Works by Salomonis, Nathan

Results: 45

AltAnalyze and DomainGraph: analyzing and visualizing exon expression data.

Published in:

Nucleic Acids Research, 2010, v. 38, n. suppl_2, p. W755, doi. 10.1093/nar/gkq405

By:

Emig, Dorothea;
Salomonis, Nathan;
Baumbach, Jan;
Lengauer, Thomas;
Conklin, Bruce R.;
Albrecht, Mario

Publication type:

Article

Sinus venosus adaptation models prolonged cardiovascular disease and reveals insights into evolutionary transitions of the vertebrate heart.

Published in:

Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-41184-y

By:

Gafranek, Jacob T.;
D'Aniello, Enrico;
Ravisankar, Padmapriyadarshini;
Thakkar, Kairavee;
Vagnozzi, Ronald J.;
Lim, Hee-Woong;
Salomonis, Nathan;
Waxman, Joshua S.

Publication type:

Article

Development of a Single-Neurosphere Culture to Assess Radiation Toxicity and Pre-Clinical Cancer Combination Therapy Safety.

Published in:

Cancers, 2023, v. 15, n. 20, p. 4916, doi. 10.3390/cancers15204916

By:

Pathak, Bedika;
Lange, Taylor E.;
Lampe, Kristin;
Hollander, Ella;
Oria, Marina;
Murphy, Kendall P.;
Salomonis, Nathan;
Sertorio, Mathieu;
Oria, Marc

Publication type:

Article

The kSORT Assay to Detect Renal Transplant Patients at High Risk for Acute Rejection: Results of the Multicenter AART Study.

Published in:

PLoS Medicine, 2014, v. 11, n. 11, p. 1, doi. 10.1371/journal.pmed.1001759

By:

Roedder, Silke;
Sigdel, Tara;
Salomonis, Nathan;
Hsieh, Sue;
Dai, Hong;
Bestard, Oriol;
Metes, Diana;
Zeevi, Andrea;
Gritsch, Albin;
Cheeseman, Jennifer;
Macedo, Camila;
Peddy, Ram;
Medeiros, Mara;
Vincenti, Flavio;
Asher, Nancy;
Salvatierra, Oscar;
Shapiro, Ron;
Kirk, Allan;
Reed, Elaine;
Sarwal, Minnie M.

Publication type:

Article

Short-term exposure to intermittent hypoxia leads to changes in gene expression seen in chronic pulmonary disease.

Published in:

eLife, 2021, p. 1, doi. 10.7554/eLife.63003

By:

Gang Wu;
Yin Yeng Lee;
Gulla, Evelyn M.;
Potter, Andrew;
Kitzmiller, Joseph;
Ruben, Marc D.;
Salomonis, Nathan;
Whitsett, Jeffery A.;
Francey, Lauren J.;
Hogenesch, John B.;
Smith, David F.

Publication type:

Article

Defective transcription elongation in a subset of cancers confers immunotherapy resistance.

Published in:

Nature Communications, 2018, v. 9, p. 1, doi. 10.1038/s41467-018-06810-0

By:

Modur, Vishnu;
Singh, Navneet;
Mohanty, Vakul;
Chung, Eunah;
Muhammad, Belal;
Choi, Kwangmin;
Chen, Xiaoting;
Chetal, Kashish;
Ratner, Nancy;
Salomonis, Nathan;
Weirauch, Matthew T.;
Waltz, Susan;
Huang, Gang;
Privette-Vinnedge, Lisa;
Park, Joo-Seop;
Janssen, Edith M.;
Komurov, Kakajan

Publication type:

Article

Splicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy.

Published in:

Science Translational Medicine, 2024, v. 16, n. 730, p. 1, doi. 10.1126/scitranslmed.ade2886

By:

Li, Guangyuan;
Mahajan, Shweta;
Ma, Siyuan;
Jeffery, Erin D.;
Zhang, Xuan;
Bhattacharjee, Anukana;
Venkatasubramanian, Meenakshi;
Weirauch, Matthew T.;
Miraldi, Emily R.;
Grimes, H. Leighton;
Sheynkman, Gloria M.;
Tilburgs, Tamara;
Salomonis, Nathan

Publication type:

Article

Ontogeny and function of the circadian clock in intestinal organoids.

