pypi: BioVenn | Projects | Ecosyste.ms: Papers

10.7554/eLife.54186

Epigenetic inheritance of circadian period in clonal cells
Cited by: 12
Author(s): Yan Li, Yongli Shan, Gokhul Kilaru, Stefano Berto, Guang-Zhong Wang, Kimberly Cox, Seung-Hee Yoo, Shao Nian Yang, Genevieve Konopka, Joseph S. Takahashi
Software Mentions: 13
Published: over 4 years ago

10.1371/journal.pgen.1009240

Analysis of cell-type-specific chromatin modifications and gene expression in Drosophila neurons that direct reproductive behavior
Cited by: 5
Author(s): Colleen M Palmateer, Shawn C. Moseley, Surjyendu Ray, Savannah G Brovero, Michelle N. Arbeitman
Software Mentions: 11
Published: over 3 years ago

10.7554/eLife.69431

Inflammation drives alternative first exon usage to regulate immune genes including a novel iron-regulated isoform of Aim2
Cited by: 18
Author(s): Elektra Kantzari Robinson, Pratibha Jagannatha, Sergio Covarrubias, Matthew Cattle, Valeriya Smaliy, Rojin Safavi, Barbara Shapleigh, Robin Abu-Shumays, Miten Jain, Suzanne M. Cloonan, Mark Akeson, Angela N. Brooks
Software Mentions: 9
Published: over 3 years ago

10.1186/s12870-019-2182-3

A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference
Cited by: 9
Author(s): Enrique Ostria‐Gallardo, Giovanni Larama, Graciela Berríos, Ana Fallard, Ana Gutiérrez-Moraga, Ingo Ensminger, León A. Bravo
Software Mentions: 8
Published: almost 5 years ago

10.1371/journal.pgen.1006864

Functional convergence of histone methyltransferases EHMT1 and KMT2C involved in intellectual disability and autism spectrum disorder
Cited by: 101
Author(s): Tom S. Koemans, Tjitske Kleefstra, Melissa C. Chubak, Max H. Stone, Margot R.F. Reijnders, Sonja de Munnik, Marjolein H. Willemsen, Michaela Fencková, Connie Stumpel, Levinus A. Bok, Margarita Saenz, Kyna A. Byerly, Linda B. Baughn, Alexander P.A. Stegmann, Rolph Pfundt, Huiqing Zhou, Hans van Bokhoven, Annette Schenck, Jamie M. Kramer
Software Mentions: 7
Published: about 7 years ago

10.3390/brainsci10020109

Chronic Chemogenetic Stimulation of the Nucleus Accumbens Produces Lasting Reductions in Binge Drinking and Ameliorates Alcohol-Related Morphological and Transcriptional Changes
Cited by: 27
Author(s): Dar'ya Pozhidayeva, Sean P. Farris, Calla M Goeke, Evan Firsick, Kayla G. Townsley, Marina Guizzetti, Angela R. Ozburn
Software Mentions: 7
Published: over 4 years ago

10.1038/s41598-017-16353-x

The microbiomes of blowflies and houseflies as bacterial transmission reservoirs
Cited by: 85
Author(s): Ana Carolina M. Junqueira, Aakrosh Ratan, Enzo Acerbi, Daniela I. Drautz–Moses, Balakrishnan N. V. Premkrishnan, Paul Igor Costea, Bodo Linz, Rikky W. Purbojati, Daniel F. Paulo, Nicolas E. Gaultier, Poorani Subramanian, Nur A. Hasan, Rita R. Colwell, Peer Bork, Ana Maria Lima de Azeredo-Espin, Donald A. Bryant, Stephan C. Schuster
Software Mentions: 7
Published: almost 7 years ago

10.1186/s40478-020-01020-6

Innate immune response in neuronopathic forms of Gaucher disease confers resistance against viral-induced encephalitis
Cited by: 7
Author(s): Sharon Melamed, Roy Avraham, Deborah E. Rothbard, Noam Erez, Tomer Israely, Ziv Klausner, Anthony H. Futerman, Nir Paran, Einat B. Vitner
Software Mentions: 7
Published: about 4 years ago

10.3389/fnbeh.2019.00157

Early Life Stress Restricts Translational Reactivity in CA3 Neurons Associated With Altered Stress Responses in Adulthood
Cited by: 37
Author(s): Jordan Marrocco, Jason D. Gray, Joshua F. Kogan, Nathan R. Einhorn, Emma M. O’Cinneide, Todd G. Rubin, Thomas Carroll, Eric F. Schmidt, Bruce S. McEwen
Software Mentions: 7
Published: over 5 years ago

10.3389/fcell.2019.00283

A Combined Mass Spectrometry and Data Integration Approach to Predict the Mitochondrial Poly(A) RNA Interacting Proteome
Cited by: 2
Author(s): Selma L van Esveld, Şirin Cansız-Arda, Fenna Hensen, Robin van der Lee, Martijn Huynen, Johannes N. Spelbrink
Software Mentions: 7
Published: almost 5 years ago

10.15252/msb.20188689

Defining the <scp>RNA</scp> interactome by total <scp>RNA</scp> ‐associated protein purification
Cited by: 103
Author(s): Vadim Shchepachev, Stefan Bresson, Christos Spanos, Elisabeth Petfalski, Lutz Fischer, Juri Rappsilber, David Tollervey
Software Mentions: 7
Published: over 5 years ago

