cran: STAR | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0199902

Annotation, classification, genomic organization and expression of the Vitis vinifera CYPome
Cited by: 8
Author(s): Tina Ilc, Gautier Arista, Raquel Tavares, Nicolas Navrot, Éric Duchêne, Amandine Velt, Frédéric Choulet, Etienne Paux, Marc Fischer, David R. Nelson, Philippe Hugueney, Danièle Werck‐Reichhart, Camille Rustenholz
Software Mentions: 4
Published: over 8 years ago

10.1002/ece3.7401

Transcriptome assembly and differential gene expression of the invasive avian malaria parasite Plasmodium relictum in Hawaiʻi
Cited by: 8
Author(s): Elin Videvall, Kristina L. Paxton, Michael G. Campana, Loren Cassin-Sackett, Carter T. Atkinson, Robert C. Fleischer
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0089445

RNA CoMPASS: A Dual Approach for Pathogen and Host Transcriptome Analysis of RNA-Seq Datasets
Cited by: 38
Author(s): Guiyin Xu, Michael J. Strong, Michelle Lacey, Carl Baribault, Erik K. Flemington, Christopher M. Taylor
Software Mentions: 4
Published: over 12 years ago

10.1186/s12870-020-02706-8

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

10.7554/eLife.43882

Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury
Cited by: 349
Author(s): Nona Farbehi, Ralph Patrick, Aude Dorison, Munira Xaymardan, Vaibhao Janbandhu, Katharina Wystub-Lis, Joshua W. K. Ho, Robert E. Nordon, Richard P. Harvey
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0201690

Strap associates with Csde1 and affects expression of select Csde1-bound transcripts
Cited by: 5
Author(s): Kat Moore, Nurcan Yağcı, Floris van Alphen, Alexander B. Meijer, Peter A.C. ’t Hoen, Marieke von Lindern
Software Mentions: 4
Published: about 8 years ago

10.3389/fpls.2021.666310

Aux/IAA and ARF Gene Families in Salix suchowensis: Identification, Evolution, and Dynamic Transcriptome Profiling During the Plant Growth Process
Cited by: 9
Author(s): Suyun Wei, Yingnan Chen, Jing Hou, Yonghua Yang, Tongming Yin
Software Mentions: 4
Published: over 5 years ago

10.3389/fpls.2018.00049

Non-parent of Origin Expression of Numerous Effector Genes Indicates a Role of Gene Regulation in Host Adaption of the Hybrid Triticale Powdery Mildew Pathogen
Cited by: 28
Author(s): Coraline R. Praz, Fabrizio Menardo, Mark D. Robinson, Marion Müller, Thomas Wicker, Salim Bourras, Beat Keller
Software Mentions: 4
Published: over 8 years ago

10.7554/eLife.66749

Murine muscle stem cell response to perturbations of the neuromuscular junction are attenuated with aging
Cited by: 11
Author(s): Jacqueline Larouche, Mahir Mohiuddin, Jeongmoon J. Choi, Peter Ulintz, Paula Fraczek, Kaitlyn Sabin, Sethuramasundaram Pitchiaya, Sarah J Kurpiers, Jesus A. Castor-Macias, Wenxuan Liu, Robert Louis Hastings, Lemuel A. Brown, James F. Markworth, Kanishka de Silva, Benjamin Levi, Sofía D. Merajver, Gregorio Valdez, Joe V. Chakkalakal, Young C. Jang, Susan V. Brooks, Carlos A. Aguilar
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0251121

Melanocytes determine angiogenesis gene expression across human tissues
Cited by: 3
Author(s): Shirly Freilikhman, Marianna Halasi, Alal Eran, Irit Adini
Software Mentions: 4
Published: over 5 years ago

10.3389/fpls.2018.01222

Generalist and Specialist Mite Herbivores Induce Similar Defense Responses in Maize and Barley but Differ in Susceptibility to Benzoxazinoids
Cited by: 35
Author(s): Huyen Bui, Robert Greenhalgh, Alice Ruckert, Gunbharpur S. Gill, Sarah Lee, Ricardo A. Ramirez, Richard M. Clark
Software Mentions: 4
Published: about 8 years ago

10.7554/eLife.24570

EED orchestration of heart maturation through interaction with HDACs is H3K27me3-independent
Cited by: 36
Author(s): Shanshan Ai, Yong Peng, Chen Li, Fei Gu, Xianhong Yu, Yanzhu Yue, Qing Ma, Jinghai Chen, Zhiqiang Lin, Pingzhu Zhou, Huafeng Xie, Terence Prendiville, Wen Zheng, Yuli Liu, Stuart H. Orkin, Dazhi Wang, Jia Yu, William T. Pu, Aibin He
Software Mentions: 4
Published: over 9 years ago

10.1186/s12868-021-00622-7

Construction of competitive endogenous RNA network reveals regulatory role of long non-coding RNAs in intracranial aneurysm
Cited by: 7
Author(s): Yutong Pan, Jianing Lu, Biao Yang, Cameron Lenahan, Jianmin Zhang, Anwen Shao
Software Mentions: 4
Published: over 5 years ago

10.3389/fpls.2021.649634

Cotranscriptional and Posttranscriptional Features of the Transcriptome in Soybean Shoot Apex and Leaf
Cited by: 5
Author(s): Jiafu Zhu, Han Zhao, Fanjiang Kong, Baohui Liu, Min Liu, Zhicheng Dong
Software Mentions: 4
Published: over 5 years ago

10.3389/fpls.2020.588846

Genome-Wide Identification of Populus Malectin/Malectin-Like Domain-Containing Proteins and Expression Analyses Reveal Novel Candidates for Signaling and Regulation of Wood Development
Cited by: 8
Author(s): Vikash Kumar, Evgeniy N. Donev, Félix Barbut, Sunita Kushwah, Chanaka Mannapperuma, János Urbancsok, Ewa J. Mellerowicz
Software Mentions: 4
Published: almost 6 years ago

