthony J. Aldave
Software Mentions: 2
Published: over 4 years ago
10.1038/s41598-020-77593-y
Genome-wide identification of Argonautes in Solanaceae with emphasis on potato
Cited by: 10
Author(s): Zhen Liao, Kristian Persson Hodén, Ravi Singh, Christina Dixelius
Software Mentions: 2
Published: almost 4 years ago
10.26508/lsa.202000792
The Paf1 complex positively regulates enhancer activity in mouse embryonic stem cells
Cited by: 12
Author(s): Li Ding, Maciej Paszkowski‐Rogacz, Jovan Mircetic, Debojyoti Chakraborty, Frank Buchholz
Software Mentions: 2
Published: almost 4 years ago
10.1038/s41598-020-78942-7
Reliable and accurate diagnostics from highly multiplexed sequencing assays
Cited by: 12
Author(s): A. Sina Booeshaghi, Nathan B. Lubock, Aaron Cooper, Scott W. Simpkins, Joshua S. Bloom, Jase Gehring, Laura Luebbert, Sriram Kosuri, Lior Pachter
Software Mentions: 2
Published: almost 4 years ago
10.1186/s12935-020-01457-8
Evaluation of the upregulation and surface expression of hypoxanthine guanine phosphoribosyltransferase in acute lymphoblastic leukemia and Burkitt’s B cell lymphoma
Cited by: 1
Author(s): Michelle H. Townsend, Zac E. Ence, Taylor P. Cox, John Lattin, Weston Burrup, Michael K. Boyer, Stephen R. Piccolo, Richard A. Robison, Kim L. O’Neill
Software Mentions: 2
Published: over 4 years ago
10.1038/s41598-021-87503-5
Changes in the gene expression profile during spontaneous migraine attacks
Cited by: 10
Author(s): Lisette J. A. Kogelman, Katrine Falkenberg, Alfonso Buil, Pau Erola, Julie Courraud, Susan Svane Laursen, Tom Michoel, Jes Olesen, Thomas Folkmann Hansen
Software Mentions: 2
Published: over 3 years ago
10.3390/ijms22031469
Priming with a Seaweed Extract Strongly Improves Drought Tolerance in Arabidopsis
Cited by: 27
Author(s): Fiaz Rasul, Saurabh Gupta, Justyna Jadwiga Olas, Tsanko Gechev, Neerakkal Sujeeth, Bernd Mueller‐Roeber
Software Mentions: 2
Published: almost 4 years ago
10.1128/mBio.03173-20
Metagenomic Quantification of Genes with Internal Standards
Cited by: 17
Author(s): Emily Crossette, Jordan Gumm, Kathryn Langenfeld, Lutgarde Raskin, Melissa B. Duhaime, Krista Wigginton
Software Mentions: 2
Published: over 3 years ago
10.3390/biom10060929
Genome-Wide Identification of RNA Silencing-Related Genes and Their Expressional Analysis in Response to Heat Stress in Barley (Hordeum vulgare L.)
