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Items: 1 to 50 of 449

1.

KBase: The United States Department of Energy Systems Biology Knowledgebase.

Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, Sneddon MW, Henderson ML, Riehl WJ, Murphy-Olson D, Chan SY, Kamimura RT, Kumari S, Drake MM, Brettin TS, Glass EM, Chivian D, Gunter D, Weston DJ, Allen BH, Baumohl J, Best AA, Bowen B, Brenner SE, Bun CC, Chandonia JM, Chia JM, Colasanti R, Conrad N, Davis JJ, Davison BH, DeJongh M, Devoid S, Dietrich E, Dubchak I, Edirisinghe JN, Fang G, Faria JP, Frybarger PM, Gerlach W, Gerstein M, Greiner A, Gurtowski J, Haun HL, He F, Jain R, Joachimiak MP, Keegan KP, Kondo S, Kumar V, Land ML, Meyer F, Mills M, Novichkov PS, Oh T, Olsen GJ, Olson R, Parrello B, Pasternak S, Pearson E, Poon SS, Price GA, Ramakrishnan S, Ranjan P, Ronald PC, Schatz MC, Seaver SMD, Shukla M, Sutormin RA, Syed MH, Thomason J, Tintle NL, Wang D, Xia F, Yoo H, Yoo S, Yu D.

Nat Biotechnol. 2018 Jul 6;36(7):566-569. doi: 10.1038/nbt.4163. No abstract available.

PMID:
29979655
2.

Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line.

Nattestad M, Goodwin S, Ng K, Baslan T, Sedlazeck FJ, Rescheneder P, Garvin T, Fang H, Gurtowski J, Hutton E, Tseng E, Chin CS, Beck T, Sundaravadanam Y, Kramer M, Antoniou E, McPherson JD, Hicks J, McCombie WR, Schatz MC.

Genome Res. 2018 Aug;28(8):1126-1135. doi: 10.1101/gr.231100.117. Epub 2018 Jun 28.

PMID:
29954844
3.

Mitotic defects in fission yeast lipid metabolism 'cut' mutants are suppressed by ammonium chloride.

Zach R, Tvaružková J, Schätz M, Tupa O, Grallert B, Prevorovský M.

FEMS Yeast Res. 2018 Sep 1;18(6). doi: 10.1093/femsyr/foy064.

4.

Controller therapy in Asians and whites with persistent Asthma.

Chen W, Schatz M, Liang Z, Li Q, Sadikova E, Zhang Z, Bagga S, Zeiger RS.

Asian Pac J Allergy Immunol. 2018 Jun 11. doi: 10.12932/AP-210617-0105. [Epub ahead of print]

5.

Cyclophilin A enables specific HIV-1 Tat palmitoylation and accumulation in uninfected cells.

Chopard C, Tong PBV, Tóth P, Schatz M, Yezid H, Debaisieux S, Mettling C, Gross A, Pugnière M, Tu A, Strub JM, Mesnard JM, Vitale N, Beaumelle B.

Nat Commun. 2018 Jun 8;9(1):2251. doi: 10.1038/s41467-018-04674-y.

6.

Precise detection of de novo single nucleotide variants in human genomes.

Gómez-Romero L, Palacios-Flores K, Reyes J, García D, Boege M, Dávila G, Flores M, Schatz MC, Palacios R.

Proc Natl Acad Sci U S A. 2018 May 22;115(21):5516-5521. doi: 10.1073/pnas.1802244115. Epub 2018 May 7.

7.

Critical Care Nurses' Cognitive Ergonomics Related to Medical Device Alarms.

Wung SF, Schatz MR.

Crit Care Nurs Clin North Am. 2018 Jun;30(2):191-202. doi: 10.1016/j.cnc.2018.02.002. Epub 2018 Mar 20.

PMID:
29724438
8.

Accurate detection of complex structural variations using single-molecule sequencing.

Sedlazeck FJ, Rescheneder P, Smolka M, Fang H, Nattestad M, von Haeseler A, Schatz MC.

Nat Methods. 2018 Jun;15(6):461-468. doi: 10.1038/s41592-018-0001-7. Epub 2018 Apr 30.

PMID:
29713083
9.

