pypi: AltAnalyze | Projects | Ecosyste.ms: Papers

10.1016/j.xpro.2020.100085

Protocol for Identification and Removal of Doublets with DoubletDecon
Cited by: 7
Author(s): Erica A. K. DePasquale, Daniel Schnell, Kashish Chetal, Nathan Salomonis
Software Mentions: 25
Published: over 4 years ago

10.7554/eLife.63003

Short-term exposure to intermittent hypoxia leads to changes in gene expression seen in chronic pulmonary disease
Cited by: 17
Author(s): Gang Wu, Yin Yeng Lee, Evelyn M. Gulla, Andrew Potter, Joseph A. Kitzmiller, Marc D. Ruben, Nathan Salomonis, JA Whitsett, Lauren J. Francey, John B. Hogenesch, Smith Dl
Software Mentions: 12
Published: almost 4 years ago

10.1093/bioinformatics/btaa201

Resolving single-cell heterogeneity from hundreds of thousands of cells through sequential hybrid clustering and NMF
Cited by: 37
Author(s): Meenakshi Venkatasubramanian, Kashish Chetal, Daniel Schnell, Gowtham Atluri, Nathan Salomonis
Software Mentions: 10
Published: almost 5 years ago

10.1093/bib/bbz096

Evaluation of single-cell classifiers for single-cell RNA sequencing data sets
Cited by: 54
Author(s): Xinlei Zhao, Shuang Wu, Nan Fang, Xiao Sun, Jue Fan
Software Mentions: 8
Published: about 5 years ago

10.1186/s12864-016-2816-x

EventPointer: an effective identification of alternative splicing events using junction arrays
Cited by: 28
Author(s): Juan Pablo Romero, Ander Muniategui, Fernando J. de Miguel, Ander Aramburu, Luis M. Montuenga, Rubén Pı́o, Ángel Rubio
Software Mentions: 7
Published: over 8 years ago

10.1186/1471-2105-15-69

MAAMD: a workflow to standardize meta-analyses and comparison of affymetrix microarray data
Cited by: 15
Author(s): Gan Zhang, Jianwu Wang, Nathan Salomonis, Jennifer Stowe, Gabriel G. Haddad, Andrew D. McCulloch, Ilkay Altıntaş, Alexander C. Zambon
Software Mentions: 7
Published: almost 11 years ago

10.1016/j.celrep.2019.09.082

DoubletDecon: Deconvoluting Doublets from Single-Cell RNA-Sequencing Data
Cited by: 120
Author(s): Erica A. K. DePasquale, Daniel Schnell, Pieter-Jan Van Camp, Íñigo Valiente-Alandí, Burns C. Blaxall, H. Leighton Grimes, Harinder Singh, Nathan Salomonis
Software Mentions: 5
Published: about 5 years ago

10.1186/s12864-018-5082-2

Comparison of RNA-seq and microarray platforms for splice event detection using a cross-platform algorithm
Cited by: 17
Author(s): Juan Pablo Romero, María Ortiz-Estévez, Ander Muniategui, Soraya Carrancio, Fernando J. de Miguel, Fernando Carazo, Luis M. Montuenga, Remco Loos, Rubén Pı́o, Matthew Trotter, Ángel Rubio
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pcbi.1005187

MinePath: Mining for Phenotype Differential Sub-paths in Molecular Pathways
Cited by: 24
Author(s): Lefteris Koumakis, Alexandros Kanterakis, Evgenia Kartsaki, Maria Chatzimina, Michalis Zervakis, Manolis Tsiknakis, Despoina Vassou, Dimitris Kafetzopoulos, Kostas Marias, Vassilis Moustakis, George Potamias
Software Mentions: 5
Published: about 8 years ago

10.1038/cr.2017.135

Endothelial cell-derived GABA signaling modulates neuronal migration and postnatal behavior
Cited by: 66
Author(s): Suyan Li, Peeyush Kumar T, Sampada Joshee, Timo Kirschstein, Sivan Subburaju, Jahan S. Khalili, Jonas Kloepper, Chuang Du, Abdallah Elkhal, Gábor Szabó, Rakesh K. Jain, Rüdiger Köhling, Anju Vasudevan
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0144409

The Activation-Induced Assembly of an RNA/Protein Interactome Centered on the Splicing Factor U2AF2 Regulates Gene Expression in Human CD4 T Cells
Cited by: 14
Author(s): Thomas Whisenant, Eigen Peralta, Lauren Aarreberg, Nana Gao, Steven R. Head, Phillip Ordoukhanian, James R. Williamson, Daniel R. Salomon
Software Mentions: 4
Published: about 9 years ago

10.3390/ijms19041140

Aging and Intermittent Fasting Impact on Transcriptional Regulation and Physiological Responses of Adult Drosophila Neuronal and Muscle Tissues
Cited by: 14
Author(s): Sharon Zhang, Eric P. Ratliff, Brandon Molina, Nadja El-Mecharrafie, Jessica Mastroianni, Roxanne W. Kotzebue, Madhulika Achal, Ruth E. Mauntz, Arysa Gonzalez, Ayeh Barekat, William A. Bray, Andrew M Macias, Daniel J. Daugherty, Greg L. Harris, Robert A. Edwards, Kim D. Finley
Software Mentions: 4
Published: over 6 years ago

