Cotter, J. (2010).  Reforming the European Common Fisheries Policy: a case for capacity and effort controls.  Fish and Fisheries 11(2), 210-219.

Petitgas, P., Cotter, J., Trenkel, V., and Mesnil, B. - Editors (2009).  Fish stock assessments using surveys and indicators.  Aquatic Living Resources 22(2) (special volume with 14 articles, available freely at http://www.alr-journal.org ).

Trenkel, V.M., and Cotter, A.J.R.  (2009).  Choosing survey time series as part of an ecosystem approach to fishery management.  Aquatic Living Resources 22(2), 121-126.

Cotter, J.  (2009).  Statistical estimation of mean values of fish stock indicators from trawl surveys. Aquatic Living Resources 22(2), 127-134.

Cotter, J., Mesnil, B., Witthames, P., and Parker-Humphreys, M. (2009).  Notes on nine biological indicators estimable from trawl surveys with an illustrative assessment for North Sea cod.  Aquatic Living Resources 22(2), 135-154.

Cotter, J.  (2009).  A selection of nonparametric statistical methods for assessing trends in trawl survey indicators as part of an ecosystem approach to fisheries management (EAFM).  Aquatic Living Resources 22(2), 173-186.

Mesnil, B., Cotter, A.J.R., Fryer, R.J., Needle, C.L., and Trenkel, V.M. (In press, 2009). A review of fishery-independent assessment models, and initial evaluation based on simulated data. In: Petitgas, P., et al. - Eds. Aquatic Living Resources (see above).

Cotter, J., Petitgas, P., Abella, A., Apostolaki, P., Mesnil, B., Politou, C.-Y., Rivoirard, J., Rochet, M.-J., Spedicato, M., Trenkel, V.M., and Woillez, M. (In press, 2009). Towards an Ecosystem Approach to Management of Fisheries when trawl surveys provide the main source of information. In: Petitgas, P., et al. - Eds. Aquatic Living Resources (see above).

Trenkel, V.M., and Cotter, A.J.R. (In press, 2009). Choosing survey time series for non-target species of fish as part of an ecosystem approach to fishery management. In: Petitgas, P., et al. - Eds. Aquatic Living Resources (see above).

Payne, A., Cotter, J., and Potter, T. - Editors (2008). Advances in fisheries science 50 years on from Beverton and Holt, Blackwell Publishing. 546pp.

Cotter, A.J.R. (2008). The 'soundscape' of the sea, underwater navigation, and why we should be listening more. pp. 451-471 In: Advances in fisheries science 50 years on from Beverton and Holt, Ed. A. Payne, J. Cotter, and T. Potter, Blackwell Publishing.

Armstrong, M.J., Payne, A.I.L., and Cotter, A.J.R. (2008). Contributions of the fishing industry to research through partnerships. pp. 63-84 In: Advances in fisheries science 50 years on from Beverton and Holt, Ed. A. Payne, J. Cotter, and T. Potter, Blackwell Publishing.

Pilling, G.M., van der Kooij, J., Daskalov, G.M., Cotter, A.J.R., Metcalfe, J.D. (2007). Overview of current best world practice in fish stock assessment and management, with specific reference to Caspian Sea fisheries. Cefas Tech. Rep. 141, 158pp.

Revill, A.S., Cotter, J., Armstrong, J.M., Ashworth, J., Forster, R., Caslake, G., and Holst, R. (2007). The selectivity of gill-nets used to target hake (Merluccius merluccius) in the Cornish and Irish offshore fisheries. Fisheries Research, 85, 142-147.

Callaway, R., Engelhard, G.H., Dann, J., Cotter, J., and Rumohr, H. (2007). One century of North Sea epibenthos: comparison between 1902-1912, 1982-1985 and 2000. Marine Ecology Progress Series 346, 27-43.

Cotter, A.J.R., and Pilling, G. (2007). Landings, logbooks and observer surveys: improving the protocols for sampling commercial fisheries. Fish and Fisheries 8, 123-152.

Cotter, A.J.R., Mesnil, B., and Piet, G. (2007). Estimating stock parameters from trawl cpue-at-age series using year-class curves. ICES Journal of marine Science, 64, 234-247.

Cotter, A.J.R., Course, G., Ashworth, J., Forster, R., Enever, R., Goad, D., Bush, R., Shaw, S., Mainprize, R., and Garrod, C. (2006). Summary of commercial marine fishing by English and Welsh vessels ≥ 10 metres LOA for 2004. Sci. Ser. Tech. Rep., Cefas, Lowestoft, 134, 93pp.

Cotter, A.J.R., Burt, L., Paxton, C.G.M., Fernandez, C., Buckland, S.T., and Pan, J-X. (2004). Are stock assessment methods too complicated? Fish and Fisheries, 5, 235-254.

Cotter, A.J.R., and Buckland, S.T. (2004). Using the EM algorithm to weight data sets of unknown precision when modelling fish stocks. Mathematical Biosciences 190, 1-7.

Callaway, R., Alvsvaag, J., de Boois, I., Cotter, J., + 8 other authors (2002). Diversity and community structure of epibenthic invertebrates and fish in the North Sea. ICES J. mar. Sci., 59, 1199-1214.