Cited by: 10
Author(s): Éva Hamar, Henrik Mihály Szaker, András Kis, Ágnes Dalmadi, Fabio Miloro, György Szittya, János Taller, Péter Gyula, Tibor Csorba
Software Mentions: 2
Published: over 4 years ago
10.1128/mSystems.00156-18
<i>Neisseria gonorrhoeae</i> Exposed to Sublethal Levels of Hydrogen Peroxide Mounts a Complex Transcriptional Response
Cited by: 14
Author(s): Sarah J. Quillin, Adam J. Hockenberry, Michael C. Jewett, H. Steven Seifert
Software Mentions: 2
Published: about 6 years ago
10.1186/s12870-021-03080-9
The report of anthocyanins in the betalain-pigmented genus Hylocereus is not well evidenced and is not a strong basis to refute the mutual exclusion paradigm
Cited by: 5
Author(s): Boas Pucker, Hidam Bishworjit Singh, Monika Kumari, Mohammad Imtiyaj Khan, Samuel F. Brockington
Software Mentions: 2
Published: over 3 years ago
10.1128/mSystems.01202-20
Molecular and Physiological Adaptations to Low Temperature in <i>Thioalkalivibrio</i> Strains Isolated from Soda Lakes with Different Temperature Regimes
Cited by: 2
Author(s): Anne-Catherine Ahn, Evelien Jongepier, J. Merijn Schuurmans, W. Irene C. Rijpstra, Jaap S. Sinninghe Damsté, Erwin A. Galinski, Pawel Roman, Dimitry Y. Sorokin, Gerard Muyzer
Software Mentions: 2
Published: over 3 years ago
10.1101/2021.08.31.21262938
Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification
Cited by: 18
Author(s): Jasmijn A. Baaijens, Alessandro Zulli, Isabel M. Ott, Petrone Me, Tara Alpert, Joseph R. Fauver, Chaney C. Kalinich, Chantal B.F. Vogels, Mallery I. Breban, Claire Duvallet, Kyle A. McElroy, Newsha Ghaeli, Maxim Imakaev, Malaika F. Mckenzie-Bennett, Keith Robison, Alex Plocik, Rebecca Schilling, M Pierson, Rebecca Littlefield, Michelle Spencer, Birgitte B. Simen, Yale SARS-CoV Genomic Surveillance Initiative, William P. Hanage, Nathan D. Grubaugh, Jordan Peccia, Michael Baym
Software Mentions: 2
Published: about 3 years ago
10.1186/s12864-021-07557-7
Post-diapause transcriptomic restarts: insight from a high-latitude copepod
Cited by: 5
Author(s): Vittoria Roncalli, Matthew Cieslak, Ann M. Castelfranco, Russell R. Hopcroft, Daniel K. Hartline, Petra H. Lenz
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pone.0218279
ZEB1 insufficiency causes corneal endothelial cell state transition and altered cellular processing
Cited by: 21
Author(s): Ricardo F. Frausto, Dang Huu Chung, Payton Boere, Vinay Swamy, Huong Duong, Liyo Kao, Rustam Azimov, Wenlin Zhang, Liam Carrigan, Davey Wong, Marco Morselli, Marina Zakharevich, E. Maryam Hanser, Austin Connor Kassels, Ira Kurtz, Matteo Pellegrini, Anthony J. Aldave
Software Mentions: 2
Published: over 5 years ago
10.1186/s12864-017-3786-3
Co-expressed Pathways DataBase for Tomato: a database to predict pathways relevant to a query gene
Cited by: 9
Author(s): Takafumi Narise, Nozomu Sakurai, Takeshi Obayashi, Hiroyuki Ohta, Daisuke Shibata
Software Mentions: 2
Published: over 7 years ago
10.1186/s13075-021-02418-w
Is gene expression among women with rheumatoid arthritis dysregulated during a postpartum flare?