10.1038/s41375-020-0965-z

A transcriptomic continuum of differentiation arrest identifies myeloid interface acute leukemias with poor prognosis
Cited by: 6
Author(s): Jonathan Bond, Aleksandra Krzywon, Ludovic Lhermitte, Christophe Roumier, Anne Roggy, Mohamed Belhocine, Alexander Abdulkader Kheirallah, Patrick Villarèse, Guillaume Hypolite, Francine Garnache‐Ottou, Sylvie Castaigné, Nicolas Boissel, Vahid Asnafi, Claude Preudhomme, Hervé Dombret, Elisa Laurenti, Elizabeth Macintyre
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0143742

Functional Cross-Talking between Differentially Expressed and Alternatively Spliced Genes in Human Liver Cancer Cells Treated with Berberine
Cited by: 11
Author(s): Zhonghua Sheng, Yi Sun, Ruixin Zhu, Na Jiao, Kailin Tang, Zhen Cao, Chao Ma
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0110134

Integrated Exon Level Expression Analysis of Driver Genes Explain Their Role in Colorectal Cancer
Cited by: 20
Author(s): Mohammad Azhar Aziz, Sathish Periyasamy, Zeyad Yousef, Ibrahim AlAbdulkarim, Majed Al Otaibi, Abdulaziz Alfahed, Glowi Alasiri
Software Mentions: 4
Published: about 10 years ago

10.2174/1389202911314030004

Review: Alternative Splicing (AS) of Genes As An Approach for Generating Protein Complexity
Cited by: 75
Author(s): Bishakha Roy, Larisa M. Haupt, Lyn R. Griffiths
Software Mentions: 3
Published: almost 12 years ago

10.3390/biology9090260

Computational and Transcriptome Analyses Revealed Preferential Induction of Chemotaxis and Lipid Synthesis by SARS-CoV-2
Cited by: 7
Author(s): Hibah Shaath, Nehad M. Alajez
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-018-36057-0

Chromatin accessibility identifies diversity in mesenchymal stem cells from different tissue origins
Cited by: 27
Author(s): Yen-Ting Ho, Takashi Shimbo, Edward Wijaya, Yuya Ouchi, Eiichi Takaki, Ryusuke Yamamoto, Yasushi Kikuchi, Yasufumi Kaneda, Katsuto Tamai
Software Mentions: 3
Published: about 6 years ago

10.14338/2331-5180-5-2-000

Proceedings of the 57<sup>th</sup> Annual Meeting of the Particle Therapy Cooperative Group (PTCOG)
Cited by: 3
Author(s):
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pcbi.1003517

Long Non-Coding RNA and Alternative Splicing Modulations in Parkinson's Leukocytes Identified by RNA Sequencing
Cited by: 145
Author(s): Lilach Soreq, Alessandro Guffanti, Nathan Salomonis, Alon Simchovitz, Zvi Israel, Hagai Bergman, Hermona Soreq
Software Mentions: 3
Published: almost 11 years ago

10.3389/fmicb.2017.02121

Different Non-Saccharomyces Yeast Species Stimulate Nutrient Consumption in S. cerevisiae Mixed Cultures
Cited by: 57
Author(s): José Antonio Curiel, Pilar Morales, Ramón González, Jordi Tronchoni
Software Mentions: 3
Published: about 7 years ago

10.3390/genes11070760

Protein Coding and Long Noncoding RNA (lncRNA) Transcriptional Landscape in SARS-CoV-2 Infected Bronchial Epithelial Cells Highlight a Role for Interferon and Inflammatory Response
Cited by: 90
Author(s): Radhakrishnan Vishnubalaji, Hibah Shaath, Nehad M. Alajez
Software Mentions: 3
Published: over 4 years ago

10.18632/oncotarget.7248

MicroRNA-34a promotes genomic instability by a broad suppression of genome maintenance mechanisms downstream of the oncogene KSHV-vGPCR
Cited by: 14
Author(s): Claudia J. Krause, Oliver Popp, Nanthakumar Thirunarayanan, Gunnar Dittmar, Martin Lipp, Gerd Müller
Software Mentions: 3
Published: almost 9 years ago

10.1186/1471-2164-15-879

A robust estimation of exon expression to identify alternative spliced genes applied to human tissues and cancer samples
Cited by: 13
Author(s): Alberto Risueño, Beatriz Rosón-Burgo, Anna Dolnik, Jesús María Hernández-Rivas, Lars Bullinger, Javier De Las Rivas
Software Mentions: 3
Published: about 10 years ago

10.3389/fimmu.2020.00558

TNF-Signaling Modulates Neutrophil-Mediated Immunity at the Feto-Maternal Interface During LPS-Induced Intrauterine Inflammation
Cited by: 30
Author(s): Pietro Presicce, Monica Cappelletti, Paranthaman Senthamaraikannan, Feiyang Ma, Marco Morselli, Courtney M. Jackson, Shibabrata Mukherjee, Lisa Miller, Matteo Pellegrini, Alan H. Jobe, Claire Chougnet, Suhas G. Kallapur
Software Mentions: 3
Published: over 4 years ago

