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Year Number of Results
2011 1
2012 5
2013 6
2014 4
2015 7
2016 6
2017 7
2018 7
2019 10
2020 18
2021 24
2022 20
2023 32
2024 23

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Page 1
Predicting Preterm Birth Using Proteomics.
Marić I, Stevenson DK, Aghaeepour N, Gaudillière B, Wong RJ, Angst MS. Marić I, et al. Among authors: aghaeepour n. Clin Perinatol. 2024 Jun;51(2):391-409. doi: 10.1016/j.clp.2024.02.011. Epub 2024 Mar 23. Clin Perinatol. 2024. PMID: 38705648 Free PMC article. Review.
Evaluation of Sleep in Pregnant Inpatients Compared With Outpatients.
Panelli DM, Miller HE, Simpson SL, Hurtado J, Shu CH, Boncompagni AC, Chueh J, Barwick F, Carvalho B, Sultan P, Aghaeepour N, Druzin ML. Panelli DM, et al. Among authors: aghaeepour n. Obstet Gynecol. 2024 Jun 1;143(6):803-810. doi: 10.1097/AOG.0000000000005591. Epub 2024 Apr 25. Obstet Gynecol. 2024. PMID: 38663016
Comprehensive overview of the anesthesiology research landscape: A machine Learning Analysis of 737 NIH-funded anesthesiology primary Investigator's publication trends.
Ghanem M, Espinosa C, Chung P, Reincke M, Harrison N, Phongpreecha T, Shome S, Saarunya G, Berson E, James T, Xie F, Shu CH, Hazra D, Mataraso S, Kim Y, Seong D, Chakraborty D, Studer M, Xue L, Marić I, Chang AL, Tjoa E, Gaudillière B, Tawfik VL, Mackey S, Aghaeepour N. Ghanem M, et al. Among authors: aghaeepour n. Heliyon. 2024 Apr 3;10(7):e29050. doi: 10.1016/j.heliyon.2024.e29050. eCollection 2024 Apr 15. Heliyon. 2024. PMID: 38623206 Free PMC article.
Intra- and post-pandemic impact of the COVID-19 outbreak on Stanford Health Care.
Phongpreecha T, Berson E, Xue L, Shome S, Saarunya G, Fralick J, Ruiz-Tagle BG, Foody A, Chin AL, Lim M, Arthofer R, Albini C, Montine K, Folkins AK, Kong CS, Aghaeepour N, Montine T, Kerr A. Phongpreecha T, et al. Among authors: aghaeepour n. Acad Pathol. 2024 Mar 25;11(2):100113. doi: 10.1016/j.acpath.2024.100113. eCollection 2024 Apr-Jun. Acad Pathol. 2024. PMID: 38562568 Free PMC article.
Physical activity among pregnant inpatients and outpatients and associations with anxiety.
Panelli DM, Miller HE, Simpson SL, Hurtado J, Shu CH, Boncompagni AC, Chueh J, Carvalho B, Sultan P, Aghaeepour N, Druzin ML. Panelli DM, et al. Among authors: aghaeepour n. Eur J Obstet Gynecol Reprod Biol. 2024 Jun;297:8-14. doi: 10.1016/j.ejogrb.2024.03.033. Epub 2024 Mar 28. Eur J Obstet Gynecol Reprod Biol. 2024. PMID: 38554481
An immune signature of postoperative cognitive decline in elderly patients.
Verdonk F, Cambriel A, Hedou J, Ganio E, Bellan G, Gaudilliere D, Einhaus J, Sabayev M, Stelzer IA, Feyaerts D, Bonham AT, Ando K, Choisy B, Drover D, Heifets B, Chretien F, Aghaeepour N, Angst MS, Molliex S, Sharshar T, Gaillard R, Gaudilliere B. Verdonk F, et al. Among authors: aghaeepour n. bioRxiv [Preprint]. 2024 Mar 5:2024.03.02.582845. doi: 10.1101/2024.03.02.582845. bioRxiv. 2024. PMID: 38496400 Free PMC article. Preprint.
Leveraging electronic health records and knowledge networks for Alzheimer's disease prediction and sex-specific biological insights.
Tang AS, Rankin KP, Cerono G, Miramontes S, Mills H, Roger J, Zeng B, Nelson C, Soman K, Woldemariam S, Li Y, Lee A, Bove R, Glymour M, Aghaeepour N, Oskotsky TT, Miller Z, Allen IE, Sanders SJ, Baranzini S, Sirota M. Tang AS, et al. Among authors: aghaeepour n. Nat Aging. 2024 Mar;4(3):379-395. doi: 10.1038/s43587-024-00573-8. Epub 2024 Feb 21. Nat Aging. 2024. PMID: 38383858 Free PMC article.
RETRACTED: 60 Predicting chorioamnionitis using AI-based methods: a retrospective cohort study.
Waldrop AR, James TK, Suharwardy S, Studer M, Chang A, Bernal CE, Xie F, Shome S, Hazra D, Kim Y, Clarke G, Chakraborty D, Mataraso S, Berson E, Xue L, Payrovnaziri S, Mohammadi N, Haberkorn W, Maric I, El-Sayed YY, Carvalho B, Aghaeepour N. Waldrop AR, et al. Among authors: aghaeepour n. Am J Obstet Gynecol. 2024 Jan;230(1S):S46. doi: 10.1016/j.ajog.2023.11.081. Epub 2024 Jan 18. Am J Obstet Gynecol. 2024. PMID: 38355237
Multimodal machine learning for modeling infant head circumference, mothers' milk composition, and their shared environment.
Becker M, Fehr K, Goguen S, Miliku K, Field C, Robertson B, Yonemitsu C, Bode L, Simons E, Marshall J, Dawod B, Mandhane P, Turvey SE, Moraes TJ, Subbarao P, Rodriguez N, Aghaeepour N, Azad MB. Becker M, et al. Among authors: aghaeepour n. Sci Rep. 2024 Feb 5;14(1):2977. doi: 10.1038/s41598-024-52323-w. Sci Rep. 2024. PMID: 38316895 Free PMC article.
Understanding the molecular basis of resilience to Alzheimer's disease.
Montine KS, Berson E, Phongpreecha T, Huang Z, Aghaeepour N, Zou JY, MacCoss MJ, Montine TJ. Montine KS, et al. Among authors: aghaeepour n. Front Neurosci. 2023 Dec 19;17:1311157. doi: 10.3389/fnins.2023.1311157. eCollection 2023. Front Neurosci. 2023. PMID: 38192507 Free PMC article. Review.
Discovery of sparse, reliable omic biomarkers with Stabl.
Hédou J, Marić I, Bellan G, Einhaus J, Gaudillière DK, Ladant FX, Verdonk F, Stelzer IA, Feyaerts D, Tsai AS, Ganio EA, Sabayev M, Gillard J, Amar J, Cambriel A, Oskotsky TT, Roldan A, Golob JL, Sirota M, Bonham TA, Sato M, Diop M, Durand X, Angst MS, Stevenson DK, Aghaeepour N, Montanari A, Gaudillière B. Hédou J, et al. Among authors: aghaeepour n. Nat Biotechnol. 2024 Jan 2:10.1038/s41587-023-02033-x. doi: 10.1038/s41587-023-02033-x. Online ahead of print. Nat Biotechnol. 2024. PMID: 38168992
Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research.
Golob JL, Oskotsky TT, Tang AS, Roldan A, Chung V, Ha CWY, Wong RJ, Flynn KJ, Parraga-Leo A, Wibrand C, Minot SS, Oskotsky B, Andreoletti G, Kosti I, Bletz J, Nelson A, Gao J, Wei Z, Chen G, Tang ZZ, Novielli P, Romano D, Pantaleo E, Amoroso N, Monaco A, Vacca M, De Angelis M, Bellotti R, Tangaro S, Kuntzleman A, Bigcraft I, Techtmann S, Bae D, Kim E, Jeon J, Joe S; Preterm Birth DREAM Community; Theis KR, Ng S, Lee YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Stolovitzky G, Lynch SV, Albrecht J, Gomez-Lopez N, Romero R, Stevenson DK, Aghaeepour N, Tarca AL, Costello JC, Sirota M. Golob JL, et al. Among authors: aghaeepour n. Cell Rep Med. 2024 Jan 16;5(1):101350. doi: 10.1016/j.xcrm.2023.101350. Epub 2023 Dec 21. Cell Rep Med. 2024. PMID: 38134931 Free PMC article.
Large-scale correlation network construction for unraveling the coordination of complex biological systems.
