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Items: 46

1.

Differential Dynamics of the Maternal Immune System in Healthy Pregnancy and Preeclampsia.

Han X, Ghaemi MS, Ando K, Peterson LS, Ganio EA, Tsai AS, Gaudilliere DK, Stelzer IA, Einhaus J, Bertrand B, Stanley N, Culos A, Tanada A, Hedou J, Tsai ES, Fallahzadeh R, Wong RJ, Judy AE, Winn VD, Druzin ML, Blumenfeld YJ, Hlatky MA, Quaintance CC, Gibbs RS, Carvalho B, Shaw GM, Stevenson DK, Angst MS, Aghaeepour N, Gaudilliere B.

Front Immunol. 2019 Jun 11;10:1305. doi: 10.3389/fimmu.2019.01305. eCollection 2019.

2.

Systemic Immunologic Consequences of Chronic Periodontitis.

Gaudilliere DK, Culos A, Djebali K, Tsai AS, Ganio EA, Choi WM, Han X, Maghaireh A, Choisy B, Baca Q, Einhaus JF, Hedou JJ, Bertrand B, Ando K, Fallahzadeh R, Ghaemi MS, Okada R, Stanley N, Tanada A, Tingle M, Alpagot T, Helms JA, Angst MS, Aghaeepour N, Gaudilliere B.

J Dent Res. 2019 Aug;98(9):985-993. doi: 10.1177/0022034519857714. Epub 2019 Jun 21.

PMID:
31226001
3.

Predicting Acute Pain After Surgery: A Multivariate Analysis.

Baca Q, Marti F, Poblete B, Gaudilliere B, Aghaeepour N, Angst MS.

Ann Surg. 2019 Jun 7. doi: 10.1097/SLA.0000000000003400. [Epub ahead of print]

PMID:
31188202
4.

How Clinical Flow Cytometry Rebooted Sepsis Immunology.

Monneret G, Gossez M, Aghaeepour N, Gaudilliere B, Venet F.

Cytometry A. 2019 Apr;95(4):431-441. doi: 10.1002/cyto.a.23749. Epub 2019 Mar 19. Review.

PMID:
30887636
5.

A year-long immune profile of the systemic response in acute stroke survivors.

Tsai AS, Berry K, Beneyto MM, Gaudilliere D, Ganio EA, Culos A, Ghaemi MS, Choisy B, Djebali K, Einhaus JF, Bertrand B, Tanada A, Stanley N, Fallahzadeh R, Baca Q, Quach LN, Osborn E, Drag L, Lansberg MG, Angst MS, Gaudilliere B, Buckwalter MS, Aghaeepour N.

Brain. 2019 Apr 1;142(4):978-991. doi: 10.1093/brain/awz022.

PMID:
30860258
6.

A topological view of human CD34+ cell state trajectories from integrated single-cell output and proteomic data.

Knapp DJHF, Hammond CA, Wang F, Aghaeepour N, Miller PH, Beer PA, Pellacani D, VanInsberghe M, Hansen C, Bendall SC, Nolan GP, Eaves CJ.

Blood. 2019 Feb 28;133(9):927-939. doi: 10.1182/blood-2018-10-878025. Epub 2019 Jan 8.

7.

Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy.

Ghaemi MS, DiGiulio DB, Contrepois K, Callahan B, Ngo TTM, Lee-McMullen B, Lehallier B, Robaczewska A, Mcilwain D, Rosenberg-Hasson Y, Wong RJ, Quaintance C, Culos A, Stanley N, Tanada A, Tsai A, Gaudilliere D, Ganio E, Han X, Ando K, McNeil L, Tingle M, Wise P, Maric I, Sirota M, Wyss-Coray T, Winn VD, Druzin ML, Gibbs R, Darmstadt GL, Lewis DB, Partovi Nia V, Agard B, Tibshirani R, Nolan G, Snyder MP, Relman DA, Quake SR, Shaw GM, Stevenson DK, Angst MS, Gaudilliere B, Aghaeepour N.

Bioinformatics. 2019 Jan 1;35(1):95-103. doi: 10.1093/bioinformatics/bty537.

8.

Understanding health disparities.