10.18632/oncotarget.19848

IL2RG, identified as overexpressed by RNA-seq profiling of pancreatic intraepithelial neoplasia, mediates pancreatic cancer growth
Cited by: 13
Author(s): Michael Ayars, Eileen O’Sullivan, Anne M. Macgregor-Das, Koji Shindo, Haeryoung Kim, Michael Borges, Jun Yu, Ralph H. Hruban, Michael Goggins
Software Mentions: 2
Published: over 7 years ago

10.3390/cells9112374

Single-Cell Transcriptome Analysis Highlights a Role for Neutrophils and Inflammatory Macrophages in the Pathogenesis of Severe COVID-19
Cited by: 133
Author(s): Hibah Shaath, Radhakrishnan Vishnubalaji, Eyad Elkord, Nehad M. Alajez
Software Mentions: 2
Published: about 4 years ago

10.1016/j.exphem.2018.09.004

The Human Cell Atlas bone marrow single-cell interactive web portal
Cited by: 152
Author(s): Stuart Hay, Kyle Ferchen, Kashish Chetal, H. Leighton Grimes, Nathan Salomonis
Software Mentions: 2
Published: about 6 years ago

10.1016/j.exphem.2018.04.002

Synergistic action of dual IGF1/R and MEK inhibition sensitizes childhood acute lymphoblastic leukemia (ALL) cells to cytotoxic agents and involves downregulation of STAT6 and PDAP1
Cited by: 8
Author(s): Victoria Weston, Wenbin Wei, Tatjana Stankovic, Pamela Kearns
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-019-5794-y

Events of alternative splicing in head and neck cancer via RNA sequencing – an update
Cited by: 4
Author(s): Vishwas Sharma, Amrita Nandan, Harpreet Singh, Suyash Agarwal, Richa Tripathi, Dhirendra N Sinha, Ravi Mehrotra
Software Mentions: 2
Published: over 5 years ago

10.1186/s12969-017-0185-x

Proceedings of the 24th Paediatric Rheumatology European Society Congress: Part one
Cited by: 5
Author(s):
Software Mentions: 2
Published: over 7 years ago

10.3389/fmed.2017.00080

Assessment of Circulating Protein Signatures for Kidney Transplantation in Pediatric Recipients
Cited by: 9
Author(s): Tara K. Sigdel, Minnie M. Sarwal
Software Mentions: 2
Published: over 7 years ago

10.3390/pharmaceutics13091485

Ultrasound and Transcriptomics Identify a Differential Impact of Cisplatin and Histone Deacetylation on Tumor Structure and Microenvironment in a Patient-Derived In Vivo Model of Gastric Cancer
Cited by: 4
Author(s): Aïna Venkatasamy, Éric Guérin, Anaïs Blanchet, Christophe Orvain, Véronique Devignot, Matthieu Jung, Alain C. Jung, Marie‐Pierre Chenard, B. Romain, Christian Gaiddon, Georg Mellitzer
Software Mentions: 2
Published: over 3 years ago

10.3389/fphar.2018.00318

The Effects of PPAR Stimulation on Cardiac Metabolic Pathways in Barth Syndrome Mice
Cited by: 30
Author(s): Caitlin Schafer, Vicky Moore, Nupur Dasgupta, Sabzali Javadov, Jeanne James, А.И. Глухов, Arnold W. Strauss, Zaza Khuchua
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0049978

Contextualization Procedure and Modeling of Monocyte Specific TLR Signaling
Cited by: 5
Author(s): Maike Kathrin Aurich, Ines Thiele
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0061975

Genome-Wide Analysis of Alternative Splicing during Dendritic Cell Response to a Bacterial Challenge
Cited by: 26
Author(s): Renata Rodrigues, Ana Rita Grosso, Luís F. Moita
Software Mentions: 2
Published: over 11 years ago

10.1038/sdata.2017.30

Molecular, phenotypic, and sample-associated data to describe pluripotent stem cell lines and derivatives
Cited by: 41
Author(s): Kenneth Daily, Shannan Ho Sui, Lynn M. Schriml, Phillip Dexheimer, Nathan Salomonis, Robin Schroll, Stacy Bush, Mehdi Keddache, Christopher N. Mayhew, Samad Lotia, Thanneer M. Perumal, Kristen K. Dang, Lorena Pantano, Alexander Pico, Elke Grassman, Diana Nordling, Winston Hide, Antonis K. Hatzopoulos, Punam Malik, José A. Cancelas, Carolyn Lutzko, Bruce J. Aronow, Larsson Omberg
Software Mentions: 2
Published: almost 8 years ago

10.1186/1471-2105-13-S4-S21

BEAT: Bioinformatics Exon Array Tool to store, analyze and visualize Affymetrix GeneChip Human Exon Array data from disease experiments
Cited by: 5
Author(s): Arianna Consiglio, Massimo Carella, Giorgio De, Gianfranco Delle Foglie, Candida Giovannelli, Giorgio Grillo, Massimo Ianigro, Flavio Licciulli, Orazio Palumbo, Ada Piepoli, Elena Ranieri, Sabino Liuni
Software Mentions: 2
Published: almost 13 years ago