Becker M, Nassar H, Espinosa C, Stelzer IA, Feyaerts D, Berson E, Bidoki NH, Chang AL, Saarunya G, Culos A, De Francesco D, Fallahzadeh R, Liu Q, Kim Y, Marić I, Mataraso SJ, Payrovnaziri SN, Phongpreecha T, Ravindra NG, Stanley N, Shome S, Tan Y, Thuraiappah M, Xenochristou M, Xue L, Shaw G, Stevenson D, Angst MS, Gaudilliere B, Aghaeepour N. Becker M, et al. Among authors: aghaeepour n. Nat Comput Sci. 2023 Apr;3(4):346-359. doi: 10.1038/s43588-023-00429-y. Epub 2023 Apr 13. Nat Comput Sci. 2023. PMID: 38116462 Free PMC article.
Quantitative estimate of cognitive resilience and its medical and genetic associations.
Phongpreecha T, Godrich D, Berson E, Espinosa C, Kim Y, Cholerton B, Chang AL, Mataraso S, Bukhari SA, Perna A, Yakabi K, Montine KS, Poston KL, Mormino E, White L, Beecham G, Aghaeepour N, Montine TJ. Phongpreecha T, et al. Among authors: aghaeepour n. Alzheimers Res Ther. 2023 Nov 6;15(1):192. doi: 10.1186/s13195-023-01329-z. Alzheimers Res Ther. 2023. PMID: 37926851 Free PMC article.
Deep representation learning identifies associations between physical activity and sleep patterns during pregnancy and prematurity.
Ravindra NG, Espinosa C, Berson E, Phongpreecha T, Zhao P, Becker M, Chang AL, Shome S, Marić I, De Francesco D, Mataraso S, Saarunya G, Thuraiappah M, Xue L, Gaudillière B, Angst MS, Shaw GM, Herzog ED, Stevenson DK, England SK, Aghaeepour N. Ravindra NG, et al. Among authors: aghaeepour n. NPJ Digit Med. 2023 Sep 28;6(1):171. doi: 10.1038/s41746-023-00911-x. NPJ Digit Med. 2023. PMID: 37770643 Free PMC article.
Cross-species comparative analysis of single presynapses.
Berson E, Gajera CR, Phongpreecha T, Perna A, Bukhari SA, Becker M, Chang AL, De Francesco D, Espinosa C, Ravindra NG, Postupna N, Latimer CS, Shively CA, Register TC, Craft S, Montine KS, Fox EJ, Keene CD, Bendall SC, Aghaeepour N, Montine TJ. Berson E, et al. Among authors: aghaeepour n. Sci Rep. 2023 Aug 24;13(1):13849. doi: 10.1038/s41598-023-40683-8. Sci Rep. 2023. PMID: 37620363 Free PMC article.
Whole genome deconvolution unveils Alzheimer's resilient epigenetic signature.
Berson E, Sreenivas A, Phongpreecha T, Perna A, Grandi FC, Xue L, Ravindra NG, Payrovnaziri N, Mataraso S, Kim Y, Espinosa C, Chang AL, Becker M, Montine KS, Fox EJ, Chang HY, Corces MR, Aghaeepour N, Montine TJ. Berson E, et al. Among authors: aghaeepour n. Nat Commun. 2023 Aug 16;14(1):4947. doi: 10.1038/s41467-023-40611-4. Nat Commun. 2023. PMID: 37587197 Free PMC article.
Comparative predictive power of serum vs plasma proteomic signatures in feto-maternal medicine.
Espinosa C, Ali SM, Khan W, Khanam R, Pervin J, Price JT, Rahman S, Hasan T, Ahmed S, Raqib R, Rahman M, Aktar S, Nisar MI, Khalid J, Dhingra U, Dutta A, Deb S, Stringer JSA, Wong RJ, Shaw GM, Stevenson DK, Darmstadt GL, Gaudilliere B, Baqui AH, Jehan F, Rahman A, Sazawal S, Vwalika B, Aghaeepour N, Angst MS. Espinosa C, et al. Among authors: aghaeepour n. AJOG Glob Rep. 2023 Jun 12;3(3):100244. doi: 10.1016/j.xagr.2023.100244. eCollection 2023 Aug. AJOG Glob Rep. 2023. PMID: 37456144 Free PMC article.
Multiomic signals associated with maternal epidemiological factors contributing to preterm birth in low- and middle-income countries.
Espinosa CA, Khan W, Khanam R, Das S, Khalid J, Pervin J, Kasaro MP, Contrepois K, Chang AL, Phongpreecha T, Michael B, Ellenberger M, Mehmood U, Hotwani A, Nizar A, Kabir F, Wong RJ, Becker M, Berson E, Culos A, De Francesco D, Mataraso S, Ravindra N, Thuraiappah M, Xenochristou M, Stelzer IA, Marić I, Dutta A, Raqib R, Ahmed S, Rahman S, Hasan ASMT, Ali SM, Juma MH, Rahman M, Aktar S, Deb S, Price JT, Wise PH, Winn VD, Druzin ML, Gibbs RS, Darmstadt GL, Murray JC, Stringer JSA, Gaudilliere B, Snyder MP, Angst MS, Rahman A, Baqui AH, Jehan F, Nisar MI, Vwalika B, Sazawal S, Shaw GM, Stevenson DK, Aghaeepour N. Espinosa CA, et al. Among authors: aghaeepour n. Sci Adv. 2023 May 24;9(21):eade7692. doi: 10.1126/sciadv.ade7692. Epub 2023 May 26. Sci Adv. 2023. PMID: 37224249 Free PMC article.
Evidence for human milk as a biological system and recommendations for study design-a report from "Breastmilk Ecology: Genesis of Infant Nutrition (BEGIN)" Working Group 4.
Donovan SM, Aghaeepour N, Andres A, Azad MB, Becker M, Carlson SE, Järvinen KM, Lin W, Lönnerdal B, Slupsky CM, Steiber AL, Raiten DJ. Donovan SM, et al. Among authors: aghaeepour n. Am J Clin Nutr. 2023 Apr;117 Suppl 1(Suppl 1):S61-S86. doi: 10.1016/j.ajcnut.2022.12.021. Am J Clin Nutr. 2023. PMID: 37173061 Free PMC article.
Advances and potential of omics studies for understanding the development of food allergy.
Sindher SB, Chin AR, Aghaeepour N, Prince L, Maecker H, Shaw GM, Stevenson DK, Nadeau KC, Snyder M, Khatri P, Boyd SD, Winn VD, Angst MS, Chinthrajah RS. Sindher SB, et al. Among authors: aghaeepour n. Front Allergy. 2023 Mar 24;4:1149008. doi: 10.3389/falgy.2023.1149008. eCollection 2023. Front Allergy. 2023. PMID: 37034151 Free PMC article. Review.
Author Correction: Early response evaluation by single cell signaling profiling in acute myeloid leukemia.
Tislevoll BS, Hellesøy M, Fagerholt OHE, Gullaksen SE, Srivastava A, Birkeland E, Kleftogiannis D, Ayuda-Durán P, Piechaczyk L, Tadele DS, Skavland J, Baliakas P, Hovland R, Andresen V, Seternes OM, Tvedt THA, Aghaeepour N, Gavasso S, Porkka K, Jonassen I, Fløisand Y, Enserink J, Blaser N, Gjertsen BT. Tislevoll BS, et al. Among authors: aghaeepour n. Nat Commun. 2023 Mar 30;14(1):1767. doi: 10.1038/s41467-023-37488-8. Nat Commun. 2023. PMID: 36997540 Free PMC article. No abstract available.
Leveraging electronic health records to identify risk factors for recurrent pregnancy loss across two medical centers: a case-control study.
Roger J, Xie F, Costello J, Tang A, Liu J, Oskotsky T, Woldemariam S, Kosti I, Le B, Snyder MP, Giudice LC, Torgerson D, Shaw GM, Stevenson DK, Rajkovic A, Glymour MM, Aghaeepour N, Cakmak H, Lathi RB, Sirota M. Roger J, et al. Among authors: aghaeepour n. Res Sq [Preprint]. 2023 Mar 31:rs.3.rs-2631220. doi: 10.21203/rs.3.rs-2631220/v1. Res Sq. 2023. PMID: 36993325 Free PMC article. Preprint.
VMAP: Vaginal Microbiome Atlas During Pregnancy.
Parraga-Leo A, Oskotsky TT, Oskotsky B, Wibrand C, Roldan A, Tang A, Ha CWY, Wong RJ, Minot SS, Andreoletti G, Kosti I, Theis KR, Ng S, Lee YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Lynch SV, Romero R, Tarca AL, Stevenson DK, Aghaeepour N, Golob J, Sirota M. Parraga-Leo A, et al. Among authors: aghaeepour n. medRxiv [Preprint]. 2023 Apr 5:2023.03.21.23286947. doi: 10.1101/2023.03.21.23286947. medRxiv. 2023. PMID: 36993193 Free PMC article. Preprint.
Microbiome Preterm Birth DREAM Challenge: Crowdsourcing Machine Learning Approaches to Advance Preterm Birth Research.