Cited by: 0
Author(s): Matthew Wright, Mette Kiel Smed, J. Lee Nelson, Jørn Olsen, Merete Lund Hetland, Vibeke Zoffmann, Damini Jawaheer
Software Mentions: 2
Published: almost 4 years ago
10.1186/s12864-020-6470-y
Gene regulatory response to hyposalinity in the brown seaweed Fucus vesiculosus
Cited by: 9
Author(s): Luca Rugiu, Marina Panova, Ricardo T. Pereyra, Veijo Jormalainen
Software Mentions: 2
Published: almost 5 years ago
10.1186/s13098-019-0473-3
22nd Brazilian Diabetes Society Congress
Cited by: 5
Author(s):
Software Mentions: 2
Published: about 5 years ago
10.1016/j.ebiom.2020.103030
CUP-AI-Dx: A tool for inferring cancer tissue of origin and molecular subtype using RNA gene-expression data and artificial intelligence
Cited by: 54
Author(s): Yue Zhao, Zikang Pan, Sandeep Namburi, Andrew Pattison, Atara Posner, Shiva Balachander, Carolyn Paisie, Honey V. Reddi, Jens Rueter, Anthony J. Gill, Stephen B. Fox, Kanwal Raghav, William F. Flynn, Richard W. Tothill, Sheng Li, R. Krishna Murthy Karuturi, Joshy George
Software Mentions: 2
Published: about 4 years ago
10.1038/s42003-020-01522-y
Molecularly targeted photothermal ablation improves tumor specificity and immune modulation in a rat model of hepatocellular carcinoma
Cited by: 13
Author(s): Nina M. Muñoz, Crystal Dupuis, Madison H. Williams, Kathleen Dixon, Amanda McWatters, Rony Avritscher, Richard R. Bouchard, Ahmed O. Kaseb, Kyle M. Schachtschneider, Arvind Rao, Rahul A. Sheth
Software Mentions: 2
Published: almost 4 years ago
10.1038/s42003-019-0565-5
Regional heterogeneity impacts gene expression in the subarctic zooplankter Neocalanus flemingeri in the northern Gulf of Alaska
Cited by: 8
Author(s): Vittoria Roncalli, Matthew Cieslak, Martina Germano, Russell R. Hopcroft, Petra H. Lenz
Software Mentions: 2
Published: about 5 years ago
10.1002/ece3.7138
Comparative transcriptomics of spotted seatrout (<i>Cynoscion nebulosus</i>) populations to cold and heat stress
Cited by: 6
Author(s): Jingwei Song, Jan R. McDowell
Software Mentions: 2
Published: almost 4 years ago
10.1530/ERC-20-0464
Pan-genomic characterization of high-risk pediatric papillary thyroid carcinoma
Cited by: 10
Author(s): Adam Stenman, Samuel Backman, Klara Johansson, Johan O. Paulsson, Peter Stålberg, Jan Zedenius, Carl Christofer Juhlin
Software Mentions: 2
Published: over 3 years ago
10.1038/s42003-018-0068-9
Coding variants in RPL3L and MYZAP increase risk of atrial fibrillation
Cited by: 37
Author(s): Rósa B. Þórólfsdóttir, Garðar Sveinbjörnsson, Patrick Sulem, Nielsen Jb, Stefan Jönsson, Gisli H. Halldorsson, Páll Melsted, Erna V. Ívarsdóttir, Olafur B. Davidsson, Ragnar P. Kristjansson, Guðmar Þorleifsson, Anna Helgadóttir, Sólveig Grétarsdóttir, Gudmundur L. Norddahl, Sridharan Rajamani, Bjarni Torfason, Atli S Valgardsson, Jon Th. Sverrisson, Vinicius Tragante, Oddgeir L. Holmen, Folkert W. Asselbergs, Dan M. Roden, Dawood Darbar, Terje R. Pedersen, Marc S. Sabatine, Cristen J. Willer, Maja‐Lisa Løchen, Bjarni V. Halldórsson, Ingileif Jónsdóttir, Kristian Hveem, Davíð O. Arnar, Unnur Þorsteinsdóttir, Daníel F. Guðbjartsson, Hilma Hólm, Kāri Stefánsson
Software Mentions: 2
