Yawen Zou | The Chinese University of Hong Kong, Shenzhen (original) (raw)
Papers by Yawen Zou
PLOS ONE, 2018
Systems biology is a discipline that studies biological systems from a holistic and interdiscipli... more Systems biology is a discipline that studies biological systems from a holistic and interdisciplinary perspective. It brings together biologists, mathematicians, computer scientists, physicists, and engineers, so it has both biology-oriented components and systems-oriented components. We applied several computational tools to analyze the bibliographic information of published articles in systems biology to answer the question: Did the research topics of systems biology become more biology-oriented or more systems-oriented from 1992 to 2013? We analyzed the metadata of 9923 articles on systems biology from the Web of Science database. We identified the most highly cited 330 references using computational tools and through close reading we divided them into nine categories of research types in systems biology. Interestingly, we found that articles in one category, namely, systems biology's applications in medical research, increased tremendously. This finding was corroborated by computational analysis of the abstracts, which also suggested that the percentages of topics on vaccines, diseases, drugs and cancers increased over time. In addition, we analyzed the institutional backgrounds of the corresponding authors of those 9923 articles and identified the most highly cited 330 authors over time. We found that before the mid-1990s, systems-oriented scientists had made the most referenced contributions. However, in recent years, researchers from biology-oriented institutions not only represented a huge percentage of the total number of researchers, but also had made the most referenced contributions. Notably, interdisciplinary institutions only produced a small percentage of researchers, but had made disproportionate contributions to this field.
Systems biology is a discipline that studies biological systems from a holistic and interdisci-pl... more Systems biology is a discipline that studies biological systems from a holistic and interdisci-plinary perspective. It brings together biologists, mathematicians, computer scientists, physicists , and engineers, so it has both biology-oriented components and systems-oriented components. We applied several computational tools to analyze the bibliographic information of published articles in systems biology to answer the question: Did the research topics of systems biology become more biology-oriented or more systems-oriented from 1992 to 2013? We analyzed the metadata of 9923 articles on systems biology from the Web of Science database. We identified the most highly cited 330 references using computational tools and through close reading we divided them into nine categories of research types in systems biology. Interestingly, we found that articles in one category, namely, systems biol-ogy's applications in medical research, increased tremendously. This finding was corroborated by computational analysis of the abstracts, which also suggested that the percentages of topics on vaccines, diseases, drugs and cancers increased over time. In addition, we analyzed the institutional backgrounds of the corresponding authors of those 9923 articles and identified the most highly cited 330 authors over time. We found that before the mid-1990s, systems-oriented scientists had made the most referenced contributions. However, in recent years, researchers from biology-oriented institutions not only represented a huge percentage of the total number of researchers, but also had made the most referenced contributions. Notably, interdisciplinary institutions only produced a small percentage of researchers, but had made disproportionate contributions to this field.
Gavin de Beer (1899–1972) was an evolutionary embryologist considered by many as a forerunner of ... more Gavin de Beer (1899–1972) was an evolutionary embryologist considered by many as a forerunner of modern evolutionary developmental biology (evo-devo). This entry discusses de Beer’s works with a special focus on his contributions to evo-devo. De Beer was trained in zoology and later became interested in com- parative and evolutionary embryology. De Beer joined the attack on Ernst Haeckel’s biogenetic law and argued that ontogeny did not recapitulate phylog- eny, but ontogeny caused phylogeny instead. Influenced by the advancements of the Modern Synthesis and the rise of genetics, de Beer advocated for the integration of embryology, heredity, and evolution and emphasized on the impor- tance of embryology in evolutionary theory in many of his writings. Although de Beer failed to make a significant impact on the Modern Synthesis, his work on heterochrony influenced modern evo-devo biologists such as Stephen Jay Gould, and his views on homology are still revisited today.
Systems biology is a new field of biology that has great implications for agriculture , medicine,... more Systems biology is a new field of biology that has great implications for agriculture , medicine, and sustainability. In this article we explore the contributions of Chinese authors to systems biology through analysis of the metadata of more than 9000 articles on systems biology. Our big-data approach includes scientometric analysis, GIS analysis, co-word network analysis, and comparative analysis. By 2013 China has become second in the number of publications on systems biology. Similar to previous studies on Chinese science, we find an unequal distribution of research power in China, favoring big cities and coastal cities. Overall, 75% of the articles in systems biology were published by scholars from universities, 15% by scholars from the Chinese of Academy of Sciences institutions, and 9% from other institutions. Many Chinese scholars' research topics are similar to those in the US, Japan, and Germany, but one salient difference is that traditional Chinese medicine is an important topic among Chinese systems biologists. 25% of Chinese systems biologists cooperate with scientists abroad, suggesting that they take advantage of the opening-up policy. From the year 2011–2013, the average impact factor of the journals that Chinese scholars publish in is generally lower than that of their counterparts in the US, but the trend points to a gradual increase in impact.