10.1038/srep28261

Fibroblasts profiling in scarring trachoma identifies IL-6 as a functional component of a fibroblast-macrophage pro-fibrotic and pro-inflammatory feedback loop
Cited by: 28
Author(s): Jenny Z. Kechagia, Daniel G. Ezra, Matthew J. Burton, Maryse Bailly
Software Mentions: 2
Published: over 8 years ago

10.1186/1755-8794-4-35

Exon array analysis reveals neuroblastoma tumors have distinct alternative splicing patterns according to stage and MYCN amplification status
Cited by: 37
Author(s): Xiang Guo, Qingrong Chen, Young K. Song, Jun S. Wei, Javed Khan
Software Mentions: 2
Published: over 13 years ago

10.1038/srep39276

Molecular Characterization of Pediatric Restrictive Cardiomyopathy from Integrative Genomics
Cited by: 19
Author(s): Tara N. Rindler, Robert B. Hinton, Nathan Salomonis, Stephanie M. Ware
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-018-26695-9

The Usage of Exon-Exon Splice Junctions for the Detection of Alternative Splicing using the REIDS model
Cited by: 4
Author(s): Marijke Van Moerbeke, Adetayo Kasim, Ziv Shkedy
Software Mentions: 2
Published: over 6 years ago

10.1186/s12920-015-0138-5

Systems biology evaluation of cell-free amniotic fluid transcriptome of term and preterm infants to detect fetal maturity
Cited by: 22
Author(s): Beena D. Kamath‐Rayne, Yina Du, Maria Hughes, E Wagner, Louis J. Muglia, Emily DeFranco, Jeffrey A. Whitsett, Nathan Salomonis, Yan Xu
Software Mentions: 2
Published: about 9 years ago

10.1186/s12915-015-0220-7

iCLIP identifies novel roles for SAFB1 in regulating RNA processing and neuronal function
Cited by: 22
Author(s): Caroline A Rivers, Jalilah Idris, Helen L. Scott, Mark F. Rogers, Youn‐Bok Lee, Jess R Gaunt, Leonidas A. Phylactou, Tomaž Curk, Colin Campbell, Jernej Ule, M. R. Norman, James B. Uney
Software Mentions: 2
Published: about 9 years ago

10.1038/s41598-019-39489-4

Aspirin impairs acetyl-coenzyme A metabolism in redox-compromised yeast cells
Cited by: 4
Author(s): Gianluca Farrugia, Maria Azzopardi, Christian Saliba, Godfrey Grech, Angelina S. Gross, Jelena Pistolic, Vladimír Beneš, Neville Vassallo, Joseph Borg, Frank Madeo, Tobias Eisenberg, Rena Balzan
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-94514-9

Epigenetic regulation of triple negative breast cancer (TNBC) by TGF-β signaling
Cited by: 35
Author(s): Radhakrishnan Vishnubalaji, Nehad M. Alajez
Software Mentions: 2
Published: over 3 years ago

10.3390/cancers11121994

Transcriptomic Analyses Revealed Systemic Alterations in Gene Expression in Circulation and Tumor Microenvironment of Colorectal Cancer Patients
Cited by: 27
Author(s): Hibah Shaath, Salman M Toor, Varun Sasidharan Nair, Eyad Elkord, Nehad M. Alajez
Software Mentions: 2
Published: about 5 years ago

10.1038/cddis.2014.566

Reactive oxygen species-mediated therapeutic response and resistance in glioblastoma
Cited by: 181
Author(s): Eric A. Singer, Jonathon Judkins, Nathan Salomonis, Lisa Matlaf, Patricia Soteropoulos, Sean D. McAllister, Liliana Soroceanu
Software Mentions: 2
Published: almost 10 years ago

10.1186/1479-7364-8-3

A survey of software for genome-wide discovery of differential splicing in RNA-Seq data
Cited by: 63
Author(s): Joan E. Hooper
Software Mentions: 2
Published: almost 11 years ago

10.1093/jmcb/mju026

The conserved ubiquitin-like protein Hub1 plays a critical role in splicing in human cells
Cited by: 30
Author(s): Tim Ammon, Sudhish Mishra, Kaja Kowalska, Grzegorz M. Popowicz, Tad A. Holak, Stefan Jentsch
Software Mentions: 2
Published: over 10 years ago

10.3390/cells9020448

A System Based-Approach to Examine Host Response during Infection with Influenza A Virus Subtype H7N9 in Human and Avian Cells
Cited by: 2
Author(s): Biruhalem Taye, Hui Chen, David Yeo, Shirley Gek Kheng Seah, Michelle Wong, Richard J. Sugrue, Boon Huan Tan
Software Mentions: 2
Published: almost 5 years ago

10.3390/ijms21030961

Bioinformatics for Renal and Urinary Proteomics: Call for Aggrandization
Cited by: 9
Author(s): Piby Paul, A. Vimala, Judy Gopal, Steve Haga, Nazim Hasan, Jae-Wook Oh
Software Mentions: 2
Published: almost 5 years ago

10.18632/aging.202755

Aging and pathological aging signatures of the brain: through the focusing lens of SIRT6
Cited by: 10
Author(s): Daniel Stein, Amir Mizrahi, Anastasia V. Golova, Adam Saretzky, Alfredo Garcia Venzor, Zeev Slobodnik, Shai Kaluski, Monica Einav, Ekaterina E. Khrameeva, Debra Toiber
Software Mentions: 2
Published: almost 4 years ago

