Changde Cheng

Changde Cheng

Senior Bioinformatics Research Scientist

St. Jude Children's Research Hospital

Welcome

As a research scientist at St. Jude, I work on machine learning with applications in cancer research (single-cell sequencing, spatial genomics, and multi-omics).

I led research projects on evolutionary/population genomics at the University of Texas, Austin before joining St. Jude. I worked on infectious diseases and genomics at Notre Dame, and I did statistical modeling at UCLA.

I read Balzac or walk my dog when I am not working.

Interests
  • Machine Learning
  • Cancer
  • Evolution
  • Population Genetics
  • Infectious Diseases
Education

  • PhD in Genetics/Genomics

    University of Notre Dame

  • MA in Ecology & Evolutionary Biology (completed coursework in Biomath, and Biostatistics)

    University of California, Los Angeles

  • BS in Cell Biology and Genetics

    Peking University

Working Papers

Preprints / Conference Submissions

4) Genome-wide mapping of oncogenic pathways and genetic modifiers of chemotherapy using a high-risk hepatoblastoma genetic model
Genome-wide mapping of oncogenic pathways.
4) Genome-wide mapping of oncogenic pathways and genetic modifiers of chemotherapy using a high-risk hepatoblastoma genetic model
3) Innate T cells regulate early inflammation and neurological outcomes after cardiac arrest and resuscitation
Among patients hospitalized for cardiac arrest (CA), most deaths are driven by neurological injury. Despite its clinical importance, there are no effective pharmacological therapies targeting post-CA neurological injury. In single-cell RNA-sequencing of peripheral blood mononuclear cells …
3) Innate T cells regulate early inflammation and neurological outcomes after cardiac arrest and resuscitation
2) Single-cell RNA-sequencing reveals hyperacute NK cell and Monocyte states correlating with poor neurological outcomes after cardiac arrest
We determined the immunological network after clinical CA and identified cell states correlating with poor neurological outcomes using single-cell RNA-sequencing..
2) Single-cell RNA-sequencing reveals hyperacute NK cell and Monocyte states correlating with poor neurological outcomes after cardiac arrest
1) Sexually antagonistic selection and sex chromosome evolution in Sticklebacks
A presentation submitted to the 2017 Society for Molecular Biology & Evolution meeting at Austin.
1) Sexually antagonistic selection and sex chromosome evolution in Sticklebacks

Featured Publications

Molecular evolution and the decline of purifying selection with age
Life history theory predicts that the intensity of selection declines with age, and this trend should impact how genes expressed at …
C. Cheng, M. Kirkpatrick
PDF Cite Slides DOI
Molecular evolution and the decline of purifying selection with age
Predicting multivariate responses of sexual dimorphism to direct and indirect selection
Sexual dimorphism is often assumed to result from balancing the strength of antagonistic selection in favor of dimorphism against the …
C. Cheng, D. Houle
PDF Cite DOI
Predicting multivariate responses of sexual dimorphism to direct and indirect selection
Systems genetic analysis of inversion polymorphisms in the malaria mosquito Anopheles gambiae
Inversion polymorphisms in the African malaria vector Anopheles gambiae segregate along climatic gradients of aridity. Despite indirect …
C. Cheng, J. C. Tan, M. W. Hahn, N. J. Besansky
PDF Cite DOI
Systems genetic analysis of inversion polymorphisms in the malaria mosquito Anopheles gambiae
Ecological genomics of Anopheles gambiae along a latitudinal cline: a population-resequencing approach
The association between fitness-related phenotypic traits and an environmental gradient offers one of the best opportunities to study …
C. Cheng, B. J. White, C. Kamdem, K. Mockaitis, C. Costantini, M. W. Hahn, N. J. Besansky
PDF Cite DOI
Ecological genomics of Anopheles gambiae along a latitudinal cline: a population-resequencing approach
Genetic association of physically unlinked islands of genomic divergence in incipient species of Anopheles gambiae
Previous efforts to uncover the genetic underpinnings of ongoing ecological speciation of the M and S forms of the African malaria …
B. J. White, C. Cheng, F. Simard, C. Costantini, N. J. Besansky
PDF Cite DOI
Genetic association of physically unlinked islands of genomic divergence in incipient species of Anopheles gambiae