10.3389/fpls.2019.01249

Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence
Cited by: 9
Author(s): Anna Furches, David Kainer, Deborah Weighill, Annabel Large, Piet Jones, Angelica M. Walker, Jonathon Romero, João Gabriel Felipe Machado Gazolla, Wayne Joubert, Manesh Shah, Jared Streich, Priya Ranjan, Jeremy Schmutz, Avinash Sreedasyam, David Macaya‐Sanz, Nan Zhao, Madhavi Z. Martin, Xiaolan Rao, Richard A. Dixon, Stephen P. DiFazio, Timothy J. Tschaplinski, Jay Chen, Gerald A. Tuskan, Daniel Jacobson
Software Mentions: 4
Published: about 7 years ago

10.1186/s12872-021-02147-7

Integration of transcriptomic data identifies key hallmark genes in hypertrophic cardiomyopathy
Cited by: 2
Author(s): Jing Xu, Xiangdong Liu, Qiang Dai
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.64680

Urocortin-3 neurons in the mouse perifornical area promote infant-directed neglect and aggression
Cited by: 23
Author(s): Anita E. Autry, Wu Zheng, Vikrant Kapoor, Johannes Kohl, Dhananjay Bambah-Mukku, Nimrod D. Rubinstein, Brenda Marin-Rodriguez, Ilaria Carta, Victoria Sedwick, Ming Tang, Catherine Dulac
Software Mentions: 4
Published: about 5 years ago

10.15252/embr.201846557

Tamoxifen mechanically reprograms the tumor microenvironment via <scp>HIF</scp> ‐1A and reduces cancer cell survival
Cited by: 55
Author(s): Ernesto Cortés, Dariusz Lachowski, Benjamin Robinson, Müge Sarper, Jaakko Teppo, Stephen D. Thorpe, Tyler J Lieberthal, Kenji Iwamoto, David A. Lee, Mariko Okada‐Hatakeyama, Markku Varjosalo, Armando E. del Río Hernández
Software Mentions: 4
Published: almost 8 years ago

10.3389/fpls.2018.01209

Nuclear Speckle RNA Binding Proteins Remodel Alternative Splicing and the Non-coding Arabidopsis Transcriptome to Regulate a Cross-Talk Between Auxin and Immune Responses
Cited by: 39
Author(s): Jérémie Bazin, Natali Romero, Richard Rigo, Céline Charon, Thomas Blein, Federico Ariel, Martín Crespi
Software Mentions: 4
Published: about 8 years ago

10.3389/fpls.2020.587185

Comprehensive Identification and Expression Profiling of Circular RNAs During Nodule Development in Phaseolus vulgaris
Cited by: 9
Author(s): Zhihua Wu, Wen Huang, Erdai Qin, Shuo Liu, Huan Liu, Aleel K. Grennan, Hong Liu, Rui Qin
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0181902

EINCR1 is an EGF inducible lincRNA overexpressed in lung adenocarcinomas
Cited by: 4
Author(s): Karol Nowicki-Osuch, Yaoyong Li, Mairi Challinor, Dave T. Gerrard, Neil A. Hanley, Andrew D. Sharrocks
Software Mentions: 4
Published: about 9 years ago

10.15252/embr.201948882

Mitochondrial protein biogenesis in the synapse is supported by local translation
Cited by: 56
Author(s): Bożena Kuźniewska, Dominik Cysewski, Michał Wasilewski, Paulina Sakowska, Jacek Miłek, Tomasz M. Kuliński, M. Winiarski, Paweł Kozielewicz, Ewelina Knapska, Michał Dadlez, Agnieszka Chacińska, Andrzej Dziembowski, Magdalena Dziembowska
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0245602

Cabozantinib can block growth of neuroendocrine prostate cancer patient-derived xenografts by disrupting tumor vasculature
Cited by: 4
Author(s): Mark P. Labrecque, Lisha G. Brown, Ilsa M. Coleman, Holly M. Nguyen, Daniel W. Lin, Eva Corey, Peter S. Nelson, Colm Morrissey
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0117818

mRNA Profiling Reveals Determinants of Trastuzumab Efficiency in HER2-Positive Breast Cancer
Cited by: 33
Author(s): Silvia von der Heyde, Sven Wagner, Czerny Alexander, M. Nietert, Fabian Ludewig, Gabriela Salinas-Riester, Dorit Arlt, Tim Beißbarth
Software Mentions: 4
Published: over 11 years ago

10.18632/aging.103516

ASNEO: Identification of personalized alternative splicing based neoantigens with RNA-seq
Cited by: 18
Author(s): Zhanbing Zhang, Chi Zhou, Lihua Tang, Yukang Gong, Zhiting Wei, Gongchen Zhang, Feng Wang, Qi Liu, Jing Yu
Software Mentions: 4
Published: about 6 years ago

10.7554/eLife.65856

CRISPR-based functional genomics in human dendritic cells
Cited by: 10
Author(s): Marco Jost, Amy N. Jacobson, Jeffrey A. Hussmann, Giana Cirolia, Michael A. Fischbach, Jonathan S. Weissman
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.57603

Endothelial TGF-β signaling instructs smooth muscle cell development in the cardiac outflow tract
Cited by: 16
Author(s): Giulia L. M. Boezio, Anabela Bensimon-Brito, Janett Piesker, Stefan Guenther, Christian S. M. Helker, Didier Y.R. Stainier
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0228514

