526
References
Adams SM (1990) Status and use of biological indicators for evaluating the effects of stress in fish.
Am Fish Soc Symp 8:1–8
Al-Sabti K (1985) Frequency of chromosomal aberrations in the rainbow trout, Salmo gairdneri
Rich., exposed to five pollutants. J Fish Biol 26(1):13–19. https://doi.org/
10.1111/j.1095-8649.1985.tb04235.x
Aluru N, Kuo E, Helfrich LW, Karchner SI, Linney EA, Pais JE, Franks DG (2015) Developmental
exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin alters DNA methyltransferase (dnmt)
expression in zebrafish (Danio rerio). Toxicol Appl Pharmacol 284(2):142–151. https://doi.
org/10.1016/j.taap.2015.02.016
Anders S, Pyl PT, Huber W (2014) HTSeq–a Python framework to work with high-throughput
sequencing data. Bioinformatics 31:166–169
Andersson DI, Hughes D (2010) Antibiotic resistance and its cost: is it possible to reverse resistance? Nat Rev Microbiol 8:260. https://doi.org/10.1038/nrmicro2319
Androutsopoulos VP, Tsatsakis AM, Spandidos DA (2009) Cytochrome P450 CYP1A1:
wider roles in cancer progression and prevention. BMC Cancer 9(1):187. https://doi.
org/10.1186/1471-2407-9-187
Antonovics J, Bradshaw AD, Turner RG (1971) Heavy metal tolerance in plants. In: Cragg JB
(ed) Advances in ecological research, vol 7. Academic Press, pp 1–85. https://doi.org/10.1016/
S0065-2504(08)60202-0
Behjati S, Tarpey PS (2013) What is next generation sequencing? Arch Dis Child Educ Pract Ed
98(6):236
Belfiore NM, Anderson SL (2001) Effects of contaminants on genetic patterns in aquatic organisms: a review. Mutat Res 489(2):97–122. https://doi.org/10.1016/S1383-5742(01)00065-5
Bickham JW, Sandhu S, Hebert PDN, Chikhi L, Athwal R (2000) Effects of chemical contaminants on genetic diversity in natural populations: implications for biomonitoring and ecotoxicology. Mutat Res 463(1):33–51. https://doi.org/10.1016/S1383-5742(00)00004-1
Bijlsma R, Loeschcke V (2011) Genetic erosion impedes adaptive responses to stressful environments. Evol Appl 5(2):117–129. https://doi.org/10.1111/j.1752-4571.2011.00214.x
Blake GET, Watson ED (2016) Unravelling the complex mechanisms of transgenerational epigenetic inheritance. Curr Opin Chem Biol 33:101–107. https://doi.org/10.1016/j.cbpa.2016.06.008
Brette F, Machado B, Cros C, Incardona JP, Scholz NL, Block BA (2014) Crude oil impairs cardiac
excitation-contraction coupling in fish. Science 343(6172):772–776
Carls MG, Rice SD, Hose JE (1999) Sensitivity of fish embryos to weathered crude oil: part
I. Low-level exposure during incubation causes malformations, genetic damage, and mortality
in larval pacific herring (Clupea pallasi). Environ Toxicol Chem 18(3):481–493. https://doi.
org/10.1002/etc.5620180317
Carney SA, Chen J, Burns CG, Xiong KM, Peterson RE, Heideman W (2006) Aryl hydrocarbon
receptor activation produces heart-specific transcriptional and toxic responses in developing
zebrafish. Mol Pharmacol 70(2):549–561. https://doi.org/10.1124/mol.106.025304
Chanda S, Dasgupta UB, GuhaMazumder D, Gupta M, Chaudhuri U, Lahiri S, Das S, Ghosh
N, Chatterjee D (2006) DNA hypermethylation of promoter of gene p53 and p16 in arsenicexposed people with and without malignancy. Toxicol Sci 89(2):431–437. https://doi.
org/10.1093/toxsci/kfj030
Chen G, Shi T, Shi L (2017) Characterizing and annotating the genome using RNA-seq data. Sci
China Life Sci 60(2):116–125
Collotta M, Bertazzi PA, Bollati V (2013) Epigenetics and pesticides. Toxicology 307:35–41.
https://doi.org/10.1016/j.tox.2013.01.017
Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW,
Gaffney DJ, Elo LL, Zhang X (2016) A survey of best practices for RNA-seq data analysis.