Published: over 6 years ago
10.3390/ani10010091
Expression Changes of MHC and Other Immune Genes in Frog Skin during Ontogeny
Cited by: 3
Author(s): Quintin Lau, Takeshi Igawa, Shohei Komaki, Yoko Satta
Software Mentions: 2
Published: almost 5 years ago
10.1038/s41419-020-03349-1
Targeting the autophagy promoted antitumor effect of T-DM1 on HER2-positive gastric cancer
Cited by: 8
Author(s): Jinghui Zhang, Jiajun Fan, Xian Zeng, Mingming Nie, Wei Chen, Yichen Wang, Jingyun Luan, Zeguo Zhu, Xusheng Chang, Dianwen Ju, Feng Li, Kai Yin
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pone.0240386
Identification of novel regulators of dendrite arborization using cell type-specific RNA metabolic labeling
Cited by: 2
Author(s): Mohamed Aboukilila, Josephine D. Sami, Jingtian Wang, Whitney England, Robert C. Spitale, ML Cleary
Software Mentions: 2
Published: almost 4 years ago
10.7554/eLife.55414
Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment
Cited by: 22
Author(s): Zachary D. Blount, Rohan Maddamsetti, Nkrumah A. Grant, Sumaya T Ahmed, Tanush Jagdish, Jessica Baxter, Brooke A. Sommerfeld, Alice Tillman, Jeremy P. Moore, Joan L. Slonczewski, Jeffrey E. Barrick, Richard E. Lenski
Software Mentions: 2
Published: over 4 years ago
10.3389/fimmu.2020.568630
IL-12-Induced Immune Suppressive Deficit During CD8+ T-Cell Differentiation
Cited by: 5
Author(s): Pranav S Renavikar, Sushmita Sinha, Ashley A. Brate, Nicholas Borcherding, Michael P. Crawford, Scott Steward-Tharp, Nitin J. Karandikar
Software Mentions: 2
Published: about 4 years ago
10.3389/fimmu.2019.00975
Identification of Renal Long Non-coding RNA RP11-2B6.2 as a Positive Regulator of Type I Interferon Signaling Pathway in Lupus Nephritis
Cited by: 46
Author(s): Zhuojun Liao, Zhizhong Ye, Zhonghui Xue, Lingling Wu, Ye Ouyang, Chao Yao, Chaojie Cui, Ning Xu, Jianyang Ma, Guojun Hou, Jiehua Wang, Yao Meng, Zhihua Yin, Ya Liu, Jie Qian, Chunyan Zhang, Huihua Ding, Qiang Guo, Bo Qu, Nan Shen
Software Mentions: 2
Published: over 5 years ago
10.1534/g3.116.032672
Evolutionary Genomics of Peach and Almond Domestication
Cited by: 52
Author(s): Dianne Velasco, Josh Hough, Mallikarjuna K. Aradhya, Jeffrey Ross‐Ibarra
Software Mentions: 1
Published: almost 8 years ago
10.1186/s12864-021-07532-2
The transcriptional landscape of a hepatoma cell line grown on scaffolds of extracellular matrix proteins
Cited by: 0
Author(s): Souvik Ghosh, Anastasiya Börsch, Shreemoyee Ghosh, Mihaela Zavolan
Software Mentions: 1
Published: over 3 years ago
10.3390/v10110607
Transcriptomics Reveal Antiviral Gene Induction in the Egyptian Rousette Bat Is Antagonized In Vitro by Marburg Virus Infection
Cited by: 17
Author(s): Catherine Arnold, Jonathan C. Guito, Louis A. Altamura, Sean Lovett, Elyse R. Nagle, Gustavo Palacios, Mariano Sánchez-Lockhart, Jonathan S. Towner
Software Mentions: 1
Published: about 6 years ago
10.14814/phy2.14671
RNA‐Seq identifies genes whose proteins are upregulated during syncytia development in murine C2C12 myoblasts and human BeWo trophoblasts
Cited by: 3
Author(s): C G Azar, Mark C. Valentine, Julie S. Trausch-Azar, Lisa E. Rois, Moe R. Mahjoub, D. Michael Nelson, Alan L. Schwartz
