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Items: 1 to 50 of 119

1.

Applying Citizen Science to Gene, Drug, and Disease Relationship Extraction from Biomedical Abstracts.

Tsueng G, Nanis M, Fouquier JT, Mayers M, Good BM, Su AI.

Bioinformatics. 2019 Sep 3. pii: btz678. doi: 10.1093/bioinformatics/btz678. [Epub ahead of print]

PMID:
31504205
2.

Aligning Needs: Integrating Citizen Science Efforts into Schools Through Service Requirements.

Tsueng G, Kumar A, Nanis SM, Su AI.

Hum Comput (Fairfax). 2019;6(1):56-82.

3.

The Healthy Pregnancy Research Program: transforming pregnancy research through a ResearchKit app.

Radin JM, Steinhubl SR, Su AI, Bhargava H, Greenberg B, Bot BM, Doerr M, Topol EJ.

NPJ Digit Med. 2018 Sep 5;1:45. doi: 10.1038/s41746-018-0052-2. eCollection 2018.

4.

ChlamBase: a curated model organism database for the Chlamydia research community.

Putman T, Hybiske K, Jow D, Afrasiabi C, Lelong S, Cano MA, Stupp GS, Waagmeester A, Good BM, Wu C, Su AI.

Database (Oxford). 2019 Jan 1;2019. pii: baz091. doi: 10.1093/database/baz091. No abstract available.

5.

[Research progress on Chinese herbal medicine fermentation and profile of active substances derived].

Ai S, Tang W, Guo RL, Li JQ, Yang W, He ZG.

Zhongguo Zhong Yao Za Zhi. 2019 Mar;44(6):1110-1118. doi: 10.19540/j.cnki.cjcmm.20181227.002. Review. Chinese.

PMID:
30989972
6.

ChlamBase: a curated model organism database for the Chlamydia research community.

Putman T, Hybiske K, Jow D, Afrasiabi C, Lelong S, Cano MA, Wu C, Su AI.

Database (Oxford). 2019 Jan 1;2019. pii: baz041. doi: 10.1093/database/baz041. Erratum in: Database (Oxford). 2019 Jan 1;2019:.

7.

exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids.

Murillo OD, Thistlethwaite W, Rozowsky J, Subramanian SL, Lucero R, Shah N, Jackson AR, Srinivasan S, Chung A, Laurent CD, Kitchen RR, Galeev T, Warrell J, Diao JA, Welsh JA, Hanspers K, Riutta A, Burgstaller-Muehlbacher S, Shah RV, Yeri A, Jenkins LM, Ahsen ME, Cordon-Cardo C, Dogra N, Gifford SM, Smith JT, Stolovitzky G, Tewari AK, Wunsch BH, Yadav KK, Danielson KM, Filant J, Moeller C, Nejad P, Paul A, Simonson B, Wong DK, Zhang X, Balaj L, Gandhi R, Sood AK, Alexander RP, Wang L, Wu C, Wong DTW, Galas DJ, Van Keuren-Jensen K, Patel T, Jones JC, Das S, Cheung KH, Pico AR, Su AI, Raffai RL, Laurent LC, Roth ME, Gerstein MB, Milosavljevic A.

Cell. 2019 Apr 4;177(2):463-477.e15. doi: 10.1016/j.cell.2019.02.018.

8.

The ReFRAME library as a comprehensive drug repurposing library and its application to the treatment of cryptosporidiosis.

Janes J, Young ME, Chen E, Rogers NH, Burgstaller-Muehlbacher S, Hughes LD, Love MS, Hull MV, Kuhen KL, Woods AK, Joseph SB, Petrassi HM, McNamara CW, Tremblay MS, Su AI, Schultz PG, Chatterjee AK.

Proc Natl Acad Sci U S A. 2018 Oct 16;115(42):10750-10755. doi: 10.1073/pnas.1810137115. Epub 2018 Oct 3.

9.

Identification of transcription factors responsible for dysregulated networks in human osteoarthritis cartilage by global gene expression analysis.