10.1186/s41231-020-00066-x

C-C chemokine receptor type 5 links COVID-19, rheumatoid arthritis, and Hydroxychloroquine: in silico analysis
Cited by: 6
Author(s): Mahmood Y. Hachim, Ibrahim Y. Hachim, Kashif Naeem, Haifa Hannawi, Issa Al Salmi, Suad Hannawi
Software Mentions: 1
Published: over 4 years ago

10.1186/s13195-017-0277-3

A novel Alzheimer’s disease drug candidate targeting inflammation and fatty acid metabolism
Cited by: 32
Author(s): Daniel J. Daugherty, Joshua Goldberg, Wolfgang Fischer, Richard Dargusch, Pamela Maher, David Schubert
Software Mentions: 1
Published: over 7 years ago

10.1128/AAC.02513-17

Gene Expression of Pneumocystis murina after Treatment with Anidulafungin Results in Strong Signals for Sexual Reproduction, Cell Wall Integrity, and Cell Cycle Arrest, Indicating a Requirement for Ascus Formation for Proliferation
Cited by: 20
Author(s): Melanie T. Cushion, Alan Ashbaugh, Keeley Hendrix, Michael J. Linke, Nikeya L. Macioce-Tisdale, Steven G. Sayson, Aleksey Porollo
Software Mentions: 1
Published: over 6 years ago

10.1186/s13075-018-1603-2

Transcription factor motif enrichment in whole transcriptome analysis identifies STAT4 and BCL6 as the most prominent binding motif in systemic juvenile idiopathic arthritis
Cited by: 11
Author(s): Boris Hügle, Angela Schippers, Nadine Fischer, Kim Ohl, Bernd Denecke, Fabio Ticconi, Bas Vastert, Ivan G. Costa, Johannes Haas, Klaus Tenbrock
Software Mentions: 1
Published: over 6 years ago

10.1186/s12885-019-6045-y

Lipid accumulation impairs natural killer cell cytotoxicity and tumor control in the postoperative period
Cited by: 48
Author(s): Seyedeh Raheleh Niavarani, Christine Lawson, Orneala Bakos, Marie Boudaud, Cory Batenchuk, Samuel G. Rouleau, Lee-Hwa Tai
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-14-478

Deep brain stimulation modulates nonsense-mediated RNA decay in Parkinson’s patients leukocytes
Cited by: 13
Author(s): Lilach Soreq, Hagai Bergman, Zvi Israel, Hermona Soreq
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12864-017-3803-6

Systems-based approach to examine the cytokine responses in primary mouse lung macrophages infected with low pathogenic avian Influenza virus circulating in South East Asia
Cited by: 3
Author(s): Biruhalem Taye, Hui Chen, Myint Zu Myaing, Boon Huan Tan, Sebastian Maurer‐Stroh, Richard J. Sugrue
Software Mentions: 1
Published: over 7 years ago

10.1186/1756-0500-7-934

Computational extraction of a neural molecular network through alternative splicing
Cited by: 5
Author(s): Shafiul Alam, Huong T.T. Phan, Mio Okazaki, Masahiro Takagi, Kozo Kawahara, Toshifumi Tsukahara, Hitoshi Suzuki
Software Mentions: 1
Published: about 10 years ago

10.1242/bio.20149969

Identification of novel radiation-induced p53-dependent transcripts extensively regulated during mouse brain development
Cited by: 30
Author(s): Roel Quintens, Tine Verreet, Ann Janssen, Mieke Neefs, Liselotte Leysen, Arlette Michaux, Mieke Verslegers, Nada Samari, Giuseppe Pani, Joris Verheyde, Sarah Baatout, Mohammed Abderrafi Benotmane
Software Mentions: 1
Published: almost 10 years ago

10.1002/cam4.540

Multiple criteria optimization joint analyses of microarray experiments in lung cancer: from existing microarray data to new knowledge
Cited by: 8
Author(s): Katia I. Camacho‐Cáceres, Juan C. Acevedo‐Díaz, Lynn M. Pérez‐Marty, Michael Ortiz, Juan Irizarry, Mauricio Cabrera‐Ríos, Clara E. Isaza
Software Mentions: 1
Published: about 9 years ago

10.3390/ph14070680

Current Status of Baricitinib as a Repurposed Therapy for COVID-19
Cited by: 12
Author(s): Maha Saber-Ayad, Sarah Hammoudeh, Eman Abu‐Gharbieh, Rifat Hamoudi, Hamadeh Tarazi, Taleb H. Al‐Tel, Qutayba Hamid
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pcbi.1000553

Alternative Splicing in the Differentiation of Human Embryonic Stem Cells into Cardiac Precursors
Cited by: 82
Author(s): Nathan Salomonis, Brandon Nelson, Karen Vranizan, Alexander R. Pico, Kristina Hanspers, Allan Kuchinsky, Linda Ta, Mark Mercola, Bruce R. Conklin
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pgen.1006786