10.1038/s41422-019-0168-1

Pioneering function of Isl1 in the epigenetic control of cardiomyocyte cell fate
Cited by: 64
Author(s): Rui Gao, Xingqun Liang, Sirisha Cheedipudi, Julio Cordero, Xiyi Jiang, Qingquan Zhang, Luca Caputo, Stefan Günther, Carsten Kuenne, Yongcheng Ren, Shoumo Bhattacharya, Xuejun Yuan, Guillermo Barreto, Yihan Chen, Thomas Braun, Sylvia M. Evans, Yunfu Sun, Gergana Dobreva
Software Mentions: 7
Published: over 5 years ago

10.1186/s12859-019-3320-5

DynaVenn: web-based computation of the most significant overlap between ordered sets
Cited by: 14
Author(s): Jérémy Amand, Tobias Fehlmann, Christina Backes, Andreas Keller
Software Mentions: 6
Published: almost 5 years ago

10.7554/eLife.18591

RYBP stimulates PRC1 to shape chromatin-based communication between Polycomb repressive complexes
Cited by: 105
Author(s): Nathan R. Rose, Hamish W King, Neil P. Blackledge, Nadezda A. Fursova, Katherine Ji Ember, Román Fischer, Benedikt M. Kessler, Robert J. Klose
Software Mentions: 6
Published: about 8 years ago

10.1186/s12859-018-2338-4

Data-driven human transcriptomic modules determined by independent component analysis
Cited by: 23
Author(s): Weizhuang Zhou, Russ B. Altman
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pgen.1006279

Gain- and Loss-of-Function Mutations in the Breast Cancer Gene GATA3 Result in Differential Drug Sensitivity
Cited by: 43
Author(s): Barbara Mair, Tomasz Konopka, Claudia Kerzendorfer, Katia Sleiman, Šejla Šalic, Violeta Serra, Markus K. Muellner, Vassiliki Théodorou, Sebastian M. Nijman
Software Mentions: 6
Published: about 8 years ago

10.1186/s12915-018-0615-3

Mitochondrial unfolded protein response transcription factor ATFS-1 promotes longevity in a long-lived mitochondrial mutant through activation of stress response pathways
Cited by: 79
Author(s): Ziyun Wu, Megan M. Senchuk, Dylan J. Dues, Benjamin K. Johnson, Jason Cooper, Leira Lew, Emily Machiela, Claire E. Schaar, Heather DeJonge, T. Keith Blackwell, Jeremy M. Van Raamsdonk
Software Mentions: 6
Published: almost 6 years ago

10.1038/s42003-021-02217-8

LINE-1 transcription in round spermatids is associated with accretion of 5-carboxylcytosine in their open reading frames
Cited by: 6
Author(s): Martin Blythe, Ayhan Kocer, Alejandro Rubio-Roldán, Tom Giles, Abdulkadir Abakir, Côme Ialy-Radio, Lee M. Wheldon, Oxana Bereshchenko, Stefano Bruscoli, Alexander Kondrashov, Joël R. Drevet, Richard D. Emes, Andrew D. Johnson, John R. McCarrey, Daniel Gackowski, Julie Cocquet, José L. García‐Pérez, Alexey Ruzov
Software Mentions: 6
Published: over 3 years ago

10.1186/gb-2013-14-11-r124

AHT-ChIP-seq: a completely automated robotic protocol for high-throughput chromatin immunoprecipitation
Cited by: 27
Author(s): Sarah Aldridge, Stephen Watt, Michael A. Quail, Tim Rayner, Margus Lukk, Michael F Bimson, Daniel J. Gaffney, Duncan T. Odom
Software Mentions: 6
Published: almost 12 years ago

10.1186/s12864-021-07571-9

Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni
Cited by: 7
Author(s): Laura Foix, Anna Nadal, Maja Zagorščak, Živa Ramšak, Anna Esteve‐Codina, Kristina Gruden, María Pla
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0246695

Analysis of lung transcriptome in calves infected with Bovine Respiratory Syncytial Virus and treated with antiviral and/or cyclooxygenase inhibitor
Cited by: 5
Author(s): Maxim Lebedev, Heather McEligot, Victoria Mutua, Paul Walsh, Francisco R. Carvallo Chaigneau, Laurel J. Gershwin
Software Mentions: 6
Published: over 3 years ago

10.1128/mSystems.00954-20

Isolation of SAR11 Marine Bacteria from Cryopreserved Seawater
Cited by: 4
Author(s): Elizabeth A. Monaghan, Kelle C. Freel, Michael S. Rappé
Software Mentions: 5
Published: almost 4 years ago

10.7717/peerj.10941

Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture
Cited by: 59
Author(s): Rachel Gilroy, Anuradha Ray, María Getino, Isabella Pursley, Daniel L. Horton, Nabil-Fareed Alikhan, Dave Baker, Karim Gharbi, Neil Hall, Mick Watson, Evelien M. Adriaenssens, Ebenezer Foster-Nyarko, Sheikh Jarju, Arss Secka, Martín Antonio, Aharon Oren, Roy R. Chaudhuri, Roberto La Ragione, Falk Hildebrand, Mark J. Pallen
Software Mentions: 5
Published: over 3 years ago

10.1002/aps3.11295

An empirical assessment of a single family‐wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae
Cited by: 24
Author(s): K. Jones, Tomáš Fér, Roswitha Schmickl, Rebecca B. Dikow, Vicki A. Funk, Sonia Herrando‐Moraira, Paul R. Johnston, Norbert Kilian, Carolina M. Siniscalchi, Alfonso Susanna, Marek Slovák, Ramhari Thapa, Linda E. Watson, Jennifer R. Mandel
Software Mentions: 5
Published: about 5 years ago