Paul M. Brakefield and his research team in Leiden, the Netherlands, examined the development, pl... more Paul M. Brakefield and his research team in Leiden, the Netherlands, examined the development, plasticity, and evolution of butterfly eyespot patterns, and published their findings in Nature in 1996. Eyespots are eye-shaped color patterns that appear on the wings of some butterflies and birds as well as on the skin of some fish and reptiles. In butterflies, such as the peacock butterfly (Aglais io), the eyespots resemble the eyes of birds and help butterflies deter potential predators. Brakefield's research team described the stages through which eyespots develop, identified the genes and environmental signals that affect eye-spot appearance in some species, and demonstrated that small genetic variations can change butterfly eyespot color and shape. The research focused on a few butterfly species, but it contributed to more general claims of how the environment may affect the development of coloration and how specific color patterns may have evolved.
August Friedrich Leopold Weismann studied how the traits of organisms developed and evolved in a ... more August Friedrich Leopold Weismann studied how the traits of organisms developed and evolved in a variety of organisms, mostly insects and aquatic animals, in Germany in the
late nineteenth and early twentieth centuries. Weismann proposed the theory of the continuity of germ-plasm, a theory of heredity. Weismann postulated that germ-plasm was the hereditary material in cells, and parents transmitted to their offspring only the germ-plasm present in germ-cells (sperm and egg cells) rather than somatic or body cells. Weismann also promoted Charles Darwin's 1859 theory of the evolution of species. Weismann argued that only changes to the germ cells, and not body cells, could be inherited, a theory that
influenced theories of heredity throughout later centuries.
Green fluorescent protein (GFP) is a protein in the jellyfish Aequorea Victoria that exhibits gre... more Green fluorescent protein (GFP) is a protein in the jellyfish Aequorea Victoria that exhibits green fluorescence when exposed to light. The protein has 238 amino acids, three of them (Numbers 65 to 67) form a structure that emits visible green fluorescent light. In the jellyfish, GFP interacts with another protein, called aequorin, which emits blue light when added with calcium. Biologists use GFP to study cells in embryos and fetuses during developmental processes.
In 1868 in England, Charles Darwin proposed his pangenesis theory to describe the units of inher... more In 1868 in England, Charles Darwin proposed his pangenesis theory to describe the units of inheritance between parents and offspring and the processes by which those units control development in offspring. Darwin coined the concept of gemmules, which he said referred to hypothesized minute particles of inheritance thrown off by all cells of the body. The theory suggested that an organism's environment could modify the gemmules in any parts of the body, and that these modified gemmules would congregate in the reproductive organs of parents to be passed on to their offspring. Darwin's theory of pangenesis gradually lost popularity in the 1890s when biologists increasingly abandoned the theory of inheritance of acquired characteristics (IAC), on which the pangenesis theory partially relied. Around the turn of the twentieth century, biologists replaced the theory of pangenesis with germ plasm theory and then with chromosomal theories of inheritance, and they replaced the concept of gemmules with that of genes.
Dizhou Tong, also called Ti Chou Tung, studied marine animals and helped introduce and organize e... more Dizhou Tong, also called Ti Chou Tung, studied marine animals and helped introduce and organize experimental embryology in China during the twentieth century. He introduced cellular nuclear transfer technology to the Chinese biological community, developed methods
to clone organisms from many marine species, and investigated the role of cytoplasm in early development. Tong's administrative and scientific leadership in the fields of marine, cellular, and developmental biology contributed to China's experimental embryology research programs.
Friedrich Leopold August Weismann published Das Keimplasma: eine Theorie der Vererbung (The Germ-... more Friedrich Leopold August Weismann published Das Keimplasma: eine Theorie der Vererbung (The Germ-Plasm: a Theory of Heredity, hereafter The Germ-Plasm) while
working at the University of Freiburg in Freiburg, Germany in 1892. William N. Parker, a professor in the University College of South Wales and Monmouthshire in Cardiff, UK,
translated The Germ-Plasm into English in 1893. In The Germ-Plasm, Weismann proposed a theory of heredity based on the concept of the germ plasm, a substance in the germ cell that
carries hereditary information. The Germ-Plasm compiled Weismann's theoretical work and analyses of other biologists' experimental work in the 1880s, and it provided a framework to study development, evolution [7] and heredity. Weismann anticipated that the germ-plasm theory would enable researchers to investigate the functions and material of hereditary substances.