Age-dependent electrical and morphological remodeling of the Drosophila heart caused by hERG/seizure mutations
Cited by: 13
Author(s): Karen Ocorr, Alexander C. Zambon, Yoav Nudell, Santiago Pineda, Soda Balla Diop, Min Tang, Takeshi Akasaka, E. P. Taylor
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0109631

Urinary Exosomes: A Novel Means to Non-Invasively Assess Changes in Renal Gene and Protein Expression
Cited by: 36
Author(s): Silvia Spanu, Claudia R.C. van Roeyen, Bernd Denecke, Jürgen Floege, Anja Mühlfeld
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0198492

Drug discovery with an RBM20 dependent titin splice reporter identifies cardenolides as lead structures to improve cardiac filling
Cited by: 21
Author(s): Martin Liss, Michaël Radkë, Jamina Eckhard, Martin Neuenschwander, Vita Dauksaite, Jens-Peter von Kries, Michael Gotthardt
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0096636

Growth Factor Independence 1b (Gfi1b) Is Important for the Maturation of Erythroid Cells and the Regulation of Embryonic Globin Expression
Cited by: 39
Author(s): Lothar Vaßen, Hugues Beauchemin, Wafaâ Lemsaddek, Joseph Krongold, Marie Trudel, Tarik Möröy
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0146748

Advanced Running Performance by Genetic Predisposition in Male Dummerstorf Marathon Mice (DUhTP) Reveals Higher Sterol Regulatory Element-Binding Protein (SREBP) Related mRNA Expression in the Liver and Higher Serum Levels of Progesterone
Cited by: 6
Author(s): Daniela Ohde, Mark Moeller, Julia Brenmoehl, Christina Walz, Siriluck Ponsuksili, Manfred Schwerin, Georg Fuellen, Andreas Hoeflich
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0007780

Gi-Coupled GPCR Signaling Controls the Formation and Organization of Human Pluripotent Colonies
Cited by: 25
Author(s): Kenta Nakamura, Nathan Salomonis, Kiichiro Tomoda, Shinya Yamanaka, Bruce R. Conklin
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0071143

Sarcoptes scabiei Mites Modulate Gene Expression in Human Skin Equivalents
Cited by: 36
Author(s): Marjorie S. Morgan, Larry G. Arlian, Michael P. Markey
Software Mentions: 1
Published: over 11 years ago

10.3390/cells10051038

The ECM Modulator ITIH5 Affects Cell Adhesion, Motility and Chemotherapeutic Response of Basal/Squamous-Like (BASQ) Bladder Cancer Cells
Cited by: 5
Author(s): Michael Rose, Erik Noetzel, Jennifer Kistermann, Julian Eschenbruch, Sandra Rushrush, Lin Gan, Ruth Knüchel, Nadine T. Gaisa, Edgar Dahl
Software Mentions: 1
Published: over 3 years ago

10.1186/1687-4153-2011-5

Measuring and analyzing tissue specificity of human genes and protein complexes
Cited by: 17
Author(s): Dorothea Emig, Tim Kacprowski, Mario Albrecht
Software Mentions: 1
Published: over 13 years ago

10.3389/fcell.2021.641404

Wnt Signaling Is Deranged in Asthmatic Bronchial Epithelium and Fibroblasts
Cited by: 11
Author(s): Mahmood Y. Hachim, Noha Mousaad Elemam, Rakhee K. Ramakrishnan, Khuloud Bajbouj, Ronald Olivenstein, Ibrahim Y. Hachim, Saba Al Heialy, Qutayba Hamid, Hauke Busch, Rifat Hamoudi
Software Mentions: 1
Published: almost 4 years ago

10.3389/fimmu.2021.595150

Systems Immunology Analysis Reveals the Contribution of Pulmonary and Extrapulmonary Tissues to the Immunopathogenesis of Severe COVID-19 Patients
Cited by: 17
Author(s): Sarah Hammoudeh, Arabella Musa Hammoudeh, Poorna Manasa Bhamidimarri, Habiba Alsafar, Bassam Mahboub, Axel Künstner, Hauke Busch, Rabih Halwani, Qutayba Hamid, Mohamed Rahmani, Rifat Hamoudi
Software Mentions: 1
Published: over 3 years ago

10.3389/fimmu.2018.02995

Neutrophils From Children With Systemic Juvenile Idiopathic Arthritis Exhibit Persistent Proinflammatory Activation Despite Long-Standing Clinically Inactive Disease
Cited by: 47
Author(s): R. G. Brown, Maggie Henderlight, Thuy Do, Shima Yasin, Alexei A. Grom, Monica DeLay, Sherry Thornton, Grant S. Schulert
Software Mentions: 1
Published: about 6 years ago

10.3389/fimmu.2020.560074

M1 Polarization Markers Are Upregulated in Basal-Like Breast Cancer Molecular Subtype and Associated With Favorable Patient Outcome
Cited by: 15
Author(s): Mahmood Y. Hachim, Ibrahim Y. Hachim, Iman M. Talaat, Nada M. Yakout, Rifat Hamoudi
Software Mentions: 1
Published: about 4 years ago