10.7554/eLife.06942

NKX2-5 mutations causative for congenital heart disease retain functionality and are directed to hundreds of targets
Cited by: 52
Author(s): Romaric Bouveret, Ashley J. Waardenberg, Nicole Schönrock, Mirana Ramialison, Tram Doan, Daniëlle de Jong, Antoine Bondue, Gurpreet Kaur, Mohamed Salim, Hananeh Fonoudi, Chiann-mun Chen, Merridee A. Wouters, Shoumo Bhattacharya, Nicolas Plachta, Sally L. Dunwoodie, Gavin Chapman, Cédric Blanpain, Richard P. Harvey
Software Mentions: 5
Published: over 9 years ago

10.3390/ijms21051630

Alternatively Constructed Estrogen Receptor Alpha-Driven Super-Enhancers Result in Similar Gene Expression in Breast and Endometrial Cell Lines
Cited by: 1
Author(s): Dóra Bojcsuk, Gergely Nagy, Bálint László Bálint
Software Mentions: 5
Published: over 4 years ago

10.1186/s13567-021-00972-4

Transcriptomic analysis of equine chorioallantois reveals immune networks and molecular mechanisms involved in nocardioform placentitis
Cited by: 8
Author(s): Hesham A. Ali, Shavahn C. Loux, Laura Kennedy, Kirsten E. Scoggin, Pouya Dini, Carleigh E. Fedorka, Theodore S. Kalbfleisch, A. Esteller-Vico, David W. Horohov, Erdal Erol, Craig N. Carter, Jon J. Smith, Barry A. Ball
Software Mentions: 5
Published: over 3 years ago

10.3389/fonc.2020.00117

From the Clinic to the Bench and Back Again in One Dog Year: How a Cross-Species Pipeline to Identify New Treatments for Sarcoma Illuminates the Path Forward in Precision Medicine
Cited by: 17
Author(s): Satish Rao, Jason A. Somarelli, Erdem Altunel, Laura E. Selmic, Mark Byrum, Maya U. Sheth, Serene Cheng, Kathryn E. Ware, So Young Kim, Joseph A. Prinz, Nicolas Devos, David L. Corcoran, Arthur Moseley, Erik J. Soderblom, Shiaowen David Hsu, William C. Eward
Software Mentions: 5
Published: over 4 years ago

10.1186/1471-2164-15-687

Species and gene divergence in Littorina snails detected by array comparative genomic hybridization
Cited by: 20
Author(s): Marina Panova, Tomas Johansson, Björn Canbäck, Johan Bentzer, Magnus Alm Rosenblad, Kerstin Johannesson, Anders Tunlid, Carl André
Software Mentions: 5
Published: almost 11 years ago

10.1371/journal.pbio.3000557

BMPR2 acts as a gatekeeper to protect endothelial cells from increased TGFβ responses and altered cell mechanics
Cited by: 65
Author(s): Christian Hiepen, Jerome Jatzlau, Susanne Hildebrandt, Branka Kampfrath, Melis Göktas, Arunima Murgai, José Luis Cuellar Camacho, Rainer Haag, Clemens Ruppert, Gerhard Sengle, Elisabetta Ada Cavalcanti‐Adam, Kerstin Blank, Petra Knaus
Software Mentions: 5
Published: almost 5 years ago

10.1186/1471-2105-12-35

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R
Cited by: 1,681
Author(s): Hanbo Chen, Paul C. Boutros
Software Mentions: 5
Published: almost 14 years ago

10.1371/journal.pone.0215987

Insights from deconvolution of cell subtype proportions enhance the interpretation of functional genomic data
Cited by: 18
Author(s): Yu Kong, Deepa Rastogi, Cathal Seoighe, John M. Greally, Masako Suzuki
Software Mentions: 5
Published: over 5 years ago

10.1186/s12859-021-04121-8

Euler diagrams drawn with ellipses area-proportionally (Edeap)
Cited by: 6
Author(s): Michael Wybrow, Peter Rodgers, Fadi K. Dib
Software Mentions: 5
Published: over 3 years ago

10.1172/jci.insight.142501

Surfactant protein C mutation links postnatal type 2 cell dysfunction to adult disease
Cited by: 10
Author(s): Sneha Sitaraman, Emily P. Martin, Cheng-Lun Na, Shuyang Zhao, Jenna Green, Hitesh Deshmukh, Anne‐Karina T. Perl, James P. Bridges, Yan Xu, Timothy E. Weaver
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0072238

Effect of Doxorubicin/Pluronic SP1049C on Tumorigenicity, Aggressiveness, DNA Methylation and Stem Cell Markers in Murine Leukemia
Cited by: 73
Author(s): Daria Y. Alakhova, Yi Zhao, Shu Li, Alexander V. Kabanov
Software Mentions: 5
Published: about 11 years ago

10.1186/s40168-017-0261-y

Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome
Cited by: 127
Author(s): Dorottya Nagy‐Szakal, Brent L. Williams, Nischay Mishra, Xiaoyu Che, Bohyun Lee, Lucinda Bateman, Nancy G. Klimas, Anthony L. Komaroff, Susan Levine, José G. Montoya, Daniel L. Peterson, Devi Ramanan, Komal Jain, M L Eddy, Mady Hornig, W. Ian Lipkin
Software Mentions: 5
Published: over 7 years ago

10.1186/s12859-019-3008-x

An equivalence approach to the integrative analysis of feature lists
Cited by: 1
Author(s): Álex Sánchez-Pla, Miquel Salicrú, Jordi Ocaña
Software Mentions: 5
Published: about 5 years ago

10.1186/s12885-021-08635-5

Clinical application of whole transcriptome sequencing for the classification of patients with acute lymphoblastic leukemia
Cited by: 12
Author(s): Wencke Walter, Rabia Shahswar, Anna Stengel, Manja Meggendorfer, Wolfgang Kern, Torsten Haferlach, Claudia Haferlach
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-020-72750-9

