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Items: 1 to 50 of 86

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.

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.

14.

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
15.

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
16.

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
17.

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.

18.

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.

19.

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
20.

Conversion of intraovarian patterns from preovulation to postovulation based on location of dominant follicle and corpus luteum in heifers.

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

Theriogenology. 2015 Jan 15;83(2):153-61. doi: 10.1016/j.theriogenology.2014.08.020. Epub 2014 Oct 18.

PMID:
25457678
21.

Comparative analysis of metazoan chromatin organization.

Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, Egelhofer TA, Hu SS, Alekseyenko AA, Rechtsteiner A, Asker D, Belsky JA, Bowman SK, Chen QB, Chen RA, Day DS, Dong Y, Dose AC, Duan X, Epstein CB, Ercan S, Feingold EA, Ferrari F, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM, Strome S, Elgin SC, Liu XS, Lieb JD, Ahringer J, Karpen GH, Park PJ.

Nature. 2014 Aug 28;512(7515):449-52. doi: 10.1038/nature13415.

22.

Effect of intraovarian proximity between dominant follicle and corpus luteum on dimensions and blood flow of each structure in heifers.

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

Theriogenology. 2014 Oct 1;82(6):875-83. doi: 10.1016/j.theriogenology.2014.06.022. Epub 2014 Jul 10.

PMID:
25091526
23.

ADRA2B deletion variant selectively predicts stress-induced enhancement of long-term memory in females.

Zoladz PR, Kalchik AE, Hoffman MM, Aufdenkampe RL, Lyle SM, Peters DM, Brown CM, Cadle CE, Scharf AR, Dailey AM, Wolters NE, Talbot JN, Rorabaugh BR.

Psychoneuroendocrinology. 2014 Oct;48:111-22. doi: 10.1016/j.psyneuen.2014.06.012. Epub 2014 Jun 20.

PMID:
24997351
24.

Blood flow to follicles and CL during development of the periovulatory follicular wave in heifers.

Ginther OJ, Rakesh HB, Hoffman MM.

Theriogenology. 2014 Jul 15;82(2):304-11. doi: 10.1016/j.theriogenology.2014.04.009. Epub 2014 Apr 16.

PMID:
24835640
25.

Intraovarian effect of dominant follicle and corpus luteum on number of follicles during a follicular wave in heifers.

Ginther OJ, Hoffman MM.

Theriogenology. 2014 Jul 1;82(1):169-75. doi: 10.1016/j.theriogenology.2014.03.013. Epub 2014 Mar 26.

PMID:
24768007
26.

Selective fluorescence sensing of copper(II) and water via competing imine hydrolysis and alcohol oxidation pathways sensitive to water content in aqueous acetonitrile mixtures.

Mariappan K, Alaparthi M, Caple G, Balasubramanian V, Hoffman MM, Hudspeth M, Sykes AG.

Inorg Chem. 2014 Mar 17;53(6):2953-62. doi: 10.1021/ic402723c. Epub 2014 Mar 6.

PMID:
24601554
27.

Brief, pre-learning stress reduces false memory production and enhances true memory selectively in females.

Zoladz PR, Peters DM, Kalchik AE, Hoffman MM, Aufdenkampe RL, Woelke SA, Wolters NE, Talbot JN.

Physiol Behav. 2014 Apr 10;128:270-6. doi: 10.1016/j.physbeh.2014.02.028. Epub 2014 Feb 21.

PMID:
24560841
28.

Brief, pre-retrieval stress differentially influences long-term memory depending on sex and corticosteroid response.

Zoladz PR, Kalchik AE, Hoffman MM, Aufdenkampe RL, Burke HM, Woelke SA, Pisansky JM, Talbot JN.

Brain Cogn. 2014 Mar;85:277-85. doi: 10.1016/j.bandc.2014.01.010. Epub 2014 Feb 6.

PMID:
24509087
29.

Relationship between days of the luteolytic period and locations of the preovulatory follicle and CL in interovulatory intervals with two or three follicular waves in heifers.

Ginther OJ, Rakesh HB, Bashir ST, Hoffman MM.

Theriogenology. 2014 Apr 1;81(6):787-96. doi: 10.1016/j.theriogenology.2013.12.025. Epub 2014 Jan 7.

PMID:
24503108
30.

Complex interrelationships among CL, preovulatory follicle, number of follicular waves, and right or left ovaries in heifers.

Ginther OJ, Rakesh HB, Hoffman MM.

Theriogenology. 2014 Feb;81(3):481-9. doi: 10.1016/j.theriogenology.2013.11.003. Epub 2013 Nov 11.

PMID:
24315685
31.

Minor FSH surge, minor follicular wave, and resurgence of preovulatory follicle several days before ovulation in heifers.

Ginther OJ, Rakesh HB, Bashir ST, Hoffman MM.

Theriogenology. 2014 Feb;81(3):437-45. doi: 10.1016/j.theriogenology.2013.10.019. Epub 2013 Oct 26.

PMID:
24268017
32.

Hormone concentrations temporally associated with contralateral and ipsilateral relationships between the CL and preovulatory follicle during the third follicular wave in heifers.