Golob JL, Oskotsky TT, Tang AS, Roldan A, Chung V, Ha CWY, Wong RJ, Flynn KJ, Parraga-Leo A, Wibrand C, Minot SS, Andreoletti G, Kosti I, Bletz J, Nelson A, Gao J, Wei Z, Chen G, Tang ZZ, Novielli P, Romano D, Pantaleo E, Amoroso N, Monaco A, Vacca M, De Angelis M, Bellotti R, Tangaro S, Kuntzleman A, Bigcraft I, Techtmann S, Bae D, Kim E, Jeon J, Joe S; Preterm Birth DREAM Community; Theis KR, Ng S, Lee Li YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Stolovitzky G, Lynch SV, Albrecht J, Gomez-Lopez N, Romero R, Stevenson DK, Aghaeepour N, Tarca AL, Costello JC, Sirota M. Golob JL, et al. Among authors: aghaeepour n. medRxiv [Preprint]. 2023 Apr 11:2023.03.07.23286920. doi: 10.1101/2023.03.07.23286920. medRxiv. 2023. Update in: Cell Rep Med. 2024 Jan 16;5(1):101350. doi: 10.1016/j.xcrm.2023.101350. PMID: 36945505 Free PMC article. Updated. Preprint.
Stabl: sparse and reliable biomarker discovery in predictive modeling of high-dimensional omic data.
Hédou J, Marić I, Bellan G, Einhaus J, Gaudillière DK, Ladant FX, Verdonk F, Stelzer IA, Feyaerts D, Tsai AS, Ganio EA, Sabayev M, Gillard J, Bonham TA, Sato M, Diop M, Angst MS, Stevenson D, Aghaeepour N, Montanari A, Gaudillière B. Hédou J, et al. Among authors: aghaeepour n. Res Sq [Preprint]. 2023 Feb 28:rs.3.rs-2609859. doi: 10.21203/rs.3.rs-2609859/v1. Res Sq. 2023. Update in: Nat Biotechnol. 2024 Jan 2. doi: 10.1038/s41587-023-02033-x. PMID: 36909508 Free PMC article. Updated. Preprint.
Changes in preterm birth and stillbirth during COVID-19 lockdowns in 26 countries.
Calvert C, Brockway MM, Zoega H, Miller JE, Been JV, Amegah AK, Racine-Poon A, Oskoui SE, Abok II, Aghaeepour N, Akwaowo CD, Alshaikh BN, Ayede AI, Bacchini F, Barekatain B, Barnes R, Bebak K, Berard A, Bhutta ZA, Brook JR, Bryan LR, Cajachagua-Torres KN, Campbell-Yeo M, Chu DT, Connor KL, Cornette L, Cortés S, Daly M, Debauche C, Dedeke IOF, Einarsdóttir K, Engjom H, Estrada-Gutierrez G, Fantasia I, Fiorentino NM, Franklin M, Fraser A, Gachuno OW, Gallo LA, Gissler M, Håberg SE, Habibelahi A, Häggström J, Hookham L, Hui L, Huicho L, Hunter KJ, Huq S, Kc A, Kadambari S, Kelishadi R, Khalili N, Kippen J, Le Doare K, Llorca J, Magee LA, Magnus MC, Man KKC, Mburugu PM, Mediratta RP, Morris AD, Muhajarine N, Mulholland RH, Bonnard LN, Nakibuuka V, Nassar N, Nyadanu SD, Oakley L, Oladokun A, Olayemi OO, Olutekunbi OA, Oluwafemi RO, Ogunkunle TO, Orton C, Örtqvist AK, Ouma J, Oyapero O, Palmer KR, Pedersen LH, Pereira G, Pereyra I, Philip RK, Pruski D, Przybylski M, Quezada-Pinedo HG, Regan AK, Rhoda NR, Rihs TA, Riley T, Rocha TAH, Rolnik DL, Saner C, Schneuer FJ, Souter VL, Stephansson O, Sun S, Swift EM, Szabó M, Temmerman M, Tooke L, Urquia ML, von Dadelszen P, Wellenius GA, … See abstract for full author list ➔ Calvert C, et al. Among authors: aghaeepour n. Nat Hum Behav. 2023 Apr;7(4):529-544. doi: 10.1038/s41562-023-01522-y. Epub 2023 Feb 27. Nat Hum Behav. 2023. PMID: 36849590 Free PMC article.
Data-driven longitudinal characterization of neonatal health and morbidity.
De Francesco D, Reiss JD, Roger J, Tang AS, Chang AL, Becker M, Phongpreecha T, Espinosa C, Morin S, Berson E, Thuraiappah M, Le BL, Ravindra NG, Payrovnaziri SN, Mataraso S, Kim Y, Xue L, Rosenstein MG, Oskotsky T, Marić I, Gaudilliere B, Carvalho B, Bateman BT, Angst MS, Prince LS, Blumenfeld YJ, Benitz WE, Fuerch JH, Shaw GM, Sylvester KG, Stevenson DK, Sirota M, Aghaeepour N. De Francesco D, et al. Among authors: aghaeepour n. Sci Transl Med. 2023 Feb 15;15(683):eadc9854. doi: 10.1126/scitranslmed.adc9854. Epub 2023 Feb 15. Sci Transl Med. 2023. PMID: 36791208 Free PMC article.
Towards multiomic analysis of oral mucosal pathologies.
Einhaus J, Han X, Feyaerts D, Sunwoo J, Gaudilliere B, Ahmad SH, Aghaeepour N, Bruckman K, Ojcius D, Schürch CM, Gaudilliere DK. Einhaus J, et al. Among authors: aghaeepour n. Semin Immunopathol. 2023 Jan;45(1):111-123. doi: 10.1007/s00281-022-00982-0. Epub 2023 Feb 15. Semin Immunopathol. 2023. PMID: 36790488 Free PMC article. Review.
Prediction of neuropathologic lesions from clinical data.
Phongpreecha T, Cholerton B, Bukhari S, Chang AL, De Francesco D, Thuraiappah M, Godrich D, Perna A, Becker MG, Ravindra NG, Espinosa C, Kim Y, Berson E, Mataraso S, Sha SJ, Fox EJ, Montine KS, Baker LD, Craft S, White L, Poston KL, Beecham G, Aghaeepour N, Montine TJ. Phongpreecha T, et al. Among authors: aghaeepour n. Alzheimers Dement. 2023 Jul;19(7):3005-3018. doi: 10.1002/alz.12921. Epub 2023 Jan 21. Alzheimers Dement. 2023. PMID: 36681388 Free PMC article.
Early response evaluation by single cell signaling profiling in acute myeloid leukemia.
Tislevoll BS, Hellesøy M, Fagerholt OHE, Gullaksen SE, Srivastava A, Birkeland E, Kleftogiannis D, Ayuda-Durán P, Piechaczyk L, Tadele DS, Skavland J, Baliakas P, Hovland R, Andresen V, Seternes OM, Tvedt THA, Aghaeepour N, Gavasso S, Porkka K, Jonassen I, Fløisand Y, Enserink J, Blaser N, Gjertsen BT. Tislevoll BS, et al. Among authors: aghaeepour n. Nat Commun. 2023 Jan 7;14(1):115. doi: 10.1038/s41467-022-35624-4. Nat Commun. 2023. PMID: 36611026 Free PMC article.
Revealing the impact of lifestyle stressors on the risk of adverse pregnancy outcomes with multitask machine learning.
Becker M, Dai J, Chang AL, Feyaerts D, Stelzer IA, Zhang M, Berson E, Saarunya G, De Francesco D, Espinosa C, Kim Y, Marić I, Mataraso S, Payrovnaziri SN, Phongpreecha T, Ravindra NG, Shome S, Tan Y, Thuraiappah M, Xue L, Mayo JA, Quaintance CC, Laborde A, King LS, Dhabhar FS, Gotlib IH, Wong RJ, Angst MS, Shaw GM, Stevenson DK, Gaudilliere B, Aghaeepour N. Becker M, et al. Among authors: aghaeepour n. Front Pediatr. 2022 Dec 13;10:933266. doi: 10.3389/fped.2022.933266. eCollection 2022. Front Pediatr. 2022. PMID: 36582513 Free PMC article.
Early prediction and longitudinal modeling of preeclampsia from multiomics.
Marić I, Contrepois K, Moufarrej MN, Stelzer IA, Feyaerts D, Han X, Tang A, Stanley N, Wong RJ, Traber GM, Ellenberger M, Chang AL, Fallahzadeh R, Nassar H, Becker M, Xenochristou M, Espinosa C, De Francesco D, Ghaemi MS, Costello EK, Culos A, Ling XB, Sylvester KG, Darmstadt GL, Winn VD, Shaw GM, Relman DA, Quake SR, Angst MS, Snyder MP, Stevenson DK, Gaudilliere B, Aghaeepour N. Marić I, et al. Among authors: aghaeepour n. Patterns (N Y). 2022 Dec 9;3(12):100655. doi: 10.1016/j.patter.2022.100655. eCollection 2022 Dec 9. Patterns (N Y). 2022. PMID: 36569558 Free PMC article.