Cell type specific gene expression profiling reveals a role for complement component C3 in neutrophil responses to tissue damage
Cited by: 16
Author(s): Ruth A. Houseright, Emily E. Rosowski, Pui-ying Lam, Sébastien Tauzin, Oscar Mulvaney, Colin N. Dewey, Anna Huttenlocher
Software Mentions: 5
Published: about 4 years ago

10.1111/acel.13280

Modeling the human aging transcriptome across tissues, health status, and sex
Cited by: 23
Author(s): Maxim N. Shokhirev, Adiv A. Johnson
Software Mentions: 5
Published: almost 4 years ago

10.3390/cancers12051084

Multimodal Targeted Deep Sequencing of Circulating Tumor Cells and Matched Cell-Free DNA Provides a More Comprehensive Tool to Identify Therapeutic Targets in Metastatic Breast Cancer Patients
Cited by: 13
Author(s): Corinna Keup, Markus Storbeck, Siegfried Hauch, Peter F. Hahn, Markus Sprenger-Haussels, Oliver Hoffmann, Rainer Kimmig, Sabine Kasimir‐Bauer
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.ppat.1009290

Shiga toxin remodels the intestinal epithelial transcriptional response to Enterohemorrhagic Escherichia coli
Cited by: 8
Author(s): Alyson R. Warr, Carole J. Kuehl, Matthew K. Waldor
Software Mentions: 5
Published: almost 4 years ago

10.1093/gbe/evu251

Diversity and Variability of NOD-Like Receptors in Fungi
Cited by: 77
Author(s): Witold Dyrka, Marina Lamacchia, Pascal Durrens, Boštjan Kobe, Asen Daskalov, Mathieu Paoletti, David James Sherman, Sven J. Saupe
Software Mentions: 5
Published: almost 10 years ago

10.3390/ijms20133315

Alu RNA Modulates the Expression of Cell Cycle Genes in Human Fibroblasts
Cited by: 10
Author(s): Simona Cantarella, Davide Carnevali, Marco Morselli, Anastasia Conti, Matteo Pellegrini, Barbara Montanini, Giorgio Dieci
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.49044

NEIL1 and NEIL2 DNA glycosylases protect neural crest development against mitochondrial oxidative stress
Cited by: 22
Author(s): Dongdong Han, Lars Schomacher, Katrin M. Schüle, Medhavi Mallick, Michael U. Musheev, Emil Karaulanov, Laura Krebs, Annika von Seggern, Christof Niehrs
Software Mentions: 5
Published: about 5 years ago

10.7554/eLife.46327

Identification of RBPMS as a mammalian smooth muscle master splicing regulator via proximity of its gene with super-enhancers
Cited by: 21
Author(s): Erick E Nakagaki-Silva, Clare Gooding, Miriam Llorian, Aishwarya G. Jacob, Fred Richards, Adrian Buckroyd, Sanjay Sinha, Christopher W.J. Smith
Software Mentions: 5
Published: over 5 years ago

10.1038/s42003-021-01656-7

Molecular characterization of a marine turtle tumor epizootic, profiling external, internal and postsurgical regrowth tumors
Cited by: 19
Author(s): Kelsey Yetsko, Jessica Farrell, Nicholas B. Blackburn, Liam Whitmore, Maximilian R Stammnitz, Jenny Whilde, Catherine B. Eastman, Devon Rollinson Ramia, Rachel Thomas, Aleksandar Krstić, Paul J. Linser, Simon Creer, Gary R. Carvalho, Mariana A. Devlin, Nina Nahvi, Ana C Leandro, Thomas W. deMaar, Brooke Burkhalter, Elizabeth P. Murchison, Christine E. Schnitzler, David J. Duffy
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0236586

Transcriptome analysis of contrasting resistance to herbivory by Empoasca fabae in two shrub willow species and their hybrid progeny
Cited by: 5
Author(s): Wanyan Wang, Craig H. Carlson, Lawrence B. Smart, John E. Carlson
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pgen.1007268

Activation of DAF-16/FOXO by reactive oxygen species contributes to longevity in long-lived mitochondrial mutants in Caenorhabditis elegans
Cited by: 106
Author(s): Megan M. Senchuk, Dylan J. Dues, Claire E. Schaar, Benjamin K. Johnson, Zachary Madaj, Megan J. Bowman, Mary E. Winn, Jeremy M. Van Raamsdonk
Software Mentions: 5
Published: over 6 years ago

10.1186/s12915-017-0359-5

Low-cell-number, single-tube amplification (STA) of total RNA revealed transcriptome changes from pluripotency to endothelium
Cited by: 5
Author(s): Yi‐Hsuan Lee, Ya Wen Hsueh, Yunyan Peng, Kung Chao Chang, Kuen‐Jer Tsai, Han Sun, Ih Jen Su, Po Min Chiang
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pgen.1009260

TDP-43 mutations link Amyotrophic Lateral Sclerosis with R-loop homeostasis and R loop-mediated DNA damage
Cited by: 43
Author(s): Marta Gianini, Aleix Bayona-Feliú, Daisy Sproviero, Sónia Barroso, Cristina Cereda, Andrés Aguilera
Software Mentions: 5
Published: almost 4 years ago

10.1021/acsomega.1c03681

Interactome Networks of FOSL1 and FOSL2 in Human Th17 Cells
Cited by: 5
Author(s): Ankitha Shetty, Santosh D. Bhosale, Subhash Tripathi, Tanja Buchacher, Rahul Biradar, Omid Rasool, Robert Moulder, Sanjeev Galande, Riitta Lahesmaa
Software Mentions: 5
Published: about 3 years ago