Fisch KM, Gamini R, Alvarez-Garcia O, Akagi R, Saito M, Muramatsu Y, Sasho T, Koziol JA, Su AI, Lotz MK.

Osteoarthritis Cartilage. 2018 Nov;26(11):1531-1538. doi: 10.1016/j.joca.2018.07.012. Epub 2018 Aug 3.

PMID:
30081074
10.

Triflic Acid Treatment Enables LC-MS/MS Analysis of Insoluble Bacterial Biomass.

Wang AY, Thuy-Boun PS, Stupp GS, Su AI, Wolan DW.

J Proteome Res. 2018 Sep 7;17(9):2978-2986. doi: 10.1021/acs.jproteome.8b00166. Epub 2018 Aug 8.

PMID:
30019906
11.

Correcting the F508del-CFTR variant by modulating eukaryotic translation initiation factor 3-mediated translation initiation.

Hutt DM, Loguercio S, Roth DM, Su AI, Balch WE.

J Biol Chem. 2018 Aug 31;293(35):13477-13495. doi: 10.1074/jbc.RA118.003192. Epub 2018 Jul 13.

12.

A genome-wide survey of mutations in the Jurkat cell line.

Gioia L, Siddique A, Head SR, Salomon DR, Su AI.

BMC Genomics. 2018 May 8;19(1):334. doi: 10.1186/s12864-018-4718-6.

13.

Common PIEZO1 Allele in African Populations Causes RBC Dehydration and Attenuates Plasmodium Infection.

Ma S, Cahalan S, LaMonte G, Grubaugh ND, Zeng W, Murthy SE, Paytas E, Gamini R, Lukacs V, Whitwam T, Loud M, Lohia R, Berry L, Khan SM, Janse CJ, Bandell M, Schmedt C, Wengelnik K, Su AI, Honore E, Winzeler EA, Andersen KG, Patapoutian A.

Cell. 2018 Apr 5;173(2):443-455.e12. doi: 10.1016/j.cell.2018.02.047. Epub 2018 Mar 22.

14.

Exploring applications of crowdsourcing to cryo-EM.

Bruggemann J, Lander GC, Su AI.

J Struct Biol. 2018 Jul;203(1):37-45. doi: 10.1016/j.jsb.2018.02.006. Epub 2018 Feb 24.

15.

FoxO transcription factors modulate autophagy and proteoglycan 4 in cartilage homeostasis and osteoarthritis.

Matsuzaki T, Alvarez-Garcia O, Mokuda S, Nagira K, Olmer M, Gamini R, Miyata K, Akasaki Y, Su AI, Asahara H, Lotz MK.

Sci Transl Med. 2018 Feb 14;10(428). pii: eaan0746. doi: 10.1126/scitranslmed.aan0746.

16.

Cross-linking BioThings APIs through JSON-LD to facilitate knowledge exploration.

Xin J, Afrasiabi C, Lelong S, Adesara J, Tsueng G, Su AI, Wu C.

BMC Bioinformatics. 2018 Feb 1;19(1):30. doi: 10.1186/s12859-018-2041-5.

17.

Metaproteomics of Colonic Microbiota Unveils Discrete Protein Functions among Colitic Mice and Control Groups.

Moon C, Stupp GS, Su AI, Wolan DW.

Proteomics. 2018 Feb;18(3-4). doi: 10.1002/pmic.201700391. Epub 2018 Feb 2.

18.

Gene Profiling and T Cell Receptor Sequencing from Antigen-Specific CD4 T Cells.

Holt M, Costanzo A, Gioia L, Abe B, Su AI, Teyton L.

Methods Mol Biol. 2018;1712:217-238. doi: 10.1007/978-1-4939-7514-3_14.

PMID:
29224077
19.

Academics can help shape Wikipedia.

Shafee T, Mietchen D, Su AI.

Science. 2017 Aug 11;357(6351):557-558. doi: 10.1126/science.aao0462. Epub 2017 Aug 10. No abstract available.

PMID:
28798122
20.

WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata.

Putman TE, Lelong S, Burgstaller-Muehlbacher S, Waagmeester A, Diesh C, Dunn N, Munoz-Torres M, Stupp GS, Wu C, Su AI, Good BM.