Ginther OJ, Bashir ST, Rakesh HB, Hoffman MM.

Theriogenology. 2013 Oct 15;80(7):738-47. doi: 10.1016/j.theriogenology.2013.06.011. Epub 2013 Aug 9.

PMID:
23932169
33.

Endocrinology of number of follicular waves per estrous cycle and contralateral or ipsilateral relationship between corpus luteum and preovulatory follicle in heifers.

Ginther OJ, Bashir ST, Hoffman MM, Beg MA.

Domest Anim Endocrinol. 2013 Aug;45(2):64-71. doi: 10.1016/j.domaniend.2013.05.002. Epub 2013 Jun 12.

PMID:
23806855
34.

Two-way coupling between FSH and the dominant follicle in heifers.

Ginther OJ, Bashir ST, Rakesh HB, Hoffman MM.

Theriogenology. 2013 Sep 15;80(5):463-9. doi: 10.1016/j.theriogenology.2013.05.008. Epub 2013 Jun 10.

PMID:
23756042
35.

Integrative annotation of chromatin elements from ENCODE data.

Hoffman MM, Ernst J, Wilder SP, Kundaje A, Harris RS, Libbrecht M, Giardine B, Ellenbogen PM, Bilmes JA, Birney E, Hardison RC, Dunham I, Kellis M, Noble WS.

Nucleic Acids Res. 2013 Jan;41(2):827-41. doi: 10.1093/nar/gks1284. Epub 2012 Dec 5.

36.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M.

Genome Res. 2012 Sep;22(9):1813-31. doi: 10.1101/gr.136184.111.

37.

Unsupervised pattern discovery in human chromatin structure through genomic segmentation.

Hoffman MM, Buske OJ, Wang J, Weng Z, Bilmes JA, Noble WS.

Nat Methods. 2012 Mar 18;9(5):473-6. doi: 10.1038/nmeth.1937.

38.

Exploratory analysis of genomic segmentations with Segtools.

Buske OJ, Hoffman MM, Ponts N, Le Roch KG, Noble WS.

BMC Bioinformatics. 2011 Oct 26;12:415. doi: 10.1186/1471-2105-12-415.

39.

In vitro efficacy of 7-benzylamino-1-isoquinolinamines against Plasmodium falciparum related to the efficacy of chalcones.

Gutteridge CE, Hoffman MM, Bhattacharjee AK, Milhous WK, Gerena L.

Bioorg Med Chem Lett. 2011 Jan 15;21(2):786-9. doi: 10.1016/j.bmcl.2010.11.099. Epub 2010 Nov 26.

PMID:
21168330
40.

A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data.

Chen X, Hoffman MM, Bilmes JA, Hesselberth JR, Noble WS.

Bioinformatics. 2010 Jun 15;26(12):i334-42. doi: 10.1093/bioinformatics/btq175.

41.

The Genomedata format for storing large-scale functional genomics data.

Hoffman MM, Buske OJ, Noble WS.

Bioinformatics. 2010 Jun 1;26(11):1458-9. doi: 10.1093/bioinformatics/btq164. Epub 2010 Apr 29.

42.

An effective model for natural selection in promoters.

Hoffman MM, Birney E.

Genome Res. 2010 May;20(5):685-92. doi: 10.1101/gr.096719.109. Epub 2010 Mar 1.

43.

Another case of severe, chronically symptomatic, nonhealing gastroduodenal injury after radioembolization of hepatic tumor.

Yarze JC, Hoffman MM.

Am J Gastroenterol. 2007 Dec;102(12):2863. No abstract available.

PMID:
18042123
44.

Estimating the neutral rate of nucleotide substitution using introns.

Hoffman MM, Birney E.

Mol Biol Evol. 2007 Feb;24(2):522-31. Epub 2006 Nov 22.

PMID:
17122369
45.

Rethinking the coagulation cascade.

Hoffman MM, Monroe DM.

Curr Hematol Rep. 2005 Sep;4(5):391-6. Review.

PMID:
16131441
46.

Volume-dependent glutamate permeation depends on transmembrane ionic strength and extracellular Cl-.

Hoffman MM, Garber SS.

J Membr Biol. 2004 Feb 1;197(3):193-202.

PMID:
15042350
47.

AANT: the Amino Acid-Nucleotide Interaction Database.

Hoffman MM, Khrapov MA, Cox JC, Yao J, Tong L, Ellington AD.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D174-81.

48.

Cl(-) and glutamate(-) competition for a volume-regulated anion channel.

Garber SS, Hoffman MM.

Biol Bull. 2002 Oct;203(2):194-5. No abstract available.

PMID:
12414573
49.

Focal renal mass: an unusual manifestation of chronic lymphocytic leukemia.

Ahmed S, Karim A, Hoffman MM, Bhuiya TA, Mattana J.

Clin Nephrol. 2002 Oct;58(4):324-7. No abstract available.

PMID:
12400852
50.

Modulation of volume regulated anion current by I(Cln).

Hubert MD, Levitan I, Hoffman MM, Zraggen M, Hofreiter ME, Garber SS.

Biochim Biophys Acta. 2000 Jun 1;1466(1-2):105-14.

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