10.1371/journal.pone.0161504

Comparison of Normal and Pre-Eclamptic Placental Gene Expression: A Systematic Review with Meta-Analysis
Cited by: 58
Author(s): Obed Brew, Mark Sullivan, Anthony C. Woodman
Software Mentions: 5
Published: about 8 years ago

10.3389/fcell.2020.00552

Id Proteins Promote a Cancer Stem Cell Phenotype in Mouse Models of Triple Negative Breast Cancer via Negative Regulation of Robo1
Cited by: 15
Author(s): Wee Siang Teo, Holly Holliday, N. Karthikeyan, Aurélie Cazet, Daniel Roden, Kate Harvey, Christina Valbirk Konrad, Reshma Murali, Binitha Anu Varghese, Archana P. Thankamony, Chia-Ling Chan, Andrea McFarland, Simon Junankar, Sunny Ye, Jessica Yang, Iva Nikolić, Jaynish S. Shah, Laura A. Baker, Ewan K.A. Millar, Matthew J. Naylor, Christopher J. Ormandy, Sunil R. Lakhani, Warren Kaplan, Albert S. Mellick, Sandra A. O’Toole, Alexander Swarbrick, Radhika Nair
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-018-29472-w

RNA-seq and flow-cytometry of conventional, scalp, and palmoplantar psoriasis reveal shared and distinct molecular pathways
Cited by: 28
Author(s): Richard Ahn, Di Yan, Hsin-Wen Chang, Kristina Lee, Shrishti Bhattarai, Zhiming Huang, Mio Nakamura, Rasnik Singh, Ladan Afifi, Keyon Taravati, Priscila Muñoz-Sandoval, Mariela Pauli, Michael D. Rosenblum, Wilson Liao
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pgen.1005755

Preferential Allele Expression Analysis Identifies Shared Germline and Somatic Driver Genes in Advanced Ovarian Cancer
Cited by: 12
Author(s): Najeeb Halabi, Alejandra Martinez, Halema Al-Farsi, Eliane Mery-Lamarche, Laurence Puydenus, Pascal Pujol, Hanif Khalak, Cameron Mclurcan, Gwénaël Ferron, Denis Querleu, Iman K. Al-Azwani, Eman K. Al-Dous, Yasmin Ali Mohamoud, Joel A. Malek, Arash Rafii
Software Mentions: 4
Published: almost 9 years ago

10.3389/fpls.2019.01605

De Novo Transcriptome Analysis of Durum Wheat Flag Leaves Provides New Insights Into the Regulatory Response to Elevated CO2 and High Temperature
Cited by: 26
Author(s): Rubén Vicente, Anthony Bolger, Rafael Martínez‐Carrasco, Pilar Pérez Pérez, Elena Gutiérrez, Björn Usadel, Rosa Morcuende
Software Mentions: 4
Published: almost 5 years ago

10.1128/mSystems.00127-17

Genomic, Transcriptomic, and Phenotypic Analyses of Neisseria meningitidis Isolates from Disease Patients and Their Household Contacts
Cited by: 2
Author(s): Xiaoyun Ren, David Eccles, Gabrielle Greig, Jane Clapham, Nicole E. Wheeler, Stinus Lindgreen, Paul Geeleher, Joanna K. MacKichan
Software Mentions: 4
Published: almost 7 years ago

10.3389/fmicb.2021.615416

Correlations Between Intestinal Microbial Community and Hematological Profile in Native Tibetans and Han Immigrants
Cited by: 7
Author(s): Yan Ma, Qin Ga, Ri-Li Ge, Shuang Ma
Software Mentions: 4
Published: over 3 years ago

10.1007/s00401-020-02217-8

Extrinsic immune cell-derived, but not intrinsic oligodendroglial factors contribute to oligodendroglial differentiation block in multiple sclerosis
Cited by: 47
Author(s): Laura Starost, Maren Lindner, Martin Herold, Yu Xu, Hannes C.A. Drexler, Katharina Heß, Marc Ehrlich, Linda Ottoboni, Francesca Ruffini, Martin Stehling, Albrecht Röpke, Christian Thomas, Hans R. Schöler, Jack Antel, Jürgen Winkler, Gianvito Martino, Luisa Klotz, Tanja Kuhlmann
Software Mentions: 4
Published: about 4 years ago

10.3389/fimmu.2019.02902

Rainbow Trout IgM+ B Cells Preferentially Respond to Thymus-Independent Antigens but Are Activated by CD40L
Cited by: 14
Author(s): Aitor G. Granja, Pedro Perdiguero, Alba Martín-Martín, Patricia Díaz‐Rosales, Irene Soleto, Carolina Tafalla
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pgen.1008761

Functional and transcriptional profiling of non-coding RNAs in yeast reveal context-dependent phenotypes and in trans effects on the protein regulatory network
Cited by: 13
Author(s): Laura Natalia Balarezo-Cisneros, Steven J. Parker, Marcin G. Fraczek, Soukaina Timouma, Ping Wang, Raymond T. O’Keefe, Catherine B. Millar, Daniela Delneri
Software Mentions: 4
Published: almost 4 years ago

10.3390/ijms21061910

NR2F2 Orphan Nuclear Receptor is Involved in Estrogen Receptor Alpha-Mediated Transcriptional Regulation in Luminal A Breast Cancer Cells
Cited by: 8
Author(s): Edina Erdős, Bálint László Bálint
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0063234

Beyond the Binding Site: In Vivo Identification of tbx2, smarca5 and wnt5b as Molecular Targets of CNBP during Embryonic Development
Cited by: 15
Author(s): Pablo Armas, Ezequiel Margarit, Valeria S. Mouguelar, Miguel L. Allende, Nora B. Calcaterra
Software Mentions: 4
Published: over 11 years ago