Published in:

EMBO Journal, 2022, v. 41, n. 2, p. 1, doi. 10.15252/embj.2020106973

By:

Rosselot, Andrew E;
Park, Miri;
Kim, Mari;
Matsu‐Ura, Toru;
Wu, Gang;
Flores, Danilo E;
Subramanian, Krithika R;
Lee, Suengwon;
Sundaram, Nambirajan;
Broda, Taylor R;
McCauley, Heather A;
Hawkins, Jennifer A;
Chetal, Kashish;
Salomonis, Nathan;
Shroyer, Noah F;
Helmrath, Michael A;
Wells, James M;
Hogenesch, John B;
Moore, Sean R;
Hong, Christian I

Publication type:

Article

Long Non-Coding RNA and Alternative Splicing Modulations in Parkinson's Leukocytes Identified by RNA Sequencing.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 3, p. 1, doi. 10.1371/journal.pcbi.1003517

By:

Soreq, Lilach;
Guffanti, Alessandro;
Salomonis, Nathan;
Simchovitz, Alon;
Israel, Zvi;
Bergman, Hagai;
Soreq, Hermona

Publication type:

Article

Alternative Splicing in the Differentiation of Human Embryonic Stem Cells into Cardiac Precursors.

Published in:

PLoS Computational Biology, 2009, v. 5, n. 11, p. 1, doi. 10.1371/journal.pcbi.1000553

By:

Salomonis, Nathan;
Nelson, Brandon;
Vranizan, Karen;
Pico, Alexander R.;
Hanspers, Kristina;
Kuchinsky, Allan;
Ta, Linda;
Mercola, Mark;
Conklin, Bruce R.

Publication type:

Article

Small RNA sequencing-microarray analyses in Parkinson leukocytes reveal deep brain stimulation-induced splicing changes that classify brain region transcriptomes.

Published in:

Frontiers in Molecular Neuroscience, 2013, v. 6, p. 1, doi. 10.3389/fnmol.2013.00010

By:

Soreq, Lilach;
Salomonis, Nathan;
Bronstein, Michal;
Greenberg, David S.;
Israel, Zvi;
Bergman, Hagai;
Soreq, Hermona

Publication type:

Article

Obesity Uncovers the Presence of Inflammatory Lung Macrophage Subsets With an Adipose Tissue Transcriptomic Signature in Influenza Virus Infection.

Published in:

Journal of Infectious Diseases, 2025, v. 231, n. 2, p. e317, doi. 10.1093/infdis/jiae535

By:

Alarcon, Pablo C;
Ulanowicz, Cassidy J;
Damen, Michelle S M A;
Eom, John;
Sawada, Keisuke;
Chung, Hak;
Alahakoon, Tara;
Oates, Jarren R;
Wayland, Jennifer L;
Stankiewicz, Traci E;
Moreno-Fernandez, Maria E;
Zacharias, William J;
Salomonis, Nathan;
Divanovic, Senad

Publication type:

Article

GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways.

Published in:

Nature Genetics, 2002, v. 31, n. 1, p. 19, doi. 10.1038/ng0502-19

By:

Dahlquist, Kam D.;
Salomonis, Nathan;
Vranizan, Karen;
Lawlor, Steven C.;
Conklin, Bruce R.

Publication type:

Article

Defining human cardiac transcription factor hierarchies using integrated single-cell heterogeneity analysis.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-07333-4

By:

Churko, Jared M.;
Garg, Priyanka;
Treutlein, Barbara;
Venkatasubramanian, Meenakshi;
Wu, Haodi;
Lee, Jaecheol;
Wessells, Quinton N.;
Chen, Shih-Yu;
Chen, Wen-Yi;
Chetal, Kashish;
Mantalas, Gary;
Neff, Norma;
Jabart, Eric;
Sharma, Arun;
Nolan, Garry P.;
Salomonis, Nathan;
Wu, Joseph C.

Publication type:

Article

The balance between protective and pathogenic immune responses to pneumonia in the neonatal lung is enforced by gut microbiota.

Published in:

Science Translational Medicine, 2022, v. 14, n. 649, p. 1, doi. 10.1126/scitranslmed.abl3981

By:

Stevens, Joseph;
Steinmeyer, Shelby;
Bonfield, Madeline;
Peterson, Laura;
Wang, Timothy;
Gray, Jerilyn;
Lewkowich, Ian;
Xu, Yan;
Du, Yina;
Guo, Minzhe;
Wynn, James L.;
Zacharias, William;
Salomonis, Nathan;
Miller, Lisa;
Chougnet, Claire;
O'Connor, Dennis Hartigan;
Deshmukh, Hitesh

Publication type:

Article

RNA Isoforms as Broad Targets for Cancer Immunotherapy.