Innate immune gene expression in Acropora palmata is consistent despite variance in yearly disease events
Cited by: 12
Author(s): Benjamin Young, Xaymara M. Serrano, Stephanie M. Rosales, Margaret W. Miller, Dana E. Williams, Nikki Traylor-Knowles
Software Mentions: 4
Published: almost 6 years ago

10.7554/eLife.56221

Ageing compromises mouse thymus function and remodels epithelial cell differentiation
Cited by: 83
Author(s): Jeanette Baran-Gale, Michael D. Morgan, Stefano Maio, Fatima Dhalla, Irene Calvo‐Asensio, Mary E. Deadman, Adam E. Handel, Ashley Maynard, Steven Chen, Foad Green, Rene Sit, Norma Neff, Spyros Darmanis, Weilun Tan, Andy P May, John C. Marioni, Chris P. Ponting, Georg A. Holländer
Software Mentions: 4
Published: about 6 years ago

10.1186/s12885-019-5501-z

Elucidating the transcriptional program of feline injection-site sarcoma using a cross-species mRNA-sequencing approach
Cited by: 7
Author(s): Qi Wei, Stephen A. Ramsey, Maureen K. Larson, Noah Berlow, Donasian O. Ochola, Christopher Shiprack, Amita Kashyap, Bernard Séguin, Charles Keller, Christiane V. Löhr
Software Mentions: 4
Published: over 7 years ago

10.3389/fpls.2021.612382

High-Resolution Transcriptome Atlas and Improved Genome Assembly of Common Buckwheat, Fagopyrum esculentum
Cited by: 15
Author(s): Aleksey A. Penin, Artem S. Kasianov, Anna V. Klepikova, Ilya Kirov, Evgeny S. Gerasimov, А Н Фесенко, Maria D. Logacheva
Software Mentions: 4
Published: over 5 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: about 5 years ago

10.1186/s12920-020-00785-y

Transcriptome analysis of peripheral whole blood identifies crucial lncRNAs implicated in childhood asthma
Cited by: 12
Author(s): Peiyan Zheng, Chen Huang, Dongliang Leng, Baoqing Sun, Xiaohua Douglas Zhang
Software Mentions: 4
Published: about 6 years ago

10.3389/fpls.2020.00180

Distinctive Gene Expression Patterns Define Endodormancy to Ecodormancy Transition in Apricot and Peach
Cited by: 32
Author(s): Jiali Yu, Anna O. Conrad, Véronique Decroocq, Tetyana Zhebentyayeva, Daniel E. Williams, Dennis Bennett, Guillaume Roch, Jean Marc Audergon, Christopher Dardick, Zongrang Liu, Albert G. Abbott, Margaret Staton
Software Mentions: 4
Published: over 6 years ago

10.3389/fphys.2021.616055

Phenotypic Changes in T Cell and Macrophage Subtypes in Perivascular Adipose Tissues Precede High-Fat Diet-Induced Hypertension
Cited by: 6
Author(s): Ramya Kumar, Yongliang Yang, Andres Contreras, Hannah Garver, Sudin Bhattacharya, Gregory D. Fink, Cheryl E. Rockwell, Stephanie W. Watts
Software Mentions: 4
Published: over 5 years ago

10.1186/s12920-020-00772-3

Expression correlation attenuates within and between key signaling pathways in chronic kidney disease
Cited by: 9
Author(s): Hui Yu, Dan-Qian Chen, Olufunmilola Oyebamiji, Zhao Yan, Yan Guo
Software Mentions: 4
Published: about 6 years ago

10.3390/antiox10040618

Differential and Overlapping Effects of Melatonin and Its Metabolites on Keratinocyte Function: Bioinformatics and Metabolic Analyses
Cited by: 4
Author(s): Joanna Stefan, Tae Kang Kim, Fiona Schedel, Zorica Janjetovic, David K. Crossman, Kerstin Steinbrink, Radomir M. Slominski, Jaroslaw W. Żmijewski, Meri K. Tulić, Russel J. Reíter, Konrad Kleszczyński, Andrzej Słomiński
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0192947

Modulation of the peripheral blood transcriptome by the ingestion of probiotic yoghurt and acidified milk in healthy, young men
Cited by: 26
Author(s): Kathryn Burton, Grégory Pimentel, Nadine Zangger, Nathalie Vionnet, Jocelyne Drai, P. G. McTernan, François P. Pralong, Mauro Delorenzi, Guy Vergères
Software Mentions: 4
Published: over 8 years ago

10.1186/s12920-020-00800-2

TOP2A and CENPF are synergistic master regulators activated in cervical cancer
Cited by: 17
Author(s): Beiwei Yu, Long Chen, Weina Zhang, Yue Li, Yibiao Zhang, Yuan Gao, Xianlin Teng, Libo Zou, Qian Wang, Huiying Jia, Xiangtao Liu, Hui Zheng, Ping Hou, Hongyan Yu, Ying Sun, Zhiqin Zhang, Ping Zhang, Liqin Zhang
Software Mentions: 4
Published: about 6 years ago

10.7554/eLife.56720

CARD14E138A signalling in keratinocytes induces TNF-dependent skin and systemic inflammation
Cited by: 14
Author(s): Joan Manils, Louise V. Webb, Ashleigh Howes, Julia Janzen, Stefan Boeing, Anne M. Bowcock, Steven C. Ley
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.22536

Transcriptional networks specifying homeostatic and inflammatory programs of gene expression in human aortic endothelial cells
Cited by: 68
Author(s): Nicholas T Hogan, Michael B. Whalen, Lindsey K Stolze, Nizar K Hadeli, Michael T. Lam, James R. Springstead, Christopher K. Glass, Casey E. Romanoski
Software Mentions: 4
Published: over 9 years ago