10.1007/s00401-021-02347-7

Targeting cancer stem cells in medulloblastoma by inhibiting AMBRA1 dual function in autophagy and STAT3 signalling
Cited by: 17
Author(s): Francesca Nazio, Agnese Pò, Luana Abballe, Claudio Ballabio, Francesca Diomedi Camassei, Matteo Bordi, Antonio Camera, Simona Caruso, Ignazio Caruana, Marco Pezzullo, Caterina Ferraina, Giacomo Milletti, Matteo Gianesello, Sofia Reddel, Luca Compagnucci, Donatella Ceglie, Sara Marinelli, Silvia Campello, Elena Papaleo, Evelina Miele, Antonella Cacchione, Andrea Carai, Maria Vinci, Enrico Velardi, Biagio De Angelis, Luca Tiberi, Concetta Quintarelli, Angela Mastronuzzi, Elisabetta Ferretti, Franco Locatelli, Francesco Cecconi
Software Mentions: 4
Published: over 3 years ago

10.3389/fmicb.2019.00250

Transcriptomic Analysis of the Brucella melitensis Rev.1 Vaccine Strain in an Acidic Environment: Insights Into Virulence Attenuation
Cited by: 13
Author(s): Mali Salmon‐Divon, Tamar Zahavi, Jonathan D. Kornspan
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.64370

SATB2 induction of a neural crest mesenchyme-like program drives melanoma invasion and drug resistance
Cited by: 8
Author(s): Maurizio Fazio, Ellen van Rooijen, Michelle Dang, Glenn van de Hoek, Julien Ablain, Jeffrey K. Mito, Song Yang, Andrew Thomas, Jonathan Michael, Tania Fabo, Rodsy Modhurima, Patrizia Pessina, Charles Kaufman, Yi Zhou, Richard M. White, Leonard I. Zon
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13100-019-0174-3

AluMine: alignment-free method for the discovery of polymorphic Alu element insertions
Cited by: 10
Author(s): Tarmo Puurand, Viktoria Kukuškina, Fanny-Dhelia Pajuste, Maido Remm
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0186794

A deep transcriptomic resource for the copepod crustacean Labidocera madurae: A potential indicator species for assessing near shore ecosystem health
Cited by: 16
Author(s): Vittoria Roncalli, Andrew E. Christie, Stephanie A. Sommer, Matthew Cieslak, Daniel K. Hartline, Petra H. Lenz
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0154315

VennPainter: A Tool for the Comparison and Identification of Candidate Genes Based on Venn Diagrams
Cited by: 61
Author(s): Guoliang Lin, Jing Chai, Shuo Yuan, Chao Mai, Li Cai, Robert W. Murphy, Wei Zhou, Jing Luo
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-020-78682-8

Gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by NF-Y
Cited by: 1
Author(s): Tatsuhiko Yamanaka, Haruko Miyazaki, Asako Tosaki, Sankar N. Maity, Tomomi Shimogori, Nobutaka Hattori, Nobuyuki Nukina
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-020-65137-3

Morphological, genotypic and metabolomic signatures confirm interfamilial hybridization between the ubiquitous kelps Macrocystis (Arthrothamnaceae) and Lessonia (Lessoniaceae)
Cited by: 9
Author(s): Pedro Murúa, Ru Angelie Edrada-Ebel, Liliana Muñoz, Sylvia Soldatou, Nathalie Legrave, Dieter G. Müller, David J. Patiño, Pieter van West, Frithjof C. Küpper, R. Westermeier, Rainer Ebel, Akira F. Peters
Software Mentions: 4
Published: over 4 years ago

10.1007/s12015-020-10103-9

ActivinA Induced SMAD1/5 Signaling in an iPSC Derived EC Model of Fibrodysplasia Ossificans Progressiva (FOP) Can Be Rescued by the Drug Candidate Saracatinib
Cited by: 9
Author(s): Susanne Hildebrandt, Branka Kampfrath, Kristin Fischer, Laura de Campos Hildebrand, Julia Haupt, Harald Stachelscheid, Petra Knaus
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-019-48979-4

Comparative analysis demonstrates cell type-specific conservation of SOX9 targets between mouse and chicken
Cited by: 22
Author(s): Satoshi Yamashita, Kensuke Kataoka, Hiroto Yamamoto, Tomoko Kato, Satoshi Hara, Katsushi Yamaguchi, Claire Renard-Guillet, Yuki Katou, Katsuhiko Shirahige, Haruki Ochi, Hitoshi Ogino, Tatsuo Uchida, Masafumi Inui, Shuji Takada, Shuji Shigenobu, Hiroshi Asahara
Software Mentions: 4
Published: about 5 years ago

10.1242/dev.139857

Cooperative binding of AP-1 and TEAD4 modulates the balance between vascular smooth muscle and hemogenic cell fate
Cited by: 41
Author(s): Nadine Obier, Pierre Cauchy, Salam A. Assi, Jane Gilmour, Michael Lie-A-Ling, Monika Lichtinger, Maarten Hoogenkamp, Laura Noailles, Peter N. Cockerill, Georges Lacaud, Valérie Kouskoff, Constanze Bonifer
Software Mentions: 4
Published: almost 9 years ago

10.1038/s41598-020-62139-z

Colorectal cancer-associated anaerobic bacteria proliferate in tumor spheroids and alter the microenvironment
Cited by: 35
Author(s): Stephen H. Kasper, Carolina Morell-Perez, Thomas P. Wyche, Theodore R. Sana, Linda A. Lieberman, Erik C. Hett
Software Mentions: 4
Published: over 4 years ago