Nicotine Alters Estrogen Receptor-Beta-Regulated Inflammasome Activity and Exacerbates Ischemic Brain Damage in Female Rats.

d'Adesky ND, de Rivero Vaccari JP, Bhattacharya P, Schatz M, Perez-Pinzon MA, Bramlett HM, Raval AP.

Int J Mol Sci. 2018 Apr 30;19(5). pii: E1330. doi: 10.3390/ijms19051330.

10.

Clinical Updates in Women's Health Care Summary: Asthma.

Namazy JA, Schatz M, Dombrowski M.

Obstet Gynecol. 2018 May;131(5):954. doi: 10.1097/AOG.0000000000002630.

PMID:
29683908
11.

Antibiotic pressure on the acquisition and loss of antibiotic resistance genes in Klebsiella pneumoniae.

Simner PJ, Antar AAR, Hao S, Gurtowski J, Tamma PD, Rock C, Opene BNA, Tekle T, Carroll KC, Schatz MC, Timp W.

J Antimicrob Chemother. 2018 Apr 10. doi: 10.1093/jac/dky121. [Epub ahead of print]

PMID:
29648629
12.

Piercing the dark matter: bioinformatics of long-range sequencing and mapping.

Sedlazeck FJ, Lee H, Darby CA, Schatz MC.

Nat Rev Genet. 2018 Jun;19(6):329-346. doi: 10.1038/s41576-018-0003-4. Review.

PMID:
29599501
13.

Unconventional secretion of viral proteins.

Schatz M, Tong PBV, Beaumelle B.

Semin Cell Dev Biol. 2018 Mar 24. pii: S1084-9521(17)30113-1. doi: 10.1016/j.semcdb.2018.03.008. [Epub ahead of print] Review.

PMID:
29571970
14.

Patterns of prednisone use during pregnancy in women with rheumatoid arthritis: Daily and cumulative dose.

Palmsten K, Rolland M, Hebert MF, Clowse MEB, Schatz M, Xu R, Chambers CD.

Pharmacoepidemiol Drug Saf. 2018 Apr;27(4):430-438. doi: 10.1002/pds.4410. Epub 2018 Feb 28.

PMID:
29488292
15.

Claims-based risk model for first severe COPD exacerbation.

Stanford RH, Nag A, Mapel DW, Lee TA, Rosiello R, Schatz M, Vekeman F, Gauthier-Loiselle M, Merrigan JFP, Duh MS.

Am J Manag Care. 2018 Feb 1;24(2):e45-e53.

16.

Proper experimental design requires randomization/balancing of molecular ecology experiments.

Bálint M, Márton O, Schatz M, Düring RA, Grossart HP.

Ecol Evol. 2018 Jan 10;8(3):1786-1793. doi: 10.1002/ece3.3687. eCollection 2018 Feb.

17.

Management of Asthma during Pregnancy: Optimizing Outcomes and Minimizing Risk.

Namazy JA, Schatz M.

Semin Respir Crit Care Med. 2018 Feb;39(1):29-35. doi: 10.1055/s-0037-1606216. Epub 2018 Feb 10.

PMID:
29427983
18.

Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library.

Hulse-Kemp AM, Maheshwari S, Stoffel K, Hill TA, Jaffe D, Williams SR, Weisenfeld N, Ramakrishnan S, Kumar V, Shah P, Schatz MC, Church DM, Van Deynze A.

Hortic Res. 2018 Jan 12;5:4. doi: 10.1038/s41438-017-0011-0. eCollection 2018.

19.

The Journal of Allergy and Clinical Immunology: In Practice 2017 Year in Review.

Schatz M, Sicherer SH, Zeiger RS.

J Allergy Clin Immunol Pract. 2018 Mar - Apr;6(2):328-352. doi: 10.1016/j.jaip.2017.12.016. Epub 2018 Feb 1. Review.

PMID:
29397373
20.

Scikit-ribo Enables Accurate Estimation and Robust Modeling of Translation Dynamics at Codon Resolution.

Fang H, Huang YF, Radhakrishnan A, Siepel A, Lyon GJ, Schatz MC.

Cell Syst. 2018 Feb 28;6(2):180-191.e4. doi: 10.1016/j.cels.2017.12.007. Epub 2018 Jan 17.

PMID:
29361467
21.