Original Articles

Identification and targeting of a HES1‐YAP1‐CDKN1C functional interaction in fusion‐negative rhabdomyosarcoma
Rhabdomyosarcoma (RMS), a cancer characterized by features of skeletal muscle, is the most common soft-tissue sarcoma of childhood. …
Alexander R Kovach, Kristianne M Oristian, David G Kirsch, Rex C Bentley, Changde Cheng, Xiang Chen, Po‐Han Chen, Jen‐Tsan Ashley Chi, Corinne M Linardic
PDF DOI
Identification and targeting of a HES1‐YAP1‐CDKN1C functional interaction in fusion‐negative rhabdomyosarcoma
Predicting the evolution of sexual dimorphism in gene expression
Sexual dimorphism in gene expression is likely to be the underlying source of dimorphism in a variety of traits. Many analyses …
D. Houle, C. Cheng
PDF Cite DOI
Predicting the evolution of sexual dimorphism in gene expression
Complex interactions between day length and diurnal patterns of gene expression drive photoperiodic responses in a perennial C4 grass
Photoperiod is a key environmental cue affecting flowering and biomass traits in plants. Key components of the photoperiodic flowering …
X. Weng, J. T. Lovell, S. L. Schwartz, C. Cheng, T. Haque, L. Zhang, S. Razzaque, T. E. Juenger
PDF Cite DOI
Complex interactions between day length and diurnal patterns of gene expression drive photoperiodic responses in a perennial C4 grass
Inversions are bigger on the X chromosome
In many insects, X-linked inversions fix at a higher rate and are much less polymorphic than autosomal inversions. Here, we report that …
C. Cheng, M. Kirkpatrick
PDF Cite Slides DOI
Inversions are bigger on the X chromosome
Latent cellular analysis robustly reveals subtle diversity in large-scale single-cell RNA-seq data
Single-cell RNA sequencing (scRNA-seq) is a powerful tool for characterizing the cell-to-cell variation and cellular dynamics in …
C. Cheng, J. Easton, C. Rosencrance, Y. Li, B. Ju, J. Williams, H. L. Mulder, Y. Pang, W. Chen, X. Chen
PDF Cite DOI
Latent cellular analysis robustly reveals subtle diversity in large-scale single-cell RNA-seq data
Metabolic signaling directs the reciprocal lineage decisions of alphabeta and gammadelta T cells
The interaction between extrinsic factors and intrinsic signal strength governs thymocyte development, but the mechanisms linking them …
K. Yang, D. B. Blanco, X. Chen, P. Dash, G. Neale, C. Rosencrance, J. Easton, W. Chen, C. Cheng, Y. Dhungana, A. Kc, W. Awad, X. J. Guo, P. G. Thomas, H. Chi
PDF Cite DOI
Metabolic signaling directs the reciprocal lineage decisions of alphabeta and gammadelta T cells
Sex differences in recombination in sticklebacks
Recombination often differs markedly between males and females. Here we present the first analysis of sex-specific recombination in …
J. M. Sardell, C. Cheng, A. J. Dagilis, A. Ishikawa, J. Kitano, C. L. Peichel, M. Kirkpatrick
PDF Cite DOI
Sex differences in recombination in sticklebacks
Environmental plasticity in the intersexual correlation and sex bias of gene expression
Intersexual genetic correlations are expected to constrain the evolution of sexual dimorphic traits, including the degree of sex-biased …
C. Cheng, M. Kirkpatrick
PDF Cite DOI
Environmental plasticity in the intersexual correlation and sex bias of gene expression
Extensive genetic differentiation between homomorphic sex chromosomes in the mosquito vector, Aedes aegypti
Mechanisms and evolutionary dynamics of sex-determination systems are of particular interest in insect vectors of human pathogens like …
A. Fontaine, I. Filipovic, T. Fansiri, A. A. Hoffmann, C. Cheng, M. Kirkpatrick, G. Rasic, L. Lambrechts
PDF Cite DOI
Extensive genetic differentiation between homomorphic sex chromosomes in the mosquito vector, Aedes aegypti
Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes
Y chromosomes control essential male functions in many species, including sex determination and fertility. However, because of …
A. B. Hall, P. A. Papathanos, A. Sharma, C. Cheng, O. S. Akbari, L. Assour, N. H. Bergman, A. Cagnetti, A. Crisanti, T. Dottorini, E. Fiorentini, R. Galizi, J. Hnath, X. Jiang, S. Koren, T. Nolan, D. Radune, M. V. Sharakhova, A. Steele, V. A. Timoshevskiy, N. Windbichler, S. Zhang, M. W. Hahn, A. M. Phillippy, S. J. Emrich, I. V. Sharakhov, Z. J. Tu, N. J. Besansky