In-silico generation of high-dimensional immune response data in patients using a deep neural network.
Fallahzadeh R, Bidoki NH, Stelzer IA, Becker M, Marić I, Chang AL, Culos A, Phongpreecha T, Xenochristou M, De Francesco D, Espinosa C, Berson E, Verdonk F, Angst MS, Gaudilliere B, Aghaeepour N. Fallahzadeh R, et al. Among authors: aghaeepour n. Cytometry A. 2023 May;103(5):392-404. doi: 10.1002/cyto.a.24709. Epub 2022 Dec 27. Cytometry A. 2023. PMID: 36507780 Free PMC article.
The Childhood Acute Illness and Nutrition (CHAIN) network nested case-cohort study protocol: a multi-omics approach to understanding mortality among children in sub-Saharan Africa and South Asia.
Njunge JM, Tickell K, Diallo AH, Sayeem Bin Shahid ASM, Gazi MA, Saleem A, Kazi Z, Ali S, Tigoi C, Mupere E, Lancioni CL, Yoshioka E, Chisti MJ, Mburu M, Ngari M, Ngao N, Gichuki B, Omer E, Gumbi W, Singa B, Bandsma R, Ahmed T, Voskuijl W, Williams TN, Macharia A, Makale J, Mitchel A, Williams J, Gogain J, Janjic N, Mandal R, Wishart DS, Wu H, Xia L, Routledge M, Gong YY, Espinosa C, Aghaeepour N, Liu J, Houpt E, Lawley TD, Browne H, Shao Y, Rwigi D, Kariuki K, Kaburu T, Uhlig HH, Gartner L, Jones K, Koulman A, Walson J, Berkley J. Njunge JM, et al. Among authors: aghaeepour n. Gates Open Res. 2022 Nov 3;6:77. doi: 10.12688/gatesopenres.13635.2. eCollection 2022. Gates Open Res. 2022. PMID: 36415883 Free PMC article.
Author Correction: Prediction of gestational age using urinary metabolites in term and preterm pregnancies.
Contrepois K, Chen S, Ghaemi MS, Wong RJ, Jehan F, Sazawal S, Baqui AH, Stringer JSA, Rahman A, Nisar MI, Dhingra U, Khanam R, Ilyas M, Dutta A, Mehmood U, Deb S, Hotwani A, Ali SM, Rahman S, Nizar A, Ame SM, Muhammad S, Chauhan A, Khan W, Raqib R, Das S, Ahmed S, Hasan T, Khalid J, Juma MH, Chowdhury NH, Kabir F, Aftab F, Quaiyum A, Manu A, Yoshida S, Bahl R, Pervin J, Price JT, Rahman M, Kasaro MP, Litch JA, Musonda P, Vwalika B, Shaw G, Stevenson DK, Aghaeepour N, Snyder MP. Contrepois K, et al. Among authors: aghaeepour n. Sci Rep. 2022 Nov 17;12(1):19753. doi: 10.1038/s41598-022-23715-7. Sci Rep. 2022. PMID: 36396676 Free PMC article. No abstract available.
Integrated plasma proteomic and single-cell immune signaling network signatures demarcate mild, moderate, and severe COVID-19.
Feyaerts D, Hédou J, Gillard J, Chen H, Tsai ES, Peterson LS, Ando K, Manohar M, Do E, Dhondalay GKR, Fitzpatrick J, Artandi M, Chang I, Snow TT, Chinthrajah RS, Warren CM, Wittman R, Meyerowitz JG, Ganio EA, Stelzer IA, Han X, Verdonk F, Gaudillière DK, Mukherjee N, Tsai AS, Rumer KK, Jacobsen DR, Bjornson-Hooper ZB, Jiang S, Saavedra SF, Valdés Ferrer SI, Kelly JD, Furman D, Aghaeepour N, Angst MS, Boyd SD, Pinsky BA, Nolan GP, Nadeau KC, Gaudillière B, McIlwain DR. Feyaerts D, et al. Among authors: aghaeepour n. Cell Rep Med. 2022 Jul 19;3(7):100680. doi: 10.1016/j.xcrm.2022.100680. Epub 2022 Jun 28. Cell Rep Med. 2022. PMID: 35839768 Free PMC article.
Signature for Pain Recovery IN Teens (SPRINT): protocol for a multisite prospective signature study in chronic musculoskeletal pain.
Simons L, Moayedi M, Coghill RC, Stinson J, Angst MS, Aghaeepour N, Gaudilliere B, King CD, López-Solà M, Hoeppli ME, Biggs E, Ganio E, Williams SE, Goldschneider KR, Campbell F, Ruskin D, Krane EJ, Walker S, Rush G, Heirich M. Simons L, et al. Among authors: aghaeepour n. BMJ Open. 2022 Jun 8;12(6):e061548. doi: 10.1136/bmjopen-2022-061548. BMJ Open. 2022. PMID: 35676017 Free PMC article.
Prediction of gestational age using urinary metabolites in term and preterm pregnancies.
Contrepois K, Chen S, Ghaemi MS, Wong RJ, Jehan F, Sazawal S, Baqui AH, Stringer JSA, Rahman A, Nisar MI, Dhingra U, Khanam R, Ilyas M, Dutta A, Mehmood U, Deb S, Hotwani A, Ali SM, Rahman S, Nizar A, Ame SM, Muhammad S, Chauhan A, Khan W, Raqib R, Das S, Ahmed S, Hasan T, Khalid J, Juma MH, Chowdhury NH, Kabir F, Aftab F, Quaiyum A, Manu A, Yoshida S, Bahl R, Pervin J, Price JT, Rahman M, Kasaro MP, Litch JA, Musonda P, Vwalika B; Alliance for Maternal and Newborn Health Improvement (AMANHI); Global Alliance to Prevent Prematurity and Stillbirth (GAPPS); Shaw G, Stevenson DK, Aghaeepour N, Snyder MP. Contrepois K, et al. Among authors: aghaeepour n. Sci Rep. 2022 May 16;12(1):8033. doi: 10.1038/s41598-022-11866-6. Sci Rep. 2022. PMID: 35577875 Free PMC article.
A data-driven health index for neonatal morbidities.
De Francesco D, Blumenfeld YJ, Marić I, Mayo JA, Chang AL, Fallahzadeh R, Phongpreecha T, Butwick AJ, Xenochristou M, Phibbs CS, Bidoki NH, Becker M, Culos A, Espinosa C, Liu Q, Sylvester KG, Gaudilliere B, Angst MS, Stevenson DK, Shaw GM, Aghaeepour N. De Francesco D, et al. Among authors: aghaeepour n. iScience. 2022 Mar 22;25(4):104143. doi: 10.1016/j.isci.2022.104143. eCollection 2022 Apr 15. iScience. 2022. PMID: 35402862 Free PMC article.
Stress and Its Consequences-Biological Strain.
Stevenson DK, Gotlib IH, Buthmann JL, Marié I, Aghaeepour N, Gaudilliere B, Angst MS, Darmstadt GL, Druzin ML, Wong RJ, Shaw GM, Katz M. Stevenson DK, et al. Among authors: aghaeepour n. Am J Perinatol. 2024 Jul;41(9):1282-1284. doi: 10.1055/a-1798-1602. Epub 2022 Mar 15. Am J Perinatol. 2024. PMID: 35292943
Increases in ambient air pollutants during pregnancy are linked to increases in methylation of IL4, IL10, and IFNγ.
Aguilera J, Han X, Cao S, Balmes J, Lurmann F, Tyner T, Lutzker L, Noth E, Hammond SK, Sampath V, Burt T, Utz PJ, Khatri P, Aghaeepour N, Maecker H, Prunicki M, Nadeau K. Aguilera J, et al. Among authors: aghaeepour n. Clin Epigenetics. 2022 Mar 14;14(1):40. doi: 10.1186/s13148-022-01254-2. Clin Epigenetics. 2022. PMID: 35287715 Free PMC article.
Objective Activity Parameters Track Patient-specific Physical Recovery Trajectories After Surgery and Link With Individual Preoperative Immune States.
Fallahzadeh R, Verdonk F, Ganio E, Culos A, Stanley N, Maric I, Chang AL, Becker M, Phongpreecha T, Xenochristou M, De Francesco D, Espinosa C, Gao X, Tsai A, Sultan P, Tingle M, Amanatullah DF, Huddleston JI, Goodman SB, Gaudilliere B, Angst MS, Aghaeepour N. Fallahzadeh R, et al. Among authors: aghaeepour n. Ann Surg. 2023 Mar 1;277(3):e503-e512. doi: 10.1097/SLA.0000000000005250. Epub 2021 Oct 8. Ann Surg. 2023. PMID: 35129529 Free PMC article.