Stevenson DK, Wong RJ, Aghaeepour N, Angst MS, Darmstadt GL, DiGiulio DB, Druzin ML, Gaudilliere B, Gibbs RS, B Gould J, Katz M, Li J, Moufarrej MN, Quaintance CC, Quake SR, Relman DA, Shaw GM, Snyder MP, Wang X, Wise PH.

J Perinatol. 2019 Mar;39(3):354-358. doi: 10.1038/s41372-018-0298-1. Epub 2018 Dec 18.

PMID:
30560947
9.

GateFinder: projection-based gating strategy optimization for flow and mass cytometry.

Aghaeepour N, Simonds EF, Knapp DJHF, Bruggner RV, Sachs K, Culos A, Gherardini PF, Samusik N, Fragiadakis GK, Bendall SC, Gaudilliere B, Angst MS, Eaves CJ, Weiss WA, Fantl WJ, Nolan GP.

Bioinformatics. 2018 Dec 1;34(23):4131-4133. doi: 10.1093/bioinformatics/bty430.

PMID:
29850785
10.

Single-cell analysis identifies a CD33+ subset of human cord blood cells with high regenerative potential.

Knapp DJHF, Hammond CA, Hui T, van Loenhout MTJ, Wang F, Aghaeepour N, Miller PH, Moksa M, Rabu GM, Beer PA, Pellacani D, Humphries RK, Hansen C, Hirst M, Eaves CJ.

Nat Cell Biol. 2018 Jun;20(6):710-720. doi: 10.1038/s41556-018-0104-5. Epub 2018 May 25.

PMID:
29802403
11.

Residential agricultural pesticide exposures and risks of preeclampsia.

Shaw GM, Yang W, Roberts EM, Aghaeepour N, Mayo JA, Weber KA, Maric I, Carmichael SL, Winn VD, Stevenson DK, English PB.

Environ Res. 2018 Jul;164:546-555. doi: 10.1016/j.envres.2018.03.020. Epub 2018 Mar 31.

12.

Single-cell developmental classification of B cell precursor acute lymphoblastic leukemia at diagnosis reveals predictors of relapse.

Good Z, Sarno J, Jager A, Samusik N, Aghaeepour N, Simonds EF, White L, Lacayo NJ, Fantl WJ, Fazio G, Gaipa G, Biondi A, Tibshirani R, Bendall SC, Nolan GP, Davis KL.

Nat Med. 2018 May;24(4):474-483. doi: 10.1038/nm.4505. Epub 2018 Mar 5.

13.

Commonly Occurring Cell Subsets in High-Grade Serous Ovarian Tumors Identified by Single-Cell Mass Cytometry.

Gonzalez VD, Samusik N, Chen TJ, Savig ES, Aghaeepour N, Quigley DA, Huang YW, Giangarrà V, Borowsky AD, Hubbard NE, Chen SY, Han G, Ashworth A, Kipps TJ, Berek JS, Nolan GP, Fantl WJ.

Cell Rep. 2018 Feb 13;22(7):1875-1888. doi: 10.1016/j.celrep.2018.01.053.

14.

A proteomic clock of human pregnancy.

Aghaeepour N, Lehallier B, Baca Q, Ganio EA, Wong RJ, Ghaemi MS, Culos A, El-Sayed YY, Blumenfeld YJ, Druzin ML, Winn VD, Gibbs RS, Tibshirani R, Shaw GM, Stevenson DK, Gaudilliere B, Angst MS.

Am J Obstet Gynecol. 2018 Mar;218(3):347.e1-347.e14. doi: 10.1016/j.ajog.2017.12.208. Epub 2017 Dec 24.

PMID:
29277631
15.

An immune clock of human pregnancy.

Aghaeepour N, Ganio EA, Mcilwain D, Tsai AS, Tingle M, Van Gassen S, Gaudilliere DK, Baca Q, McNeil L, Okada R, Ghaemi MS, Furman D, Wong RJ, Winn VD, Druzin ML, El-Sayed YY, Quaintance C, Gibbs R, Darmstadt GL, Shaw GM, Stevenson DK, Tibshirani R, Nolan GP, Lewis DB, Angst MS, Gaudilliere B.

Sci Immunol. 2017 Sep 1;2(15). pii: eaan2946. doi: 10.1126/sciimmunol.aan2946.

16.

Deep Immune Profiling of an Arginine-Enriched Nutritional Intervention in Patients Undergoing Surgery.