PDF Cite DOI
Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes
Sex-specific selection and sex-biased gene expression in humans and flies
Sexual dimorphism results from sex-biased gene expression, which evolves when selection acts differently on males and females. While …
C. Cheng, M. Kirkpatrick
PDF Cite DOI
Sex-specific selection and sex-biased gene expression in humans and flies
Transcriptomic differences between euryhaline and stenohaline malaria vector sibling species in response to salinity stress
Evolution of osmoregulatory systems is a key factor in the transition of species between fresh- and saltwater habitats. Anopheles …
H. A. Uyhelji, C. Cheng, N. J. Besansky
PDF Cite DOI
Transcriptomic differences between euryhaline and stenohaline malaria vector sibling species in response to salinity stress
Genome-wide QTL mapping of saltwater tolerance in sibling species of Anopheles (malaria vector) mosquitoes
Although freshwater (FW) is the ancestral habitat for larval mosquitoes, multiple species independently evolved the ability to survive …
H. A. Smith, B. J. White, P. Kundert, C. Cheng, J. Romero-Severson, P. Andolfatto, N. J. Besansky
PDF Cite DOI
Genome-wide QTL mapping of saltwater tolerance in sibling species of Anopheles (malaria vector) mosquitoes
Cuticular differences associated with aridity acclimation in African malaria vectors carrying alternative arrangements of inversion 2La
Principal malaria vectors in Africa, An. gambiae and An. coluzzii, share an inversion polymorphism on the left arm of chromosome 2 …
K. R. Reidenbach, C. Cheng, F. Liu, C. Liu, N. J. Besansky, Z. Syed
PDF Cite DOI
Cuticular differences associated with aridity acclimation in African malaria vectors carrying alternative arrangements of inversion 2La
Gene expression divergence between malaria vector sibling species Anopheles gambiae and An. coluzzii from rural and urban Yaounde Cameroon
Divergent selection based on aquatic larval ecology is a likely factor in the recent isolation of two broadly sympatric and …
B. J. Cassone, C. Kamdem, C. Cheng, J. C. Tan, M. W. Hahn, C. Costantini, N. J. Besansky
PDF Cite DOI
Gene expression divergence between malaria vector sibling species Anopheles gambiae and An. coluzzii from rural and urban Yaounde Cameroon
Adaptive divergence between incipient species of Anopheles gambiae increases resistance to Plasmodium
The African malaria mosquito Anopheles gambiae is diversifying into ecotypes known as M and S forms. This process is thought to be …
B. J. White, M. K. Lawniczak, C. Cheng, M. B. Coulibaly, M. D. Wilson, N. Sagnon, C. Costantini, F. Simard, G. K. Christophides, N. J. Besansky
PDF Cite DOI
Adaptive divergence between incipient species of Anopheles gambiae increases resistance to Plasmodium
Divergent transcriptional response to thermal stress by Anopheles gambiae larvae carrying alternative arrangements of inversion 2La
The African malaria mosquito Anopheles gambiae is polymorphic for chromosomal inversion 2La, whose frequency strongly correlates with …
B. J. Cassone, M. J. Molloy, C. Cheng, J. C. Tan, M. W. Hahn, N. J. Besansky
PDF Cite DOI
Divergent transcriptional response to thermal stress by Anopheles gambiae larvae carrying alternative arrangements of inversion 2La
The population genomics of trans-specific inversion polymorphisms in Anopheles gambiae
In the malaria mosquito Anopheles gambiae polymorphic chromosomal inversions may play an important role in adaptation to environmental …
B. J. White, C. Cheng, D. Sangare, N. F. Lobo, F. H. Collins, N. J. Besansky
PDF Cite DOI
The population genomics of trans-specific inversion polymorphisms in Anopheles gambiae

Slides

Molecular Evolution and the Decline of Purifying Selection with Age
A talk at Evolution 2021.
Jun 1, 2021 1:00 PM — 3:00 PM
Slides
Bigger on the X - The effect of size on the evolution of chromosome inversion
A talk at Evolution 2016.
Jun 13, 2016 1:00 PM — 3:00 PM
Slides