10.3389/fimmu.2021.663115

Immunoregulatory Monocyte Subset Promotes Metastasis Associated With Therapeutic Intervention for Primary Tumor
Cited by: 15
Author(s): Tomoki Shibuya, Asami Kamiyama, Hirotaka Sawada, Kenta Kikuchi, Mayu Maruyama, Rie Sawado, Naoki Ikeda, Kenichi Asano, Daisuke Kurotaki, Tomohide Tamura, Atsuko Yoneda, Katsumi Imada, Takashi Satoh, Shizuo Akira, Masato Tanaka, Satoshi Yotsumoto
Software Mentions: 1
Published: over 3 years ago

10.3389/fnmol.2013.00010

Small RNA sequencing-microarray analyses in Parkinson leukocytes reveal deep brain stimulation-induced splicing changes that classify brain region transcriptomes
Cited by: 94
Author(s): Lilach Soreq, Nathan Salomonis, Michal Bronstein, David Greenberg, Zvi Israel, Hagai Bergman, Hermona Soreq
Software Mentions: 1
Published: almost 12 years ago

10.3389/fnmol.2019.00188

miR-30 Family miRNAs Mediate the Effect of Chronic Social Defeat Stress on Hippocampal Neurogenesis in Mouse Depression Model
Cited by: 24
Author(s): Nitin Khandelwal, Sandeep Kumar Dey, Sumana Chakravarty, Arvind Kumar
Software Mentions: 1
Published: over 5 years ago

10.3389/fonc.2019.00482

Laser Capture Microdissection and RNA-Seq Analysis: High Sensitivity Approaches to Explain Histopathological Heterogeneity in Human Glioblastoma FFPE Archived Tissues
Cited by: 34
Author(s): Prospero Civita, Sara Franceschi, Paolo Aretini, Valerio Ortenzi, Michele Menicagli, Francesca Lessi, Francesco Pasqualetti, Antonio Giuseppe Naccarato, Chiara Maria Mazzanti
Software Mentions: 1
Published: over 5 years ago

10.3389/fonc.2021.642940

Overexpression of Multifunctional Protein p32 Promotes a Malignant Phenotype in Colorectal Cancer Cells
Cited by: 8
Author(s): Carlos Alejandro Egusquiza-Alvarez, M. Cristina Castañeda-Patlán, Sara Albarran-Gutierrez, Héctor González-Aguilar, Ángela Patricia Moreno-Londoño, Vilma Maldonado, Jorge Meléndez-Zajgla, Martha Robles-Flores
Software Mentions: 1
Published: over 3 years ago

10.3389/fonc.2019.01119

Tissues Harvested Using an Automated Surgical Approach Confirm Molecular Heterogeneity of Glioblastoma and Enhance Specimen's Translational Research Value
Cited by: 6
Author(s): Edie E. Zusman, Maxim Sidorov, Alexandria Ayala, Jimmin Chang, Eric A. Singer, Michelle Chen, Pierre-Yves Desprez, Sean D. McAllister, Nathan Salomonis, Kashish Chetal, Gautam Prasad, Tyler Y. Kang, Joseph Mark, Lawrence Dickinson, Liliana Soroceanu
Software Mentions: 1
Published: about 5 years ago

10.3389/fphys.2020.555039

Regulation of Angiotensin- Converting Enzyme 2 in Obesity: Implications for COVID-19
Cited by: 76
Author(s): Saba Al Heialy, Mahmood Y. Hachim, Abiola Senok, Mellissa Gaudet, Ahmad Abou Tayoun, Rifat Hamoudi, Alawi A. Alsheikh‐Ali, Qutayba Hamid
Software Mentions: 1
Published: over 4 years ago

10.3389/fphys.2018.01045

The Role of Abnormal Placentation in Congenital Heart Disease; Cause, Correlate, or Consequence?
Cited by: 51
Author(s): Jennifer Courtney, James Cnota, Helen Jones
Software Mentions: 1
Published: over 6 years ago

10.1172/jci.insight.128722

Cell-specific ablation of Hsp47 defines the collagen-producing cells in the injured heart
Cited by: 57
Author(s): Hadi Khalil, Onur Kanisicak, Ronald J. Vagnozzi, Anne Katrine Johansen, Bryan D. Maliken, Vikram Prasad, Justin G. Boyer, Matthew J. Brody, Tobias G. Schips, Katja Kilian, Robert N. Correll, Kunito Kawasaki, Kazuhiro Nagata, Jeffery D. Molkentin
Software Mentions: 1
Published: over 5 years ago

10.1038/srep12292

Hyperosmotic stress activates the expression of members of the miR-15/107 family and induces downregulation of anti-apoptotic genes in rat liver
Cited by: 18
Author(s): David Santosa, Mirco Castoldi, Martha Paluschinski, Annika Sommerfeld, Dieter Häussinger
Software Mentions: 1
Published: over 9 years ago

10.1038/srep18493

Ammonia-induced miRNA expression changes in cultured rat astrocytes
Cited by: 25
Author(s): Jessica Oenarto, Ayşe Karababa, Mirco Castoldi, Hans‐Jürgen Bidmon, Boris Görg, Dieter Häussinger
Software Mentions: 1
Published: almost 9 years ago