Aghaeepour N, Kin C, Ganio EA, Jensen KP, Gaudilliere DK, Tingle M, Tsai A, Lancero HL, Choisy B, McNeil LS, Okada R, Shelton AA, Nolan GP, Angst MS, Gaudilliere BL.

J Immunol. 2017 Aug 9. pii: ji1700421. doi: 10.4049/jimmunol.1700421. [Epub ahead of print]

17.

Subglottic Stenosis Following Cardiac Surgery With Cardiopulmonary Bypass in Infants and Children.

Kruse KE, Purohit PJ, Cadman CR, Su F, Aghaeepour N, Hammer GB.

Pediatr Crit Care Med. 2017 May;18(5):429-433. doi: 10.1097/PCC.0000000000001125.

PMID:
28277376
18.

Multicenter Systems Analysis of Human Blood Reveals Immature Neutrophils in Males and During Pregnancy.

Blazkova J, Gupta S, Liu Y, Gaudilliere B, Ganio EA, Bolen CR, Saar-Dover R, Fragiadakis GK, Angst MS, Hasni S, Aghaeepour N, Stevenson D, Baldwin N, Anguiano E, Chaussabel D, Altman MC, Kaplan MJ, Davis MM, Furman D.

J Immunol. 2017 Mar 15;198(6):2479-2488. doi: 10.4049/jimmunol.1601855. Epub 2017 Feb 8.

19.

SESSION INTRODUCTION.

Samusik N, Aghaeepour N, Bendall S.

Pac Symp Biocomput. 2017;22:557-563. doi: 10.1142/9789813207813_0051.

20.

Distinct signaling programs control human hematopoietic stem cell survival and proliferation.

Knapp DJ, Hammond CA, Aghaeepour N, Miller PH, Pellacani D, Beer PA, Sachs K, Qiao W, Wang W, Humphries RK, Sauvageau G, Zandstra PW, Bendall SC, Nolan GP, Hansen C, Eaves CJ.

Blood. 2017 Jan 19;129(3):307-318. doi: 10.1182/blood-2016-09-740654. Epub 2016 Nov 8.

21.

Mapping the Fetomaternal Peripheral Immune System at Term Pregnancy.

Fragiadakis GK, Baca QJ, Gherardini PF, Ganio EA, Gaudilliere DK, Tingle M, Lancero HL, McNeil LS, Spitzer MH, Wong RJ, Shaw GM, Darmstadt GL, Sylvester KG, Winn VD, Carvalho B, Lewis DB, Stevenson DK, Nolan GP, Aghaeepour N, Angst MS, Gaudilliere BL.

J Immunol. 2016 Dec 1;197(11):4482-4492. Epub 2016 Oct 28.

22.

In Reply.

Angst MS, Fragiadakis GK, Gaudillière B, Aghaeepour N, Nolan GP.

Anesthesiology. 2016 Jun;124(6):1414-5. doi: 10.1097/ALN.0000000000001091. No abstract available.

23.

Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium.

Finak G, Langweiler M, Jaimes M, Malek M, Taghiyar J, Korin Y, Raddassi K, Devine L, Obermoser G, Pekalski ML, Pontikos N, Diaz A, Heck S, Villanova F, Terrazzini N, Kern F, Qian Y, Stanton R, Wang K, Brandes A, Ramey J, Aghaeepour N, Mosmann T, Scheuermann RH, Reed E, Palucka K, Pascual V, Blomberg BB, Nestle F, Nussenblatt RB, Brinkman RR, Gottardo R, Maecker H, McCoy JP.

Sci Rep. 2016 Feb 10;6:20686. doi: 10.1038/srep20686.

24.

Automated analysis of flow cytometry data comes of age.

Brinkman RR, Aghaeepour N, Finak G, Gottardo R, Mosmann T, Scheuermann RH.

Cytometry A. 2016 Jan;89(1):13-5. doi: 10.1002/cyto.a.22810. No abstract available.

25.

Patient-specific Immune States before Surgery Are Strong Correlates of Surgical Recovery.

Fragiadakis GK, Gaudillière B, Ganio EA, Aghaeepour N, Tingle M, Nolan GP, Angst MS.

Anesthesiology. 2015 Dec;123(6):1241-55. doi: 10.1097/ALN.0000000000000887.