PLOS ONE, 2018
Systems biology is a discipline that studies biological systems from a holistic and interdiscipli... more Systems biology is a discipline that studies biological systems from a holistic and interdisciplinary perspective. It brings together biologists, mathematicians, computer scientists, physicists, and engineers, so it has both biology-oriented components and systems-oriented components. We applied several computational tools to analyze the bibliographic information of published articles in systems biology to answer the question: Did the research topics of systems biology become more biology-oriented or more systems-oriented from 1992 to 2013? We analyzed the metadata of 9923 articles on systems biology from the Web of Science database. We identified the most highly cited 330 references using computational tools and through close reading we divided them into nine categories of research types in systems biology. Interestingly, we found that articles in one category, namely, systems biology's applications in medical research, increased tremendously. This finding was corroborated by computational analysis of the abstracts, which also suggested that the percentages of topics on vaccines, diseases, drugs and cancers increased over time. In addition, we analyzed the institutional backgrounds of the corresponding authors of those 9923 articles and identified the most highly cited 330 authors over time. We found that before the mid-1990s, systems-oriented scientists had made the most referenced contributions. However, in recent years, researchers from biology-oriented institutions not only represented a huge percentage of the total number of researchers, but also had made the most referenced contributions. Notably, interdisciplinary institutions only produced a small percentage of researchers, but had made disproportionate contributions to this field.
Systems biology is a discipline that studies biological systems from a holistic and interdisci-pl... more Systems biology is a discipline that studies biological systems from a holistic and interdisci-plinary perspective. It brings together biologists, mathematicians, computer scientists, physicists , and engineers, so it has both biology-oriented components and systems-oriented components. We applied several computational tools to analyze the bibliographic information of published articles in systems biology to answer the question: Did the research topics of systems biology become more biology-oriented or more systems-oriented from 1992 to 2013? We analyzed the metadata of 9923 articles on systems biology from the Web of Science database. We identified the most highly cited 330 references using computational tools and through close reading we divided them into nine categories of research types in systems biology. Interestingly, we found that articles in one category, namely, systems biol-ogy's applications in medical research, increased tremendously. This finding was corroborated by computational analysis of the abstracts, which also suggested that the percentages of topics on vaccines, diseases, drugs and cancers increased over time. In addition, we analyzed the institutional backgrounds of the corresponding authors of those 9923 articles and identified the most highly cited 330 authors over time. We found that before the mid-1990s, systems-oriented scientists had made the most referenced contributions. However, in recent years, researchers from biology-oriented institutions not only represented a huge percentage of the total number of researchers, but also had made the most referenced contributions. Notably, interdisciplinary institutions only produced a small percentage of researchers, but had made disproportionate contributions to this field.
Gavin de Beer (1899–1972) was an evolutionary embryologist considered by many as a forerunner of ... more Gavin de Beer (1899–1972) was an evolutionary embryologist considered by many as a forerunner of modern evolutionary developmental biology (evo-devo). This entry discusses de Beer’s works with a special focus on his contributions to evo-devo. De Beer was trained in zoology and later became interested in com- parative and evolutionary embryology. De Beer joined the attack on Ernst Haeckel’s biogenetic law and argued that ontogeny did not recapitulate phylog- eny, but ontogeny caused phylogeny instead. Influenced by the advancements of the Modern Synthesis and the rise of genetics, de Beer advocated for the integration of embryology, heredity, and evolution and emphasized on the impor- tance of embryology in evolutionary theory in many of his writings. Although de Beer failed to make a significant impact on the Modern Synthesis, his work on heterochrony influenced modern evo-devo biologists such as Stephen Jay Gould, and his views on homology are still revisited today.
Systems biology is a new field of biology that has great implications for agriculture , medicine,... more Systems biology is a new field of biology that has great implications for agriculture , medicine, and sustainability. In this article we explore the contributions of Chinese authors to systems biology through analysis of the metadata of more than 9000 articles on systems biology. Our big-data approach includes scientometric analysis, GIS analysis, co-word network analysis, and comparative analysis. By 2013 China has become second in the number of publications on systems biology. Similar to previous studies on Chinese science, we find an unequal distribution of research power in China, favoring big cities and coastal cities. Overall, 75% of the articles in systems biology were published by scholars from universities, 15% by scholars from the Chinese of Academy of Sciences institutions, and 9% from other institutions. Many Chinese scholars' research topics are similar to those in the US, Japan, and Germany, but one salient difference is that traditional Chinese medicine is an important topic among Chinese systems biologists. 25% of Chinese systems biologists cooperate with scientists abroad, suggesting that they take advantage of the opening-up policy. From the year 2011–2013, the average impact factor of the journals that Chinese scholars publish in is generally lower than that of their counterparts in the US, but the trend points to a gradual increase in impact.
