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Alignment-free sequence comparison: benefits, applications, and tools.

Zielezinski A, Vinga S, Almeida J, Karlowski WM.

Genome Biol. 2017 Oct 3;18(1):186. doi: 10.1186/s13059-017-1319-7. Review.


Towards Generation, Management, and Exploration of Combined Radiomics and Pathomics Datasets for Cancer Research.

Saltz J, Almeida J, Gao Y, Sharma A, Bremer E, DiPrima T, Saltz M, Kalpathy-Cramer J, Kurc T.

AMIA Jt Summits Transl Sci Proc. 2017 Jul 26;2017:85-94. eCollection 2017.


Safe "cloudification" of large images through picker APIs.

Bremer E, Kurc T, Gao Y, Saltz J, Almeida JS.

AMIA Annu Symp Proc. 2017 Feb 10;2016:342-351. eCollection 2016.


Construction and Validation of a Multi-Institutional Tissue Microarray of Invasive Ductal Carcinoma From Racially and Ethnically Diverse Populations.

Seijo E, Lima D, Iriabho E, Almeida J, Monico J, Echeverri M, Gutierrez S, Flores I, Lee JH, Fisher K, Grizzle WE, Sica GL, Butler C, Hicks C, Meade CD, Sodeke SO, Moroz K, Coppola D, Munoz-Antonia T.

Cancer Control. 2016 Oct;23(4):383-389.


Mechanistic Parameterization of the Kinomic Signal in Peptide Arrays.

Dussaq A, Anderson JC, Willey CD, Almeida JS.

J Proteomics Bioinform. 2016 May;9(5):151-157. Epub 2016 May 24.


Computational Pathology: A Path Ahead.

Louis DN, Feldman M, Carter AB, Dighe AS, Pfeifer JD, Bry L, Almeida JS, Saltz J, Braun J, Tomaszewski JE, Gilbertson JR, Sinard JH, Gerber GK, Galli SJ, Golden JA, Becich MJ.

Arch Pathol Lab Med. 2016 Jan;140(1):41-50. doi: 10.5858/arpa.2015-0093-SA. Epub 2015 Jun 22.


Proteomic Analysis of Plasma from California Sea Lions (Zalophus californianus) Reveals Apolipoprotein E as a Candidate Biomarker of Chronic Domoic Acid Toxicosis.

Neely BA, Ferrante JA, Chaves JM, Soper JL, Almeida JS, Arthur JM, Gulland FM, Janech MG.

PLoS One. 2015 Apr 28;10(4):e0123295. doi: 10.1371/journal.pone.0123295. eCollection 2014.


OpenHealth Platform for Interactive Contextualization of Population Health Open Data.

Almeida JS, Hajagos J, Crnosija I, Kurc T, Saltz M, Saltz J.

AMIA Annu Symp Proc. 2015 Nov 5;2015:297-305. eCollection 2015.


QMachine: commodity supercomputing in web browsers.

Wilkinson SR, Almeida JS.

BMC Bioinformatics. 2014 Jun 9;15:176. doi: 10.1186/1471-2105-15-176.


Mining genome sequencing data to identify the genomic features linked to breast cancer histopathology.

Ping Z, Siegal GP, Almeida JS, Schnitt SJ, Shen D.

J Pathol Inform. 2014 Jan 31;5(1):3. doi: 10.4103/2153-3539.126147. eCollection 2014.


Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data.

Cole C, Krampis K, Karagiannis K, Almeida JS, Faison WJ, Motwani M, Wan Q, Golikov A, Pan Y, Simonyan V, Mazumder R.

BMC Bioinformatics. 2014 Jan 27;15:28. doi: 10.1186/1471-2105-15-28.


TopFed: TCGA tailored federated query processing and linking to LOD.

Saleem M, Padmanabhuni SS, Ngomo AC, Iqbal A, Almeida JS, Decker S, Deus HF.

J Biomed Semantics. 2014 Dec 3;5:47. doi: 10.1186/2041-1480-5-47. eCollection 2014.


Sequence analysis by iterated maps, a review.

Almeida JS.

Brief Bioinform. 2014 May;15(3):369-75. doi: 10.1093/bib/bbt072. Epub 2013 Oct 25. Review.


Machine learning to predict extubation outcome in premature infants.

Mueller M, Wagner CC, Stanislaus R, Almeida JS.

Proc Int Jt Conf Neural Netw. 2013 Aug;2013:1-6.


A self-updating road map of The Cancer Genome Atlas.

Robbins DE, Grüneberg A, Deus HF, Tanik MM, Almeida JS.

Bioinformatics. 2013 May 15;29(10):1333-40. doi: 10.1093/bioinformatics/btt141. Epub 2013 Apr 17.


Identification of prognostic gene signatures of glioblastoma: a study based on TCGA data analysis.

Kim YW, Koul D, Kim SH, Lucio-Eterovic AK, Freire PR, Yao J, Wang J, Almeida JS, Aldape K, Yung WK.

Neuro Oncol. 2013 Jul;15(7):829-39. doi: 10.1093/neuonc/not024. Epub 2013 Mar 15.


Can Machine Learning Methods Predict Extubation Outcome in Premature Infants as well as Clinicians?

Mueller M, Almeida JS, Stanislaus R, Wagner CL.

J Neonatal Biol. 2013;2. pii: 1000118.


ImageJS: Personalized, participated, pervasive, and reproducible image bioinformatics in the web browser.

Almeida JS, Iriabho EE, Gorrepati VL, Wilkinson SR, Grüneberg A, Robbins DE, Hackney JR.

J Pathol Inform. 2012;3:25. doi: 10.4103/2153-3539.98813. Epub 2012 Jul 20.


Fractal MapReduce decomposition of sequence alignment.

Almeida JS, Grüneberg A, Maass W, Vinga S.

Algorithms Mol Biol. 2012 May 2;7(1):12. doi: 10.1186/1748-7188-7-12.


Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis.

Vinga S, Carvalho AM, Francisco AP, Russo LM, Almeida JS.

Algorithms Mol Biol. 2012 May 2;7(1):10. doi: 10.1186/1748-7188-7-10.

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