Callaway, R., Jennings, S., Lancaster, J., and Cotter, J. (2002). Mesh-size matters in epibenthic surveys. Journal of the marine biological Association UK, 82(1): 1-8.

Zuhlke, R, Alvsvaag, J., de Boois, I., Cotter, J., + 8 other authors in alphabetic order (2002). Epibenthic diversity in the North Sea. Senckenbergiana maritima 31(2), 269-281.

Cotter, A.J.R. (2001). A PPS sample survey of English fishing vessels to estimate discarding and retention of North Sea cod, haddock, and whiting. Fisheries Res. 55, 25-35.

Cotter, A.J.R. (2001). Intercalibration of North Sea international bottom trawl surveys by fitting year-class curves. ICES J. Marine Science, 58, 622-632, and Erratum 1340.

Course G. and Cotter A.J.R., Joliffe R.O., Kay B.J. and Rolfe M.S. (1999). Safe practices for sampling commercial trawler catches at sea. Fisheries Research 41, 99-104.

Jennings, S., Warr, K.J., Greenstreet, S.P.R., and Cotter, A.J. (2000). Effects of fishing on non-target species and habitats: biological conservation and socio-economic issues (ed. M.J. Kaiser and S.J. de Groot). Oxford: Blackwell Science.

Jennings, S., Alvsvåg, J., Cotter, A.J., Ehrich, S., Greenstreet, S.P.R., Jarre-Teichmann, A., Mergardt, N., Rijnsdorp, A.D. and Smedstad, O. (1998/9). Fishing effects in northeast Atlantic shelf seas: patterns in fishing effort, diversity and community structure. III. International fishing effort in the North Sea: an analysis of temporal and spatial trends. Fisheries Research 40, 125-134.

Jennings, S. and Cotter, A.J. (1998/9). Fishing effects in northeast Atlantic shelf seas: patterns in fishing effort, diversity and community structure. I. Introduction. Fisheries Research 40, 103-104.

Jennings, S., Lancaster, J.E., Woolmer, A. and Cotter, J. (1998/9). Distribution, diversity and abundance of epibenthic fauna in the North Sea. Journal of the Marine Biological Association of the United Kingdom 79, 385-399.

Cotter, A.J.R. (1998). Method for estimating variability due to sampling of catches on a trawl survey. Can. J. Fish. Aquat. Sci. 55, 1607-1617.

Cotter, A.J.R., Boon, T.W. and Brown, C.G. 1997. Statistical aspects of trials of a separator trawl using a twin rig trawler. Fisheries Res. 29, 25-32.

Cotter, A.J.R., Walker, P., Coates, P., Cook, W. and Dare, P.J. 1997 Trial of a tractor dredger for cockles in Burry Inlet, South Wales. ICES J. mar. Sci. 54, 72-83.

Cotter, A.J.R. 1994 Compliance testing of two or more water quality determinands using quantiles. Environmetrics 5, 29-45.

Cotter, A.J.R. 1988 Sea disposal - licensing and enforcement. Chem. & Industr.

Cotter, A.J.R. 1985 Water quality surveys; a statistical method based on determinism, quantiles and the binomial distribution. Water Res. 19, 1179-1189.

Cotter, A.J.R., Phillips, D.J.H., and Ahsanullah, M. 1982 The significance of temperature, salinity and zinc as lethal factors for the mussel, Mytilus edulis, in a polluted estuary. Marine Biol. 68, 135-141.

Cotter, A.J.R. 1978 Reinvestigation of size, axial gradients, and light as factors affecting the respiration of certain marine sponges. Comp. Biochem. Physiol. 60A, 117-122.


3. ICES papers

Cotter, A.J.R. + 10 coauthors. Manual of indicators and methods for assessing fish stocks using only fishery-independent, survey based information. ICES CM 2007/O:27

Mesnil, B. Cotter, A.J.R., Fryer, R.J., Needle, C., Skagen, D., Spedicato, M.T. and Trenkel, V.M. Review of fishery-independent assessment methods. ICES CM2007/O:04

Cotter, A.J.R. Can groundfish surveys be improved without breaking the series? ICES CM 1997/Y:24.

Armstrong, M.J., Beveridge, D., Cotter, A.J.R., Revill, A.S., and Dann, J. Fisheries Science Partnership programmes of the NE and SW coasts of England and in the Irish Sea: experiences gained and future directions. ICES CM 2005/Y:06.

Kell, L.T., Cotter, J., van Keeken, O., Pastoors, M., O'Brien, C.M., Piet, G.J., and Rackham, B.R. The influence on stock assessment advice of sampling error in research survey and international market sampling data for North Sea cod (Gadus morhua L.) and plaice (Pleuronectes platessa L.). ICES CM 2003/X:05.

Cotter, A.J.R., Walker, P., Coates, P., Cook, W. and Dare, P. An experiment on the effects of tractor dredging on cockles in Burry Inlet, South Wales. ICES CM 1993/K:24

Cotter, A.J.R. and Rees, H. Univariate approaches to the derivation of quality standards for marine benthos. ICES CM 1993/E:16

Cotter, A.J.R. Intercalibration of groundfish surveys using regression analysis of yearclass mortalities. ICES CM 1993/G:21