EVITA-a double-blind, vehicle-controlled, randomized phase II trial of vitamin K1 cream as prophylaxis for cetuximab-induced skin toxicity.

Hofheinz RD, Lorenzen S, Trojan J, Ocvirk J, Ettrich TJ, Al-Batran SE, Schulz H, Homann N, Feustel HP, Schatz M, Kripp M, Schulte N, Tetyusheva M, Heeger S, Vlassak S, Merx K.

Ann Oncol. 2018 Apr 1;29(4):1010-1015. doi: 10.1093/annonc/mdy015.

PMID:
29360920
22.

LRSim: A Linked-Reads Simulator Generating Insights for Better Genome Partitioning.

Luo R, Sedlazeck FJ, Darby CA, Kelly SM, Schatz MC.

Comput Struct Biotechnol J. 2017 Nov 9;15:478-484. doi: 10.1016/j.csbj.2017.10.002. eCollection 2017.

23.

Relationship of Blood Eosinophil Count to Exacerbations in Chronic Obstructive Pulmonary Disease.

Zeiger RS, Tran TN, Butler RK, Schatz M, Li Q, Khatry DB, Martin U, Kawatkar AA, Chen W.

J Allergy Clin Immunol Pract. 2018 May - Jun;6(3):944-954.e5. doi: 10.1016/j.jaip.2017.10.004. Epub 2017 Nov 15.

PMID:
29153881
24.

Comparative effectiveness trials in asthma - how will I recognize one?

Nyenhuis SM, Apter AJ, Schatz M, Krishnan JA.

Curr Opin Pulm Med. 2018 Jan;24(1):78-82. doi: 10.1097/MCP.0000000000000442.

PMID:
29076829
25.

Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin.

Afanasyev P, Seer-Linnemayr C, Ravelli RBG, Matadeen R, De Carlo S, Alewijnse B, Portugal RV, Pannu NS, Schatz M, van Heel M.

IUCrJ. 2017 Aug 31;4(Pt 5):678-694. doi: 10.1107/S2052252517010922. eCollection 2017 Sep 1.

26.

The Association of Maternal Asthma and Early Pregnancy Vitamin D with Risk of Preeclampsia: An Observation From Vitamin D Antenatal Asthma Reduction Trial (VDAART).

Mirzakhani H, Carey VJ, McElrath TF, Laranjo N, O'Connor G, Iverson RE, Lee-Parritz A, Strunk RC, Bacharier LB, Macones GA, Zeiger RS, Schatz M, Hollis BW, Litonjua AA, Weiss ST.

J Allergy Clin Immunol Pract. 2018 Mar - Apr;6(2):600-608.e2. doi: 10.1016/j.jaip.2017.07.018. Epub 2017 Sep 8.

PMID:
28923490
27.

Erratum to: The advantages of SMRT sequencing.

Roberts RJ, Carneiro MO, Schatz MC.

Genome Biol. 2017 Aug 16;18(1):156. doi: 10.1186/s13059-017-1295-y. No abstract available.

28.

Hybrid assembly with long and short reads improves discovery of gene family expansions.

Miller JR, Zhou P, Mudge J, Gurtowski J, Lee H, Ramaraj T, Walenz BP, Liu J, Stupar RM, Denny R, Song L, Singh N, Maron LG, McCouch SR, McCombie WR, Schatz MC, Tiffin P, Young ND, Silverstein KAT.

BMC Genomics. 2017 Jul 19;18(1):541. doi: 10.1186/s12864-017-3927-8.

29.

Drivers of health care costs for adults with persistent asthma.

Zeiger RS, Tran TN, Schatz M, Li Q, Chen W, Khatry DB, Davis J, Kawatkar AA.

J Allergy Clin Immunol Pract. 2018 Jan - Feb;6(1):265-268.e4. doi: 10.1016/j.jaip.2017.05.026. Epub 2017 Jul 12. No abstract available.

PMID:
28709819
30.

16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model.

Luo R, Schatz MC, Salzberg SL.

Gigascience. 2017 Jul 1;6(7):1-4. doi: 10.1093/gigascience/gix045.

31.

The Utility of the Reflux Symptom Index for Diagnosis of Laryngopharyngeal Reflux in an Allergy Patient Population.

