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Items: 1 to 20 of 89

1.

DNAmod: the DNA modification database.

Sood AJ, Viner C, Hoffman MM.

J Cheminform. 2019 Apr 23;11(1):30. doi: 10.1186/s13321-019-0349-4.

2.

Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities.

Zitnik M, Nguyen F, Wang B, Leskovec J, Goldenberg A, Hoffman MM.

Inf Fusion. 2019 Oct;50:71-91. doi: 10.1016/j.inffus.2018.09.012. Epub 2018 Sep 21.

PMID:
30467459
3.

Sensitive tumour detection and classification using plasma cell-free DNA methylomes.

Shen SY, Singhania R, Fehringer G, Chakravarthy A, Roehrl MHA, Chadwick D, Zuzarte PC, Borgida A, Wang TT, Li T, Kis O, Zhao Z, Spreafico A, Medina TDS, Wang Y, Roulois D, Ettayebi I, Chen Z, Chow S, Murphy T, Arruda A, O'Kane GM, Liu J, Mansour M, McPherson JD, O'Brien C, Leighl N, Bedard PL, Fleshner N, Liu G, Minden MD, Gallinger S, Goldenberg A, Pugh TJ, Hoffman MM, Bratman SV, Hung RJ, De Carvalho DD.

Nature. 2018 Nov;563(7732):579-583. doi: 10.1038/s41586-018-0703-0. Epub 2018 Nov 14.

4.

Umap and Bismap: quantifying genome and methylome mappability.

Karimzadeh M, Ernst C, Kundaje A, Hoffman MM.

Nucleic Acids Res. 2018 Nov 16;46(20):e120. doi: 10.1093/nar/gky677.

5.

Iriomoteolides: novel chemical tools to study actin dynamics.

Unzue A, Cribiú R, Hoffman MM, Knehans T, Lafleur K, Caflisch A, Nevado C.

Chem Sci. 2018 Apr 3;9(15):3793-3802. doi: 10.1039/c7sc04286h. eCollection 2018 Apr 21.

6.

Opportunities and obstacles for deep learning in biology and medicine.

Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow PM, Zietz M, Hoffman MM, Xie W, Rosen GL, Lengerich BJ, Israeli J, Lanchantin J, Woloszynek S, Carpenter AE, Shrikumar A, Xu J, Cofer EM, Lavender CA, Turaga SC, Alexandari AM, Lu Z, Harris DJ, DeCaprio D, Qi Y, Kundaje A, Peng Y, Wiley LK, Segler MHS, Boca SM, Swamidass SJ, Huang A, Gitter A, Greene CS.

J R Soc Interface. 2018 Apr;15(141). pii: 20170387. doi: 10.1098/rsif.2017.0387. Review.

7.

Classification and interaction in random forests.

Denisko D, Hoffman MM.

Proc Natl Acad Sci U S A. 2018 Feb 20;115(8):1690-1692. doi: 10.1073/pnas.1800256115. Epub 2018 Feb 12. No abstract available.

8.

4SC-202 as a Potential Treatment for the Pediatric Brain Tumor Medulloblastoma.

Messerli SM, Hoffman MM, Gnimpieba EZ, Kohlhof H, Bhardwaj RD.

Brain Sci. 2017 Nov 3;7(11). pii: E147. doi: 10.3390/brainsci7110147.

9.

Segway 2.0: Gaussian mixture models and minibatch training.

Chan RCW, Libbrecht MW, Roberts EG, Bilmes JA, Noble WS, Hoffman MM.

Bioinformatics. 2018 Feb 15;34(4):669-671. doi: 10.1093/bioinformatics/btx603.

10.

Therapeutic Targeting of PTK7 is Cytotoxic in Atypical Teratoid Rhabdoid Tumors.

Messerli SM, Hoffman MM, Gnimpieba EZ, Bhardwaj RD.

Mol Cancer Res. 2017 Aug;15(8):973-983. doi: 10.1158/1541-7786.MCR-16-0432. Epub 2017 Apr 25.

11.

Genome Informatics 2016.

Chicco D, Hoffman MM.

Genome Biol. 2017 Jan 16;18(1):5. doi: 10.1186/s13059-016-1135-5.

12.

Top considerations for creating bioinformatics software documentation.

Karimzadeh M, Hoffman MM.

Brief Bioinform. 2018 Jul 20;19(4):693-699. doi: 10.1093/bib/bbw134.

13.

Genome-Wide Association of CKD Progression: The Chronic Renal Insufficiency Cohort Study.

Parsa A, Kanetsky PA, Xiao R, Gupta J, Mitra N, Limou S, Xie D, Xu H, Anderson AH, Ojo A, Kusek JW, Lora CM, Hamm LL, He J, Sandholm N, Jeff J, Raj DE, Böger CA, Bottinger E, Salimi S, Parekh RS, Adler SG, Langefeld CD, Bowden DW; FIND Consortium, Groop PH, Forsblom C, Freedman BI, Lipkowitz M, Fox CS, Winkler CA, Feldman HI; and the Chronic Renal Insufficiency Cohort (CRIC) Study Investigators.

J Am Soc Nephrol. 2017 Mar;28(3):923-934. doi: 10.1681/ASN.2015101152. Epub 2016 Oct 11.

14.

ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data.

Lundberg SM, Tu WB, Raught B, Penn LZ, Hoffman MM, Lee SI.

Genome Biol. 2016 Apr 30;17:82. doi: 10.1186/s13059-016-0925-0.

15.

Interactions of side (left and right ovary) with the number of follicles per ovary and with the intraovarian relationships between dominant follicle and corpus luteum in heifers.

Ginther OJ, Hoffman MM.

Theriogenology. 2016 Sep 1;86(4):907-913. doi: 10.1016/j.theriogenology.2016.03.013. Epub 2016 Mar 17.

PMID:
27106400
16.

Stimulation of regressing subordinate follicles of wave 2 with a gonadotropin product in heifers.

Ginther OJ, Siddiqui MA, Baldrighi JM, Hoffman MM.

Domest Anim Endocrinol. 2016 Apr;55:46-50. doi: 10.1016/j.domaniend.2015.11.006. Epub 2015 Nov 30.

PMID:
26773367
17.

Determining the epigenome using DNA alone.

Viner C, Hoffman MM.

Nat Methods. 2015 Mar;12(3):191-2. doi: 10.1038/nmeth.3291. No abstract available.

PMID:
25719827
18.

Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression.

Libbrecht MW, Ay F, Hoffman MM, Gilbert DM, Bilmes JA, Noble WS.

Genome Res. 2015 Apr;25(4):544-57. doi: 10.1101/gr.184341.114. Epub 2015 Feb 12.

19.

Extending reference assembly models.

Church DM, Schneider VA, Steinberg KM, Schatz MC, Quinlan AR, Chin CS, Kitts PA, Aken B, Marth GT, Hoffman MM, Herrero J, Mendoza ML, Durbin R, Flicek P.

Genome Biol. 2015 Jan 24;16:13. doi: 10.1186/s13059-015-0587-3.

20.

Intraovarian factors associated with switching of a future dominant follicle to a subordinate follicle during induced luteolysis in heifers.

Ginther OJ, Siddiqui MA, Baldrighi JM, Hoffman MM.

Theriogenology. 2015 Mar 15;83(5):786-96. doi: 10.1016/j.theriogenology.2014.11.014. Epub 2014 Nov 18.

PMID:
25523834

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