pypi: voom | Projects | Ecosyste.ms: Papers

10.5808/GI.2020.18.1.e8

Bioinformatics services for analyzing massive genomic datasets
Cited by: 6
Author(s): Gunhwan Ko, Pan-Gyu Kim, Youngbum Cho, Seongmun Jeong, Jae-Yoon Kim, Kyoung Hyoun Kim, Hoyeon Lee, Jiyeon Han, Namhee Yu, Seokjin Ham, Insoon Jang, Byung Ha Kang, Sunguk Shin, Lian Kim, Seungwon Lee, Dougu Nam, Jihyun F. Kim, Namshin Kim, Seon‐Young Kim, Sanghyuk Lee, Tae-Young Roh, Byung-Wook Lee
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0199392

Whole blood transcriptome changes following controlled human malaria infection in malaria pre-exposed volunteers correlate with parasite prepatent period
Cited by: 17
Author(s): Julian Rothen, Carl Murie, Jason Carnes, Atashi Anupama, Salim Abdulla, Mwajuma Chemba, Maxmillian Mpina, Marcel Tanner, B. Kim Lee Sim, Stephen L. Hoffman, Raphaël Gottardo, Claudia Daubenberger, Ken Stuart
Software Mentions: 3
Published: over 6 years ago

10.1038/srep24061

Empirical insights into the stochasticity of small RNA sequencing
Cited by: 5
Author(s): Li‐Xuan Qin, Thomas Tuschl, Samuel Singer
Software Mentions: 3
Published: over 8 years ago

10.1038/srep27514

Cross-talk between AMPK and EGFR dependent Signaling in Non-Small Cell Lung Cancer
Cited by: 8
Author(s): Paurush Praveen, H. Hülsmann, Holger Sültmann, Ruprecht Kuner, Holger Fröhlich
Software Mentions: 3
Published: over 8 years ago

10.1186/s12974-019-1628-8

Midbrain microglia mediate a specific immunosuppressive response under inflammatory conditions
Cited by: 28
Author(s): Miguel A. Abellanas, Marta Zamarbide, Leyre Basurco, Esther Luquin, Marta Garcı́a-Granero, Pedro Clavero, Patxi San Martín-Úriz, Amaia Vilas, Elisa Mengual, Sandra Hervás-Stubbs, Marta Aymerich
Software Mentions: 3
Published: almost 5 years ago

10.18632/oncotarget.8308

Dynamic epigenetic changes to <i>VHL</i> occur with sunitinib in metastatic clear cell renal cancer
Cited by: 14
Author(s): Grant D. Stewart, Thomas Powles, Christophe Van Neste, Alison Meynert, Fiach C. O’Mahony, A. Douglas Laird, Dieter Deforce, Filip Van Nieuwerburgh, Geert Trooskens, Wim Van Criekinge, Tim De Meyer, David J. Harrison
Software Mentions: 3
Published: over 8 years ago

10.7554/eLife.52707

The transcriptomic response of cells to a drug combination is more than the sum of the responses to the monotherapies
Cited by: 19
Author(s): Jennifer E. L. Diaz, Mehmet Eren Ahsen, Thomas Schaffter, Xintong Chen, Ronald Realubit, Charles Karan, Andrea Califano, Bojan Losic, Gustavo Stolovitzky
Software Mentions: 3
Published: about 4 years ago

10.7554/eLife.10809

An aspartyl protease defines a novel pathway for export of Toxoplasma proteins into the host cell
Cited by: 93
Author(s): Michael Coffey, Brad E. Sleebs, Alessandro D. Uboldi, Alexandra L. Garnham, Magdalena Franco, Nicole D. Marino, Michael W. Panas, David J. P. Ferguson, Marta Enciso, Matthew T O'Neill, Sash Lopaticki, Rebecca J. Stewart, Grant Dewson, Gordon K. Smyth, Brian J. Smith, Seth L. Masters, John C. Boothroyd, Justin A Boddey, Christopher J. Tonkin
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0159197

Comparative Transcriptome Profiling of Human Foreskin Fibroblasts Infected with the Sylvio and Y Strains of Trypanosoma cruzi
Cited by: 22
Author(s): Genevieve A. Houston-Ludlam, Ashton T. Belew, Najib M. El-Sayed
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2164-15-565

Highly sensitive amplicon-based transcript quantification by semiconductor sequencing
Cited by: 28
Author(s): Jitao David Zhang, Tobias Schindler, Erich Küng, Martin Ebeling, Ulrich Certa
Software Mentions: 2
Published: over 10 years ago

