Michael Deem

Michael Deem
Rice University · Department of Bioengineering

PhD

About

291
Publications
29,733
Reads
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8,591
Citations
Citations since 2016
77 Research Items
3943 Citations
20162017201820192020202120220100200300400500600
20162017201820192020202120220100200300400500600
20162017201820192020202120220100200300400500600
20162017201820192020202120220100200300400500600
Introduction
Michael Deem is the John W. Cox Professor at Rice University. Deem works in the Bioengineering and Physics & Astronomy Departments. His work is in the areas of Michael W. Deem works in the area of evolution, immunology, physiology, and materials. He has brought tools from statistical physics to bear on problems in these areas. Deem has developed methods to quantify vaccine effectiveness and antigenic distance for influenza, methods to sculpt the immune system to mitigate immunodominance in dengue fever, a hierarchical approach to protein molecular evolution, elucidated how static and dynamic measures of human brain connectivity predict complementary aspects of human cognitive performance, and developed the widely-used DIFFAX and ZEFSA and OSDA design methods for zeolites.
Education
June 1995 - June 1996
Harvard University
Field of study
August 1991 - May 1994
August 1987 - June 1991

Publications

Publications (291)
Article
Large single crystals of pure-silica STW-type molecular sieves are prepared using 1,2,3,4,5-pentamethylimidazolium (12345PMI) and 2-ethyl-1,3,4-trimethylimidazolium (2E134TMI) as organic structure-directing agents (OSDAs) and α-amino acid additives. The effects of the amount and type of amino acid on the crystallization of pure-silica STW materials...
Article
Full-text available
Industrial production of ethylene entails a costly separation from the ethane by-product, and this separation is the dominant consumer of energy in the process. Zeolites have been proposed as a next generation material for this separation process, and a molecular screen of all known zeolites has revealed several promising candidate materials. None...
Article
Full-text available
An increasing number of newly synthesized materials have been found to be previously present in databases of predicted porous materials. This has been observed not only for zeolites, but also for other inorganic materials and for MOFs. We here quantify the number of synthesized zeolites that are present in a large database of predicted zeolite stru...
Article
The cover feature shows organic structure‐directing agents that have been designed by using a de novo algorithm to control the synthesis of four zeolites selected for their applications in carbon capture and storage. Specifically, a molecule designed to direct the synthesis of the zeolite PCOD8186909 is shown here. These directing agents simplify s...
Article
Full-text available
Zeolites more efficient at carbon capture than scrubbing with aqueous monoethanolamine, and the best OSDAs designed for the synthesis of each.
Article
Full-text available
One strategy to mitigate global warming is carbon capture and sequestration. Membrane separation is one promising approach to separation of CO2 from feed streams. Here we report the investigation of four zeolites that have been predicted to be effective at separating CO2 from methane, but which have not to date been synthesized experimentally as me...
Article
Full-text available
The modular binding sites on the influenza A(H3N2) hemagglutinin protein are under significant pressure to acquire mutations in order to evade human antibody recognition. Analysis of these hemagglutinin epitopes in the strains circulating during 2017/18 and early 2018/19 identified the emergence of a new antigenic cluster that has grown from 4% of...
Article
We have designed chiral organic structure directing agents (OSDAs) to direct the formation of enantiomerically enriched zeolite BEA. The in silico design was a combination of a multi‐objective scoring function with exhaustive and stochastic virtual combinatorial chemistry and de novo design algorithms. Importantly, the algorithms used directly cons...
Article
Full-text available
Significance Zeolite beta is one of the top-six zeolites of commercial interest. It has been synthesized through the use of a number of organic structure directing agents (OSDAs). Pure zeolite beta A has not yet been synthesized, nor has chiral zeolite beta A. We here report a machine-learning strategy to aid the computational design of chemically...
Article
Full-text available
Zeolite beta is a crystalline material with layer-type faulting.
Article
Full-text available
We have applied in silico materials design in an effort to design chiral organic structure directing agents (OSDAs) for the synthesis of enantiomerically enriched STW zeolite. To do so, we have used both exhaustive virtual screening of a limited set of symmetrical imidazolium dimers and a multi-objective genetic algorithm to effectively search a la...