10.1136/jitc-2020-001610

Neoadjuvant chemoradiation alters biomarkers of anticancer immunotherapy responses in locally advanced rectal cancer
Cited by: 17
Author(s): Incheol Seo, Hye Won Lee, Sang Jun Byun, Jee Young Park, Hyeonji Min, Sung Hwan Lee, Ju-Seog Lee, Shin Kim, Sung Uk Bae
Software Mentions: 4
Published: over 5 years ago

10.1186/s40425-019-0556-6

Collagen density regulates the activity of tumor-infiltrating T cells
Cited by: 199
Author(s): Dorota Ewa Kuczek, Axel Larsen, Marie-Louise Thorseth, Marco Carretta, Adrija Kalviša, Majken Siersbæk, Ana Micaela Carnaz Simões, Anne Roslind, Lars H. Engelholm, Elfriede Noeßner, Marco Donia, Inge Marie Svane, Per thor Straten, Lars Grøntved, Daniel H. Madsen
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0192704

Immune checkpoint inhibitor PD-1 pathway is down-regulated in synovium at various stages of rheumatoid arthritis disease progression
Cited by: 71
Author(s): Yanxia Guo, Alice M. Walsh, Mary Canavan, Mihir D. Wechalekar, Suzanne Cole, Xiaoli Yin, Brian Scott, Matthew J. Loza, Carl Orr, Trudy McGarry, Michèle Bombardieri, Frances Humby, Susanna Proudman, Costantino Pitzalis, Malcolm D. Smith, Joshua R. Friedman, I.E. Anderson, Loui Madakamutil, Douglas J. Veale, Ursula Fearon, Sunil Nagpal
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0102398

JAGuaR: Junction Alignments to Genome for RNA-Seq Reads
Cited by: 51
Author(s): Yaron S.N. Butterfield, Maayan Kreitzman, Nina Thiessen, Richard Corbett, Yisu Li, Johnson Pang, P. Yussanne, Steven J.M. Jones, İnanç Birol
Software Mentions: 4
Published: about 12 years ago

10.4049/jimmunol.1901358

TNF-α Regulates Human Plasmacytoid Dendritic Cells by Suppressing IFN-α Production and Enhancing T Cell Activation
Cited by: 29
Author(s): Antonios Psarras, Agne Antanaviciute, Adewonuola Alase, Ian Carr, Miriam Wittmann, Paul Emery, George C. Tsokos, Edward M Vital
Software Mentions: 4
Published: over 5 years ago

10.15252/emmm.202013074

Impairment of the ER/mitochondria compartment in human cardiomyocytes with PLN p.Arg14del mutation
Cited by: 25
Author(s): Friederike Cuello, Anika E. Knaust, Umber Saleem, Malte Loos, Janice Raabe, Diogo Mosqueira, Sandra D. Laufer, Michaela Schweizer, Petra van der Kraak, Frederik Flenner, Bärbel Ulmer, Ingke Braren, Xiaoke Yin, Konstantinos Theofilatos, Jorge Ruiz-Orera, Giannino Patone, Birgit Klampe, Thomas G. Schulze, Angelika Piasecki, Yigal M. Pinto, Aryan Vink, Norbert Hübner, Siân E. Harding, Manuel Mayr, Chris Denning, Thomas Eschenhagen, Arne Hansen
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0226057

Estrogen receptor β exerts tumor suppressive effects in prostate cancer through repression of androgen receptor activity
Cited by: 16
Author(s): Surendra Chaurasiya, Scott Widmann, Cindy Botero, Chin-Yo Lin, Jan‐Åke Gustafsson, Anders Ström
Software Mentions: 4
Published: over 6 years ago

10.1186/s12862-017-0902-6

Transcriptomic insights into the genetic basis of mammalian limb diversity
Cited by: 19
Author(s): Jennifer Maier, Marcelo Rivas‐Astroza, Jenny Deng, Anna Dowling, Paige Oboikovitz, Xiaoyi Cao, Richard R. Behringer, Chris J. Cretekos, John J. Rasweiler, Sheng Zhong, Karen E. Sears
Software Mentions: 4
Published: over 9 years ago

10.1186/s12885-021-08388-1

Pooled CRISPR screening in pancreatic cancer cells implicates co-repressor complexes as a cause of multiple drug resistance via regulation of epithelial-to-mesenchymal transition
Cited by: 10
Author(s): Ryne C. Ramaker, Andrew A. Hardigan, Emily R. Gordon, Carter A Wright, R Myers, Sara J. Cooper
Software Mentions: 4
Published: over 5 years ago

10.7150/ijms.36255

Transcriptome Profiling Reveals Distinct Phenotype of Human Bone Marrow Mesenchymal Stem Cell-derived Hepatocyte-like cells
Cited by: 9
Author(s): Dongyan Shi, Jiaojiao Xin, Yingyan Lu, Wenchao Ding, Jing Jiang, Qian Zhou, Suwan Sun, Beibei Guo, Xingping Zhou, Li Jun
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pntd.0007640

Regulation of hepatic microRNAs in response to early stage Echinococcus multilocularis egg infection in C57BL/6 mice
Cited by: 11
Author(s): Ghalia Boubaker, Sebastian Strempel, Andrew Hemphill, Norbert Müller, Junhua Wang, Bruno Gottstein, Markus Spiliotis
Software Mentions: 4
Published: over 6 years ago

10.3389/fphys.2021.707116

Transcriptional Time Course After Rotator Cuff Tear
Cited by: 3
Author(s): Laura S Vasquez-Bolanos, Michael C. Gibbons, Severin Ruoss, Isabella T. Wu, Mario Vargas-Vila, Sydnee A Hyman, Mary C. Esparza, Donald C. Fithian, Joseph R. Lane, Anshuman Singh, Chanond A. Nasamran, Kathleen M. Fisch, Samuel R. Ward
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pntd.0005791