10.1155/2020/4737969

RNA-Seq-Based Breast Cancer Subtypes Classification Using Machine Learning Approaches
Cited by: 12
Author(s): Zhezhou Yu, Zhuo Wang, Xiangchun Yu, Zhe Zhang
Software Mentions: 2
Published: about 4 years ago

10.1186/s12931-020-01336-w

Heme metabolism genes Downregulated in COPD Cachexia
Cited by: 3
Author(s): A.C. Wilson, Preeti Lakshman Kumar, Sool Lee, Margaret M. Parker, Itika Arora, Jarrett Morrow, Emiel F.M. Wouters, Richard Casaburi, Stephen I. Rennard, David A. Lomas, Àlvar Agustí, Ruth Tal‐Singer, Mark T. Dransfield, James M. Wells, Surya P. Bhatt, George R. Washko, Victor J. Thannickal, Hemant K. Tiwari, Craig P. Hersh, Peter J. Castaldi, Edwin K. Silverman, Merry-Lynn McDonald
Software Mentions: 2
Published: over 4 years ago

10.3390/cancers12113169

Id1 and PD-1 Combined Blockade Impairs Tumor Growth and Survival of KRAS-mutant Lung Cancer by Stimulating PD-L1 Expression and Tumor Infiltrating CD8+ T Cells
Cited by: 8
Author(s): Iosune Baraibar, Marta Cimavilla Román, María Rodríguez‐Remírez, Inés López, Anna Vilalta, Elizabeth Guruceaga, Margarita Ecay, María Collantes, Teresa Lozano, Diego Alignani, A. Puyalto, Carolina Oliver, Sergio Ortiz‐Espinosa, Haritz Moreno, María Dolores Torregrosa, Christian Rolfo, Christian Caglevic, David García-Ros, María Villalba-Esparza, Carlos de Andrea, Silvestre Vicent, Rubén Pı́o, Juan José Lasarte, Alfonso Calvo, Daniel Ajona, Ignacio Gil‐Bazo
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pgen.1008295

Age- and stress-associated C. elegans granulins impair lysosomal function and induce a compensatory HLH-30/TFEB transcriptional response
Cited by: 17
Author(s): Victoria Butler, Fuying Gao, Christian I. Corrales, Wilian A. Cortopassi, Benjamı́n Caballero, Mihir Vohra, Kaveh Ashrafi, Ana María Cuervo, Matthew P. Jacobson, Giovanni Coppola, Aimee W. Kao
Software Mentions: 2
Published: over 5 years ago

10.1186/s12920-019-0542-3

Integrative analysis of loss-of-function variants in clinical and genomic data reveals novel genes associated with cardiovascular traits
Cited by: 8
Author(s): Benjamin S. Glicksberg, Letizia Amadori, Nicholas K. Akers, Katyayani Sukhavasi, Oscar Franzén, Li Li, Gillian M. Belbin, Kristin L. Akers, Khader Shameer, Marcus A. Badgeley, Kipp W. Johnson, Ben Readhead, Bruce Darrow, Eimear E. Kenny, Christer Betsholtz, Raili Ermel, Josefin Skogsberg, Arno Ruusalepp, Eric E. Schadt, Joel T. Dudley, Hongxia Ren, Jason C. Kovacic, Chiara Giannarelli, Shuyu D. Li, Johan Björkegren, Rong Chen
Software Mentions: 2
Published: over 5 years ago

10.15252/emmm.201910681

Neutrophils suppress tumor‐infiltrating T cells in colon cancer via matrix metalloproteinase‐mediated activation of <scp>TGF</scp> β
Cited by: 85
Author(s): Markus Germann, Nadine Zangger, Marc‐Olivier Sauvain, Christine Sempoux, Amber D. Bowler, Pratyaksha Wirapati, Lana E. Kandalaft, Mauro Delorenzi, Sabine Tejpar, George Coukos, Freddy Radtke
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12933-017-0567-x

Joint analysis of left ventricular expression and circulating plasma levels of Omentin after myocardial ischemia
Cited by: 13
Author(s): Louis A. Saddic, Sarah M. Nicoloro, Olga T. Gupta, Michael P. Czech, Joshua M. Gorham, Stanton K. Shernan, Christine E. Seidman, J. G. Seidman, Sary F. Aranki, Simon C. Body, Timothy P. Fitzgibbons, Jochen D. Muehlschlegel
Software Mentions: 2
Published: over 7 years ago