Database (Oxford). 2017 Jan 1;2017(1). doi: 10.1093/database/bax025.

21.

CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer.

Griffith M, Spies NC, Krysiak K, McMichael JF, Coffman AC, Danos AM, Ainscough BJ, Ramirez CA, Rieke DT, Kujan L, Barnell EK, Wagner AH, Skidmore ZL, Wollam A, Liu CJ, Jones MR, Bilski RL, Lesurf R, Feng YY, Shah NM, Bonakdar M, Trani L, Matlock M, Ramu A, Campbell KM, Spies GC, Graubert AP, Gangavarapu K, Eldred JM, Larson DE, Walker JR, Good BM, Wu C, Su AI, Dienstmann R, Margolin AA, Tamborero D, Lopez-Bigas N, Jones SJ, Bose R, Spencer DH, Wartman LD, Wilson RK, Mardis ER, Griffith OL.

Nat Genet. 2017 Jan 31;49(2):170-174. doi: 10.1038/ng.3774. No abstract available.

22.

Quantitative Metaproteomics and Activity-Based Probe Enrichment Reveals Significant Alterations in Protein Expression from a Mouse Model of Inflammatory Bowel Disease.

Mayers MD, Moon C, Stupp GS, Su AI, Wolan DW.

J Proteome Res. 2017 Feb 3;16(2):1014-1026. doi: 10.1021/acs.jproteome.6b00938. Epub 2017 Jan 23.

23.

Dysregulated circadian rhythm pathway in human osteoarthritis: NR1D1 and BMAL1 suppression alters TGF-β signaling in chondrocytes.

Akagi R, Akatsu Y, Fisch KM, Alvarez-Garcia O, Teramura T, Muramatsu Y, Saito M, Sasho T, Su AI, Lotz MK.

Osteoarthritis Cartilage. 2017 Jun;25(6):943-951. doi: 10.1016/j.joca.2016.11.007. Epub 2016 Nov 22.

24.

Data-Driven Approach To Determine Popular Proteins for Targeted Proteomics Translation of Six Organ Systems.

Lam MP, Venkatraman V, Xing Y, Lau E, Cao Q, Ng DC, Su AI, Ge J, Van Eyk JE, Ping P.

J Proteome Res. 2016 Nov 4;15(11):4126-4134. Epub 2016 Jul 19.

25.

A comprehensive and scalable database search system for metaproteomics.

Chatterjee S, Stupp GS, Park SK, Ducom JC, Yates JR 3rd, Su AI, Wolan DW.

BMC Genomics. 2016 Aug 16;17(1):642. doi: 10.1186/s12864-016-2855-3.

26.

YY1 plays an essential role at all stages of B-cell differentiation.

Kleiman E, Jia H, Loguercio S, Su AI, Feeney AJ.

Proc Natl Acad Sci U S A. 2016 Jul 5;113(27):E3911-20. doi: 10.1073/pnas.1606297113. Epub 2016 Jun 22.

27.

Combining machine learning, crowdsourcing and expert knowledge to detect chemical-induced diseases in text.

Bravo À, Li TS, Su AI, Good BM, Furlong LI.

Database (Oxford). 2016 Jun 15;2016. pii: baw094. doi: 10.1093/database/baw094. Print 2016.

28.

High-performance web services for querying gene and variant annotation.

Xin J, Mark A, Afrasiabi C, Tsueng G, Juchler M, Gopal N, Stupp GS, Putman TE, Ainscough BJ, Griffith OL, Torkamani A, Whetzel PL, Mungall CJ, Mooney SD, Su AI, Wu C.

Genome Biol. 2016 May 6;17(1):91. doi: 10.1186/s13059-016-0953-9.

29.

Gene Wiki Reviews-Raising the quality and accessibility of information about the human genome.

Tsueng G, Good BM, Ping P, Golemis E, Hanukoglu I, van Wijnen AJ, Su AI.

Gene. 2016 Nov 5;592(2):235-8. doi: 10.1016/j.gene.2016.04.053. Epub 2016 May 2.