Perinatal infection, inflammation, preterm birth, and brain injury: A review with proposals for future investigations.
Reiss JD, Peterson LS, Nesamoney SN, Chang AL, Pasca AM, Marić I, Shaw GM, Gaudilliere B, Wong RJ, Sylvester KG, Bonifacio SL, Aghaeepour N, Gibbs RS, Stevenson DK. Reiss JD, et al. Among authors: aghaeepour n. Exp Neurol. 2022 May;351:113988. doi: 10.1016/j.expneurol.2022.113988. Epub 2022 Jan 23. Exp Neurol. 2022. PMID: 35081400 Review.
Integrated Single-cell and Plasma Proteomic Modeling to Predict Surgical Site Complications: A Prospective Cohort Study.
Rumer KK, Hedou J, Tsai A, Einhaus J, Verdonk F, Stanley N, Choisy B, Ganio E, Bonham A, Jacobsen D, Warrington B, Gao X, Tingle M, McAllister TN, Fallahzadeh R, Feyaerts D, Stelzer I, Gaudilliere D, Ando K, Shelton A, Morris A, Kebebew E, Aghaeepour N, Kin C, Angst MS, Gaudilliere B. Rumer KK, et al. Among authors: aghaeepour n. Ann Surg. 2022 Mar 1;275(3):582-590. doi: 10.1097/SLA.0000000000005348. Ann Surg. 2022. PMID: 34954754 Free PMC article.
Single-synapse analyses of Alzheimer's disease implicate pathologic tau, DJ1, CD47, and ApoE.
Phongpreecha T, Gajera CR, Liu CC, Vijayaragavan K, Chang AL, Becker M, Fallahzadeh R, Fernandez R, Postupna N, Sherfield E, Tebaykin D, Latimer C, Shively CA, Register TC, Craft S, Montine KS, Fox EJ, Poston KL, Keene CD, Angelo M, Bendall SC, Aghaeepour N, Montine TJ. Phongpreecha T, et al. Among authors: aghaeepour n. Sci Adv. 2021 Dec 17;7(51):eabk0473. doi: 10.1126/sciadv.abk0473. Epub 2021 Dec 15. Sci Adv. 2021. PMID: 34910503 Free PMC article.
Harnessing the Potential of Multiomics Studies for Precision Medicine in Infectious Disease.
Ward RA, Aghaeepour N, Bhattacharyya RP, Clish CB, Gaudillière B, Hacohen N, Mansour MK, Mudd PA, Pasupneti S, Presti RM, Rhee EP, Sen P, Spec A, Tam JM, Villani AC, Woolley AE, Hsu JL, Vyas JM. Ward RA, et al. Among authors: aghaeepour n. Open Forum Infect Dis. 2021 Sep 25;8(11):ofab483. doi: 10.1093/ofid/ofab483. eCollection 2021 Nov. Open Forum Infect Dis. 2021. PMID: 34805429 Free PMC article. Review.
Human influenza virus challenge identifies cellular correlates of protection for oral vaccination.
McIlwain DR, Chen H, Rahil Z, Bidoki NH, Jiang S, Bjornson Z, Kolhatkar NS, Martinez CJ, Gaudillière B, Hedou J, Mukherjee N, Schürch CM, Trejo A, Affrime M, Bock B, Kim K, Liebowitz D, Aghaeepour N, Tucker SN, Nolan GP. McIlwain DR, et al. Among authors: aghaeepour n. Cell Host Microbe. 2021 Dec 8;29(12):1828-1837.e5. doi: 10.1016/j.chom.2021.10.009. Epub 2021 Nov 15. Cell Host Microbe. 2021. PMID: 34784508 Free PMC article.
Black swans and ambitious overgeneralization in newborn intensive care.
Stevenson DK, Wong RJ, Shaw GM, Aghaeepour N, Maric I, Prince LS, Reiss JD, Katz M. Stevenson DK, et al. Among authors: aghaeepour n. Pediatr Res. 2022 Aug;92(2):357-359. doi: 10.1038/s41390-021-01771-5. Epub 2021 Oct 2. Pediatr Res. 2022. PMID: 34601493 No abstract available.
A Peripheral Immune Signature of Labor Induction.
Ando K, Hédou JJ, Feyaerts D, Han X, Ganio EA, Tsai ES, Peterson LS, Verdonk F, Tsai AS, Marić I, Wong RJ, Angst MS, Aghaeepour N, Stevenson DK, Blumenfeld YJ, Sultan P, Carvalho B, Stelzer IA, Gaudillière B. Ando K, et al. Among authors: aghaeepour n. Front Immunol. 2021 Sep 9;12:725989. doi: 10.3389/fimmu.2021.725989. eCollection 2021. Front Immunol. 2021. PMID: 34566984 Free PMC article.
Single-Cell Analysis of the Neonatal Immune System Across the Gestational Age Continuum.
Peterson LS, Hedou J, Ganio EA, Stelzer IA, Feyaerts D, Harbert E, Adusumelli Y, Ando K, Tsai ES, Tsai AS, Han X, Ringle M, Houghteling P, Reiss JD, Lewis DB, Winn VD, Angst MS, Aghaeepour N, Stevenson DK, Gaudilliere B. Peterson LS, et al. Among authors: aghaeepour n. Front Immunol. 2021 Aug 23;12:714090. doi: 10.3389/fimmu.2021.714090. eCollection 2021. Front Immunol. 2021. PMID: 34497610 Free PMC article.
Crowdsourcing assessment of maternal blood multi-omics for predicting gestational age and preterm birth.
Tarca AL, Pataki BÁ, Romero R, Sirota M, Guan Y, Kutum R, Gomez-Lopez N, Done B, Bhatti G, Yu T, Andreoletti G, Chaiworapongsa T; DREAM Preterm Birth Prediction Challenge Consortium; Hassan SS, Hsu CD, Aghaeepour N, Stolovitzky G, Csabai I, Costello JC. Tarca AL, et al. Among authors: aghaeepour n. Cell Rep Med. 2021 Jun 15;2(6):100323. doi: 10.1016/j.xcrm.2021.100323. eCollection 2021 Jun 15. Cell Rep Med. 2021. PMID: 34195686 Free PMC article.
Improvement in Glucose Regulation Using a Digital Tracker and Continuous Glucose Monitoring in Healthy Adults and Those with Type 2 Diabetes.
Dehghani Zahedani A, Shariat Torbaghan S, Rahili S, Karlin K, Scilley D, Thakkar R, Saberi M, Hashemi N, Perelman D, Aghaeepour N, McLaughlin T, Snyder MP. Dehghani Zahedani A, et al. Among authors: aghaeepour n. Diabetes Ther. 2021 Jul;12(7):1871-1886. doi: 10.1007/s13300-021-01081-3. Epub 2021 May 28. Diabetes Ther. 2021. PMID: 34047962 Free PMC article.
Integrated trajectories of the maternal metabolome, proteome, and immunome predict labor onset.
Stelzer IA, Ghaemi MS, Han X, Ando K, Hédou JJ, Feyaerts D, Peterson LS, Rumer KK, Tsai ES, Ganio EA, Gaudillière DK, Tsai AS, Choisy B, Gaigne LP, Verdonk F, Jacobsen D, Gavasso S, Traber GM, Ellenberger M, Stanley N, Becker M, Culos A, Fallahzadeh R, Wong RJ, Darmstadt GL, Druzin ML, Winn VD, Gibbs RS, Ling XB, Sylvester K, Carvalho B, Snyder MP, Shaw GM, Stevenson DK, Contrepois K, Angst MS, Aghaeepour N, Gaudillière B. Stelzer IA, et al. Among authors: aghaeepour n. Sci Transl Med. 2021 May 5;13(592):eabd9898. doi: 10.1126/scitranslmed.abd9898. Sci Transl Med. 2021. PMID: 33952678 Free PMC article.
Understanding how biologic and social determinants affect disparities in preterm birth and outcomes of preterm infants in the NICU.
Stevenson DK, Aghaeepour N, Maric I, Angst MS, Darmstadt GL, Druzin ML, Gaudilliere B, Ling XB, Moufarrej MN, Peterson LS, Quake SR, Relman DA, Snyder MP, Sylvester KG, Shaw GM, Wong RJ. Stevenson DK, et al. Among authors: aghaeepour n. Semin Perinatol. 2021 Jun;45(4):151408. doi: 10.1016/j.semperi.2021.151408. Epub 2021 Mar 24. Semin Perinatol. 2021. PMID: 33875265 Free PMC article.
High-dimensional profiling clusters asthma severity by lymphoid and non-lymphoid status.