Published in:

DNA & Cell Biology, 2024, v. 43, n. 8, p. 363, doi. 10.1089/dna.2024.0108

By:

Li, Guangyuan;
Salomonis, Nathan

Publication type:

Article

Whole-Genome rVISTA: a tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomic data.

Published in:

Bioinformatics, 2013, v. 29, n. 16, p. 2059, doi. 10.1093/bioinformatics/btt318

By:

Dubchak, Inna;
Munoz, Matthew;
Poliakov, Alexandre;
Salomonis, Nathan;
Minovitsky, Simon;
Bodmer, Rolf;
Zambon, Alexander C.

Publication type:

Article

GO-Elite: a flexible solution for pathway and ontology over-representation.

Published in:

Bioinformatics, 2012, v. 28, n. 16, p. 2209, doi. 10.1093/bioinformatics/bts366

By:

Zambon, Alexander C.;
Gaj, Stan;
Ho, Isaac;
Hanspers, Kristina;
Vranizan, Karen;
Evelo, Chris T.;
Conklin, Bruce R.;
Pico, Alexander R.;
Salomonis, Nathan

Publication type:

Article

Mosaic: making biological sense of complex networks.

Published in:

Bioinformatics, 2012, v. 28, n. 14, p. 1943, doi. 10.1093/bioinformatics/bts278

By:

Zhang, Chao;
Hanspers, Kristina;
Kuchinsky, Allan;
Salomonis, Nathan;
Xu, Dong;
Pico, Alexander R.

Publication type:

Article

ANOSVA: a statistical method for detecting splice variation from expression data.

Published in:

Bioinformatics, 2005, v. 21, p. i107, doi. 10.1093/bioinformatics/bti1010

By:

Cline, Melissa S.;
Blume, John;
Cawley, Simon;
Clark, Tyson A.;
Hu, Jing-Shan;
Lu, Gang;
Salomonis, Nathan;
Wang, Hui;
Williams, Alan

Publication type:

Article

ANOSVA: a statistical method for detecting splice variation from expression data.

Published in:

Bioinformatics, 2005, v. 21, n. 1, p. i107, doi. 10.1093/bioinformatics/bti1010

By:

Melissa S. Cline;
John Blume;
Simon Cawley;
Tyson A. Clark;
Jing-Shan Hu;
Gang Lu;
Nathan Salomonis;
Hui Wang;
Alan Williams

Publication type:

Article

MAAMD: a workflow to standardize meta-analyses and comparison of affymetrix microarray data.

Published in:

BMC Bioinformatics, 2014, v. 15, n. 1, p. 1, doi. 10.1186/1471-2105-15-69

By:

Zhuohui Gan;
Jianwu Wang;
Salomonis, Nathan;
Stowe, Jennifer C.;
Haddad, Gabriel G.;
McCulloch, Andrew D.;
Altintas, Ilkay;
Zambon, Alexander C.

Publication type:

Article

GenMAPP 2: new features and resources for pathway analysis.

Published in:

BMC Bioinformatics, 2007, v. 8, p. 217, doi. 10.1186/1471-2105-8-217

By:

Salomonis, Nathan;
Hanspers, Kristina;
Zambon, Alexander C;
Vranizan, Karen;
Lawlor, Steven C;
Dahlquist, Kam D;
Doniger, Scott W;
Stuart, Josh;
Conklin, Bruce R;
Pico, Alexander R

Publication type:

Article

Pseudocell Tracer—A method for inferring dynamic trajectories using scRNAseq and its application to B cells undergoing immunoglobulin class switch recombination.

Published in:

PLoS Computational Biology, 2021, v. 17, n. 5, p. 1, doi. 10.1371/journal.pcbi.1008094

By:

Reiman, Derek;
Manakkat Vijay, Godhev Kumar;
Xu, Heping;
Sonin, Andrew;
Chen, Dianyu;
Salomonis, Nathan;
Singh, Harinder;
Khan, Aly A.

Publication type:

Article

pyInfinityFlow: optimized imputation and analysis of high-dimensional flow cytometry data for millions of cells.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad287

By:

Ferchen, Kyle;
Salomonis, Nathan;
Grimes, H Leighton

Publication type:

Article

Resolving single-cell heterogeneity from hundreds of thousands of cells through sequential hybrid clustering and NMF.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3773, doi. 10.1093/bioinformatics/btaa201

By:

Venkatasubramanian, Meenakshi;
Chetal, Kashish;
Schnell, Daniel J;
Atluri, Gowtham;
Salomonis, Nathan

Publication type:

Article

Tissues Harvested Using an Automated Surgical Approach Confirm Molecular Heterogeneity of Glioblastoma and Enhance Specimen's Translational Research Value.