30.

Branch: an interactive, web-based tool for testing hypotheses and developing predictive models.

Gangavarapu K, Babji V, Meißner T, Su AI, Good BM.

Bioinformatics. 2016 Jul 1;32(13):2072-2074. doi: 10.1093/bioinformatics/btw117. Epub 2016 Mar 7.

31.

Suppression of REDD1 in osteoarthritis cartilage, a novel mechanism for dysregulated mTOR signaling and defective autophagy.

Alvarez-Garcia O, Olmer M, Akagi R, Akasaki Y, Fisch KM, Shen T, Su AI, Lotz MK.

Osteoarthritis Cartilage. 2016 Sep;24(9):1639-47. doi: 10.1016/j.joca.2016.04.015. Epub 2016 Apr 23.

32.

A crowdsourcing workflow for extracting chemical-induced disease relations from free text.

Li TS, Bravo À, Furlong LI, Good BM, Su AI.

Database (Oxford). 2016 Apr 17;2016. pii: baw051. doi: 10.1093/database/baw051. Print 2016.

33.

Extending gene ontology in the context of extracellular RNA and vesicle communication.

Cheung KH, Keerthikumar S, Roncaglia P, Subramanian SL, Roth ME, Samuel M, Anand S, Gangoda L, Gould S, Alexander R, Galas D, Gerstein MB, Hill AF, Kitchen RR, Lötvall J, Patel T, Procaccini DC, Quesenberry P, Rozowsky J, Raffai RL, Shypitsyna A, Su AI, Théry C, Vickers K, Wauben MH, Mathivanan S, Milosavljevic A, Laurent LC.

J Biomed Semantics. 2016 Apr 12;7:19. doi: 10.1186/s13326-016-0061-5. eCollection 2016.

34.

Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes.

Putman TE, Burgstaller-Muehlbacher S, Waagmeester A, Wu C, Su AI, Good BM.

Database (Oxford). 2016 Mar 28;2016. pii: baw028. doi: 10.1093/database/baw028. Print 2016.

35.

Gene Expression in Biopsies of Acute Rejection and Interstitial Fibrosis/Tubular Atrophy Reveals Highly Shared Mechanisms That Correlate With Worse Long-Term Outcomes.

Modena BD, Kurian SM, Gaber LW, Waalen J, Su AI, Gelbart T, Mondala TS, Head SR, Papp S, Heilman R, Friedewald JJ, Flechner SM, Marsh CL, Sung RS, Shidban H, Chan L, Abecassis MM, Salomon DR.

Am J Transplant. 2016 Jul;16(7):1982-98. doi: 10.1111/ajt.13728. Epub 2016 Mar 15.

36.

Wikidata as a semantic framework for the Gene Wiki initiative.

Burgstaller-Muehlbacher S, Waagmeester A, Mitraka E, Turner J, Putman T, Leong J, Naik C, Pavlidis P, Schriml L, Good BM, Su AI.

Database (Oxford). 2016 Mar 17;2016. pii: baw015. doi: 10.1093/database/baw015. Print 2016.

37.

The Implicitome: A Resource for Rationalizing Gene-Disease Associations.

Hettne KM, Thompson M, van Haagen HH, van der Horst E, Kaliyaperumal R, Mina E, Tatum Z, Laros JF, van Mulligen EM, Schuemie M, Aten E, Li TS, Bruskiewich R, Good BM, Su AI, Kors JA, den Dunnen J, van Ommen GJ, Roos M, 't Hoen PA, Mons B, Schultes EA.

PLoS One. 2016 Feb 26;11(2):e0149621. doi: 10.1371/journal.pone.0149621. eCollection 2016.

38.

Increased DNA Methylation and Reduced Expression of Transcription Factors in Human Osteoarthritis Cartilage.

Alvarez-Garcia O, Fisch KM, Wineinger NE, Akagi R, Saito M, Sasho T, Su AI, Lotz MK.

Arthritis Rheumatol. 2016 Aug;68(8):1876-86. doi: 10.1002/art.39643.

39.

Citizen Science for Mining the Biomedical Literature.