Software Mentions: 1
Published: almost 4 years ago
10.7554/eLife.45905
Gain-of-function mutations in the UNC-2/CaV2α channel lead to excitation-dominant synaptic transmission in Caenorhabditis elegans
Cited by: 23
Author(s): Yu‐Tung Huang, Jennifer K. Pirri, Diego Rayes, Shangbang Gao, Ben Mulcahy, Jeff Grant, Yasunori Saheki, Michael M. Francis, Mei Zhen, Mark J Alkema
Software Mentions: 1
Published: over 5 years ago
10.1111/tpj.14591
Inhibition of<i>Arabidopsis thaliana</i>CIN‐like TCP transcription factors by<i>Agrobacterium</i>T‐DNA‐encoded 6B proteins
Cited by: 4
Author(s): Thomas Potuschak, Javier F. Palatnik, Carla Schommer, Nicolas Sierro, Nikolai V. Ivanov, Yerim Kwon, Pascal Genschik, Jean-Michel Davière, Léon Otten
Software Mentions: 1
Published: almost 5 years ago
10.1186/s13059-016-0970-8
Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts
Cited by: 106
Author(s): Vasilis Ntranos, Govinda M. Kamath, Jesse M. Zhang, Lior Pachter, David Tse
Software Mentions: 1
Published: over 8 years ago
10.18632/oncotarget.27907
Genomic and neoantigen evolution from primary tumor to first metastases in head and neck squamous cell carcinoma
Cited by: 6
Author(s): Charles R. Schutt, Hua Sun, Jaya Sarin Pradhan, Yvonne M. Saenger, Jessica Ley, Douglas R. Adkins, Matthew Ingham, Ding Li, Brian A. Van Tine
Software Mentions: 1
Published: over 3 years ago
10.3390/cells10040860
MECP2 Increases the Pro-Inflammatory Response of Microglial Cells and Phosphorylation at Serine 423 Regulates Neuronal Gene Expression upon Neuroinflammation
Cited by: 8
Author(s): Rebekka Wittrahm, Mari Takalo, Mikael Marttinen, Teemu Kuulasmaa, Petra Mäkinen, Susanna Kemppainen, Henna Martiskainen, Tuomas Rauramaa, Ian Pike, Ville Leinonen, Teemu Natunen, Annakaisa Haapasalo, Mikko Hiltunen
Software Mentions: 1
Published: over 3 years ago
10.1186/s12864-021-07671-6
Exploring genetic resistance to infectious salmon anaemia virus in Atlantic salmon by genome-wide association and RNA sequencing
Cited by: 10
Author(s): Ophélie Gervais, Agustín Barría, Athina Papadopoulou, Remi L. Gratacap, Borghild Hillestad, A. E. Tinch, Samuel Martín, Diego Robledo, Ross D. Houston
Software Mentions: 1
Published: over 3 years ago
10.1371/journal.pone.0208237
CRISPR-Cas9 interrogation of a putative fetal globin repressor in human erythroid cells
Cited by: 24
Author(s): Jennifer E Chung, Wendy Magis, Jonathan T. Vu, Seongkook Heo, Kirmo Wartiovaara, Mark C. Walters, Ryo Kurita, Yukio Nakamura, Dario Boffelli, David I. K. Martin, Jacob E. Corn, Mark Dewitt
Software Mentions: 1
Published: almost 6 years ago
10.1038/s41598-021-84011-4
Notch signaling drives development of Barrett’s metaplasia from Dclk1-positive epithelial tuft cells in the murine gastric mucosa
Cited by: 8
Author(s): Bettina Kunze, Moritz Middelhoff, H. Carlo Maurer, Т. В. Агибалова, Akanksha Anand, Anne-Marie Bührer, Hsin-Yu Fang, Theresa Baumeister, Katja Steiger, Julia Strangmann, Roland M. Schmid, Yichen Wang, Michael Quante
Software Mentions: 1
Published: over 3 years ago
10.1242/dmm.037069
Integrative analysis of Paneth cell proteomic and transcriptomic data from intestinal organoids reveals functional processes dependent on autophagy
