Publications

Google Scholar

πŸ„

2024

28. Yamada K†, Menon JA, Kim Y, Changde Cheng, Chen W, Shih JA, Villasenor-Altamirano AB, Chen X, Immunology of Cardiac Arrest Network (I-CAN), Tamura T, Merriam LT, Kim EY†, Weissman AJ†.
Protocol for immunophenotyping out-of-hospital cardiac arrest patients
STAR Protocols 5 (1), 102874.

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2023

27. Murphy AJβˆ—β€ , Changde Cheng βˆ—, Williams J, Shaw TI, Pinto EM, Dieseldorff-Jones K, Brzezinski J, Renfro LA, Tornwall B, Huff V, Hong AL, Mullen EA, Crompton B, Dome JS, Fernandez CV, Geller JI, Ehrlich PF, Mulder H, Oak N, Maciezsek J, Jablonowski C, Fleming AM, Pichavaram P, Morton CL, Easton J, Nichols KE, Clay MR, Santiago T, Zhang J, Yang J, Zambetti GP, Wang Z, Davidoff AM, Chen X β€ .
Genetic and epigenetic features of bilateral Wilms tumor predisposition in patients from the Children’s Oncology Group AREN18B5-Q
Nat Commun. 14, 8006 (2023).

26. Changde Cheng βˆ—, Chen Wβˆ—, Jin Hβˆ—, Chen X.
A review of single-cell rna-seq annotation, integration, and cell-cell communication
Cells. 2023 Jul 30;12(15). Review.

25. Tamura Tβˆ—, Changde Cheng βˆ—, Chen W, Merriam LT, Athar H, Kim YH, Manandhar R, Amir Sheikh MD, Pinilla-Vera M, Varon J, Hou PC, Lawler PR, Oldham WM, Seethala RR, Tesfaigzi Y, Weissman AJ, Baron RM, Ichinose F, Berg KM, Bohula EA, Morrow DA, Chen X, Kim EY.
Single-cell transcriptomics reveal a hyperacute cytokine and immune checkpoint axis after cardiac arrest in patients with poor neurological outcome
Med. 2023 Jul 14;4(7):432-456.e6.

24. Fang Jβˆ—, Singh Sβˆ—, Changde Cheng βˆ—, Natarajan Sβˆ—, Sheppard Hβˆ—, Abu-Zaid A, Durbin AD, Lee HW, Wu Q, Steele J, Connelly JP, Jin H, Chen W, Fan Y, Pruett-Miller SM, Rehg JE, Koo SC, Santiago T, Emmons J, Cairo S, Wang R, Glazer ES, Murphy AJ, Chen T, Davidoff AM, Armengol C, Easton J, Chen X, Yang J.
Genome-wide mapping of cancer dependency genes and genetic modifiers of chemotherapy in high-risk hepatoblastoma
Nat Commun. 2023 Jul 6;14(1):4003.

πŸ„

2022

23. Kovach AR, Oristian KM, Kirsch DG, Bentley RC, Changde Cheng, Chen X, Chen PH, Chi JA, Linardic CM.
Identification and targeting of a HES1-YAP1-CDKN1C functional interaction in fusion-negative rhabdomyosarcoma
Mol Oncol. 2022 Oct;16(20):3587-3605.

πŸ„πŸ„

2021

22. Changde Cheng, Kirkpatrick M.
Molecular evolution and the decline of purifying selection with age
Nat Commun. 2021 May 11;12(1):2657.

21. Houle D, Changde Cheng.
Predicting the evolution of sexual dimorphism in gene expression
Mol Biol Evol. 2021 May 4;38(5):1847-1859.

πŸ„

2020

20. Changde Cheng, Houle D.
Predicting multivariate responses of sexual dimorphism to direct and indirect selection
Am Nat. 2020 Oct;196(4):391-405.

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2019

19. Changde Cheng, Easton J, Rosencrance C, Li Y, Ju B, Williams J, Mulder HL, Pang Y, Chen W, Chen X.
Latent cellular analysis robustly reveals subtle diversity in large-scale single-cell RNA-seq data
Nucleic Acids Res. 2019 Dec 16;47(22):e143.

18. Weng X, Lovell JT, Schwartz SL, Changde Cheng, Haque T, Zhang L, Razzaque S, Juenger TE.
Complex interactions between day length and diurnal patterns of gene expression drive photoperiodic responses in a perennial C(4) grass
Plant Cell Environ. 2019 Jul;42(7):2165-2182.

17. Changde Cheng, Kirkpatrick M.
Inversions are bigger on the X chromosome
Mol Ecol. 2019 Mar;28(6):1238-1245.

πŸ„πŸ„πŸ„

2018

16. Changde Cheng, Tan JC, Hahn MW, Besansky NJ.
Systems genetic analysis of inversion polymorphisms in the malaria mosquito Anopheles gambiae
Proc Natl Acad Sci U S A. 2018 Jul 24;115(30):E7005-E7014.