Paul M. Brakefield and his research team in Leiden, the Netherlands, examined the development, pl... more Paul M. Brakefield and his research team in Leiden, the Netherlands, examined the development, plasticity, and evolution of butterfly eyespot patterns, and published their findings in Nature in 1996. Eyespots are eye-shaped color patterns that appear on the wings of some butterflies and birds as well as on the skin of some fish and reptiles. In butterflies, such as the peacock butterfly (Aglais io), the eyespots resemble the eyes of birds and help butterflies deter potential predators. Brakefield's research team described the stages through which eyespots develop, identified the genes and environmental signals that affect eye-spot appearance in some species, and demonstrated that small genetic variations can change butterfly eyespot color and shape. The research focused on a few butterfly species, but it contributed to more general claims of how the environment may affect the development of coloration and how specific color patterns may have evolved.
August Friedrich Leopold Weismann studied how the traits of organisms developed and evolved in a ... more August Friedrich Leopold Weismann studied how the traits of organisms developed and evolved in a variety of organisms, mostly insects and aquatic animals, in Germany in the
late nineteenth and early twentieth centuries. Weismann proposed the theory of the continuity of germ-plasm, a theory of heredity. Weismann postulated that germ-plasm was the hereditary material in cells, and parents transmitted to their offspring only the germ-plasm present in germ-cells (sperm and egg cells) rather than somatic or body cells. Weismann also promoted Charles Darwin's 1859 theory of the evolution of species. Weismann argued that only changes to the germ cells, and not body cells, could be inherited, a theory that
influenced theories of heredity throughout later centuries.
Green fluorescent protein (GFP) is a protein in the jellyfish Aequorea Victoria that exhibits gre... more Green fluorescent protein (GFP) is a protein in the jellyfish Aequorea Victoria that exhibits green fluorescence when exposed to light. The protein has 238 amino acids, three of them (Numbers 65 to 67) form a structure that emits visible green fluorescent light. In the jellyfish, GFP interacts with another protein, called aequorin, which emits blue light when added with calcium. Biologists use GFP to study cells in embryos and fetuses during developmental processes.
In 1868 in England, Charles Darwin proposed his pangenesis theory to describe the units of inher... more In 1868 in England, Charles Darwin proposed his pangenesis theory to describe the units of inheritance between parents and offspring and the processes by which those units control development in offspring. Darwin coined the concept of gemmules, which he said referred to hypothesized minute particles of inheritance thrown off by all cells of the body. The theory suggested that an organism's environment could modify the gemmules in any parts of the body, and that these modified gemmules would congregate in the reproductive organs of parents to be passed on to their offspring. Darwin's theory of pangenesis gradually lost popularity in the 1890s when biologists increasingly abandoned the theory of inheritance of acquired characteristics (IAC), on which the pangenesis theory partially relied. Around the turn of the twentieth century, biologists replaced the theory of pangenesis with germ plasm theory and then with chromosomal theories of inheritance, and they replaced the concept of gemmules with that of genes.
Dizhou Tong, also called Ti Chou Tung, studied marine animals and helped introduce and organize e... more Dizhou Tong, also called Ti Chou Tung, studied marine animals and helped introduce and organize experimental embryology in China during the twentieth century. He introduced cellular nuclear transfer technology to the Chinese biological community, developed methods
to clone organisms from many marine species, and investigated the role of cytoplasm in early development. Tong's administrative and scientific leadership in the fields of marine, cellular, and developmental biology contributed to China's experimental embryology research programs.
Friedrich Leopold August Weismann published Das Keimplasma: eine Theorie der Vererbung (The Germ-... more Friedrich Leopold August Weismann published Das Keimplasma: eine Theorie der Vererbung (The Germ-Plasm: a Theory of Heredity, hereafter The Germ-Plasm) while
working at the University of Freiburg in Freiburg, Germany in 1892. William N. Parker, a professor in the University College of South Wales and Monmouthshire in Cardiff, UK,
translated The Germ-Plasm into English in 1893. In The Germ-Plasm, Weismann proposed a theory of heredity based on the concept of the germ plasm, a substance in the germ cell that
carries hereditary information. The Germ-Plasm compiled Weismann's theoretical work and analyses of other biologists' experimental work in the 1880s, and it provided a framework to study development, evolution [7] and heredity. Weismann anticipated that the germ-plasm theory would enable researchers to investigate the functions and material of hereditary substances.