Cited by: 17
Author(s): Emily Jones, Zoe J. Matthews, Lejla Gul, Padhmanand Sudhakar, Agatha Treveil, Devina Divekar, Jasmine Buck, Tomasz Wrzesiński, Matthew Jefferson, Stuart D. Armstrong, Lindsay J. Hall, Alastair Watson, Simon R. Carding, Wilfried Haerty, Federica Di Palma, Ulrike Mayer, Penny P. Powell, Isabelle Hautefort, Tom Wileman, Tamás Korcsmáros
Software Mentions: 1
Published: almost 6 years ago
10.1371/journal.pgen.1008484
Spontaneous mutations that confer resistance to 2-deoxyglucose act through Hxk2 and Snf1 pathways to regulate gene expression and HXT endocytosis
Cited by: 11
Author(s): Samantha R. Soncini, Dakshayini G. Chandrashekarappa, David A. Augustine, Kenny P. Callahan, Allyson F. O’Donnell, Martin C. Schmidt
Software Mentions: 1
Published: over 4 years ago
10.1038/s41416-020-0749-2
Alternative promoters control UGT2B17-dependent androgen catabolism in prostate cancer and its influence on progression
Cited by: 11
Author(s): Éric Lévesque, Adrien Labriet, Hélène Hovington, Éric P. Allain, Luciana Melo-Garcia, Michèle Rouleau, Hervé Brisson, Véronique Turcotte, Patrick Caron, Lyne Villeneuve, Mickaël Leclercq, Arnaud Droit, Étienne Audet-Walsh, David Simonyan, Yves Fradet, Louis Lacombe, Chantal Guillemette
Software Mentions: 1
Published: almost 5 years ago
10.1038/s41598-020-79057-9
Comparative transcriptomics indicates endogenous differences in detoxification capacity after formic acid treatment between honey bees and varroa mites
Cited by: 8
Author(s): Antonia Genath, Soroush Sharbati, Benjamin Buer, Ralf Nauen, Ralf Einspanier
Software Mentions: 1
Published: almost 4 years ago
10.1038/s41598-020-72888-6
Spidroin profiling of cribellate spiders provides insight into the evolution of spider prey capture strategies
Cited by: 21
Author(s): Nobuaki Kono, Hiroyuki Nakamura, Masaru Mori, Masaru Tomita, Kazuharu Arakawa
Software Mentions: 1
Published: about 4 years ago
10.1007/s00018-019-03202-5
A novel seed plants gene regulates oxidative stress tolerance in Arabidopsis thaliana
Cited by: 10
Author(s): Neerakkal Sujeeth, Nikolay Mehterov, Saurabh Gupta, Muhammad Kamran Qureshi, Axel Fischer, Sebastian Proost, Mohammad Amin Omidbakhshfard, Toshihiro Obata, Maria Benina, Nikola Staykov, Salma Balazadeh, Dirk Walther, Alisdair R. Fernie, Bernd Mueller‐Roeber, Jacques Hille, Tsanko Gechev
Software Mentions: 1
Published: over 5 years ago
10.1038/s41598-019-46734-3
Cell type specific transcriptional reprogramming of maize leaves during Ustilago maydis induced tumor formation
Cited by: 16
Author(s): Mitzi Villajuana-Bonequi, Alexandra Matei, Corinna Ernst, Asis Hallab, Björn Usadel, Gunther Doehlemann
Software Mentions: 1
Published: over 5 years ago
10.3389/fmicb.2021.694508
Retention of Prey Genetic Material by the Kleptoplastidic Ciliate Strombidium cf. basimorphum
Cited by: 2
Author(s): Maira Maselli, Konstantinos Anestis, Kerstin Klemm, Per Juel Hansen, Uwe John
Software Mentions: 1
Published: over 3 years ago
10.1038/s41598-019-44775-2
Orb-weaving spider Araneus ventricosus genome elucidates the spidroin gene catalogue
Cited by: 67