15. Yang K, Blanco DB, Chen X, Dash P, Neale G, Rosencrance C, Easton J, Chen W, Changde Cheng, Dhungana Y, Kc A, Awad W, Guo XJ, Thomas PG, Chi H.
Metabolic signaling directs the reciprocal lineage decisions of Ξ±Ξ² and Ξ³Ξ΄ T cells
Sci Immunol. 2018 Jul 6;3(25).

14. Sardell JM, Changde Cheng, Dagilis AJ, Ishikawa A, Kitano J, Peichel CL, Kirkpatrick M.
Sex differences in recombination in sticklebacks
G3 (Bethesda) . 2018 May 31;8(6):1971-1983.

πŸ„πŸ„

2017

13. Changde Cheng, Kirkpatrick M.
Environmental plasticity in the intersexual correlation and sex bias of gene xxpression
J Hered. 2017 Oct 30;108(7):754-758.

12. Fontaine A, Filipovic I, Fansiri T, Hoffmann AA, Changde Cheng, Kirkpatrick M, RaΕ‘ic G, Lambrechts L.
Extensive genetic differentiation between homomorphic sex chromosomes in the sosquito vector, Aedes aegypti
Genome Biol Evol. 2017 Sep 1;9(9):2322-2335.

πŸ„πŸ„πŸ„

2016

11. Changde Cheng, Kirkpatrick M.
Sex-Specific selection and sex-biased gene expression in humans and flies
PLoS Genet. 2016 Sep;12(9):e1006170.

10. Uyhelji HA, Changde Cheng, Besansky NJ.
Transcriptomic differences between euryhaline and stenohaline malaria vector sibling species in response to salinity stress
Mol Ecol. 2016 May;25(10):2210-25.

9. Hall ABβˆ—, Papathanos PAβˆ—, Sharma Aβˆ—, Changde Cheng βˆ—, Akbari OS, Assour L, Bergman NH, Cagnetti A, Crisanti A, Dottorini T, Fiorentini E, Galizi R, Hnath J, Jiang X, Koren S, Nolan T, Radune D, Sharakhova MV, Steele A, Timoshevskiy VA, Windbichler N, Zhang S, Hahn MW, Phillippy AM, Emrich SJ, Sharakhov IV, Tu ZJ, Besansky NJ.
Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes
Proc Natl Acad Sci U S A. 2016 Apr 12;113(15):E2114-23.

πŸ„

2015

8. Smith HA, White BJ, Kundert P, Changde Cheng, Romero-Severson J, Andolfatto P, Besansky NJ.
Genome-wide QTL mapping of saltwater tolerance in sibling species of Anopheles (malaria vector) mosquitoes
Heredity (Edinb). 2015 Nov;115(5):471-9.

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2014

7. Cassone BJ, Kamdem C, Changde Cheng, Tan JC, Hahn MW, Costantini C, Besansky NJ.
Gene expression divergence between malaria vector sibling species Anopheles gambiae and An. coluzzii from rural and urban YaoundΓ© Cameroon
Mol Ecol. 2014 May;23(9):2242-59.

6. Reidenbach KR, Changde Cheng, Liu F, Liu C, Besansky NJ, Syed Z.
Cuticular differences associated with aridity acclimation in African malaria vectors carrying alternative arrangements of inversion 2La
Parasit Vectors. 2014 Apr 10;7:176.

πŸ„

2012

5. Changde Cheng, White BJ, Kamdem C, Mockaitis K, Costantini C, Hahn MW, Besansky NJ.
Ecological genomics of Anopheles gambiae along a latitudinal cline: a population-resequencing approach
Genetics. 2012 Apr;190(4):1417-32.

πŸ„πŸ„

2011

4. Cassone BJ, Molloy MJ, Changde Cheng, Tan JC, Hahn MW, Besansky NJ.
Divergent transcriptional response to thermal stress by Anopheles gambiae larvae carrying alternative arrangements of inversion 2La
Mol Ecol. 2011 Jun;20(12):2567-80.

3. White BJ, Lawniczak MK, Changde Cheng, Coulibaly MB, Wilson MD, Sagnon N, Costantini C, Simard F, Christophides GK, Besansky NJ.
Adaptive divergence between incipient species of Anopheles gambiae increases resistance to Plasmodium
Proc Natl Acad Sci U S A. 2011 Jan 4;108(1):244-9.

πŸ„

2010

2. White BJ, Changde Cheng, Simard F, Costantini C, Besansky NJ.
Genetic association of physically unlinked islands of genomic divergence in incipient species of Anopheles gambiae
Mol Ecol. 2010 Mar;19(5):925-39.

πŸ„

2009

1. White BJ, Changde Cheng, SangarΓ© D, Lobo NF, Collins FH, Besansky NJ.
The population genomics of trans-specific inversion polymorphisms in Anopheles gambiae
Genetics. 2009 Sep;183(1):275-88.

βˆ—: Co-first author

†: Co-corresponding author

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