Brauer DL, Tse KY, Lin JC, Schatz MX, Simon RA.

J Allergy Clin Immunol Pract. 2018 Jan - Feb;6(1):132-138.e1. doi: 10.1016/j.jaip.2017.04.039. Epub 2017 Jun 9.

PMID:
28606786
32.

Asthma control status in pregnancy, body mass index, and maternal vitamin D levels.

Mirzakhani H, O'Connor G, Bacharier LB, Zeiger RS, Schatz MX, Weiss ST, Litonjua AA.

J Allergy Clin Immunol. 2017 Nov;140(5):1453-1456.e7. doi: 10.1016/j.jaci.2017.03.053. Epub 2017 Jun 9. No abstract available.

PMID:
28606587
33.

Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma.

Feigin ME, Garvin T, Bailey P, Waddell N, Chang DK, Kelley DR, Shuai S, Gallinger S, McPherson JD, Grimmond SM, Khurana E, Stein LD, Biankin AV, Schatz MC, Tuveson DA.

Nat Genet. 2017 Jun;49(6):825-833. doi: 10.1038/ng.3861. Epub 2017 May 8.

34.

Oral corticosteroid exposure and adverse effects in asthmatic patients.

Sullivan PW, Ghushchyan VH, Globe G, Schatz M.

J Allergy Clin Immunol. 2018 Jan;141(1):110-116.e7. doi: 10.1016/j.jaci.2017.04.009. Epub 2017 Apr 27.

PMID:
28456623
35.

GenomeScope: fast reference-free genome profiling from short reads.

Vurture GW, Sedlazeck FJ, Nattestad M, Underwood CJ, Fang H, Gurtowski J, Schatz MC.

Bioinformatics. 2017 Jul 15;33(14):2202-2204. doi: 10.1093/bioinformatics/btx153.

36.

Forecasting Fluid Flows Using the Geometry of Turbulence.

Suri B, Tithof J, Grigoriev RO, Schatz MF.

Phys Rev Lett. 2017 Mar 17;118(11):114501. doi: 10.1103/PhysRevLett.118.114501. Epub 2017 Mar 15.

PMID:
28368628
37.

Nanopore sequencing meets epigenetics.

Schatz MC.

Nat Methods. 2017 Mar 31;14(4):347-348. doi: 10.1038/nmeth.4240. No abstract available.

PMID:
28362434
38.

Vitamin D supplementation in pregnancy, prenatal 25(OH)D levels, race, and subsequent asthma or recurrent wheeze in offspring: Secondary analyses from the Vitamin D Antenatal Asthma Reduction Trial.

Wolsk HM, Harshfield BJ, Laranjo N, Carey VJ, O'Connor G, Sandel M, Strunk RC, Bacharier LB, Zeiger RS, Schatz M, Hollis BW, Weiss ST, Litonjua AA.

J Allergy Clin Immunol. 2017 Nov;140(5):1423-1429.e5. doi: 10.1016/j.jaci.2017.01.013. Epub 2017 Mar 9.

PMID:
28285844
39.

Burden of Chronic Oral Corticosteroid Use by Adults with Persistent Asthma.

Zeiger RS, Schatz M, Li Q, Chen W, Khatry DB, Tran TN.

J Allergy Clin Immunol Pract. 2017 Jul - Aug;5(4):1050-1060.e9. doi: 10.1016/j.jaip.2016.12.023. Epub 2017 Feb 10.

PMID:
28215604
40.

The Journal of Allergy and Clinical Immunology: In Practice - 2016 Year in Review.

Schatz M, Sicherer SH, Zeiger RS.

J Allergy Clin Immunol Pract. 2017 Mar - Apr;5(2):218-236. doi: 10.1016/j.jaip.2016.12.002. Epub 2017 Jan 28.

PMID:
28143692
41.

TGF-β reduces DNA ds-break repair mechanisms to heighten genetic diversity and adaptability of CD44+/CD24- cancer cells.

Pal D, Pertot A, Shirole NH, Yao Z, Anaparthy N, Garvin T, Cox H, Chang K, Rollins F, Kendall J, Edwards L, Singh VA, Stone GC, Schatz MC, Hicks J, Hannon GJ, Sordella R.