10.1038/srep34927

Conditional Knockout of Breast Carcinoma Amplified Sequence 2 (BCAS2) in Mouse Forebrain Causes Dendritic Malformation via β-catenin
Cited by: 8
Author(s): Chu-Wei Huang, Yiwen Chen, Yi-Rou Lin, Po‐Han Chen, Meng-Hsuan Chou, Li-Jen Lee, Pei‐Yu Wang, June‐Tai Wu, Yeou‐Ping Tsao, Show‐Li Chen
Software Mentions: 1
Published: about 8 years ago

10.1038/srep35236

FUS/TLS acts as an aggregation-dependent modifier of polyglutamine disease model mice
Cited by: 17
Author(s): Yoshihiro Kino, Chika Washizu, Masaru Kurosawa, Masako Yamada, Hiroshi Doi, Toru Takumi, Hiroaki Adachi, Masahisa Katsuno, Gen Sobue, Geoffrey Hicks, Nobutaka Hattori, Tomomi Shimogori, Nobuyuki Nukina
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-018-38314-8

Transcriptome Analysis of Mesenchymal Stem Cells from Multiple Myeloma Patients Reveals Downregulation of Genes Involved in Cell Cycle Progression, Immune Response, and Bone Metabolism
Cited by: 16
Author(s): Rodrigo Carlini Fernando, Diego R. Mazzotti, Hátylas Azevedo, Alex Freire Sandes, Edgar Gil Rizzatti, Mariana Bleker de Oliveira, Veruska Lia Fook Alves, Angela Isabel Pereira Eugênio, Flávio Carvalho, Maria Aparecida Dalboni, David Martins, Gisele W. B. Colleoni
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-019-42513-2

Buffalo milk transcriptome: A comparative analysis of early, mid and late lactation
Cited by: 23
Author(s): Reena Arora, Anju Sharma, Upasna Sharma, Yashila Girdhar, Manpreet Kaur, Prerna Kapoor, Sonika Ahlawat, R. K. Vijh
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-021-92268-y

Insights into how environment shapes post-mortem RNA transcription in mouse brain
Cited by: 7
Author(s): Raphael Severino Bonadio, Larissa Barbosa Nunes, Patricia Moretti, Juliana Forte Mazzeu, Stefano Cagnin, Aline Pic‐Taylor, Silviene Fabiana de Oliveira
Software Mentions: 1
Published: over 3 years ago

10.1186/s13287-019-1213-1

Secretome of adipose-derived mesenchymal stem cells promotes skeletal muscle regeneration through synergistic action of extracellular vesicle cargo and soluble proteins
Cited by: 124
Author(s): Robert D. Mitchell, Ben Mellows, Jonathan Sheard, Manuela Antonioli, Oliver Kretz, David Chambers, Marie Theres Zeuner, James E. Tomkins, Bernd Denecke, Luca Musante, Barbara Joch, Florence Debacq‐Chainiaux, Harry Holthöfer, Stephen Ray, Tobias B. Huber, Jörn Dengjel, Paolo De Coppi, Darius Widera, Ketan Patel
Software Mentions: 1
Published: over 5 years ago

10.1186/s13287-020-01828-y

Transcriptional profiling reveals altered biological characteristics of chorionic stem cells from women with gestational diabetes
Cited by: 4
Author(s): Liyun Chen, Chung-Teng Wang, Nicholas R. Forsyth, Pensée Wu
Software Mentions: 1
Published: over 4 years ago

10.1186/s40478-015-0202-6

FUS/TLS deficiency causes behavioral and pathological abnormalities distinct from amyotrophic lateral sclerosis
Cited by: 85
Author(s): Yoshihiro Kino, Chika Washizu, Masaru Kurosawa, Masako Yamada, Haruko Miyazaki, Tomonori Akagi, Tsutomu Hashikawa, Hiroshi Doi, Toru Takumi, Geoffrey Hicks, Nobutaka Hattori, Tomomi Shimogori, Nobuyuki Nukina
Software Mentions: 1
Published: over 9 years ago

10.7554/eLife.10528

Transcriptional activator TAp63 is upregulated in muscular atrophy during ALS and induces the pro-atrophic ubiquitin ligase Trim63
Cited by: 25
Author(s): Yannick von Grabowiecki, Paula Abreu, Orphée Blanchard, Lavinia Palamiuc, Samir Benosman, Sophie B. Mériaux, Véronique Devignot, Isabelle Groß, Georg Mellitzer, José Luis González de Aguilar, Christian Gaiddon
Software Mentions: 1
Published: almost 9 years ago

10.3390/ijms16011755

Novel Transcription Factor Variants through RNA-Sequencing: The Importance of Being “Alternative”
Cited by: 7
Author(s): Margherita Scarpato, Antonio Federico, Alfredo Ciccodicola, Valerio Costa
Software Mentions: 1
Published: almost 10 years ago

10.3390/ijms18091956

Alignment of Mitotic Chromosomes in Human Cells Involves SR-Like Splicing Factors Btf and TRAP150
Cited by: 4
Author(s): Sapna N. Varia, Divya Cheedu, Michael P. Markey, Keshia Torres-Shafer, Vishnu Priya Battini, Athanasios Bubulya, Paula A. Bubulya
Software Mentions: 1
Published: over 7 years ago

Projects: pypi: AltAnalyze

Papers Mentioning AltAnalyze 102