10.1128/mBio.02391-19

Cause and Effectors: Whole-Genome Comparisons Reveal Shared but Rapidly Evolving Effector Sets among Host-Specific Plant-Castrating Fungi
Cited by: 25
Author(s): William C. Beckerson, Ricardo C. Rodrı́guez de la Vega, Fanny E. Hartmann, Marine Duhamel, Tatiana Giraud, Michael H. Perlin
Software Mentions: 4
Published: almost 5 years ago

10.3390/cancers12030709

Proteome and Phosphoproteome Changes Associated with Prognosis in Acute Myeloid Leukemia
Cited by: 30
Author(s): Elise Aasebø, Frode S. Berven, Sushma Bartaula-Brevik, Tomasz Stokowy, Randi Hovland, Marc Vaudel, Stein Ove Døskeland, Emmet McCormack, Tanveer S. Batth, Jesper V. Olsen, Øystein Bruserud, Frode Selheim, Maria Hernandez-Valladares
Software Mentions: 4
Published: over 4 years ago

10.26508/lsa.201900332

Kalirin-RAC controls nucleokinetic migration in ADRN-type neuroblastoma
Cited by: 4
Author(s): Elena Afanasyeva, Moritz Gartlgruber, Tatsiana Ryl, Bieke Decaesteker, Geertrui Denecker, Gregor Mönke, Umut Toprak, Andrés Flórez, Alica Torkov, Daniel Dreidax, Carl Herrmann, Konstantin Okonechnikov, Sara Ek, Ashwini Kumar Sharma, Vitaliya Sagulenko, Frank Speleman, Kai Oliver Henrich, Frank Westermann
Software Mentions: 4
Published: over 3 years ago

10.1038/srep32442

A Multi-Serotype Approach Clarifies the Catabolite Control Protein A Regulon in the Major Human Pathogen Group A Streptococcus
Cited by: 14
Author(s): Sruti DebRoy, Miguel A. Saldaña, Dante Travisany, Andrew Montano, Jessica Galloway-Peña, Nicola Horstmann, Hui Yao, Maurício González, Alejandro Maass, Mauricio Latorre, Samuel A. Shelburne
Software Mentions: 4
Published: about 8 years ago

10.3390/cancers13092143

Proteomic Studies of Primary Acute Myeloid Leukemia Cells Derived from Patients Before and during Disease-Stabilizing Treatment Based on All-Trans Retinoic Acid and Valproic Acid
Cited by: 5
Author(s): Maria Hernandez-Valladares, Rebecca Wangen, Elise Aasebø, Håkon Reikvam, Frode S. Berven, Frode Selheim, Øystein Bruserud
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-019-46594-x

SREBP1-dependent de novo fatty acid synthesis gene expression is elevated in malignant melanoma and represents a cellular survival trait
Cited by: 27
Author(s): Shi-Fang Wu, Anders M. Näär
Software Mentions: 4
Published: over 5 years ago

10.1038/srep15041

DDX3Y gene rescue of a Y chromosome AZFa deletion restores germ cell formation and transcriptional programs
Cited by: 57
Author(s): Cyril Ramathal, Benjamin Angulo, Meena Sukhwani, Jun Cui, Jens Durruthy-Durruthy, Fang Fang, Paula Schanes, Paul J. Turek, Kyle E. Orwig, Renee A. Reijo Pera
Software Mentions: 4
Published: about 9 years ago

10.1186/s12870-014-0254-y

Phosphite-induced changes of the transcriptome and secretome in Solanum tuberosum leading to resistance against Phytophthora infestans
Cited by: 77
Author(s): Dharani Dhar Burra, Oliver Berkowitz, Pete E. Hedley, Jenny Morris, Svante Resjö, Fredrik Levander, Erland Liljeroth, Erik Andréasson, Erik Alexandersson
Software Mentions: 4
Published: about 10 years ago

10.3390/microorganisms7090341

DNA- and RNA- Derived Fungal Communities in Subsurface Aquifers Only Partly Overlap but React Similarly to Environmental Factors
Cited by: 14
Author(s): Ali Nawaz, Witoon Purahong, Martina Herrmann, Kirsten Küsel, François Buscot, Tesfaye Wubet
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pbio.3001057

The dominantly expressed class II molecule from a resistant MHC haplotype presents only a few Marek’s disease virus peptides by using an unprecedented binding motif
Cited by: 11
Author(s): Samer Halabi, Michael Ghosh, Stefan Stevanović, Hans‐Georg Rammensee, Luca D. Bertzbach, Benedikt B. Kaufer, Martin C. Moncrieffe, Bernd Kaspers, Sonja Härtle, Jim Kaufman
Software Mentions: 3
Published: over 3 years ago

10.1186/s12859-016-1281-5

VennDiagramWeb: a web application for the generation of highly customizable Venn and Euler diagrams
Cited by: 27
Author(s): Felix Lam, Christopher M. Lalansingh, Holly E. Babaran, Zhiyuan Wang, Stephenie D. Prokopec, Natalie S. Fox, Paul C. Boutros
Software Mentions: 3
Published: about 8 years ago

10.3389/fphar.2020.612573

miRNome profiling of LSC-enriched CD34+CD38−CD26+ fraction in Ph+ CML-CP samples from Argentinean patients: a potential new pharmacogenomic tool
Cited by: 9
Author(s): María Sol Ruiz, María Belén Sánchez, Simone Bonecker, Carolina Furtado, Daniel Koile, Patricio Yankilevich, Santiago Cranco, Maria Del Rosario Custidiano, Josefina Freitas, Beatriz Moiraghi, Mariel Ana Pérez, Carolina Pavlovsky, Ana Inés Varela, Verónica Ventriglia, Julio César Sánchez Ávalos, Irene Larripa, Ilana Zalcberg, José Mordoh, Peter Valent, Michele Bianchini
Software Mentions: 3
Published: almost 4 years ago