Article
Full-text available
Data
Representative collective dissemination-associated gene networks for (A) epithelial cell lines and (B) mesenchymal cell lines from the study by Grosse-Wilde et al. (39), and for (C) tumor samples from IBC patients and (D) tumor samples from non-IBC breast cancer patients from the study by Iwamoto et al. (45). The nodes are collective dissemination-...
Data
Normalized CCC of different gene sets calculated for different phenotypic groups using the resistance distance (2). Normalized CCC for 13 epithelial (E) and 11 mesenchymal cell lines from the study by Grosse-Wilde et al. (39), calculated using (A) collective dissemination-associated genes and (B) IBC-associated genes. Normalized CCC for 11 epitheli...
Data
Gene set enrichment analysis on gene expression data for tumor samples from IBC and non-IBC breast cancer patients from the study by Iwamoto et al. (45) using (A) genes upregulated in cells in circulating tumor cell clusters, and (B) genes downregulated in cells in circulating tumor cell clusters. Genes are ordered from left to right in decreasing...
Data
Normalized CCC for estrogen-receptor-positive (ER+) breast cancer patients with metastatic relapse within a 30-month period posttreatment (T < 30; n = 36) or between 30 and 60 months posttreatment (T ≥ 30; n = 44): (A) normalized CCC of the collective dissemination-associated gene network and (B) normalized CCC of the IBC-associated gene network. G...
Data
Histogram of p-values calculated for the null hypothesis that the normalized CCC of a randomly generated gene set is higher in tumor samples from non-IBC breast cancer patients as compared to samples from IBC patients. Gene expression data from the study by Iwamoto et al. (45). Normalized CCC was calculated for 100 randomly generated gene sets cons...
Data
Normalized CCC for breast cancer patients with different estrogen-receptor statuses. Patients with estrogen-receptor-positive status: (A) normalized CCC of the collective dissemination-associated gene network and (B) normalized CCC of the IBC-associated gene network. In this group, there were 129 patients with no relapse during the 5-year follow-up...
Article
Full-text available
The standard genetic code is well known to be optimized for minimizing the phenotypic effects of single nucleotide substitutions, a property that was likely selected for during the emergence of a universal code. Given the fitness advantage afforded by high standing genetic diversity in a population in a dynamic environment, it is possible that sele...
Article
Full-text available
We predict vaccine efficacy with a measure of antigenic distance between influenza A(H3N2) and candidate vaccine viruses based on amino acid substitutions in the dominant epitopes. In 2016-2017, our model predicts 19% efficacy compared to 20% observed. This tool assists candidate vaccine selection by predicting human protection against circulating...
Preprint
Full-text available
We predict vaccine efficacy with a measure of antigenic distance between influenza A(H3N2) and candidate vaccine viruses based on amino acid substitutions in the dominant epitopes. In 2016-2017, our model predicts 19% efficacy compared to 20% observed. This tool assists candidate vaccine selection by predicting human protection against circulating...
Article
Full-text available
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) constitute a multi-functional, constantly evolving immune system in bacteria and archaea cells. A heritable, molecular memory is generated of phage, plasmids, or other mobile genetic elements that attempt to attack the cell. This memory is used t...
Preprint
Full-text available
Abnormal metabolism is an emerging hallmark of cancer. Cancer cells utilize both aerobic glycolysis and oxidative phosphorylation (OXPHOS) for energy production and biomass synthesis. Understanding the metabolic reprogramming in cancer can help design therapies to target metabolism and thereby to improve prognosis. We have previously argued that mo...
Article
Full-text available
Next generation sequencing (NGS) has revolutionized life sciences research. However, GC bias and costly, time-intensive library preparation make NGS an ill fit for increasing sequencing demands in the clinic. A new class of third-generation sequencing platforms has arrived to meet this need, capable of directly measuring DNA and RNA sequences at th...