Proteogenomic analysis of the total and surface-exposed proteomes of Plasmodium vivax salivary gland sporozoites
Cited by: 65
Author(s): Kristian E. Swearingen, Scott E. Lindner, Erika L. Flannery, Ashley M. Vaughan, Robert Morrison, Rapatbhorn Patrapuvich, Cristian Koepfli, Ivan Müller, Aaron R. Jex, Robert L. Moritz, Stefan H. I. Kappe, Jetsumon Sattabongkot, Sebastian A. Mikolajczak
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pmed.1002309

Contribution of systemic and somatic factors to clinical response and resistance to PD-L1 blockade in urothelial cancer: An exploratory multi-omic analysis
Cited by: 231
Author(s): Alexandra Snyder, Tavi Nathanson, Samuel A. Funt, Arun Ahuja, Jacqueline L. Buros, Matthew D. Hellmann, Eliza Chang, Bülent Arman Aksoy, Hikmat Al‐Ahmadie, Erik Yusko, Marissa Vignali, Sharon Benzeno, Mariel Elena Boyd, Meredith Maisie Moran, Gopa Iyer, Harlan Robins, Elaine R. Mardis, Taha Merghoub, Jeff Hammerbacher, Jonathan E. Rosenberg, Dean F. Bajorin
Software Mentions: 4
Published: over 9 years ago

10.1084/jem.20201729

Yolk sac, but not hematopoietic stem cell–derived progenitors, sustain erythropoiesis throughout murine embryonic life
Cited by: 40
Author(s): Francisca Soares-da-Silva, Laina Freyer, Ramy Elsaid, Odile Burlen-Defranoux, Lorea Iturri, Odile Sismeiro, Perpétua Pinto-do-Ó, Elisa Gomez Perdiguero, Ana Cumano
Software Mentions: 4
Published: over 5 years ago

10.1084/jem.20190430

An anti-CRF antibody suppresses the HPA axis and reverses stress-induced phenotypes
Cited by: 7
Author(s): Hunter S. Futch, Karen N. McFarland, Brenda D. Moore, M. Zino Kuhn, Benoit I. Giasson, Thomas B. Ladd, Karen A. Scott, Melanie R. Shapiro, Rachel L. Nosacka, Marshall S. Goodwin, Yong Ran, Pedro Cruz, Doojin Ryu, Cara L. Croft, Yona Levites, Christopher Janus, Paramita Chakrabarty, Andrew R. Judge, Todd M. Brusko, Annette D. de Kloet, Eric G. Krause, Todd E. Golde
Software Mentions: 4
Published: about 7 years ago

10.1080/07853890.2020.1858234

Increased expression of hypoxia-induced factor 1α mRNA and its related genes in myeloid blood cells from critically ill COVID-19 patients
Cited by: 40
Author(s): Keiko Taniguchi‐Ponciano, Eduardo Vadillo, Héctor Mayani, César González-Bonilla, Javier Torres, Abraham Majluf, Guillermo Flores‐Padilla, Niels H. Wacher, Juan Carlos Galán, Eduardo Ferat‐Osorio, Francisco Blanco-Favéla, Constantino López-Macı́as, Aldo Ferreira‐Hermosillo, Claudia Ramírez‐Rentería, Eduardo Peña-Martínez, Gloria Silva-Román, Sandra Vela-Patiño, Carlos Mata-Lozano, Roberto Carvente-Garcia, Lourdes Basurto-Acevedo, Renata Saucedo, Patricia Piña‐Sánchez, Antonieta Chávez‐González, Daniel Marrero‐Rodríguez, Moisés Mercado
Software Mentions: 4
Published: almost 6 years ago

10.1084/jem.20201290

Neuronal metabotropic glutamate receptor 8 protects against neurodegeneration in CNS inflammation
Cited by: 16
Author(s): Marcel S Woo, Friederike Ufer, Nicola Rothammer, Giovanni Di Liberto, Lars Binkle, Undine Haferkamp, Jana K. Sonner, Jan Broder Engler, Sönke Hornig, Simone Bauer, Ingrid Wagner, Kristóf Égervári, Jacob Raber, Robert M. Duvoisin, Ole Pleß, Doron Merkler, Manuel A. Friese
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1006636

TFAP2 paralogs regulate melanocyte differentiation in parallel with MITF
Cited by: 69
Author(s): Hannah Seberg, Eric Van Otterloo, Stacie K. Loftus, Huan Liu, Greg Bonde, Ramakrishna Sompallae, Derek Gildea, Juan Francisco de Paz Santana, J. Robert Manak, William J. Pavan, Trevor Williams, Robert A. Cornell
Software Mentions: 4
Published: over 9 years ago

10.7150/ijbs.60674

Ailanthus Altissima-derived Ailanthone enhances Gastric Cancer Cell Apoptosis by Inducing the Repression of Base Excision Repair by Downregulating p23 Expression
Cited by: 7
Author(s): Chunming Wang, Hua-Fu Li, Xiaokun Wang, Wu-Guo Li, Shan Qiao, Xing Xiao, Tong Hao, Wei Chen, Yawei Zhang, Haiyong Zhang, Wei Wu, Zhenran Hu, Guochao Zhao, Mingyu Huo, Yulong He, Changhua Zhang
Software Mentions: 4
Published: almost 6 years ago

10.3389/fphys.2020.01019

Genome-Wide Network of lncRNA–mRNA During Ovine Oocyte Development From Germinal Vesicle to Metaphase II in vitro
Cited by: 15
Author(s): Jun-Jie Wang, Menghan Niu, Teng Zhang, Wei Shen, Cao H
Software Mentions: 4
Published: about 6 years ago