Elife. 2017 Jan 16;6. pii: e21615. doi: 10.7554/eLife.21615.

42.

Correction: Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding.

Vij S, Kuhl H, Kuznetsova IS, Komissarov A, Yurchenko AA, Van Heusden P, Singh S, Thevasagayam NM, Prakki SR, Purushothaman K, Saju JM, Jiang J, Mbandi SK, Jonas M, Hin Yan Tong A, Mwangi S, Lau D, Ngoh SY, Liew WC, Shen X, Hon LS, Drake JP, Boitano M, Hall R, Chin CS, Lachumanan R, Korlach J, Trifonov V, Kabilov M, Tupikin A, Green D, Moxon S, Garvin T, Sedlazeck FJ, Vurture GW, Gopalapillai G, Katneni VK, Noble TH, Scaria V, Sivasubbu S, Jerry DR, O'Brien SJ, Schatz MC, Dalmay T, Turner SW, Lok S, Christoffels A, Orbán L.

PLoS Genet. 2016 Dec 9;12(12):e1006500. doi: 10.1371/journal.pgen.1006500. eCollection 2016 Dec.

43.

Pharmacological difficulties in the treatment of asthma in pregnant women.

Namazy JA, Schatz M.

Expert Rev Clin Pharmacol. 2017 Mar;10(3):285-292. doi: 10.1080/17512433.2017.1268914. Epub 2016 Dec 26. Review.

PMID:
27927045
44.

Indel variant analysis of short-read sequencing data with Scalpel.

Fang H, Bergmann EA, Arora K, Vacic V, Zody MC, Iossifov I, O'Rawe JA, Wu Y, Jimenez Barron LT, Rosenbaum J, Ronemus M, Lee YH, Wang Z, Dikoglu E, Jobanputra V, Lyon GJ, Wigler M, Schatz MC, Narzisi G.

Nat Protoc. 2016 Dec;11(12):2529-2548. doi: 10.1038/nprot.2016.150. Epub 2016 Nov 17.

45.

The evolution of inflorescence diversity in the nightshades and heterochrony during meristem maturation.

Lemmon ZH, Park SJ, Jiang K, Van Eck J, Schatz MC, Lippman ZB.

Genome Res. 2016 Dec;26(12):1676-1686. Epub 2016 Nov 7.

46.

Phased diploid genome assembly with single-molecule real-time sequencing.

Chin CS, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, Clum A, Dunn C, O'Malley R, Figueroa-Balderas R, Morales-Cruz A, Cramer GR, Delledonne M, Luo C, Ecker JR, Cantu D, Rank DR, Schatz MC.

Nat Methods. 2016 Dec;13(12):1050-1054. doi: 10.1038/nmeth.4035. Epub 2016 Oct 17.

47.

Blood Eosinophil Count and Outcomes in Severe Uncontrolled Asthma: A Prospective Study.

Zeiger RS, Schatz M, Dalal AA, Chen W, Sadikova E, Suruki RY, Kawatkar AA, Qian L.

J Allergy Clin Immunol Pract. 2017 Jan - Feb;5(1):144-153.e8. doi: 10.1016/j.jaip.2016.07.015. Epub 2016 Sep 21.

PMID:
27665383
48.

The Journal of Allergy Clinical Immunology: In Practice. Making An Impact.

Schatz M, Zeiger RS, Sicherer SH.

J Allergy Clin Immunol Pract. 2016 Sep-Oct;4(5):797-8. doi: 10.1016/j.jaip.2016.06.026. No abstract available.

PMID:
27587312
49.

Pharmacoepidemiological Study of Long-Acting β-agonist/Inhaled Corticosteroid Therapy and Asthma Mortality: Clinical Implications.

Camargo CA Jr, Davis KJ, Andrews EB, Stempel DA, Schatz M.

Clin Drug Investig. 2016 Dec;36(12):993-999.

PMID:
27581247
50.

Antibiotics for respiratory infections during pregnancy: prevalence and risk factors.

Namazy JA, Schatz M, Yang SJ, Chen W.

J Allergy Clin Immunol Pract. 2016 Nov - Dec;4(6):1256-1257.e2. doi: 10.1016/j.jaip.2016.06.015. Epub 2016 Jul 21. No abstract available.

PMID:
27452887

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