Tsueng G, Nanis SM, Fouquier J, Good BM, Su AI.

Citiz Sci. 2016;1(2). pii: 14. doi: 10.5334/cstp.56. Epub 2016 Dec 31.

40.

BioGPS: building your own mash-up of gene annotations and expression profiles.

Wu C, Jin X, Tsueng G, Afrasiabi C, Su AI.

Nucleic Acids Res. 2016 Jan 4;44(D1):D313-6. doi: 10.1093/nar/gkv1104. Epub 2015 Nov 17.

41.

Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies.

Subramanian SL, Kitchen RR, Alexander R, Carter BS, Cheung KH, Laurent LC, Pico A, Roberts LR, Roth ME, Rozowsky JS, Su AI, Gerstein MB, Milosavljevic A.

J Extracell Vesicles. 2015 Aug 28;4:27497. doi: 10.3402/jev.v4.27497. eCollection 2015.

42.

Prioritizing Proteomics Assay Development for Clinical Translation.

Lam MP, Venkatraman V, Cao Q, Wang D, Dincer TU, Lau E, Su AI, Xing Y, Ge J, Ping P, Van Eyk JE.

J Am Coll Cardiol. 2015 Jul 14;66(2):202-4. doi: 10.1016/j.jacc.2015.04.072. No abstract available.

43.

OncoRep: an n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing.

Meißner T, Fisch KM, Gioia L, Su AI.

BMC Med Genomics. 2015 May 21;8:24. doi: 10.1186/s12920-015-0095-z.

44.

The nicotinic α6 subunit gene determines variability in chronic pain sensitivity via cross-inhibition of P2X2/3 receptors.

Wieskopf JS, Mathur J, Limapichat W, Post MR, Al-Qazzaz M, Sorge RE, Martin LJ, Zaykin DV, Smith SB, Freitas K, Austin JS, Dai F, Zhang J, Marcovitz J, Tuttle AH, Slepian PM, Clarke S, Drenan RM, Janes J, Al Sharari S, Segall SK, Aasvang EK, Lai W, Bittner R, Richards CI, Slade GD, Kehlet H, Walker J, Maskos U, Changeux JP, Devor M, Maixner W, Diatchenko L, Belfer I, Dougherty DA, Su AI, Lummis SC, Imad Damaj M, Lester HA, Patapoutian A, Mogil JS.

Sci Transl Med. 2015 May 13;7(287):287ra72. doi: 10.1126/scitranslmed.3009986.

45.

Crowdsourcing in biomedicine: challenges and opportunities.

Khare R, Good BM, Leaman R, Su AI, Lu Z.

Brief Bioinform. 2016 Jan;17(1):23-32. doi: 10.1093/bib/bbv021. Epub 2015 Apr 17. Review.

46.

Harnessing the heart of big data.

Scruggs SB, Watson K, Su AI, Hermjakob H, Yates JR 3rd, Lindsey ML, Ping P.

Circ Res. 2015 Mar 27;116(7):1115-9. doi: 10.1161/CIRCRESAHA.115.306013. No abstract available.

47.

The cure: design and evaluation of a crowdsourcing game for gene selection for breast cancer survival prediction.

Good BM, Loguercio S, Griffith OL, Nanis M, Wu C, Su AI.

JMIR Serious Games. 2014 Jul 29;2(2):e7. doi: 10.2196/games.3350.

48.

Omics Pipe: a community-based framework for reproducible multi-omics data analysis.

Fisch KM, Meißner T, Gioia L, Ducom JC, Carland TM, Loguercio S, Su AI.

Bioinformatics. 2015 Jun 1;31(11):1724-8. doi: 10.1093/bioinformatics/btv061. Epub 2015 Jan 30.

49.

Microtask crowdsourcing for disease mention annotation in PubMed abstracts.

Good BM, Nanis M, Wu C, Su AI.

Pac Symp Biocomput. 2015:282-93.

50.

Crowdsourcing and mining crowd data.

Leaman R, Good BM, Su AI, Lu Z.

Pac Symp Biocomput. 2015:267-9.

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