Camiolo MJ, Zhou X, Oriss TB, Yan Q, Gorry M, Horne W, Trudeau JB, Scholl K, Chen W, Kolls JK, Ray P, Weisel FJ, Weisel NM, Aghaeepour N, Nadeau K, Wenzel SE, Ray A. Camiolo MJ, et al. Among authors: aghaeepour n. Cell Rep. 2021 Apr 13;35(2):108974. doi: 10.1016/j.celrep.2021.108974. Cell Rep. 2021. PMID: 33852838 Free PMC article.
Proteomic signatures predict preeclampsia in individual cohorts but not across cohorts - implications for clinical biomarker studies.
Ghaemi MS, Tarca AL, Romero R, Stanley N, Fallahzadeh R, Tanada A, Culos A, Ando K, Han X, Blumenfeld YJ, Druzin ML, El-Sayed YY, Gibbs RS, Winn VD, Contrepois K, Ling XB, Wong RJ, Shaw GM, Stevenson DK, Gaudilliere B, Aghaeepour N, Angst MS. Ghaemi MS, et al. Among authors: aghaeepour n. J Matern Fetal Neonatal Med. 2022 Dec;35(25):5621-5628. doi: 10.1080/14767058.2021.1888915. Epub 2021 Mar 2. J Matern Fetal Neonatal Med. 2022. PMID: 33653202 Free PMC article.
Integrated plasma proteomic and single-cell immune signaling network signatures demarcate mild, moderate, and severe COVID-19.
Feyaerts D, Hédou J, Gillard J, Chen H, Tsai ES, Peterson LS, Ando K, Manohar M, Do E, Dhondalay GKR, Fitzpatrick J, Artandi M, Chang I, Snow TT, Chinthrajah RS, Warren CM, Wittman R, Meyerowitz JG, Ganio EA, Stelzer IA, Han X, Verdonk F, Gaudillière DK, Mukherjee N, Tsai AS, Rumer KK, Jiang S, Valdés Ferrer SI, Kelly JD, Furman D, Aghaeepour N, Angst MS, Boyd SD, Pinsky BA, Nolan GP, Nadeau KC, Gaudillière B, McIlwain DR. Feyaerts D, et al. Among authors: aghaeepour n. bioRxiv [Preprint]. 2021 Feb 10:2021.02.09.430269. doi: 10.1101/2021.02.09.430269. bioRxiv. 2021. Update in: Cell Rep Med. 2022 Jul 19;3(7):100680. doi: 10.1016/j.xcrm.2022.100680. PMID: 33594362 Free PMC article. Updated. Preprint.
Data-Driven Modeling of Pregnancy-Related Complications.
Espinosa C, Becker M, Marić I, Wong RJ, Shaw GM, Gaudilliere B, Aghaeepour N, Stevenson DK; Prematurity Research Center at Stanford. Espinosa C, et al. Among authors: aghaeepour n. Trends Mol Med. 2021 Aug;27(8):762-776. doi: 10.1016/j.molmed.2021.01.007. Epub 2021 Feb 8. Trends Mol Med. 2021. PMID: 33573911 Free PMC article. Review.
Early prediction of preeclampsia via machine learning.
Marić I, Tsur A, Aghaeepour N, Montanari A, Stevenson DK, Shaw GM, Winn VD. Marić I, et al. Among authors: aghaeepour n. Am J Obstet Gynecol MFM. 2020 May;2(2):100100. doi: 10.1016/j.ajogmf.2020.100100. Epub 2020 Mar 14. Am J Obstet Gynecol MFM. 2020. PMID: 33345966
Multiomics Characterization of Preterm Birth in Low- and Middle-Income Countries.
Jehan F, Sazawal S, Baqui AH, Nisar MI, Dhingra U, Khanam R, Ilyas M, Dutta A, Mitra DK, Mehmood U, Deb S, Mahmud A, Hotwani A, Ali SM, Rahman S, Nizar A, Ame SM, Moin MI, Muhammad S, Chauhan A, Begum N, Khan W, Das S, Ahmed S, Hasan T, Khalid J, Rizvi SJR, Juma MH, Chowdhury NH, Kabir F, Aftab F, Quaiyum A, Manu A, Yoshida S, Bahl R, Rahman A, Pervin J, Winston J, Musonda P, Stringer JSA, Litch JA, Ghaemi MS, Moufarrej MN, Contrepois K, Chen S, Stelzer IA, Stanley N, Chang AL, Hammad GB, Wong RJ, Liu C, Quaintance CC, Culos A, Espinosa C, Xenochristou M, Becker M, Fallahzadeh R, Ganio E, Tsai AS, Gaudilliere D, Tsai ES, Han X, Ando K, Tingle M, Maric I, Wise PH, Winn VD, Druzin ML, Gibbs RS, Darmstadt GL, Murray JC, Shaw GM, Stevenson DK, Snyder MP, Quake SR, Angst MS, Gaudilliere B, Aghaeepour N; Alliance for Maternal and Newborn Health Improvement, the Global Alliance to Prevent Prematurity and Stillbirth, and the Prematurity Research Center at Stanford University. Jehan F, et al. Among authors: aghaeepour n. JAMA Netw Open. 2020 Dec 1;3(12):e2029655. doi: 10.1001/jamanetworkopen.2020.29655. JAMA Netw Open. 2020. PMID: 33337494 Free PMC article.
Integration of mechanistic immunological knowledge into a machine learning pipeline improves predictions.
Culos A, Tsai AS, Stanley N, Becker M, Ghaemi MS, McIlwain DR, Fallahzadeh R, Tanada A, Nassar H, Espinosa C, Xenochristou M, Ganio E, Peterson L, Han X, Stelzer IA, Ando K, Gaudilliere D, Phongpreecha T, Marić I, Chang AL, Shaw GM, Stevenson DK, Bendall S, Davis KL, Fantl W, Nolan GP, Hastie T, Tibshirani R, Angst MS, Gaudilliere B, Aghaeepour N. Culos A, et al. Among authors: aghaeepour n. Nat Mach Intell. 2020 Oct;2(10):619-628. doi: 10.1038/s42256-020-00232-8. Epub 2020 Oct 12. Nat Mach Intell. 2020. PMID: 33294774 Free PMC article.
Single-cell peripheral immunoprofiling of Alzheimer's and Parkinson's diseases.
Phongpreecha T, Fernandez R, Mrdjen D, Culos A, Gajera CR, Wawro AM, Stanley N, Gaudilliere B, Poston KL, Aghaeepour N, Montine TJ. Phongpreecha T, et al. Among authors: aghaeepour n. Sci Adv. 2020 Nov 25;6(48):eabd5575. doi: 10.1126/sciadv.abd5575. Print 2020 Nov. Sci Adv. 2020. PMID: 33239300 Free PMC article.
Landscape of coordinated immune responses to H1N1 challenge in humans.
Rahil Z, Leylek R, Schürch CM, Chen H, Bjornson-Hooper Z, Christensen SR, Gherardini PF, Bhate SS, Spitzer MH, Fragiadakis GK, Mukherjee N, Kim N, Jiang S, Yo J, Gaudilliere B, Affrime M, Bock B, Hensley SE, Idoyaga J, Aghaeepour N, Kim K, Nolan GP, McIlwain DR. Rahil Z, et al. Among authors: aghaeepour n. J Clin Invest. 2020 Nov 2;130(11):5800-5816. doi: 10.1172/JCI137265. J Clin Invest. 2020. PMID: 33044226 Free PMC article. Clinical Trial.
Multivariate prediction of dementia in Parkinson's disease.
Phongpreecha T, Cholerton B, Mata IF, Zabetian CP, Poston KL, Aghaeepour N, Tian L, Quinn JF, Chung KA, Hiller AL, Hu SC, Edwards KL, Montine TJ. Phongpreecha T, et al. Among authors: aghaeepour n. NPJ Parkinsons Dis. 2020 Aug 25;6:20. doi: 10.1038/s41531-020-00121-2. eCollection 2020. NPJ Parkinsons Dis. 2020. PMID: 32885039 Free PMC article.
Author Correction: Preferential inhibition of adaptive immune system dynamics by glucocorticoids in patients after acute surgical trauma.
Ganio EA, Stanley N, Lindberg-Larsen V, Einhaus J, Tsai AS, Verdonk F, Culos A, Ghaemi S, Rumer KK, Stelzer IA, Gaudilliere D, Tsai E, Fallahzadeh R, Choisy B, Kehlet H, Aghaeepour N, Angst MS, Gaudilliere B. Ganio EA, et al. Among authors: aghaeepour n. Nat Commun. 2020 Sep 3;11(1):4495. doi: 10.1038/s41467-020-18410-y. Nat Commun. 2020. PMID: 32883978 Free PMC article.
VoPo leverages cellular heterogeneity for predictive modeling of single-cell data.