10.1186/s13059-018-1451-z

Post-translational buffering leads to convergent protein expression levels between primates
Cited by: 32
Author(s): Sidney H. Wang, Chiaowen Joyce Hsiao, Zia Khan, Jonathan K. Pritchard
Software Mentions: 2
Published: over 6 years ago

10.1186/s12936-021-03839-3

Early whole blood transcriptional responses to radiation-attenuated Plasmodium falciparum sporozoite vaccination in malaria naïve and malaria pre-exposed adult volunteers
Cited by: 5
Author(s): Fergal J. Duffy, Ying Du, Jason Carnes, Judith E. Epstein, Stephen L. Hoffman, Salim Abdulla, Said Jongo, Maxmillian Mpina, Claudia Daubenberger, John D. Aitchison, Ken Stuart
Software Mentions: 2
Published: over 3 years ago

10.1128/mSphere.00541-18

Regulation of Yeast-to-Hyphae Transition in Yarrowia lipolytica
Cited by: 32
Author(s): Kyle R. Pomraning, Erin L. Bredeweg, Eduard J. Kerkhoven, Kerrie Barry, Sajeet Haridas, Hope Hundley, Kurt LaButti, Anna Lipzen, Mi Yan, Jon Magnuson, Blake A. Simmons, Igor V. Grigoriev, Jens Nielsen, Scott E. Baker
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12864-016-2668-4

Perturbation of the two-component signal transduction system, BprRS, results in attenuated virulence and motility defects in Burkholderia pseudomallei
Cited by: 18
Author(s): Natalie R. Lazar Adler, Elizabeth M. Allwood, Deanna Deveson Lucas, Paul F. Harrison, Stephen C. Watts, Alexandra Dimitropoulos, Puthayalai Treerat, Priyangi Anupama Alwis, Rodney J. Devenish, Mark Prescott, Brenda Govan, Ben Adler, Marina Harper, John D. Boyce
Software Mentions: 2
Published: over 8 years ago

10.3390/metabo10110459

Potent Antifungal Properties of Dimeric Acylphloroglucinols from Hypericum mexicanum and Mechanism of Action of a Highly Active 3′Prenyl Uliginosin B
Cited by: 2
Author(s): Noemi Tocci, Tobias Weil, Daniele Perenzoni, Marco Moretto, Nicolai M. Nürk, Santiago Madriñán, Ruggero Ferrazza, Graziano Guella, Fulvio Mattivi
Software Mentions: 2
Published: about 4 years ago

10.1038/s41389-017-0024-4

HNRNPH1 is required for rhabdomyosarcoma cell growth and survival
Cited by: 19
Author(s): Yanfeng Li, Jesse Bakke, David Finkelstein, Hu Zeng, Jing Wu, Taosheng Chen
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12864-018-4828-1

Landscape of transcriptional deregulation in lung cancer
Cited by: 24
Author(s): Shu Zhang, Mingfa Li, Hongbin Ji, Zhaoyuan Fang
Software Mentions: 2
Published: over 6 years ago

10.15252/msb.20199405

Drug mechanism‐of‐action discovery through the integration of pharmacological and <scp>CRISPR</scp> screens
Cited by: 55
Author(s): Emanuel Gonçalvès, Aldo Segura‐Cabrera, Clare Pacini, Gabriele Picco, Fiona M. Behan, Patricia Jaaks, Elizabeth A. Coker, Dieudonne van der Meer, Andrew Barthorpe, Howard Lightfoot, Tatiana Mironenko, Alexandra Beck, Laura L. Richardson, Wanjuan Yang, Ermira Lleshi, James A. Hall, Charlotte Tolley, Caitlin Hall, Iman Mali, Frances Thomas, James A. Morris, Andrew R. Leach, James T. Lynch, Ben Sidders, Claire Crafter, Francesco Iorio, Stephen E. Fawell, Mathew J. Garnett
Software Mentions: 2
Published: over 4 years ago

10.1186/s12885-018-4373-y

Cholesterol synthesis pathway genes in prostate cancer are transcriptionally downregulated when tissue confounding is minimized
Cited by: 11
Author(s): Morten Rye, Helena Bertilsson, Maria Andersen, Kjersti Rise, Tone Frost Bathen, Finn Drabløs, May‐Britt Tessem
Software Mentions: 2
Published: over 6 years ago

10.7554/eLife.27406

Histone H3G34R mutation causes replication stress, homologous recombination defects and genomic instability in S. pombe
Cited by: 33
Author(s): Rajesh K Yadav, Carolyn Jablonowski, Alfonso G. Fernandez, Brandon R Lowe, Ryan A. Henry, David Finkelstein, Kevin J Barnum, Alison L. Pidoux, Yin-Ming Kuo, Jie Huang, Matthew J. O’Connell, Andrew J. Andrews, Arzu Onar‐Thomas, Robin C. Allshire, Janet F. Partridge
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0232411