Data
Part of an IGV view of mapping. The sequence at the bottom is the reference sequence. Capital letters show the mismatch sites, black horizontal lines indicate deletion errors, and purple vertical lines denote insertions. (TIF)
Data
Error distribution for all unique mapped reads. Most of those reads have zero or one error. (TIF)
Data
Description of imaging analysis process. (DOCX)
Data
Imaging processing flow chart. (TIF)
Preprint
Full-text available
The standard genetic code is well known to be optimized for minimizing the phenotypic effects of single nucleotide substitutions, a property that was likely selected for during the emergence of a universal code. Given the fitness advantage afforded by high standing genetic diversity in a population in a dynamic environment, it is possible that sele...
Preprint
Full-text available
In cognitive network neuroscience, the connectivity and community structure of the brain network is related to cognition. Much of this research has focused on two measures of connectivity – modularity and flexibility – which frequently have been examined in isolation. By using resting state fMRI data from 52 young adults, we investigate the relatio...
Preprint
Full-text available
CRISPR is a newly discovered prokaryotic immune system. Bacteria and archaea with this system incorporate genetic material from invading viruses into their genomes, providing protection against future infection by similar viruses. The conditions for coexistence of prokaryots and viruses is an interesting problem in evolutionary biology. In this wor...
Preprint
Full-text available
Recent work in cognitive neuroscience has focused on analyzing the brain as a network, rather than as a collection of independent regions. Prior studies taking this approach have found that individual differences in the degree of modularity of the brain network relate to performance on cognitive tasks. However, inconsistent results concerning the d...
Article
Full-text available
Abnormal metabolism is an emerging hallmark of cancer. Cancer cells utilize both aerobic glycolysis and oxidative phosphorylation (OXPHOS) for energy production and biomass synthesis. Understanding the metabolic reprogramming in cancer can help design therapies to target metabolism and thereby to improve prognosis. We have previously argued that mo...
Article
Full-text available
Clusters of circulating tumor cells (CTCs), although rare, may account for more than 95% of metastases. Inflammatory breast cancer (IBC) is a highly aggressive subtype that chiefly metastasizes via CTC clusters. Theory suggests that physical systems with hierarchical organization tend to be more adaptable due to their ability to efficiently span th...
Article
Full-text available
CRISPR-Cas is a genetic adaptive immune system unique to prokaryotic cells used to combat phage and plasmid threats. The host cell adapts by incorporating DNA sequences from invading phages or plasmids into its CRISPR locus as spacers. These spacers are expressed as mobile surveillance RNAs that direct CRISPR-associated (Cas) proteins to protect ag...
Preprint
Full-text available
The demand of non-invasive prenatal testing for autosomal aneuploidy using cell-free fetal DNA (cffDNA) in maternal plasma is a highly sought-after diagnostic, with a rapidly growing market. Current approaches developed by next generation sequencing (NGS) need PCR amplifcation during sample preparation, which results in amplification bias in GC-ric...
Preprint
Background Clusters of circulating tumor cells (CTCs), despite being rare, may account for more than 95% of metastases. Cells in these clusters do not undergo a complete epithelial-to-mesenchymal transition (EMT) but retain some epithelial traits as compared to individually disseminating tumor cells. Determinants of single cell dissemination versus...
Article
Full-text available
Recent work in cognitive neuroscience has focused on analyzing the brain as a network, rather than as a collection of independent regions. Prior studies taking this approach have found that individual differences in the degree of modularity of the brain network relate to performance on cognitive tasks. However, inconsistent results concerning the d...
Article
Full-text available
In cognitive network neuroscience, the connectivity and community structure of the brain network is related to measures of cognitive performance, like attention and memory. Research in this emerging discipline has largely focused on two measures of connectivity—modularity and flexibility—which, for the most part, have been examined in isolation. Th...
Chapter
Full-text available
CRISPR-Cas is a genetic adaptive immune system unique to prokaryotic cells used to combat phage and plasmid threats. The host cell adapts by incorporating DNA sequences from invading phages or plasmids into its CRISPR locus as spacers. These spacers are expressed as mobile surveillance RNAs that direct CRISPR-associated (Cas) proteins to protect ag...