Genome Biol 17(1):13
D. S. Portnoy et al.
References
Adams SM (1990) Status and use of biological indicators for evaluating the effects of stress in fish.
Am Fish Soc Symp 8:1–8
Al-Sabti K (1985) Frequency of chromosomal aberrations in the rainbow trout, Salmo gairdneri
Rich., exposed to five pollutants. J Fish Biol 26(1):13–19. https://doi.org/
10.1111/j.1095-8649.1985.tb04235.x
Aluru N, Kuo E, Helfrich LW, Karchner SI, Linney EA, Pais JE, Franks DG (2015) Developmental
exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin alters DNA methyltransferase (dnmt)
expression in zebrafish (Danio rerio). Toxicol Appl Pharmacol 284(2):142–151. https://doi.
org/10.1016/j.taap.2015.02.016
Anders S, Pyl PT, Huber W (2014) HTSeq–a Python framework to work with high-throughput
sequencing data. Bioinformatics 31:166–169
Andersson DI, Hughes D (2010) Antibiotic resistance and its cost: is it possible to reverse resistance? Nat Rev Microbiol 8:260. https://doi.org/10.1038/nrmicro2319
Androutsopoulos VP, Tsatsakis AM, Spandidos DA (2009) Cytochrome P450 CYP1A1:
wider roles in cancer progression and prevention. BMC Cancer 9(1):187. https://doi.
org/10.1186/1471-2407-9-187
Antonovics J, Bradshaw AD, Turner RG (1971) Heavy metal tolerance in plants. In: Cragg JB
(ed) Advances in ecological research, vol 7. Academic Press, pp 1–85. https://doi.org/10.1016/
S0065-2504(08)60202-0
Behjati S, Tarpey PS (2013) What is next generation sequencing? Arch Dis Child Educ Pract Ed
98(6):236
Belfiore NM, Anderson SL (2001) Effects of contaminants on genetic patterns in aquatic organisms: a review. Mutat Res 489(2):97–122. https://doi.org/10.1016/S1383-5742(01)00065-5
Bickham JW, Sandhu S, Hebert PDN, Chikhi L, Athwal R (2000) Effects of chemical contaminants on genetic diversity in natural populations: implications for biomonitoring and ecotoxicology. Mutat Res 463(1):33–51. https://doi.org/10.1016/S1383-5742(00)00004-1
Bijlsma R, Loeschcke V (2011) Genetic erosion impedes adaptive responses to stressful environments. Evol Appl 5(2):117–129. https://doi.org/10.1111/j.1752-4571.2011.00214.x
Blake GET, Watson ED (2016) Unravelling the complex mechanisms of transgenerational epigenetic inheritance. Curr Opin Chem Biol 33:101–107. https://doi.org/10.1016/j.cbpa.2016.06.008
Brette F, Machado B, Cros C, Incardona JP, Scholz NL, Block BA (2014) Crude oil impairs cardiac
excitation-contraction coupling in fish. Science 343(6172):772–776
Carls MG, Rice SD, Hose JE (1999) Sensitivity of fish embryos to weathered crude oil: part
I. Low-level exposure during incubation causes malformations, genetic damage, and mortality
in larval pacific herring (Clupea pallasi). Environ Toxicol Chem 18(3):481–493. https://doi.
org/10.1002/etc.5620180317
Carney SA, Chen J, Burns CG, Xiong KM, Peterson RE, Heideman W (2006) Aryl hydrocarbon
receptor activation produces heart-specific transcriptional and toxic responses in developing
zebrafish. Mol Pharmacol 70(2):549–561. https://doi.org/10.1124/mol.106.025304
Chanda S, Dasgupta UB, GuhaMazumder D, Gupta M, Chaudhuri U, Lahiri S, Das S, Ghosh
N, Chatterjee D (2006) DNA hypermethylation of promoter of gene p53 and p16 in arsenicexposed people with and without malignancy. Toxicol Sci 89(2):431–437. https://doi.
org/10.1093/toxsci/kfj030
Chen G, Shi T, Shi L (2017) Characterizing and annotating the genome using RNA-seq data. Sci
China Life Sci 60(2):116–125
Collotta M, Bertazzi PA, Bollati V (2013) Epigenetics and pesticides. Toxicology 307:35–41.
https://doi.org/10.1016/j.tox.2013.01.017
Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW,
Gaffney DJ, Elo LL, Zhang X (2016) A survey of best practices for RNA-seq data analysis.
Genome Biol 17(1):13
D. S. Portnoy et al.