10.1038/s41396-020-0729-9

Transcriptome plasticity underlying plant root colonization and insect invasion by Pseudomonas protegens
Cited by: 35
Author(s): Pilar Vesga, Pascale Flury, Jordan Vacheron, Christoph Keel, Daniel Croll, M. Maurhofer
Software Mentions: 4
Published: about 6 years ago

10.1084/jem.20190730

Single-cell profiling reveals an endothelium-mediated immunomodulatory pathway in the eye choroid
Cited by: 47
Author(s): Guillermo L. Lehmann, Christin Hanke-Gogokhia, Yang Hu, Rohan Bareja, Zelda Salfati, Michael Ginsberg, Daniel J. Nolan, Santiago P. Méndez-Huergo, Tomás Dalotto-Moreno, Alexandre Wojcinski, Francisca Ochoa, Siyuan Zeng, Juan P. Cerliani, Lampros Panagis, Patrick J. Zager, Robert F. Mullins, Shuntaro Ogura, Gerard A. Lutty, Jakyung Bang, Jonathan H. Zippin, Carmelo Romano, Gabriel A. Rabinovich, Olivier Elemento, Alexandra L. Joyner, Shahin Rafii, Enrique Rodríguez-Boulan, Ignacio Benedicto
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0256148

RNA-sequencing of AVPV and ARH reveals vastly different temporal and transcriptomic responses to estradiol in the female rat hypothalamus
Cited by: 5
Author(s): Margaret A. Mohr, Angela Wong, Gauthaman Sukumar, Clifton L. Dalgard, Weizhe Hong, Tao Wu, Ye Wu, Paul E. Micevych
Software Mentions: 4
Published: about 5 years ago

10.1186/s12870-016-0926-x

Identification of nuclear genes controlling chlorophyll synthesis in barley by RNA-seq
Cited by: 9
Author(s): Nikolay A. Shmakov, Gennady V. Vasiliev, Natalya V. Shatskaya, А. В. Дорошков, Е. И. Гордеева, D. A. Afonnikov, Е. К. Хлесткина
Software Mentions: 4
Published: almost 10 years ago

10.1038/s41388-018-0273-5

KMT2C mediates the estrogen dependence of breast cancer through regulation of ERα enhancer function
Cited by: 91
Author(s): Kinisha Gala, Qing Li, Amit Sinha, Pedram Razavi, M. Dorso, Francisco Sanchez‐Vega, Young Rock Chung, Ronald C. Hendrickson, James J. Hsieh, Michael F. Berger, Nikolaus Schultz, Alessandro Pastore, Omar Abdel‐Wahab, Sarat Chandarlapaty
Software Mentions: 4
Published: over 8 years ago

10.15252/embj.2020105564

Integrator is recruited to promoter‐proximally paused RNA Pol II to generate Caenorhabditis elegans piRNA precursors
Cited by: 21
Author(s): Toni Beltran, Eleni Pahita, Subhanita Ghosh, Boris Lenhard, Peter Sarkies
Software Mentions: 4
Published: almost 6 years ago

10.15252/embj.2019103932

<scp>RNF</scp> 43 truncations trap <scp>CK</scp> 1 to drive niche‐independent self‐renewal in cancer
Cited by: 24
Author(s): Maureen Spit, Nicola Fenderico, Ingrid Jordens, Tomasz Radaszkiewicz, Rik G.H. Lindeboom, Jeroen M. Bugter, Alba Cristobal, Lars Ootes, Max van Osch, Eline Janssen, Kim E. Boonekamp, Kateřina Hanáková, David Potěšil, Zbyněk Zdráhal, Sylvia F. Boj, Jan Paul Medema, Vı́tězslav Bryja, Bon‐Kyoung Koo, Michiel Vermeulen, Madelon M. Maurice
Software Mentions: 4
Published: about 6 years ago

10.1093/hmg/ddab140

Human photoreceptor cells from different macular subregions have distinct transcriptional profiles
Cited by: 15
Author(s): Andrew P. Voigt, Nathaniel K. Mullin, S. Scott Whitmore, Adam P. DeLuca, Erin R Burnight, Xiuying Liu, Budd A. Tucker, Todd E. Scheetz, Edwin M Stone, Robert F. Mullins
Software Mentions: 4
Published: over 5 years ago

10.1534/g3.119.400998

A Collection of Pre-mRNA Splicing Mutants in Arabidopsis thaliana
Cited by: 20
Author(s): Tohru Kanno, Peter Venhuizen, Ming‐Tsung Wu, Phebe Chiou, Chia-Liang Chang, Maria Kalyna, A. J. M. Matzke, Marjori Matzke
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pgen.1008464

CRISPR editing of sftb-1/SF3B1 in Caenorhabditis elegans allows the identification of synthetic interactions with cancer-related mutations and the chemical inhibition of splicing
Cited by: 13
Author(s): Xènia Serrat, Dmytro Kukhtar, Eric Cornes, Anna Esteve‐Codina, Helena Benlloch, Germano Cecere, Julián Cerón
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12865-021-00428-6

Transcriptomics of type 2 diabetic and healthy human neutrophils
Cited by: 8
Author(s): Sarah E. Kleinstein, Jamison McCorrison, A. Razzaque Ahmed, Hatice Hastürk, Thomas E. Van Dyke, Marcelo Freire
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2018.00482

Transcriptomic Alterations in Lung Adenocarcinoma Unveil New Mechanisms Targeted by the TBX2 Subfamily of Tumor Suppressor Genes
Cited by: 10
Author(s): Athar Khalil, Batoul Dekmak, Fouad Boulos, Jake Kantrowitz, Avrum Spira, Junya Fujimoto, Humam Kadara, Nehmé El-Hachem, Georges Nemer
Software Mentions: 4
Published: almost 8 years ago