Published in:

Frontiers in Oncology, 2019, v. 9, p. 1, doi. 10.3389/fonc.2019.01119

By:

Zusman, Edie;
Sidorov, Maxim;
Ayala, Alexandria;
Chang, Jimmin;
Singer, Eric;
Chen, Michelle;
Desprez, Pierre-Yves;
McAllister, Sean;
Salomonis, Nathan;
Chetal, Kashish;
Prasad, Gautam;
Kang, Tyler;
Mark, Joseph;
Dickinson, Lawrence;
Soroceanu, Liliana

Publication type:

Article

cellHarmony: cell-level matching and holistic comparison of single-cell transcriptomes.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. e138, doi. 10.1093/nar/gkz789

By:

DePasquale, Erica A K;
Schnell, Daniel;
Dexheimer, Phillip;
Ferchen, Kyle;
Hay, Stuart;
Chetal, Kashish;
Valiente-Alandí, Íñigo;
Blaxall, Burns C;
Grimes, H Leighton;
Salomonis, Nathan

Publication type:

Article

MBNL1-mediated regulation of differentiation RNAs promotes myofibroblast transformation and the fibrotic response.

Published in:

Nature Communications, 2015, v. 6, n. 12, p. 10084, doi. 10.1038/ncomms10084

By:

Davis, Jennifer;
Salomonis, Nathan;
Ghearing, Natasha;
Lin, Suh-Chin J.;
Kwong, Jennifer Q.;
Mohan, Apoorva;
Swanson, Maurice S.;
Molkentin, Jeffery D.

Publication type:

Article

Molecular Characterization of Pediatric Restrictive Cardiomyopathy from Integrative Genomics.

Published in:

Scientific Reports, 2017, p. 39276, doi. 10.1038/srep39276

By:

Rindler, Tara N.;
Hinton, Robert B.;
Salomonis, Nathan;
Ware, Stephanie M.

Publication type:

Article

Rational targeting Cdc42 restrains Th2 cell differentiation and prevents allergic airway inflammation.

Published in:

Clinical & Experimental Allergy, 2019, v. 49, n. 1, p. 92, doi. 10.1111/cea.13293

By:

Yang, Jun‐Qi;
Kalim, Khalid W.;
Li, Yuan;
Duan, Xin;
Nguyen, Phuong;
Khurana Hershey, Gurjit K.;
Kroner, John;
Ruff, Brandy;
Zhang, Li;
Salomonis, Nathan;
Rochman, Mark;
Wen, Ting;
Zheng, Yi;
Guo, Fukun

Publication type:

Article

Single-nucleus RNA-seq identifies transcriptional heterogeneity in multinucleated skeletal myofibers.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-20063-w

By:

Petrany, Michael J.;
Swoboda, Casey O.;
Sun, Chengyi;
Chetal, Kashish;
Chen, Xiaoting;
Weirauch, Matthew T.;
Salomonis, Nathan;
Millay, Douglas P.

Publication type:

Article

Publisher Correction: MBNL1 regulates essential alternative RNA splicing patterns in MLL-rearranged leukemia.

Published in:

2020

By:

Itskovich, Svetlana S.;
Gurunathan, Arun;
Clark, Jason;
Burwinkel, Matthew;
Wunderlich, Mark;
Berger, Mikaela R.;
Kulkarni, Aishwarya;
Chetal, Kashish;
Venkatasubramanian, Meenakshi;
Salomonis, Nathan;
Kumar, Ashish R.;
Lee, Lynn H.

Publication type:

Correction Notice

MBNL1 regulates essential alternative RNA splicing patterns in MLL-rearranged leukemia.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-15733-8

By:

Itskovich, Svetlana S.;
Gurunathan, Arun;
Clark, Jason;
Burwinkel, Matthew;
Wunderlich, Mark;
Berger, Mikaela R.;
Kulkarni, Aishwarya;
Chetal, Kashish;
Venkatasubramanian, Meenakshi;
Salomonis, Nathan;
Kumar, Ashish R.;
Lee, Lynn H.

Publication type:

Article

AKAP13 Rho-GEF and PKD-Binding Domain Deficient Mice Develop Normally but Have an Abnormal Response to β-Adrenergic-Induced Cardiac Hypertrophy.

Published in:

PLoS ONE, 2013, v. 8, n. 4, p. 1, doi. 10.1371/journal.pone.0062705

By:

Spindler, Matthew J.;
Burmeister, Brian T.;
Huang, Yu;
Hsiao, Edward C.;
Salomonis, Nathan;
Scott, Mark J.;
Srivastava, Deepak;
Carnegie, Graeme K.;
Conklin, Bruce R.