Author(s): Nobuaki Kono, Hiroyuki Nakamura, Rintaro Ohtoshi, Daniel A. Pedrazzoli Moran, Asaka Shinohara, Yuki Yoshida, Masayuki Fujiwara, Masaru Mori, Masaru Tomita, Kazuharu Arakawa
Software Mentions: 1
Published: over 5 years ago
10.1038/s41598-019-39369-x
An improved estimation of tRNA expression to better elucidate the coevolution between tRNA abundance and codon usage in bacteria
Cited by: 25
Author(s): Yulong Wei, Jordan R. Silke, Xuhua Xia
Software Mentions: 1
Published: over 5 years ago
10.3389/fonc.2021.691685
A First-In-Class, Humanized Antibody Targeting Alternatively Spliced Tissue Factor: Preclinical Evaluation in an Orthotopic Model of Pancreatic Ductal Adenocarcinoma
Cited by: 3
Author(s): Clayton S. Lewis, Aniruddha Karve, Kateryna Matiash, Timothy Stone, Jingxing Li, Jordon K Wang, Henri H. Versteeg, Bruce J. Aronow, Syed A. Ahmad, Pankaj B. Desai, Vladimir Y. Bogdanov
Software Mentions: 1
Published: over 3 years ago
10.1038/s41598-018-35610-1
Neuroprotection by Heat Shock Factor-1 (HSF1) and Trimerization-Deficient Mutant Identifies Novel Alterations in Gene Expression
Cited by: 16
Author(s): Zhe Qu, Anto Sam Crosslee Louis Sam Titus, Zhenyu Xuan, Santosh R. D’Mello
Software Mentions: 1
Published: almost 6 years ago
10.1371/journal.pgen.1009800
Drug resistance in diploid yeast is acquired through dominant alleles, haploinsufficiency, gene duplication and aneuploidy
Cited by: 6
Author(s): Jordan B. Barney, Dakshayini G. Chandrashekarappa, Samantha R. Soncini, Martin C. Schmidt
Software Mentions: 1
Published: about 3 years ago
10.3390/ijms22095008
A Gene Expression Signature to Predict Nucleotide Excision Repair Defects and Novel Therapeutic Approaches
Cited by: 2
Author(s): Ran Wei, Hui Dai, Jing Zhang, David Shih, Yulong Liang, Pengfeng Xiao, Daniel J. McGrail, Shiaw-Yih Lin
Software Mentions: 1
Published: over 3 years ago
10.1038/s41598-018-29120-3
Network-based genetic investigation of virulence-associated phenotypes in methicillin-resistant Staphylococcus aureus
Cited by: 5
Author(s): Chan Yeong Kim, Muyoung Lee, Keehoon Lee, Sang Sun Yoon, Insuk Lee
Software Mentions: 1
Published: over 6 years ago
10.3390/ijms21030927
Gastric Corpus Mucosal Hyperplasia and Neuroendocrine Cell Hyperplasia, but not Spasmolytic Polypeptide-Expressing Metaplasia, Is Prevented by a Gastrin Receptor Antagonist in H+/K+ATPase Beta Subunit Knockout Mice
Cited by: 1
Author(s): Kristin Matre Aasarød, Helge L. Waldum, Astrid Kamilla Stunes, Arne K. Sandvik, Arnar Flatberg, Patricia Mjønes, Unni Syversen, Ingrid Bakke, Reidar Fossmark
Software Mentions: 1
Published: almost 5 years ago
10.3390/cancers13061364
Allelic Expression Imbalance Analysis Identified YAP1 Amplification in p53- Dependent Osteosarcoma
Cited by: 4
Author(s): Guanglin Niu, Agnieszka Bak, Melanie Nusselt, Yue Zhang, Hubert Pausch, Tatiana Flisikowska, Angelika Schnieke, Krzysztof Flisikowski
Software Mentions: 1
Published: over 3 years ago
10.1098/rsos.202023
Slaying the last unicorn: discovery of histones in the microalga <i>Nanochlorum eucaryotum</i>
Cited by: 3
Author(s): Valerie W. C. Soo, Tobias Warnecke
Software Mentions: 1
Published: almost 4 years ago