10.3389/fonc.2021.652063

Machine Learning Applicability for Classification of PAD/VCD Chemotherapy Response Using 53 Multiple Myeloma RNA Sequencing Profiles
Cited by: 15
Author(s): Nicolas Borisov, Anna Sergeeva, Maria Suntsova, Mikhail Raevskiy, Нуршат Гайфуллин, Л. П. Менделеева, Alexander Gudkov, Maria Nareiko, Andrew Garazha, Victor Tkachev, Xinmin Li, Maxim Sorokin, В. Л. Сурин, Anton Buzdin
Software Mentions: 4
Published: over 5 years ago

10.18632/aging.101691

SNCA overexpression disturbs hippocampal gene expression trajectories in midlife
Cited by: 6
Author(s): Thomas Hentrich, Zinah Wassouf, Olaf Rieß, Julia M. Schulze‐Hentrich
Software Mentions: 4
Published: almost 8 years ago

10.3389/fonc.2021.705627

Decoupling Lineage-Associated Genes in Acute Myeloid Leukemia Reveals Inflammatory and Metabolic Signatures Associated With Outcomes
Cited by: 4
Author(s): Hussein A. Abbas, Vakul Mohanty, Ruiping Wang, Yu-Ting Huang, Shaoheng Liang, Feng Wang, Jianhua Zhang, Yihua Qiu, Chenyue W. Hu, Amina A. Qutub, Monique Dail, Christopher R. Bolen, Naval Daver, Marina Konopleva, Andrew Futreal, Ken Chen, Linghua Wang, Steven M. Kornblau
Software Mentions: 4
Published: about 5 years ago

10.3389/fnins.2021.639527

Cell-Type-Specific Gene Modules Related to the Regional Homogeneity of Spontaneous Brain Activity and Their Associations With Common Brain Disorders
Cited by: 5
Author(s): Junlin Shen, Bing‐Bing Yang, Zhonghua Xie, Heng Wu, Zhanye Zheng, Jianhua Wang, Ping Wang, Peng Zhang, Wei Li, Zhaoxiang Ye, Chunshui Yu
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1008181

Hepatitis C virus leaves an epigenetic signature post cure of infection by direct-acting antivirals
Cited by: 101
Author(s): Shira Perez, Antony Kaspi, Tom Domovitz, Ateret Davidovich, Anat Lavi-Itzkovitz, Tomer Meirson, Jacinta A Holmes, Chia Yen Dai, Chung Feng Huang, Raymond T. Chung, Nimer Assy, Assam El‐Osta, Gur Yaari, Salomon M. Stemmer, Ming‐Lung Yu, Izhak Haviv, Meital Gal-Tanamy
Software Mentions: 4
Published: over 7 years ago

10.3390/genes8030090

Rapid Sampling of Escherichia coli After Changing Oxygen Conditions Reveals Transcriptional Dynamics
Cited by: 17
Author(s): Joachim von Wulffen, Andreas Ulmer, Günter Jäger, Oliver Sawodny, Ronny Feuer
Software Mentions: 4
Published: over 9 years ago

10.3389/fnins.2020.562292

Human iPSC-Derived Neuronal Cells From CTBP1-Mutated Patients Reveal Altered Expression of Neurodevelopmental Gene Networks
Cited by: 5
Author(s): S. Vijayalingam, Uthayashanker R. Ezekiel, Fenglian Xu, T. Subramanian, Elizabeth Geerling, Brittany Hoelscher, KayKay San, Aravinda Ganapathy, Kyle Pemberton, Eric Tycksen, Amelia K. Pinto, James D. Brien, David B. Beck, Wendy K. Chung, Christina A. Gurnett, G. Chinnadurai
Software Mentions: 4
Published: almost 6 years ago

10.1128/mBio.01959-21

Multifactorial Role of Mitochondria in Echinocandin Tolerance Revealed by Transcriptome Analysis of Drug-Tolerant Cells
Cited by: 13
Author(s): Rocio Garcia-Rubio, Cristina Jiménez‐Ortigosa, Lucius DeGregorio, Christopher Quinteros, Erika Shor, David S. Perlin
Software Mentions: 4
Published: about 5 years ago

10.15252/embj.2019103894

<scp>SCHENGEN</scp> receptor module drives localized <scp>ROS</scp> production and lignification in plant roots
Cited by: 67
Author(s): Satoshi Fujita, Damien De Bellis, Kai H. Edel, Philipp Köster, Tonni Grube Andersen, Emanuel Schmid‐Siegert, Valérie Dénervaud Tendon, Alexandre Pfister, Peter Marhavý, Robertas Ursache, Verónica G. Doblas, Marie Barberon, Jean Daraspe, Audrey Creff, Gwyneth Ingram, Jörg Kudla, Niko Geldner
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pgen.1006777

Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes
Cited by: 138
Author(s): Romain Blanc-Mathieu, Laetitia Perfus‐Barbeoch, Jean‐Marc Aury, Martine Da Rocha, Jérôme Gouzy, Erika Sallet, Cristina Martín-Jimenez, Marc Bailly‐Bechet, Philippe Castagnone‐Sereno, Jean‐François Flot, Djampa Kozlowski, Julie Cazareth, Arnaud Couloux, Corinne Da Silva, Julie Guy, Yujin Kim, Corinne Rancurel, Thomas Schiex, Pierre Abad, Patrick Wincker, Etienne G. J. Danchin
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pgen.1008076