Publication type:

Article

Lentiviral Vectors and Protocols for Creation of Stable hESC Lines for Fluorescent Tracking and Drug Resistance Selection of Cardiomyocytes.

Published in:

PLoS ONE, 2009, v. 4, n. 4, p. 1, doi. 10.1371/journal.pone.0005046

By:

Kita-Matsuo, Hiroko;
Barcova, Maria;
Prigozhina, Natalie;
Salomonis, Nathan;
Wei, Karen;
Jacot, Jeffrey G.;
Nelson, Brandon;
Spiering, Sean;
Haverslag, René;
Changsung Kim;
Talantova, Maria;
Bajpai, Ruchi;
Calzolari, Diego;
Terskikh, Alexey;
McCulloch, Andrew D.;
Price, Jeffrey H.;
Conklin, Bruce R.;
Chen, H. S. Vincent;
Mercola, Mark

Publication type:

Article

Identification of Spt5 Target Genes in Zebrafish Development Reveals Its Dual Activity In Vivo.

Published in:

PLoS ONE, 2008, v. 3, n. 11, p. 1, doi. 10.1371/journal.pone.0003621

By:

Krishnan, Keerthi;
Salomonis, Nathan;
Su Guo

Publication type:

Article

miR-876-3p is a tumor suppressor on 9p21 that is inactivated in melanoma and targets ERK.

Published in:

Journal of Translational Medicine, 2024, v. 22, n. 1, p. 1, doi. 10.1186/s12967-024-05527-7

By:

Bezrookove, Vladimir;
Khan, Imran;
Bhattacharjee, Anukana;
Fan, Juifang;
Jones, Robyn;
Sharma, Anima;
Nosrati, Mehdi;
Desprez, Pierre-Yves;
Salomonis, Nathan;
Shi, Yihui;
Dar, Altaf;
Kashani-Sabet, Mohammed

Publication type:

Article

Mammary Gland Involution as a Multi-step Process.

Published in:

Journal of Mammary Gland Biology & Neoplasia, 2007, v. 12, n. 1, p. 25, doi. 10.1007/s10911-007-9035-7

By:

Torsten Stein;
Nathan Salomonis;
Barry Gusterson

Publication type:

Article

CellDrift: inferring perturbation responses in temporally sampled single-cell data.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac324

By:

Jin, Kang;
Schnell, Daniel;
Li, Guangyuan;
Salomonis, Nathan;
Prasath, V B Surya;
Szczesniak, Rhonda;
Aronow, Bruce J

Publication type:

Article

DeepImmuno: deep learning-empowered prediction and generation of immunogenic peptides for T-cell immunity.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 6, p. 1, doi. 10.1093/bib/bbab160

By:

Li, Guangyuan;
Iyer, Balaji;
Prasath, V B Surya;
Ni, Yizhao;
Salomonis, Nathan

Publication type:

Article

GM-CSF Programs Hematopoietic Stem and Progenitor Cells During Candida albicans Vaccination for Protection Against Reinfection.

Published in:

Frontiers in Immunology, 2021, v. 12, p. 1, doi. 10.3389/fimmu.2021.790309

By:

Bono, Cristina;
Guerrero, Paula;
Jordán-Pla, Antonio;
Erades, Ana;
Salomonis, Nathan;
Grimes, H. Leighton;
Gil, M. Luisa;
Yáñez, Alberto

Publication type:

Article

Progenitor translatome changes coordinated by Tsc1 increase perception of Wnt signals to end nephrogenesis.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-26626-9

By:

Jarmas, Alison E.;
Brunskill, Eric W.;
Chaturvedi, Praneet;
Salomonis, Nathan;
Kopan, Raphael

Publication type:

Article

Systems biology evaluation of cell-free amniotic fluid transcriptome of term and preterm infants to detect fetal maturity.

Published in:

BMC Medical Genomics, 2015, v. 8, p. 1, doi. 10.1186/s12920-015-0138-5

By:

Kamath-Rayne, Beena D.;
Yina Du;
Hughes, Maria;
Wagner, Erin A.;
Muglia, Louis J.;
De Franco, Emily A.;
Whitsett, Jeffrey A.;
Salomonis, Nathan;
Yan Xu

Publication type:

Article

Stem cell pluripotency.

Published in:

Cell Cycle, 2010, v. 9, n. 16, p. 3133, doi. 10.4161/cc.9.16.12888

By:

Salomonis, Nathan;
Conklin, Bruce R.

Publication type:

Article