Preprint
Full-text available
Next generation sequencing (NGS) has revolutionized life sciences research. Recently, a new class of third-generation sequencing platforms has arrived to meet increasing demands in the clinic, capable of directly measuring DNA and RNA sequences at the single-molecule level without amplification. Here, we use the new GenoCare single molecule sequenc...
Preprint
Third generation sequencing is a direct measurement of DNA/RNA sequences at the single molecule level without amplification. In this study, we report sequencing of the genome of the M13 virus by a new single molecule sequencing platform. Our platform detects single molecule fluorescence by the total internal reflection microscope technique, with se...
Article
Full-text available
Significance Zeolites and zeolite-like molecular sieves are used as adsorbents and heterogeneous catalysts to prepare a wide variety of products ranging from gasoline to monomers for polymers such as polyethylene terephthalate, which is used in plastic bottles. Pharmaceuticals, pesticides, fragrances, and components in food can contain chiral cente...
Article
Full-text available
CRISPR is a newly discovered prokaryotic immune system. Bacteria and archaea with this system incorporate genetic material from invading viruses into their genomes, providing protection against future infection by similar viruses. The condition for coexistence of prokaryots and viruses is an interesting problem in evolutionary biology. In this work...
Article
Full-text available
Type 1 diabetes mellitus (T1D) is an immune-mediated disease. The autoreactive T cells in T1D patients attack and destroy their own pancreatic cells. In order to systematically investigate the potential autoreactive T cell receptors (TCRs), we used a high-throughput immune repertoire sequencing technique to profile the spectrum of TCRs in individua...
Article
Full-text available
Migration is a key mechanism for expansion of communities. In spatially heterogeneous environments, rapidly gaining knowledge about the local environment is key to the evolutionary success of a migrating population. For historical human migration, environmental heterogeneity was naturally asymmetric in the north-south (NS) and east-west (EW) direct...
Data
VJ recombination clustering The T1D patients are grouped into a cluster, except sample P6. TRBV9–TRBJ2-7 combination is significantly more used in CD4+ cells of T1D patients (P = 0.031; A), while TRBV15–TRBJ2-5 is significantly more used in CD8+ cells of T1D patients (P = 0.026; B). Statistical analysis was performed using student t-test. The frequ...
Data
Shared clones between T1D, T2D and control samples The complete list of shared HECs is shown in the heatmap. Orange and green represent HECs (⩾1% of total reads) and LECs (<1% of total reads), respectively, while gray represents sequences not found in the sample. HEC, highly-expanded clone; LEC, lowly-expanded clone; T1D, type 1 diabetes mellitus;...
Data
Clinical information for subjects included
Data
Primer sequences for amplification of human TCR CDR3
Data
Clone distribution in diabetic patients and nondiabetic controls A. Clone distribution in normalized sample size. We randomly sampled sequencing reads into the same size (50,000 reads) to reduce the bias induced from sequencing depth. Each data point represents a CDR3 clone. Y axis shows the frequency of each clone observed in different samples, ex...
Data
The VJ combination usage patterns The VJ combination of individual samples is analyzed in the 2-dimensional plot. The X and Y axes list all possible V gene and J usages, respectively, while each point in the 2-dimensional space represents a unique VJ combination. The size of the sphere at each point represents the number of reads that match to a pa...
Data
TRBV gene usage patterns in CD4 and CD8 T cells The white, gray and black bars represent the control, T2D and T1D samples. The bar charts show the percentage of each TRBV used in CD4+ (A) and CD8+ T (C) cells from each group on average. To find out TRBV genes that are significantly highly expressed in CD4+ (B) and CD8+ T (D) cells from T1D samples,...
Data
High-resolution HLA genotyping for 6 T1D patients
Article
Full-text available
Zeolites, having widespread applications in chemical industries, are often synthesized using organic templates. These can be cost-prohibitive, motivating investigations into their role in promoting crystallization. Herein, the relationship between framework structure, chemical composition, synthesis conditions and the conformation of the occluded,...