Stanley N, Stelzer IA, Tsai AS, Fallahzadeh R, Ganio E, Becker M, Phongpreecha T, Nassar H, Ghaemi S, Maric I, Culos A, Chang AL, Xenochristou M, Han X, Espinosa C, Rumer K, Peterson L, Verdonk F, Gaudilliere D, Tsai E, Feyaerts D, Einhaus J, Ando K, Wong RJ, Obermoser G, Shaw GM, Stevenson DK, Angst MS, Gaudilliere B, Aghaeepour N. Stanley N, et al. Among authors: aghaeepour n. Nat Commun. 2020 Jul 27;11(1):3738. doi: 10.1038/s41467-020-17569-8. Nat Commun. 2020. PMID: 32719375 Free PMC article.
Preferential inhibition of adaptive immune system dynamics by glucocorticoids in patients after acute surgical trauma.
Ganio EA, Stanley N, Lindberg-Larsen V, Einhaus J, Tsai AS, Verdonk F, Culos A, Ghaemi S, Rumer KK, Stelzer IA, Gaudilliere D, Tsai E, Fallahzadeh R, Choisy B, Kehlet H, Aghaeepour N, Angst MS, Gaudilliere B. Ganio EA, et al. Among authors: aghaeepour n. Nat Commun. 2020 Jul 27;11(1):3737. doi: 10.1038/s41467-020-17565-y. Nat Commun. 2020. PMID: 32719355 Free PMC article. Clinical Trial.
Discovery and validation of biomarkers to aid the development of safe and effective pain therapeutics: challenges and opportunities.
Davis KD, Aghaeepour N, Ahn AH, Angst MS, Borsook D, Brenton A, Burczynski ME, Crean C, Edwards R, Gaudilliere B, Hergenroeder GW, Iadarola MJ, Iyengar S, Jiang Y, Kong JT, Mackey S, Saab CY, Sang CN, Scholz J, Segerdahl M, Tracey I, Veasley C, Wang J, Wager TD, Wasan AD, Pelleymounter MA. Davis KD, et al. Among authors: aghaeepour n. Nat Rev Neurol. 2020 Jul;16(7):381-400. doi: 10.1038/s41582-020-0362-2. Epub 2020 Jun 15. Nat Rev Neurol. 2020. PMID: 32541893 Free PMC article. Review.
Towards personalized medicine in maternal and child health: integrating biologic and social determinants.
Stevenson DK, Wong RJ, Aghaeepour N, Maric I, Angst MS, Contrepois K, Darmstadt GL, Druzin ML, Eisenberg ML, Gaudilliere B, Gibbs RS, Gotlib IH, Gould JB, Lee HC, Ling XB, Mayo JA, Moufarrej MN, Quaintance CC, Quake SR, Relman DA, Sirota M, Snyder MP, Sylvester KG, Hao S, Wise PH, Shaw GM, Katz M. Stevenson DK, et al. Among authors: aghaeepour n. Pediatr Res. 2021 Jan;89(2):252-258. doi: 10.1038/s41390-020-0981-8. Epub 2020 May 26. Pediatr Res. 2021. PMID: 32454518 Free PMC article. No abstract available.
Changes in pregnancy-related serum biomarkers early in gestation are associated with later development of preeclampsia.
Hao S, You J, Chen L, Zhao H, Huang Y, Zheng L, Tian L, Maric I, Liu X, Li T, Bianco YK, Winn VD, Aghaeepour N, Gaudilliere B, Angst MS, Zhou X, Li YM, Mo L, Wong RJ, Shaw GM, Stevenson DK, Cohen HJ, Mcelhinney DB, Sylvester KG, Ling XB. Hao S, et al. Among authors: aghaeepour n. PLoS One. 2020 Mar 3;15(3):e0230000. doi: 10.1371/journal.pone.0230000. eCollection 2020. PLoS One. 2020. PMID: 32126118 Free PMC article.
Multiomic immune clockworks of pregnancy.
Peterson LS, Stelzer IA, Tsai AS, Ghaemi MS, Han X, Ando K, Winn VD, Martinez NR, Contrepois K, Moufarrej MN, Quake S, Relman DA, Snyder MP, Shaw GM, Stevenson DK, Wong RJ, Arck P, Angst MS, Aghaeepour N, Gaudilliere B. Peterson LS, et al. Among authors: aghaeepour n. Semin Immunopathol. 2020 Aug;42(4):397-412. doi: 10.1007/s00281-019-00772-1. Epub 2020 Feb 4. Semin Immunopathol. 2020. PMID: 32020337 Free PMC article. Review.
Cyt-Geist: Current and Future Challenges in Cytometry: Reports of the CYTO 2019 Conference Workshops.
Czechowska K, Lannigan J, Aghaeepour N, Back JB, Begum J, Behbehani G, Bispo C, Bitoun D, Fernández AB, Boova ST, Brinkman RR, Ciccolella CO, Cotleur B, Davies D, Dela Cruz GV, Del Rio-Guerra R, Des Lauriers-Cox AM, Douagi I, Dumrese C, Bonilla Escobar DL, Estevam J, Ewald C, Fossum A, Gaudillière B, Green C, Groves C, Hall C, Haque Y, Hedrick MN, Hogg K, Hsieh EWY, Irish J, Lederer J, Leipold M, Lewis-Tuffin LJ, Litwin V, Lopez P, Nasdala I, Nedbal J, Ohlsson-Wilhelm BM, Price KM, Rahman AH, Rayanki R, Rieger AM, Robinson JP, Shapiro H, Sun YS, Tang VA, Tesfa L, Telford WG, Walker R, Welsh JA, Wheeler P, Tárnok A. Czechowska K, et al. Among authors: aghaeepour n. Cytometry A. 2019 Dec;95(12):1236-1274. doi: 10.1002/cyto.a.23941. Cytometry A. 2019. PMID: 31833655 Free article. No abstract available.
iRhom2 inhibits bile duct obstruction-induced liver fibrosis.
Sundaram B, Behnke K, Belancic A, Al-Salihi MA, Thabet Y, Polz R, Pellegrino R, Zhuang Y, Shinde PV, Xu HC, Vasilevska J, Longerich T, Herebian D, Mayatepek E, Bock HH, May P, Kordes C, Aghaeepour N, Mak TW, Keitel V, Häussinger D, Scheller J, Pandyra AA, Lang KS, Lang PA. Sundaram B, et al. Among authors: aghaeepour n. Sci Signal. 2019 Oct 29;12(605):eaax1194. doi: 10.1126/scisignal.aax1194. Sci Signal. 2019. PMID: 31662486
CytoNorm: A Normalization Algorithm for Cytometry Data.
Van Gassen S, Gaudilliere B, Angst MS, Saeys Y, Aghaeepour N. Van Gassen S, et al. Among authors: aghaeepour n. Cytometry A. 2020 Mar;97(3):268-278. doi: 10.1002/cyto.a.23904. Epub 2019 Oct 21. Cytometry A. 2020. PMID: 31633883 Free PMC article.
Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition).
Cossarizza A, Chang HD, Radbruch A, Acs A, Adam D, Adam-Klages S, Agace WW, Aghaeepour N, Akdis M, Allez M, Almeida LN, Alvisi G, Anderson G, Andrä I, Annunziato F, Anselmo A, Bacher P, Baldari CT, Bari S, Barnaba V, Barros-Martins J, Battistini L, Bauer W, Baumgart S, Baumgarth N, Baumjohann D, Baying B, Bebawy M, Becher B, Beisker W, Benes V, Beyaert R, Blanco A, Boardman DA, Bogdan C, Borger JG, Borsellino G, Boulais PE, Bradford JA, Brenner D, Brinkman RR, Brooks AES, Busch DH, Büscher M, Bushnell TP, Calzetti F, Cameron G, Cammarata I, Cao X, Cardell SL, Casola S, Cassatella MA, Cavani A, Celada A, Chatenoud L, Chattopadhyay PK, Chow S, Christakou E, Čičin-Šain L, Clerici M, Colombo FS, Cook L, Cooke A, Cooper AM, Corbett AJ, Cosma A, Cosmi L, Coulie PG, Cumano A, Cvetkovic L, Dang VD, Dang-Heine C, Davey MS, Davies D, De Biasi S, Del Zotto G, Dela Cruz GV, Delacher M, Della Bella S, Dellabona P, Deniz G, Dessing M, Di Santo JP, Diefenbach A, Dieli F, Dolf A, Dörner T, Dress RJ, Dudziak D, Dustin M, Dutertre CA, Ebner F, Eckle SBG, Edinger M, Eede P, Ehrhardt GRA, Eich M, Engel P, Engelhardt B, Erdei A, Esser C, Everts B, Evrard M, Falk CS, Fehniger TA, Felipo-Benavent… See abstract for full author list ➔ Cossarizza A, et al. Among authors: aghaeepour n. Eur J Immunol. 2019 Oct;49(10):1457-1973. doi: 10.1002/eji.201970107. Eur J Immunol. 2019. PMID: 31633216 Free PMC article.