Heterogeneous pathway activation and drug response modelled in colorectal-tumor-derived 3D cultures
Cited by: 57
Author(s): Dirk Schumacher, Geoffroy Andrieux, Karsten Boehnke, Marlen Keil, Alessandra Silvestri, Maxine Silvestrov, Ulrich Keilholz, Johannes Haybaeck, Gerrit Erdmann, Christoph Sachse, Markus F. Templin, Jens Hoffmann, Melanie Boerries, Reinhold Schäfer, Christian Regenbrecht
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pgen.1006778

Gene duplication and co-evolution of G1/S transcription factor specificity in fungi are essential for optimizing cell fitness
Cited by: 11
Author(s): Adi Hendler, Edgar M. Medina, Anastasiya Kishkevich, Mehtap Abu-Qarn, Steffi Klier, Nicolas E. Buchler, Robertus A.M. de Bruin, Amir Aharoni
Software Mentions: 4
Published: over 9 years ago

10.1128/mBio.00586-21

Intraspecies Transcriptional Profiling Reveals Key Regulators of Candida albicans Pathogenic Traits
Cited by: 13
Author(s): Joshua M. Wang, Andrew L. Woodruff, Matthew J. Dunn, Robert J. Fillinger, Richard J. Bennett, Matthew Anderson
Software Mentions: 4
Published: over 5 years ago

10.1128/mSystems.00495-20

The Stringent Stress Response Controls Proteases and Global Regulators under Optimal Growth Conditions in Pseudomonas aeruginosa
Cited by: 21
Author(s): Daniel Pletzer, Travis M. Blimkie, Heidi Wolfmeier, Yicong Li, Arjun Baghela, Ahwon Lee, Reza Falsafi, Robert E. W. Hancock
Software Mentions: 4
Published: about 6 years ago

10.1038/s41388-020-01429-2

Androgen receptor signaling regulates the transcriptome of prostate cancer cells by modulating global alternative splicing
Cited by: 21
Author(s): Kalpit Shah, Teresa Gagliano, L. H. Garland, Timothy O’Hanlon, Daria Bortolotti, Valentina Gentili, Roberta Rizzo, Georgios Giamas, Michael Dean
Software Mentions: 4
Published: about 6 years ago

10.7554/eLife.67312

YAP and TAZ are transcriptional co-activators of AP-1 proteins and STAT3 during breast cellular transformation
Cited by: 43
Author(s): Lizhi He, Henry E. Pratt, Mingshi Gao, Fengxiang Wei, Zhiping Weng, Kevin Struhl
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pgen.1007807

Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay
Cited by: 79
Author(s): Michael J. Roach, Daniel L. Johnson, Jöerg Bohlmann, H. J. J. Van Vuuren, Steven J.M. Jones, Isak S. Pretorius, Simon A. Schmidt, Anthony R. Borneman
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pgen.1008273

BCDIN3D regulates tRNAHis 3’ fragment processing
Cited by: 21
Author(s): Calder Reinsborough, Hélène Ipas, Nathan S. Abell, Ryan M. Nottingham, Jun Yao, Sravan K. Devanathan, Samantha B. Shelton, Alan M. Lambowitz, Blerta Xhemalçe
Software Mentions: 4
Published: about 7 years ago

10.3389/fneur.2021.691631

Hippocampal Transcriptome Changes After Subarachnoid Hemorrhage in Mice
Cited by: 4
Author(s): Angelique Regnier-Golanov, Friederike Dündar, Paul Zumbo, Doron Betel, Magda S Hernandez, Leif E. Peterson, Eng H. Lo, Eugene V. Golanov, Gavin W. Britz
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-017-4411-1

A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of Populus trees
Cited by: 22
Author(s): Ogonna Obudulu, Niklas Mähler, Tomas Skotare, Joakim Bygdell, Ilka Nacif Abreu, Maria Ahnlund, Madhavi Latha Gandla, Anna Petterle, Thomas Moritz, Torgeir R. Hvidsten, Leif J. Jönsson, Gunnar Wingsle, Johan Trygg, Hannele Tuominen
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pgen.1007588

Numerous recursive sites contribute to accuracy of splicing in long introns in flies
Cited by: 17
Author(s): Athma A. Pai, Joseph M. Paggi, Paul Yan, Karen Adelman, Christopher B. Burge
Software Mentions: 4
Published: about 8 years ago

10.1038/s41398-019-0426-5

Alcohol-responsive genes identified in human iPSC-derived neural cultures
Cited by: 15
Author(s): Kevin P. Jensen, Richard Lieberman, Henry R. Kranzler, Joel Gelernter, Kaitlin Clinton, Jonathan Covault
Software Mentions: 4
Published: over 7 years ago

10.18632/aging.202780

circRNA expression profiling of colon tissue from mesalazine-treated mouse of inflammatory bowel disease reveals an important circRNA-miRNA-mRNA pathway
Cited by: 8
Author(s): Wei Zhou, Haiyin Zhang, Y. B. Pan, Yingbin Xu, Yongqing Cao
Software Mentions: 4
Published: over 5 years ago

10.3390/genes11060709

Extensive Involvement of Alternative Polyadenylation in Single-Nucleus Neurons
Cited by: 3
Author(s): Ying Wang, Weixing Feng, Siwen Xu, Bo He
Software Mentions: 4
Published: over 6 years ago

10.15252/embj.2019103667

Arabidopsis shoot stem cells display dynamic transcription and <scp>DNA</scp> methylation patterns
Cited by: 40
Author(s): Ruben Gutzat, Klaus Rembart, Thomas Nußbaumer, Falko Hofmann, Rahul Pisupati, Gabriele Bradamante, Nina Daubel, Angelika Gaidora, Nicole Lettner, Mattia Donà, Magnus Nordborg, Michael D. Nodine, Ortrun Mittelsten Scheid
Software Mentions: 4
Published: about 6 years ago

Projects: cran: STAR

Science Score: 100/100

Bonuses:

Papers Mentioning STAR 5,759