26.

Deletions in the cytoplasmic domain of iRhom1 and iRhom2 promote shedding of the TNF receptor by the protease ADAM17.

Maney SK, McIlwain DR, Polz R, Pandyra AA, Sundaram B, Wolff D, Ohishi K, Maretzky T, Brooke MA, Evers A, Vasudevan AA, Aghaeepour N, Scheller J, Münk C, Häussinger D, Mak TW, Nolan GP, Kelsell DP, Blobel CP, Lang KS, Lang PA.

Sci Signal. 2015 Nov 3;8(401):ra109. doi: 10.1126/scisignal.aac5356.

PMID:
26535007
27.

A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes.

Aghaeepour N, Chattopadhyay P, Chikina M, Dhaene T, Van Gassen S, Kursa M, Lambrecht BN, Malek M, McLachlan GJ, Qian Y, Qiu P, Saeys Y, Stanton R, Tong D, Vens C, Walkowiak S, Wang K, Finak G, Gottardo R, Mosmann T, Nolan GP, Scheuermann RH, Brinkman RR.

Cytometry A. 2016 Jan;89(1):16-21. doi: 10.1002/cyto.a.22732. Epub 2015 Oct 8.

28.

Implementing Mass Cytometry at the Bedside to Study the Immunological Basis of Human Diseases: Distinctive Immune Features in Patients with a History of Term or Preterm Birth.

Gaudillière B, Ganio EA, Tingle M, Lancero HL, Fragiadakis GK, Baca QJ, Aghaeepour N, Wong RJ, Quaintance C, El-Sayed YY, Shaw GM, Lewis DB, Stevenson DK, Nolan GP, Angst MS.

Cytometry A. 2015 Sep;87(9):817-29. doi: 10.1002/cyto.a.22720. Epub 2015 Jul 17.

29.

State-of-the-Art in the Computational Analysis of Cytometry Data.

Brinkman RR, Aghaeepour N, Finak G, Gottardo R, Mosmann T, Scheuermann RH.

Cytometry A. 2015 Jul;87(7):591-3. doi: 10.1002/cyto.a.22707. No abstract available.

30.

Thinking outside the gate: single-cell assessments in multiple dimensions.

Kvistborg P, Gouttefangeas C, Aghaeepour N, Cazaly A, Chattopadhyay PK, Chan C, Eckl J, Finak G, Hadrup SR, Maecker HT, Maurer D, Mosmann T, Qiu P, Scheuermann RH, Welters MJ, Ferrari G, Brinkman RR, Britten CM.

Immunity. 2015 Apr 21;42(4):591-2. doi: 10.1016/j.immuni.2015.04.006. No abstract available.

31.

Deep profiling of multitube flow cytometry data.

O'Neill K, Aghaeepour N, Parker J, Hogge D, Karsan A, Dalal B, Brinkman RR.

Bioinformatics. 2015 May 15;31(10):1623-31. doi: 10.1093/bioinformatics/btv008. Epub 2015 Jan 18.

32.

A dominant-negative isoform of IKAROS expands primitive normal human hematopoietic cells.

Beer PA, Knapp DJ, Kannan N, Miller PH, Babovic S, Bulaeva E, Aghaeepour N, Rabu G, Rostamirad S, Shih K, Wei L, Eaves CJ.

Stem Cell Reports. 2014 Nov 11;3(5):841-57. doi: 10.1016/j.stemcr.2014.09.006. Epub 2014 Oct 11.

33.

Enhanced flowType/RchyOptimyx: a BioConductor pipeline for discovery in high-dimensional cytometry data.

O'Neill K, Jalali A, Aghaeepour N, Hoos H, Brinkman RR.

Bioinformatics. 2014 May 1;30(9):1329-30. doi: 10.1093/bioinformatics/btt770. Epub 2014 Jan 8.

34.

Flow cytometry bioinformatics.

O'Neill K, Aghaeepour N, Spidlen J, Brinkman R.

PLoS Comput Biol. 2013;9(12):e1003365. doi: 10.1371/journal.pcbi.1003365. Epub 2013 Dec 5.

35.

Computational analysis optimizes the flow cytometric evaluation for lymphoma.

Craig FE, Brinkman RR, Ten Eyck S, Aghaeepour N.