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. Han X, et al. Among authors: aghaeepour n. Front Immunol. 2019 Jun 11;10:1305. doi: 10.3389/fimmu.2019.01305. eCollection 2019. Front Immunol. 2019. PMID: 31263463 Free PMC article.
Predicting Acute Pain After Surgery: A Multivariate Analysis.
Baca Q, Marti F, Poblete B, Gaudilliere B, Aghaeepour N, Angst MS. Baca Q, et al. Among authors: aghaeepour n. Ann Surg. 2021 Feb 1;273(2):289-298. doi: 10.1097/SLA.0000000000003400. Ann Surg. 2021. PMID: 31188202 Free PMC article.
How Clinical Flow Cytometry Rebooted Sepsis Immunology.
Monneret G, Gossez M, Aghaeepour N, Gaudilliere B, Venet F. Monneret G, et al. Among authors: aghaeepour n. Cytometry A. 2019 Apr;95(4):431-441. doi: 10.1002/cyto.a.23749. Epub 2019 Mar 19. Cytometry A. 2019. PMID: 30887636 Free PMC article. Review.
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. Tsai AS, et al. Among authors: aghaeepour n. Brain. 2019 Apr 1;142(4):978-991. doi: 10.1093/brain/awz022. Brain. 2019. PMID: 30860258 Free PMC article.
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. Ghaemi MS, et al. Among authors: aghaeepour n. Bioinformatics. 2019 Jan 1;35(1):95-103. doi: 10.1093/bioinformatics/bty537. Bioinformatics. 2019. PMID: 30561547 Free PMC article.
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. Stevenson DK, et al. Among authors: aghaeepour n. J Perinatol. 2019 Mar;39(3):354-358. doi: 10.1038/s41372-018-0298-1. Epub 2018 Dec 18. J Perinatol. 2019. PMID: 30560947
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. Aghaeepour N, et al. Bioinformatics. 2018 Dec 1;34(23):4131-4133. doi: 10.1093/bioinformatics/bty430. Bioinformatics. 2018. PMID: 29850785 Free PMC article.
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. Shaw GM, et al. Among authors: aghaeepour n. Environ Res. 2018 Jul;164:546-555. doi: 10.1016/j.envres.2018.03.020. Epub 2018 Mar 31. Environ Res. 2018. PMID: 29614386 Free PMC article.
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. Good Z, et al. Among authors: aghaeepour n. Nat Med. 2018 May;24(4):474-483. doi: 10.1038/nm.4505. Epub 2018 Mar 5. Nat Med. 2018. PMID: 29505032 Free PMC article.
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. Gonzalez VD, et al. Among authors: aghaeepour n. Cell Rep. 2018 Feb 13;22(7):1875-1888. doi: 10.1016/j.celrep.2018.01.053. Cell Rep. 2018. PMID: 29444438 Free PMC article.
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. Aghaeepour N, et al. Am J Obstet Gynecol. 2018 Mar;218(3):347.e1-347.e14. doi: 10.1016/j.ajog.2017.12.208. Epub 2017 Dec 24. Am J Obstet Gynecol. 2018. PMID: 29277631
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. Aghaeepour N, et al. Sci Immunol. 2017 Sep 1;2(15):eaan2946. doi: 10.1126/sciimmunol.aan2946. Sci Immunol. 2017. PMID: 28864494 Free PMC article.
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. Blazkova J, et al. Among authors: aghaeepour n. J Immunol. 2017 Mar 15;198(6):2479-2488. doi: 10.4049/jimmunol.1601855. Epub 2017 Feb 8. J Immunol. 2017. PMID: 28179497 Free PMC article.
SESSION INTRODUCTION.
Samusik N, Aghaeepour N, Bendall S. Samusik N, et al. Among authors: aghaeepour n. Pac Symp Biocomput. 2017;22:557-563. doi: 10.1142/9789813207813_0051. Pac Symp Biocomput. 2017. PMID: 27897006 Free article.
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. Knapp DJ, et al. Among authors: aghaeepour n. Blood. 2017 Jan 19;129(3):307-318. doi: 10.1182/blood-2016-09-740654. Epub 2016 Nov 8. Blood. 2017. PMID: 27827829 Free PMC article.
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. Fragiadakis GK, et al. Among authors: aghaeepour n. J Immunol. 2016 Dec 1;197(11):4482-4492. doi: 10.4049/jimmunol.1601195. Epub 2016 Oct 28. J Immunol. 2016. PMID: 27793998 Free PMC article.
In Reply.
Angst MS, Fragiadakis GK, Gaudillière B, Aghaeepour N, Nolan GP. Angst MS, et al. Among authors: aghaeepour n. Anesthesiology. 2016 Jun;124(6):1414-5. doi: 10.1097/ALN.0000000000001091. Anesthesiology. 2016. PMID: 27187126 Free PMC article. No abstract available.
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. Finak G, et al. Among authors: aghaeepour n. Sci Rep. 2016 Feb 10;6:20686. doi: 10.1038/srep20686. Sci Rep. 2016. PMID: 26861911 Free PMC article.
Automated analysis of flow cytometry data comes of age.
Brinkman RR, Aghaeepour N, Finak G, Gottardo R, Mosmann T, Scheuermann RH. Brinkman RR, et al. Among authors: aghaeepour n. Cytometry A. 2016 Jan;89(1):13-5. doi: 10.1002/cyto.a.22810. Cytometry A. 2016. PMID: 26812230 Free article. No abstract available.
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. Maney SK, et al. Among authors: aghaeepour n. Sci Signal. 2015 Nov 3;8(401):ra109. doi: 10.1126/scisignal.aac5356. Sci Signal. 2015. PMID: 26535007 Free PMC article.
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. Aghaeepour N, et al. Cytometry A. 2016 Jan;89(1):16-21. doi: 10.1002/cyto.a.22732. Epub 2015 Oct 8. Cytometry A. 2016. PMID: 26447924 Free PMC article.
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. Gaudillière B, et al. Among authors: aghaeepour n. Cytometry A. 2015 Sep;87(9):817-29. doi: 10.1002/cyto.a.22720. Epub 2015 Jul 17. Cytometry A. 2015. PMID: 26190063 Free PMC article.
State-of-the-Art in the Computational Analysis of Cytometry Data.
Brinkman RR, Aghaeepour N, Finak G, Gottardo R, Mosmann T, Scheuermann RH. Brinkman RR, et al. Among authors: aghaeepour n. Cytometry A. 2015 Jul;87(7):591-3. doi: 10.1002/cyto.a.22707. Cytometry A. 2015. PMID: 26111230 Free article. No abstract available.
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. Kvistborg P, et al. Among authors: aghaeepour n. Immunity. 2015 Apr 21;42(4):591-2. doi: 10.1016/j.immuni.2015.04.006. Immunity. 2015. PMID: 25902473 Free PMC article. No abstract available.
Deep profiling of multitube flow cytometry data.
O'Neill K, Aghaeepour N, Parker J, Hogge D, Karsan A, Dalal B, Brinkman RR. O'Neill K, et al. Among authors: aghaeepour n. Bioinformatics. 2015 May 15;31(10):1623-31. doi: 10.1093/bioinformatics/btv008. Epub 2015 Jan 18. Bioinformatics. 2015. PMID: 25600947 Free PMC article.
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. Beer PA, et al. Among authors: aghaeepour n. Stem Cell Reports. 2014 Nov 11;3(5):841-57. doi: 10.1016/j.stemcr.2014.09.006. Epub 2014 Oct 11. Stem Cell Reports. 2014. PMID: 25418728 Free PMC article.
Flow cytometry bioinformatics.
O'Neill K, Aghaeepour N, Spidlen J, Brinkman R. O'Neill K, et al. Among authors: aghaeepour n. PLoS Comput Biol. 2013;9(12):e1003365. doi: 10.1371/journal.pcbi.1003365. Epub 2013 Dec 5. PLoS Comput Biol. 2013. PMID: 24363631 Free PMC article.
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. Villanova F, et al. Among authors: aghaeepour n. PLoS One. 2013 Jul 3;8(7):e65485. doi: 10.1371/journal.pone.0065485. Print 2013. PLoS One. 2013. PMID: 23843942 Free PMC article.
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. Aghaeepour N, et al. Nat Methods. 2013 Mar;10(3):228-38. doi: 10.1038/nmeth.2365. Epub 2013 Feb 10. Nat Methods. 2013. PMID: 23396282 Free PMC article.
RchyOptimyx: cellular hierarchy optimization for flow cytometry.
Aghaeepour N, Jalali A, O'Neill K, Chattopadhyay PK, Roederer M, Hoos HH, Brinkman RR. Aghaeepour N, et al. Cytometry A. 2012 Dec;81(12):1022-30. doi: 10.1002/cyto.a.22209. Epub 2012 Oct 8. Cytometry A. 2012. PMID: 23044634 Free PMC article.