Identification of miRNA signatures associated with radiation-induced late lung injury in mice
Cited by: 27
Author(s): Claude J. Rogers, Agnès Lukaszewicz, Jason Yamada-Hanff, Ewa D. Micewicz, Josephine A. Ratikan, Mark A. Starbird, Tim Miller, Kieu Cao Diem Nguyen, Jason T. Lee, Tove Olafsen, Keisuke S. Iwamoto, William H. McBride, Dörthe Schaue, Naresh Menon
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.ppat.1007276

Cellular sheddases are induced by Merkel cell polyomavirus small tumour antigen to mediate cell dissociation and invasiveness
Cited by: 24
Author(s): Nnenna Nwogu, James R. Boyne, Samuel J. Dobson, Krzysztof Poterlowicz, G. Eric Blair, Andrew Macdonald, Jamel Mankouri, Adrian Whitehouse
Software Mentions: 2
Published: about 6 years ago

10.1186/s12864-019-5860-5

Transcriptome profiling of Puccinellia tenuiflora during seed germination under a long-term saline-alkali stress
Cited by: 29
Author(s): Xiaoxue Ye, Hao Wang, Xiuling Cao, Xuejiao Jin, Fuqiang Cui, Yuanyuan Bu, Hua Liu, Wenwu Wu, Tetsuo Takano, Shenkui Liu
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-018-28199-y

Morphological, genomic and transcriptomic responses of Klebsiella pneumoniae to the last-line antibiotic colistin
Cited by: 18
Author(s): Amy K. Cain, Christine J. Boinett, Lars Barquist, Janina Dordel, María Fookes, Matthew Mayho, Matthew J. Ellington, David Goulding, Derek Pickard, Ryan R. Wick, Kathryn E. Holt, Julian Parkhill, Nicholas R. Thomson
Software Mentions: 1
Published: over 6 years ago

10.18632/oncotarget.20827

Prognostic relevance of androgen receptor expression in renal cell carcinomas
Cited by: 14
Author(s): Sebastian Foersch, Mario Schindeldecker, Martina Keith, Katrin E. Tagscherer, Aurélie Fernandez, Philipp Stenzel, Sascha Pahernik, Markus Hohenfellner, Peter Schirmacher, Wilfried Roth, Stephan Macher-Goeppinger
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-019-39571-x

Definition of a cell surface signature for human cardiac progenitor cells after comprehensive comparative transcriptomic and proteomic characterization
Cited by: 16
Author(s): José Luis Torán, Juan Antonio López, Patrícia Gomes‐Alves, Susana Aguilar, Carlos Torroja, Marco Trevisán-Herraz, Isabel Moscoso, Maria J. Sebastião, Margarida Serra, Catarina Brito, Francisco M. Cruz, Juan Carlos Sepúlveda-Arias, José Luís Abad, Carlos Galán‐Arriola, Borja Ibáñez, Fernando Martínez, María E. Fernández, Francisco Fernández‐Avilés, Itziar Palacios, Luis R‐Borlado, Jesús Vázquez, Paula M. Alves, António Bernad
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pcbi.1006832

Pan-cancer association of a centrosome amplification gene expression signature with genomic alterations and clinical outcome
Cited by: 31
Author(s): Bernardo P. de Almeida, André Filipe Vieira, Joana Paredes, Mónica Bettencourt-Dias, Nuno L. Barbosa‐Morais
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-017-4111-x

Regulatory network changes between cell lines and their tissues of origin
Cited by: 53
Author(s): Camila M. Lopes‐Ramos, Joseph N. Paulson, Cho-Yi Chen, Marieke L. Kuijjer, Maud Fagny, John Platig, Abhijeet R. Sonawane, Dawn L. DeMeo, John Quackenbush, Kimberly Glass
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0231003

Tumor-infiltrating immune cells in hepatocellular carcinoma: Tregs is correlated with poor overall survival
Cited by: 32
Author(s): Si Yu, Yu Wang, Jie Hou, Wen Yuan Li, Wang Xiao, Luo Cheng Ling Xiang, De Li Tan, Wen Juan Wang, Li Jiang, François X. Claret, Min Jiao, Hui Guo
Software Mentions: 1
Published: over 4 years ago

Ecosyste.ms: Papers

Projects: pypi: voom

Papers Mentioning voom 136