Cytometry B Clin Cytom. 2014 Jan;86(1):18-24. doi: 10.1002/cyto.b.21115. Epub 2013 Sep 3.

36.

Computational analysis of high-dimensional flow cytometric data for diagnosis and discovery.

Aghaeepour N, Brinkman R.

Curr Top Microbiol Immunol. 2014;377:159-75. doi: 10.1007/82_2013_337. Review.

PMID:
23975083
37.

Computational analysis optimizes the flow cytometric evaluation for lymphoma.

Craig FE, Brinkman RR, Eyck ST, Aghaeepour N.

Cytometry B Clin Cytom. 2013 Jul 19. doi: 10.1002/cytob.21115. [Epub ahead of print]

38.

Integration of lyoplate based flow cytometry and computational analysis for standardized immunological biomarker discovery.

Villanova F, Di Meglio P, Inokuma M, Aghaeepour N, Perucha E, Mollon J, Nomura L, Hernandez-Fuentes M, Cope A, Prevost AT, Heck S, Maino V, Lord G, Brinkman RR, Nestle FO.

PLoS One. 2013 Jul 3;8(7):e65485. doi: 10.1371/journal.pone.0065485. Print 2013.

39.

Ensemble-based prediction of RNA secondary structures.

Aghaeepour N, Hoos HH.

BMC Bioinformatics. 2013 Apr 24;14:139. doi: 10.1186/1471-2105-14-139.

40.

Critical assessment of automated flow cytometry data analysis techniques.

Aghaeepour N, Finak G; FlowCAP Consortium; DREAM Consortium, Hoos H, Mosmann TR, Brinkman R, Gottardo R, Scheuermann RH.

Nat Methods. 2013 Mar;10(3):228-38. doi: 10.1038/nmeth.2365. Epub 2013 Feb 10. Erratum in: Nat Methods. 2013 May;10(5):445.

41.

RchyOptimyx: cellular hierarchy optimization for flow cytometry.

Aghaeepour N, Jalali A, O'Neill K, Chattopadhyay PK, Roederer M, Hoos HH, Brinkman RR.

Cytometry A. 2012 Dec;81(12):1022-30. doi: 10.1002/cyto.a.22209. Epub 2012 Oct 8.

42.

The phenotypic distribution and functional profile of tuberculin-specific CD4 T-cells characterizes different stages of TB infection.

Streitz M, Fuhrmann S, Thomas D, Cheek E, Nomura L, Maecker H, Martus P, Aghaeepour N, Brinkman RR, Volk HD, Kern F.

Cytometry B Clin Cytom. 2012 Nov;82(6):360-8. doi: 10.1002/cyto.b.21041. Epub 2012 Sep 7.

43.

Hematopoietic stem cell subtypes expand differentially during development and display distinct lymphopoietic programs.

Benz C, Copley MR, Kent DG, Wohrer S, Cortes A, Aghaeepour N, Ma E, Mader H, Rowe K, Day C, Treloar D, Brinkman RR, Eaves CJ.

Cell Stem Cell. 2012 Mar 2;10(3):273-83. doi: 10.1016/j.stem.2012.02.007.

44.

Early immunologic correlates of HIV protection can be identified from computational analysis of complex multivariate T-cell flow cytometry assays.

Aghaeepour N, Chattopadhyay PK, Ganesan A, O'Neill K, Zare H, Jalali A, Hoos HH, Roederer M, Brinkman RR.

Bioinformatics. 2012 Apr 1;28(7):1009-16. doi: 10.1093/bioinformatics/bts082. Epub 2012 Feb 29.

45.

Automated analysis of multidimensional flow cytometry data improves diagnostic accuracy between mantle cell lymphoma and small lymphocytic lymphoma.

Zare H, Bashashati A, Kridel R, Aghaeepour N, Haffari G, Connors JM, Gascoyne RD, Gupta A, Brinkman RR, Weng AP.

Am J Clin Pathol. 2012 Jan;137(1):75-85. doi: 10.1309/AJCPMMLQ67YOMGEW.

46.

Rapid cell population identification in flow cytometry data.

Aghaeepour N, Nikolic R, Hoos HH, Brinkman RR.

Cytometry A. 2011 Jan;79(1):6-13. doi: 10.1002/cyto.a.21007.

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