10.3389/fpls.2021.641232

Management After Windstorm Affects the Composition of Ectomycorrhizal Symbionts of Regenerating Trees but Not Their Mycorrhizal Networks
Cited by: 0
Author(s): Petra Veselá, Martina Vašutová, Magda Edwards‐Jonášová, Filip Holub, Peter Fleischer, Pavel Cudlín
Software Mentions: 3
Published: over 3 years ago

10.3389/fimmu.2021.535039

Complex Interplay Between MAZR and Runx3 Regulates the Generation of Cytotoxic T Lymphocyte and Memory T Cells
Cited by: 3
Author(s): Alexandra Franziska Gülich, Ramona Rica, Caroline Tizian, Csilla Viczenczová, Kseniya Khamina, Thomas Faux, Daniela Hainberger, Thomas Penz, Rémy Bosselut, Christoph Bock, Asta Laiho, Laura L. Elo, Andréas Bergthaler, Wilfried Ellmeier, Shoji Sakaguchi
Software Mentions: 3
Published: over 3 years ago

10.3389/fimmu.2018.00912

Discrimination Between Human Leukocyte Antigen Class I-Bound and Co-Purified HIV-Derived Peptides in Immunopeptidomics Workflows
Cited by: 38
Author(s): Thomas Partridge, Annalisa Nicastri, Anna E. Kliszczak, L M Yindom, Benedikt M. Kessler, Nicola Ternette, Persephone Borrow
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-015-2051-x

Defining the nitrogen regulated transcriptome of Mycobacterium smegmatis using continuous culture
Cited by: 23
Author(s): Michael Petridis, Andrej Benjak, Gregory M. Cook
Software Mentions: 3
Published: about 9 years ago

10.3389/fimmu.2021.707298

Effects of Combinatorial Ubiquitinated Protein-Based Nanovaccine and STING Agonist in Mice With Drug-Resistant and Metastatic Breast Cancer
Cited by: 4
Author(s): Fang Huang, Ning Pan, Yi-ting Wei, Jinjin Zhao, Mohanad Aldarouish, Xuru Wang, Xiaotong Sun, Wen Zhang, Yongqiang Chen, Lixin Wang
Software Mentions: 3
Published: about 3 years ago

10.3389/fimmu.2020.01430

Characterization of a Novel Compound That Stimulates STING-Mediated Innate Immune Activity in an Allele-Specific Manner
Cited by: 6
Author(s): Jinu Abraham, Sara Botto, Nobuyo Mizuno, Kara Pryke, Bryan Gall, Dylan T. Boehm, Tina Sali, Haihong Jin, Aaron Nilsen, Michael Gough, Jason R. Baird, Marita Chakhtoura, Caroline Subra, Lydie Trautmann, Elias K. Haddad, Victor R. DeFilippis
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0164533

Microbiome and Exudates of the Root and Rhizosphere of Brachypodium distachyon, a Model for Wheat
Cited by: 178
Author(s): Akitomo Kawasaki, Suzanne Donn, Peter R. Ryan, Ulrike Mathesius, Rosangela Devilla, Amanda Jones, Michelle Watt
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0086787

Effects of Sulforaphane and 3,3′-Diindolylmethane on Genome-Wide Promoter Methylation in Normal Prostate Epithelial Cells and Prostate Cancer Cells
Cited by: 90
Author(s): Carmen P. Wong, Anna Hsu, Alex Buchanan, Zoraya Palomera-Sánchez, Laura M. Beaver, E. Andrés Houseman, David E. Williams, Roderick H. Dashwood, Emily Ho
Software Mentions: 3
Published: almost 11 years ago

10.1111/mpp.12965

EffectorK, a comprehensive resource to mine for <i>Ralstonia, Xanthomonas,</i> and other published effector interactors in the <i>Arabidopsis</i> proteome
Cited by: 34
Author(s): Manuel González‐Fuente, Sébastien Carrère, Dario Monachello, Benjamin G. Marsella, Anne‐Claire Cazalé, Claudine Zischek, Raka M. Mitra, Nathalie Rézé, Ludovic Cottret, M. Shahid Mukhtar, Claire Lurin, Laurent Noël, Nemo Peeters
Software Mentions: 3
Published: about 4 years ago

10.1186/s12864-021-07756-2

RNAseq and quantitative proteomic analysis of Dictyostelium knock-out cells lacking the core autophagy proteins ATG9 and/or ATG16
Cited by: 7
Author(s): Qiuhong Xiong, Ning Song, Ping Li, Sarah Fischer, Roman Konertz, Prerana Wagle, Gernot Glöckner, Changxin Wu, Ludwig M. Eichinger
Software Mentions: 3
Published: over 3 years ago

10.3389/fimmu.2019.02708

TcellSubC: An Atlas of the Subcellular Proteome of Human T Cells
Cited by: 13
Author(s): Rubin Narayan Joshi, Charlotte Stadler, Robert Lehmann, Janne Lehtiö, Jesper Tegnér, Angelika Schmidt, Mattias Vesterlund
Software Mentions: 3
Published: almost 5 years ago

10.3389/fimmu.2019.01019

IRF1 Maintains Optimal Constitutive Expression of Antiviral Genes and Regulates the Early Antiviral Response
Cited by: 67
Author(s): Debasis Panda, Erisa Gjinaj, Mahesh Bachu, Erica Squire, Hilary Novatt, Keiko Ozato, Ronald L. Rabin
Software Mentions: 3
Published: over 5 years ago

Projects: pypi: BioVenn

Papers Mentioning BioVenn 247